From e458257b4244b89337b39eb6e018fd39d65f35b8 Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 10:43:17 -0400 Subject: [PATCH 1/9] update to 'referencePatternsFileNamesList' --- DefaultUserInput.py | 4 +- ExampleAnalysis/DefaultUserInput.py | 4 +- ExampleAnalysis/MSRESOLVE.py | 92 +++++++------- ExampleAnalysis/UserInput.py | 4 +- ExampleAnalysis/userInputValidityFunctions.py | 14 +- .../DefaultUserInput.py | 4 +- ExampleReferenceExtraction/MSRESOLVE.py | 92 +++++++------- ExampleReferenceExtraction/UserInput.py | 4 +- .../userInputValidityFunctions.py | 14 +- ExampleTuningCorrectorGasMixture/0-README.txt | 2 +- .../DefaultUserInput.py | 4 +- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 100 +++++++-------- .../MSRESOLVEBad1.py | 94 +++++++------- .../MSRESOLVEPrevious.py | 100 +++++++-------- ExampleTuningCorrectorGasMixture/UserInput.py | 4 +- .../userInputValidityFunctions.py | 16 +-- MSRESOLVE.py | 120 +++++++++--------- UnitTests/ConcentrationFinder/test_1.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/ConcentrationFinder/test_2.py | 2 +- UnitTests/ConcentrationFinder/test_3.py | 2 +- UnitTests/ConcentrationFinder/test_4.py | 2 +- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../test_3_input.py | 2 +- .../test_4_input.py | 2 +- .../test_5_input.py | 2 +- .../test_6_input.py | 2 +- .../test_1_Input_Brute_Finisher.py | 4 +- UnitTests/IonizationFactors/test_1.py | 2 +- UnitTests/IonizationFactors/test_2.py | 2 +- UnitTests/IonizationFactors/test_3.py | 2 +- UnitTests/IonizationFactors/test_4.py | 2 +- .../_iter_1/UserInput_iter_1.py | 4 +- .../_iter_2/UserInput_iter_2.py | 4 +- .../_iter_3/UserInput_iter_3.py | 4 +- .../_iter_4/UserInput_iter_4.py | 4 +- .../_iter_5/UserInput_iter_5.py | 4 +- .../_iter_6/UserInput_iter_6.py | 4 +- .../_iter_7/UserInput_iter_7.py | 4 +- .../_iter_8/UserInput_iter_8.py | 4 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../_iter_1/UserInput_iter_1.py | 4 +- .../_iter_2/UserInput_iter_2.py | 4 +- .../_iter_3/UserInput_iter_3.py | 4 +- .../_iter_4/UserInput_iter_4.py | 4 +- .../_iter_5/UserInput_iter_5.py | 4 +- .../_iter_6/UserInput_iter_6.py | 4 +- .../_iter_7/UserInput_iter_7.py | 4 +- .../_iter_8/UserInput_iter_8.py | 4 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../_iter_1/UserInput_iter_1.py | 4 +- .../_iter_2/UserInput_iter_2.py | 4 +- .../_iter_3/UserInput_iter_3.py | 4 +- .../_iter_4/UserInput_iter_4.py | 4 +- .../_iter_5/UserInput_iter_5.py | 4 +- .../_iter_6/UserInput_iter_6.py | 4 +- .../_iter_7/UserInput_iter_7.py | 4 +- .../_iter_8/UserInput_iter_8.py | 4 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../_iter_1/UserInput_iter_1.py | 4 +- .../_iter_2/UserInput_iter_2.py | 4 +- .../_iter_3/UserInput_iter_3.py | 4 +- .../_iter_4/UserInput_iter_4.py | 4 +- .../_iter_5/UserInput_iter_5.py | 4 +- .../_iter_6/UserInput_iter_6.py | 4 +- .../_iter_7/UserInput_iter_7.py | 4 +- .../_iter_8/UserInput_iter_8.py | 4 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../_iter_1/UserInput_iter_1.py | 4 +- .../_iter_2/UserInput_iter_2.py | 4 +- .../_iter_3/UserInput_iter_3.py | 4 +- .../_iter_4/UserInput_iter_4.py | 4 +- .../_iter_5/UserInput_iter_5.py | 4 +- .../_iter_6/UserInput_iter_6.py | 4 +- .../_iter_7/UserInput_iter_7.py | 4 +- .../_iter_8/UserInput_iter_8.py | 4 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/NegativeAnalyzer/test_1_Input.py | 4 +- .../test_1_inputA.py | 2 +- .../test_1_inputB.py | 2 +- .../test_1_inputC.py | 2 +- .../test_2_input.py | 2 +- UnitTests/TuningCorrector/test_1.py | 2 +- .../test_10 Manual SLS/1/test_10.turnedOff | 2 +- .../test_10 Manual SLS/1/test_5.turnedOff | 2 +- .../test_10 Manual SLS/4/test_10.turnedOff | 2 +- UnitTests/TuningCorrector/test_10.py | 2 +- .../1/test_10.turnedOff | 2 +- .../1/test_11.turnedOff | 2 +- .../4/test_11.turnedOff | 2 +- UnitTests/TuningCorrector/test_11.py | 2 +- UnitTests/TuningCorrector/test_2.py | 2 +- UnitTests/TuningCorrector/test_3.py | 4 +- UnitTests/TuningCorrector/test_4.py | 2 +- UnitTests/TuningCorrector/test_5.py | 2 +- UnitTests/TuningCorrector/test_6.py | 2 +- UnitTests/TuningCorrector/test_7.py | 2 +- UnitTests/TuningCorrector/test_8.py | 2 +- UnitTests/TuningCorrector/test_9.py | 2 +- .../TuningCorrectorGasMixture/0-README.txt | 2 +- .../UserInputGasMixture.py | 4 +- .../UserInputGasMixture2.py | 4 +- .../UserInputGasMixture3.py | 4 +- .../UserInputGasMixture4.py | 4 +- .../XYXYReferencePattern/test_1_inputXYXY.py | 4 +- .../XYXYReferencePattern/test_1_inputXYYY.py | 4 +- .../implicitSLScorrection/test_1_Input.py | 4 +- .../implicitSLScorrection/test_2_Input.py | 4 +- .../test_1_UserInput.py | 4 +- .../test_2_UserInput.py | 4 +- UnitTests/slsCommon/test_1_Input.py | 4 +- .../test_1_Input.py | 4 +- .../test_2_Input.py | 4 +- UnitTests/uncertainties/test_10_Input.py | 4 +- UnitTests/uncertainties/test_11_Input.py | 4 +- UnitTests/uncertainties/test_12_Input.py | 4 +- UnitTests/uncertainties/test_13_Input.py | 4 +- UnitTests/uncertainties/test_14_Input.py | 4 +- UnitTests/uncertainties/test_15_Input.py | 4 +- UnitTests/uncertainties/test_16_Input.py | 4 +- UnitTests/uncertainties/test_1_Input.py | 4 +- UnitTests/uncertainties/test_2_Input.py | 4 +- UnitTests/uncertainties/test_3_Input.py | 4 +- UnitTests/uncertainties/test_4_Input.py | 4 +- UnitTests/uncertainties/test_5_Input.py | 4 +- UnitTests/uncertainties/test_6_Input.py | 4 +- UnitTests/uncertainties/test_7_Input.py | 4 +- UnitTests/uncertainties/test_8_Input.py | 4 +- UnitTests/uncertainties/test_9_Input.py | 4 +- UserInput.py | 4 +- userInputValidityFunctions.py | 28 ++-- 138 files changed, 543 insertions(+), 543 deletions(-) diff --git a/DefaultUserInput.py b/DefaultUserInput.py index eb5029457..238947a58 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index eba6ce6c8..26c183b39 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index 278ea901b..1cbca7872 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -1248,22 +1248,22 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): return ReferenceData ''' -GenerateReferenceDataAndFormsList takes in the list of referenceFileNamesList and the +GenerateReferenceDataAndFormsList takes in the list of referencePatternsFileNamesList and the list of forms. A list is generated containing MSReference objects created based on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): +def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string - ##If referenceFileNamesList is a string or if form is a string then make them lists - if isinstance(referenceFileNamesList,str): - referenceFileNamesList = [referenceFileNamesList] + ##If referencePatternsFileNamesList is a string or if form is a string then make them lists + if isinstance(referencePatternsFileNamesList,str): + referencePatternsFileNamesList = [referencePatternsFileNamesList] if isinstance(referenceFormsList,str): referenceFormsList = [referenceFormsList] - #If referenceFileNamesList and forms are lists of 1 then create a list of the single MSReference object + #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referenceFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[0],referenceFormsList[0]) + if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1284,29 +1284,29 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities #TODO: low priority, remove nan values and/or populate them with zero using numpy divide. return ReferenceDataList #Otherwise we have multiple reference files and forms - #If just one form is used, make a list of forms that is the same length as referenceFileNamesList + #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList if len(referenceFormsList) == 1: - #Generate a copy of referenceFileNamesList to be overwritten with forms - listOfForms = copy.copy(referenceFileNamesList) + #Generate a copy of referencePatternsFileNamesList to be overwritten with forms + listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form - for i in range(len(referenceFileNamesList)): + for i in range(len(referencePatternsFileNamesList)): listOfForms[i] = referenceFormsList[0] - #If list of forms is the same length of referenceFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referenceFileNamesList): + #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index + elif len(referenceFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms listOfForms = referenceFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list - for i in range(len(referenceFileNamesList)): - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[i],listOfForms[i]) + for i in range(len(referencePatternsFileNamesList)): + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[i],listOfForms[i]) ReferenceDataList.append(MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)) #save each global variable into the class objects ReferenceDataList[i].ExportAtEachStep = G.ExportAtEachStep @@ -1327,7 +1327,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1658,7 +1658,7 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file @@ -1680,28 +1680,28 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): G.oldReferenceFileName = [] G.nextRefFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list #record the old file names G.oldReferenceFileName.append(RefName) #construct the file names for the current run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations - referenceFileNameTemp = G.referenceFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + referenceFileNameTemp = G.referencePatternsFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #copy the experimental and reference files into new names for this iterative run shutil.copy(RefName, referenceFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.referenceFileNamesList[RefIndex] = referenceFileNameTemp + G.referencePatternsFileNamesList[RefIndex] = referenceFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -1728,19 +1728,19 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] G.oldReferenceFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list G.oldReferenceFileName.append(RefName) #construct the file names for the first run of the program - G.referenceFileNamesList[RefIndex] = G.referenceFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + G.referencePatternsFileNamesList[RefIndex] = G.referencePatternsFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #construct file names for the second run of the program G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -1770,7 +1770,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list #Export current Reference Data #Reference data is trimmed prior to this function - ExportXYYYData(G.referenceFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') + ExportXYYYData(G.referencePatternsFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported @@ -1876,7 +1876,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file G.nextUserInputModule.collectedFileName = G.nextExpFileName - G.nextUserInputModule.referenceFileNamesList = G.nextRefFileName + G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules #Updating the selected masses for the next user input file @@ -1916,12 +1916,12 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): str(iterationDirectoryName), str(G.nextUserInputModule.collectedFileName)) shutil.copy(copyFromPath, os.getcwd()) - for RefIndex, RefName in enumerate(G.nextUserInputModule.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.referenceFileNamesList[RefIndex])) + str(G.nextUserInputModule.referencePatternsFileNamesList[RefIndex])) shutil.copy(copyFromPath, os.getcwd()) #returning to the parent directory os.chdir('..') @@ -1949,7 +1949,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### @@ -4937,7 +4937,7 @@ def PopulateLogFile(): filename6 = 'LogFile.txt' #the log file is printed here f6 = open(filename6,'a') f6.write('\n') - f6.write('referenceFileName = %s \n'%(G.referenceFileNamesList)) + f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referenceFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen @@ -5104,33 +5104,33 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names - AllMoleculesReferenceFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list - for referenceFileNameIndex in range(len(G.referenceFileNamesList)): #Loop through the reference file names list - AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referenceFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory + AllMoleculesreferencePatternsFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list + for referenceFileNameIndex in range(len(G.referencePatternsFileNamesList)): #Loop through the reference file names list + AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory - AllMoleculesReferenceFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name + AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename - AllMoleculesReferenceFileNamesList = copy.copy(G.referenceFileNamesList) + AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesReferenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' PrepareReferenceObjectsAndCorrectionValues(AllMoleculesReferenceDataList[referenceObjectIndex],AllMassFragmentsExperimentData) #Read in the molecules used before parsing the user input file - G.referenceFileNamesList = parse.listCast(G.referenceFileNamesList) - G.moleculesNames = getMoleculesFromReferenceData(G.referenceFileNamesList[0]) + G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) + G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) @@ -5168,7 +5168,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): @@ -5179,14 +5179,14 @@ def main(): prototypicalReferenceData = ReferenceDataList[0] #Prints a warning if the user has more reference files than specified time ranges - if len(G.referencePatternTimeRanges) > 0 and (len(G.referenceFileNamesList) > len(G.referencePatternTimeRanges)): + if len(G.referencePatternTimeRanges) > 0 and (len(G.referencePatternsFileNamesList) > len(G.referencePatternTimeRanges)): print("WARNING: There are more reference files given than time ranges") #save global variable into the class objects ExperimentData.ExportAtEachStep = G.ExportAtEachStep #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index 08ce9fabf..50b14c7c5 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index 3e5e11bfb..4838e1370 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -8,9 +8,9 @@ ''' def parseUserInput(currentUserInput): #Input Files - currentUserInput.referenceFileNamesList = parse.listCast(currentUserInput.referenceFileNamesList) #referenceFileName needs to be a list + currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referenceFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string @@ -204,10 +204,10 @@ def parseUserInput(currentUserInput): if currentUserInput.TSC_List_Type == 'MultipleReferencePatterns': #If using multiple reference patterns then the user must input 1 value to use for each reference file or a value for each reference file #Then parallelize these variables to have the same length as number of reference patterns - currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referenceFileNamesList)) + currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referencePatternsFileNamesList)) #NOTE: vectorizing these lists for 'SeparateMoleculesFactors' occurs in RatioFinder #Output Files @@ -248,7 +248,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #TODO: Consider if G.iterativeAnalysis = True or False should be changed to G.IterativeAnalysis_On or something like that, but will break backwards compatibility unless special care is taken. #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} - SettingsVDictionary['referenceFileNamesList'] = UserChoices['inputFiles']['referenceFileNamesList'] + SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index eba6ce6c8..26c183b39 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index 278ea901b..1cbca7872 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -1248,22 +1248,22 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): return ReferenceData ''' -GenerateReferenceDataAndFormsList takes in the list of referenceFileNamesList and the +GenerateReferenceDataAndFormsList takes in the list of referencePatternsFileNamesList and the list of forms. A list is generated containing MSReference objects created based on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): +def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string - ##If referenceFileNamesList is a string or if form is a string then make them lists - if isinstance(referenceFileNamesList,str): - referenceFileNamesList = [referenceFileNamesList] + ##If referencePatternsFileNamesList is a string or if form is a string then make them lists + if isinstance(referencePatternsFileNamesList,str): + referencePatternsFileNamesList = [referencePatternsFileNamesList] if isinstance(referenceFormsList,str): referenceFormsList = [referenceFormsList] - #If referenceFileNamesList and forms are lists of 1 then create a list of the single MSReference object + #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referenceFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[0],referenceFormsList[0]) + if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1284,29 +1284,29 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities #TODO: low priority, remove nan values and/or populate them with zero using numpy divide. return ReferenceDataList #Otherwise we have multiple reference files and forms - #If just one form is used, make a list of forms that is the same length as referenceFileNamesList + #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList if len(referenceFormsList) == 1: - #Generate a copy of referenceFileNamesList to be overwritten with forms - listOfForms = copy.copy(referenceFileNamesList) + #Generate a copy of referencePatternsFileNamesList to be overwritten with forms + listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form - for i in range(len(referenceFileNamesList)): + for i in range(len(referencePatternsFileNamesList)): listOfForms[i] = referenceFormsList[0] - #If list of forms is the same length of referenceFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referenceFileNamesList): + #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index + elif len(referenceFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms listOfForms = referenceFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list - for i in range(len(referenceFileNamesList)): - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[i],listOfForms[i]) + for i in range(len(referencePatternsFileNamesList)): + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[i],listOfForms[i]) ReferenceDataList.append(MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)) #save each global variable into the class objects ReferenceDataList[i].ExportAtEachStep = G.ExportAtEachStep @@ -1327,7 +1327,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1658,7 +1658,7 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file @@ -1680,28 +1680,28 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): G.oldReferenceFileName = [] G.nextRefFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list #record the old file names G.oldReferenceFileName.append(RefName) #construct the file names for the current run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations - referenceFileNameTemp = G.referenceFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + referenceFileNameTemp = G.referencePatternsFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #copy the experimental and reference files into new names for this iterative run shutil.copy(RefName, referenceFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.referenceFileNamesList[RefIndex] = referenceFileNameTemp + G.referencePatternsFileNamesList[RefIndex] = referenceFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -1728,19 +1728,19 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] G.oldReferenceFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list G.oldReferenceFileName.append(RefName) #construct the file names for the first run of the program - G.referenceFileNamesList[RefIndex] = G.referenceFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + G.referencePatternsFileNamesList[RefIndex] = G.referencePatternsFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #construct file names for the second run of the program G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -1770,7 +1770,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list #Export current Reference Data #Reference data is trimmed prior to this function - ExportXYYYData(G.referenceFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') + ExportXYYYData(G.referencePatternsFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported @@ -1876,7 +1876,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file G.nextUserInputModule.collectedFileName = G.nextExpFileName - G.nextUserInputModule.referenceFileNamesList = G.nextRefFileName + G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules #Updating the selected masses for the next user input file @@ -1916,12 +1916,12 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): str(iterationDirectoryName), str(G.nextUserInputModule.collectedFileName)) shutil.copy(copyFromPath, os.getcwd()) - for RefIndex, RefName in enumerate(G.nextUserInputModule.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.referenceFileNamesList[RefIndex])) + str(G.nextUserInputModule.referencePatternsFileNamesList[RefIndex])) shutil.copy(copyFromPath, os.getcwd()) #returning to the parent directory os.chdir('..') @@ -1949,7 +1949,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### @@ -4937,7 +4937,7 @@ def PopulateLogFile(): filename6 = 'LogFile.txt' #the log file is printed here f6 = open(filename6,'a') f6.write('\n') - f6.write('referenceFileName = %s \n'%(G.referenceFileNamesList)) + f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referenceFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen @@ -5104,33 +5104,33 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names - AllMoleculesReferenceFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list - for referenceFileNameIndex in range(len(G.referenceFileNamesList)): #Loop through the reference file names list - AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referenceFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory + AllMoleculesreferencePatternsFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list + for referenceFileNameIndex in range(len(G.referencePatternsFileNamesList)): #Loop through the reference file names list + AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory - AllMoleculesReferenceFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name + AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename - AllMoleculesReferenceFileNamesList = copy.copy(G.referenceFileNamesList) + AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesReferenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' PrepareReferenceObjectsAndCorrectionValues(AllMoleculesReferenceDataList[referenceObjectIndex],AllMassFragmentsExperimentData) #Read in the molecules used before parsing the user input file - G.referenceFileNamesList = parse.listCast(G.referenceFileNamesList) - G.moleculesNames = getMoleculesFromReferenceData(G.referenceFileNamesList[0]) + G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) + G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) @@ -5168,7 +5168,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): @@ -5179,14 +5179,14 @@ def main(): prototypicalReferenceData = ReferenceDataList[0] #Prints a warning if the user has more reference files than specified time ranges - if len(G.referencePatternTimeRanges) > 0 and (len(G.referenceFileNamesList) > len(G.referencePatternTimeRanges)): + if len(G.referencePatternTimeRanges) > 0 and (len(G.referencePatternsFileNamesList) > len(G.referencePatternTimeRanges)): print("WARNING: There are more reference files given than time ranges") #save global variable into the class objects ExperimentData.ExportAtEachStep = G.ExportAtEachStep #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index 078a5b99e..173055c3b 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ExistingReferencePatterns.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExistingReferencePatterns.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index 3e5e11bfb..4838e1370 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -8,9 +8,9 @@ ''' def parseUserInput(currentUserInput): #Input Files - currentUserInput.referenceFileNamesList = parse.listCast(currentUserInput.referenceFileNamesList) #referenceFileName needs to be a list + currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referenceFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string @@ -204,10 +204,10 @@ def parseUserInput(currentUserInput): if currentUserInput.TSC_List_Type == 'MultipleReferencePatterns': #If using multiple reference patterns then the user must input 1 value to use for each reference file or a value for each reference file #Then parallelize these variables to have the same length as number of reference patterns - currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referenceFileNamesList)) + currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referencePatternsFileNamesList)) #NOTE: vectorizing these lists for 'SeparateMoleculesFactors' occurs in RatioFinder #Output Files @@ -248,7 +248,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #TODO: Consider if G.iterativeAnalysis = True or False should be changed to G.IterativeAnalysis_On or something like that, but will break backwards compatibility unless special care is taken. #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} - SettingsVDictionary['referenceFileNamesList'] = UserChoices['inputFiles']['referenceFileNamesList'] + SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] diff --git a/ExampleTuningCorrectorGasMixture/0-README.txt b/ExampleTuningCorrectorGasMixture/0-README.txt index 96a031d9d..d9228906f 100644 --- a/ExampleTuningCorrectorGasMixture/0-README.txt +++ b/ExampleTuningCorrectorGasMixture/0-README.txt @@ -11,7 +11,7 @@ Proc Doc type things: -- First added at line 5351 if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: -- Now make a reference object from LiteratureReference.csv so that simulated signals can be made. - -- GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): + -- GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): -- Need to be careful because "ReferenceInputPreProcessing" is being used. diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index 6777d922e..207a438c3 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index 3871a1e5d..c68f4f612 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -507,7 +507,7 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien if measuredReferenceYorN =='yes': print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -570,7 +570,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu ReferenceDataExistingTuning = createReferenceDataObject ( G.referenceFileDesiredTuningAndForm[0],G.referenceFileDesiredTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternOriginalTuning.csv') if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. - referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. print("line 1489", referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) @@ -618,7 +618,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileExistingTuningAndForm = G.referenceFileExistingTuningAndForm if referenceFileDesiredTuningAndForm == []: print("line 622", G.referenceFormsList) - referenceFileDesiredTuningAndForm = [G.referenceFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternExternal.csv') @@ -789,7 +789,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"] if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients @@ -1640,22 +1640,22 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): return ReferenceData ''' -GenerateReferenceDataAndFormsList takes in the list of referenceFileNamesList and the +GenerateReferenceDataAndFormsList takes in the list of referencePatternsFileNamesList and the list of forms. A list is generated containing MSReference objects created based on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): +def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string - ##If referenceFileNamesList is a string or if form is a string then make them lists - if isinstance(referenceFileNamesList,str): - referenceFileNamesList = [referenceFileNamesList] + ##If referencePatternsFileNamesList is a string or if form is a string then make them lists + if isinstance(referencePatternsFileNamesList,str): + referencePatternsFileNamesList = [referencePatternsFileNamesList] if isinstance(referenceFormsList,str): referenceFormsList = [referenceFormsList] - #If referenceFileNamesList and forms are lists of 1 then create a list of the single MSReference object + #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referenceFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[0],referenceFormsList[0]) + if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1676,7 +1676,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1687,22 +1687,22 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].update_relative_standard_uncertainties() return ReferenceDataList #Otherwise we have multiple reference files and forms - #If just one form is used, make a list of forms that is the same length as referenceFileNamesList + #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList if len(referenceFormsList) == 1: - #Generate a copy of referenceFileNamesList to be overwritten with forms - listOfForms = copy.copy(referenceFileNamesList) + #Generate a copy of referencePatternsFileNamesList to be overwritten with forms + listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form - for i in range(len(referenceFileNamesList)): + for i in range(len(referencePatternsFileNamesList)): listOfForms[i] = referenceFormsList[0] - #If list of forms is the same length of referenceFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referenceFileNamesList): + #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index + elif len(referenceFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms listOfForms = referenceFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list - for i in range(len(referenceFileNamesList)): - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[i],listOfForms[i]) + for i in range(len(referencePatternsFileNamesList)): + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[i],listOfForms[i]) ReferenceDataList.append(MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)) #save each global variable into the class objects ReferenceDataList[i].ExportAtEachStep = G.ExportAtEachStep @@ -1723,7 +1723,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -2079,7 +2079,7 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file @@ -2101,28 +2101,28 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): G.oldReferenceFileName = [] G.nextRefFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list #record the old file names G.oldReferenceFileName.append(RefName) #construct the file names for the current run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations - referenceFileNameTemp = G.referenceFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + referenceFileNameTemp = G.referencePatternsFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #copy the experimental and reference files into new names for this iterative run shutil.copy(RefName, referenceFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.referenceFileNamesList[RefIndex] = referenceFileNameTemp + G.referencePatternsFileNamesList[RefIndex] = referenceFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2149,19 +2149,19 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] G.oldReferenceFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list G.oldReferenceFileName.append(RefName) #construct the file names for the first run of the program - G.referenceFileNamesList[RefIndex] = G.referenceFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + G.referencePatternsFileNamesList[RefIndex] = G.referencePatternsFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #construct file names for the second run of the program G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2191,7 +2191,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list #Export current Reference Data #Reference data is trimmed prior to this function - ExportXYYYData(G.referenceFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') + ExportXYYYData(G.referencePatternsFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported @@ -2297,7 +2297,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file G.nextUserInputModule.collectedFileName = G.nextExpFileName - G.nextUserInputModule.referenceFileNamesList = G.nextRefFileName + G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules #Updating the selected masses for the next user input file @@ -2337,12 +2337,12 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): str(iterationDirectoryName), str(G.nextUserInputModule.collectedFileName)) shutil.copy(copyFromPath, os.getcwd()) - for RefIndex, RefName in enumerate(G.nextUserInputModule.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.referenceFileNamesList[RefIndex])) + str(G.nextUserInputModule.referencePatternsFileNamesList[RefIndex])) shutil.copy(copyFromPath, os.getcwd()) #returning to the parent directory os.chdir('..') @@ -2370,7 +2370,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### @@ -5517,7 +5517,7 @@ def PopulateLogFile(): filename6 = 'LogFile.txt' #the log file is printed here f6 = open(filename6,'a') f6.write('\n') - f6.write('referenceFileName = %s \n'%(G.referenceFileNamesList)) + f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referenceFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen @@ -5685,13 +5685,13 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Read in the molecules used before parsing the user input file - G.referenceFileNamesList = parse.listCast(G.referenceFileNamesList) + G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) G.referenceFormsList = parse.listCast(G.referenceFormsList) - G.moleculesNames = getMoleculesFromReferenceData(G.referenceFileNamesList[0]) + G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #If a tuning correction is going to be done, we'll make a mixed reference pattern. #G.moleculesNamesExtended needs to be populated before the first tuning correction and before parsing of userinput. if str(G.measuredReferenceYorN).lower() == 'yes': @@ -5708,20 +5708,20 @@ def main(): #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names - AllMoleculesReferenceFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list - for referenceFileNameIndex in range(len(G.referenceFileNamesList)): #Loop through the reference file names list - AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referenceFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory + AllMoleculesreferencePatternsFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list + for referenceFileNameIndex in range(len(G.referencePatternsFileNamesList)): #Loop through the reference file names list + AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory - AllMoleculesReferenceFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name + AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename - AllMoleculesReferenceFileNamesList = copy.copy(G.referenceFileNamesList) + AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesReferenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' @@ -5759,7 +5759,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): @@ -5767,14 +5767,14 @@ def main(): G.collectedFileUncertainties = int(G.collectedFileUncertainties) #Prints a warning if the user has more reference files than specified time ranges - if len(G.referencePatternTimeRanges) > 0 and (len(G.referenceFileNamesList) > len(G.referencePatternTimeRanges)): + if len(G.referencePatternTimeRanges) > 0 and (len(G.referencePatternsFileNamesList) > len(G.referencePatternTimeRanges)): print("WARNING: There are more reference files given than time ranges") #save global variable into the class objects ExperimentData.ExportAtEachStep = G.ExportAtEachStep #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index 51b7f0934..d8a907b32 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -509,7 +509,7 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -1515,22 +1515,22 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): return ReferenceData ''' -GenerateReferenceDataAndFormsList takes in the list of referenceFileNamesList and the +GenerateReferenceDataAndFormsList takes in the list of referencePatternsFileNamesList and the list of forms. A list is generated containing MSReference objects created based on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): +def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string - ##If referenceFileNamesList is a string or if form is a string then make them lists - if isinstance(referenceFileNamesList,str): - referenceFileNamesList = [referenceFileNamesList] + ##If referencePatternsFileNamesList is a string or if form is a string then make them lists + if isinstance(referencePatternsFileNamesList,str): + referencePatternsFileNamesList = [referencePatternsFileNamesList] if isinstance(referenceFormsList,str): referenceFormsList = [referenceFormsList] - #If referenceFileNamesList and forms are lists of 1 then create a list of the single MSReference object + #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referenceFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[0],referenceFormsList[0]) + if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1551,7 +1551,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1562,22 +1562,22 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].update_relative_standard_uncertainties() return ReferenceDataList #Otherwise we have multiple reference files and forms - #If just one form is used, make a list of forms that is the same length as referenceFileNamesList + #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList if len(referenceFormsList) == 1: - #Generate a copy of referenceFileNamesList to be overwritten with forms - listOfForms = copy.copy(referenceFileNamesList) + #Generate a copy of referencePatternsFileNamesList to be overwritten with forms + listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form - for i in range(len(referenceFileNamesList)): + for i in range(len(referencePatternsFileNamesList)): listOfForms[i] = referenceFormsList[0] - #If list of forms is the same length of referenceFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referenceFileNamesList): + #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index + elif len(referenceFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms listOfForms = referenceFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list - for i in range(len(referenceFileNamesList)): - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[i],listOfForms[i]) + for i in range(len(referencePatternsFileNamesList)): + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[i],listOfForms[i]) ReferenceDataList.append(MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)) #save each global variable into the class objects ReferenceDataList[i].ExportAtEachStep = G.ExportAtEachStep @@ -1598,7 +1598,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1951,7 +1951,7 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file @@ -1973,28 +1973,28 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): G.oldReferenceFileName = [] G.nextRefFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list #record the old file names G.oldReferenceFileName.append(RefName) #construct the file names for the current run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations - referenceFileNameTemp = G.referenceFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + referenceFileNameTemp = G.referencePatternsFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #copy the experimental and reference files into new names for this iterative run shutil.copy(RefName, referenceFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.referenceFileNamesList[RefIndex] = referenceFileNameTemp + G.referencePatternsFileNamesList[RefIndex] = referenceFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2021,19 +2021,19 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] G.oldReferenceFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list G.oldReferenceFileName.append(RefName) #construct the file names for the first run of the program - G.referenceFileNamesList[RefIndex] = G.referenceFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + G.referencePatternsFileNamesList[RefIndex] = G.referencePatternsFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #construct file names for the second run of the program G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2063,7 +2063,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list #Export current Reference Data #Reference data is trimmed prior to this function - ExportXYYYData(G.referenceFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') + ExportXYYYData(G.referencePatternsFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported @@ -2169,7 +2169,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file G.nextUserInputModule.collectedFileName = G.nextExpFileName - G.nextUserInputModule.referenceFileNamesList = G.nextRefFileName + G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules #Updating the selected masses for the next user input file @@ -2209,12 +2209,12 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): str(iterationDirectoryName), str(G.nextUserInputModule.collectedFileName)) shutil.copy(copyFromPath, os.getcwd()) - for RefIndex, RefName in enumerate(G.nextUserInputModule.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.referenceFileNamesList[RefIndex])) + str(G.nextUserInputModule.referencePatternsFileNamesList[RefIndex])) shutil.copy(copyFromPath, os.getcwd()) #returning to the parent directory os.chdir('..') @@ -2242,7 +2242,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### @@ -5382,7 +5382,7 @@ def PopulateLogFile(): filename6 = 'LogFile.txt' #the log file is printed here f6 = open(filename6,'a') f6.write('\n') - f6.write('referenceFileName = %s \n'%(G.referenceFileNamesList)) + f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referenceFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen @@ -5549,33 +5549,33 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names - AllMoleculesReferenceFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list - for referenceFileNameIndex in range(len(G.referenceFileNamesList)): #Loop through the reference file names list - AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referenceFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory + AllMoleculesreferencePatternsFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list + for referenceFileNameIndex in range(len(G.referencePatternsFileNamesList)): #Loop through the reference file names list + AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory - AllMoleculesReferenceFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name + AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename - AllMoleculesReferenceFileNamesList = copy.copy(G.referenceFileNamesList) + AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesReferenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' PrepareReferenceObjectsAndCorrectionValues(AllMoleculesReferenceDataList[referenceObjectIndex],AllMassFragmentsExperimentData.mass_fragment_numbers, AllMassFragmentsExperimentData) #Read in the molecules used before parsing the user input file - G.referenceFileNamesList = parse.listCast(G.referenceFileNamesList) - G.moleculesNames = getMoleculesFromReferenceData(G.referenceFileNamesList[0]) + G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) + G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) @@ -5611,7 +5611,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): @@ -5619,14 +5619,14 @@ def main(): G.collectedFileUncertainties = int(G.collectedFileUncertainties) #Prints a warning if the user has more reference files than specified time ranges - if len(G.referencePatternTimeRanges) > 0 and (len(G.referenceFileNamesList) > len(G.referencePatternTimeRanges)): + if len(G.referencePatternTimeRanges) > 0 and (len(G.referencePatternsFileNamesList) > len(G.referencePatternTimeRanges)): print("WARNING: There are more reference files given than time ranges") #save global variable into the class objects ExperimentData.ExportAtEachStep = G.ExportAtEachStep #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index 7c75995c3..ebc144c52 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -510,7 +510,7 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -576,7 +576,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternOriginalTuning.csv') if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!! TODO: NEED TO MAKE ExportedReferencePatternDesiredTuning FOR CASE OF THIS IF STATEMENT") - referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. print("line 1489", referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) @@ -625,7 +625,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileExistingTuningAndForm = G.referenceFileExistingTuningAndForm if referenceFileDesiredTuningAndForm == []: print("line 622", G.referenceFormsList) - referenceFileDesiredTuningAndForm = [G.referenceFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternExternal.csv') @@ -796,7 +796,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"] if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients @@ -1646,22 +1646,22 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): return ReferenceData ''' -GenerateReferenceDataAndFormsList takes in the list of referenceFileNamesList and the +GenerateReferenceDataAndFormsList takes in the list of referencePatternsFileNamesList and the list of forms. A list is generated containing MSReference objects created based on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): +def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string - ##If referenceFileNamesList is a string or if form is a string then make them lists - if isinstance(referenceFileNamesList,str): - referenceFileNamesList = [referenceFileNamesList] + ##If referencePatternsFileNamesList is a string or if form is a string then make them lists + if isinstance(referencePatternsFileNamesList,str): + referencePatternsFileNamesList = [referencePatternsFileNamesList] if isinstance(referenceFormsList,str): referenceFormsList = [referenceFormsList] - #If referenceFileNamesList and forms are lists of 1 then create a list of the single MSReference object + #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referenceFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[0],referenceFormsList[0]) + if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1682,7 +1682,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1693,22 +1693,22 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].update_relative_standard_uncertainties() return ReferenceDataList #Otherwise we have multiple reference files and forms - #If just one form is used, make a list of forms that is the same length as referenceFileNamesList + #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList if len(referenceFormsList) == 1: - #Generate a copy of referenceFileNamesList to be overwritten with forms - listOfForms = copy.copy(referenceFileNamesList) + #Generate a copy of referencePatternsFileNamesList to be overwritten with forms + listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form - for i in range(len(referenceFileNamesList)): + for i in range(len(referencePatternsFileNamesList)): listOfForms[i] = referenceFormsList[0] - #If list of forms is the same length of referenceFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referenceFileNamesList): + #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index + elif len(referenceFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms listOfForms = referenceFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list - for i in range(len(referenceFileNamesList)): - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[i],listOfForms[i]) + for i in range(len(referencePatternsFileNamesList)): + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[i],listOfForms[i]) ReferenceDataList.append(MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)) #save each global variable into the class objects ReferenceDataList[i].ExportAtEachStep = G.ExportAtEachStep @@ -1729,7 +1729,7 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -2082,7 +2082,7 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file @@ -2104,28 +2104,28 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): G.oldReferenceFileName = [] G.nextRefFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list #record the old file names G.oldReferenceFileName.append(RefName) #construct the file names for the current run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations - referenceFileNameTemp = G.referenceFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + referenceFileNameTemp = G.referencePatternsFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #copy the experimental and reference files into new names for this iterative run shutil.copy(RefName, referenceFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.referenceFileNamesList[RefIndex] = referenceFileNameTemp + G.referencePatternsFileNamesList[RefIndex] = referenceFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2152,19 +2152,19 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] G.oldReferenceFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list G.oldReferenceFileName.append(RefName) #construct the file names for the first run of the program - G.referenceFileNamesList[RefIndex] = G.referenceFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + G.referencePatternsFileNamesList[RefIndex] = G.referencePatternsFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #construct file names for the second run of the program G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2194,7 +2194,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list #Export current Reference Data #Reference data is trimmed prior to this function - ExportXYYYData(G.referenceFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') + ExportXYYYData(G.referencePatternsFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported @@ -2300,7 +2300,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file G.nextUserInputModule.collectedFileName = G.nextExpFileName - G.nextUserInputModule.referenceFileNamesList = G.nextRefFileName + G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules #Updating the selected masses for the next user input file @@ -2340,12 +2340,12 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): str(iterationDirectoryName), str(G.nextUserInputModule.collectedFileName)) shutil.copy(copyFromPath, os.getcwd()) - for RefIndex, RefName in enumerate(G.nextUserInputModule.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.referenceFileNamesList[RefIndex])) + str(G.nextUserInputModule.referencePatternsFileNamesList[RefIndex])) shutil.copy(copyFromPath, os.getcwd()) #returning to the parent directory os.chdir('..') @@ -2373,7 +2373,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### @@ -5521,7 +5521,7 @@ def PopulateLogFile(): filename6 = 'LogFile.txt' #the log file is printed here f6 = open(filename6,'a') f6.write('\n') - f6.write('referenceFileName = %s \n'%(G.referenceFileNamesList)) + f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referenceFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen @@ -5688,13 +5688,13 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Read in the molecules used before parsing the user input file - G.referenceFileNamesList = parse.listCast(G.referenceFileNamesList) + G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) G.referenceFormsList = parse.listCast(G.referenceFormsList) - G.moleculesNames = getMoleculesFromReferenceData(G.referenceFileNamesList[0]) + G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #If a tuning correction is going to be done, we'll make a mixed reference pattern. #G.moleculesNamesExtended needs to be populated before the first tuning correction and before parsing of userinput. if str(G.measuredReferenceYorN).lower() == 'yes': @@ -5711,20 +5711,20 @@ def main(): #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names - AllMoleculesReferenceFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list - for referenceFileNameIndex in range(len(G.referenceFileNamesList)): #Loop through the reference file names list - AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referenceFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory + AllMoleculesreferencePatternsFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list + for referenceFileNameIndex in range(len(G.referencePatternsFileNamesList)): #Loop through the reference file names list + AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory - AllMoleculesReferenceFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name + AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename - AllMoleculesReferenceFileNamesList = copy.copy(G.referenceFileNamesList) + AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesReferenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' @@ -5762,7 +5762,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): @@ -5770,14 +5770,14 @@ def main(): G.collectedFileUncertainties = int(G.collectedFileUncertainties) #Prints a warning if the user has more reference files than specified time ranges - if len(G.referencePatternTimeRanges) > 0 and (len(G.referenceFileNamesList) > len(G.referencePatternTimeRanges)): + if len(G.referencePatternTimeRanges) > 0 and (len(G.referencePatternsFileNamesList) > len(G.referencePatternTimeRanges)): print("WARNING: There are more reference files given than time ranges") #save global variable into the class objects ExperimentData.ExportAtEachStep = G.ExportAtEachStep #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index 807829aae..c59d9d717 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index 7fd5995b7..6f846ade5 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -8,11 +8,11 @@ ''' def parseUserInput(currentUserInput): #Input Files - currentUserInput.referenceFileNamesList = parse.listCast(currentUserInput.referenceFileNamesList) #referenceFileName needs to be a list - currentUserInput.referenceFileNamesList = parse.stripListOfStrings(currentUserInput.referenceFileNamesList) + currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list + currentUserInput.referencePatternsFileNamesList = parse.stripListOfStrings(currentUserInput.referencePatternsFileNamesList) currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list currentUserInput.referenceFormsList = parse.stripListOfStrings(currentUserInput.referenceFormsList) - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referenceFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string currentUserInput.collectedFileName = currentUserInput.collectedFileName.strip() @@ -224,10 +224,10 @@ def parseUserInput(currentUserInput): if currentUserInput.TSC_List_Type == 'MultipleReferencePatterns': #If using multiple reference patterns then the user must input 1 value to use for each reference file or a value for each reference file #Then parallelize these variables to have the same length as number of reference patterns - currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referenceFileNamesList)) + currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referencePatternsFileNamesList)) #NOTE: vectorizing these lists for 'SeparateMoleculesFactors' occurs in RatioFinder #Output Files @@ -274,7 +274,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #TODO: Consider if G.iterativeAnalysis = True or False should be changed to G.IterativeAnalysis_On or something like that, but will break backwards compatibility unless special care is taken. #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} - SettingsVDictionary['referenceFileNamesList'] = UserChoices['inputFiles']['referenceFileNamesList'] + SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index 5d393d7c7..dd76dfca0 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -523,10 +523,10 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien referenceCorrectionCoefficients = [referenceCorrectionCoefficients['A'],referenceCorrectionCoefficients['B'],referenceCorrectionCoefficients['C']] if measuredReferenceYorN =='yes': if len(referenceFileDesiredTuningAndForm) == 0:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. - if '.csv' in G.referenceFileNamesList[0]: - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. - if '.tsv' in G.referenceFileNamesList[0]: - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.tsv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + if '.csv' in G.referencePatternsFileNamesList[0]: + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + if '.tsv' in G.referencePatternsFileNamesList[0]: + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.tsv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -612,7 +612,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu if len(referenceFileDesiredTuningAndForm) == 0:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. resetReferenceFileDesiredTuningAndForm = True if ReferenceDataExistingTuning.referenceFileNameExtension =='csv': - referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. if ReferenceDataExistingTuning.referenceFileNameExtension =='tsv': referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.tsv","xyyy" ] abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) @@ -659,7 +659,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileExistingTuningAndForm = G.referenceFileStandardTuningAndForm if len(referenceFileDesiredTuningAndForm) == 0: #Use the original reference pattern if blank. resetReferenceFileDesiredTuningAndForm = True - referenceFileDesiredTuningAndForm = [G.referenceFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) if ReferenceDataExistingTuning.referenceFileNameExtension == 'csv': @@ -716,7 +716,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileExistingTuningAndForm = G.referenceFileStandardTuningAndForm if len(referenceFileDesiredTuningAndForm) == 0: #Use the original reference pattern if blank. resetReferenceFileDesiredTuningAndForm = True - referenceFileDesiredTuningAndForm = [G.referenceFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) if ReferenceDataExistingTuning.referenceFileNameExtension == 'csv': @@ -1419,7 +1419,7 @@ def CorrectionValuesObtain(ReferenceData): #NEED AN IF STATEMENT TO DETERMINE THESE COEFFICENTS FROM GAS MIXTURE IF USING THAT. if str(G.referenceFileStandardTuningAndForm[0]).lower() != 'gaxmixture': if len(G.referenceFileDesiredTuningAndForm) == 0: #Use the original reference pattern if blank. - referenceFileDesiredTuningAndForm = [G.referenceFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referenceFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. else: referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm abcCoefficients, abcCoefficients_covmat = ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm=referenceFileDesiredTuningAndForm, ReferencePatternDesiredTuning_FileNameAndForm = G.referenceFileStandardTuningAndForm, exportCoefficients=False) #We will separately export the coefficents for this usage. @@ -1954,22 +1954,22 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): return ReferenceData ''' -GenerateReferenceDataAndFormsList takes in the list of referenceFileNamesList and the +GenerateReferenceDataAndFormsList takes in the list of referencePatternsFileNamesList and the list of forms. A list is generated containing MSReference objects created based on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): +def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string - ##If referenceFileNamesList is a string or if form is a string then make them lists - if isinstance(referenceFileNamesList,str): - referenceFileNamesList = [referenceFileNamesList] + ##If referencePatternsFileNamesList is a string or if form is a string then make them lists + if isinstance(referencePatternsFileNamesList,str): + referencePatternsFileNamesList = [referencePatternsFileNamesList] if isinstance(referenceFormsList,str): referenceFormsList = [referenceFormsList] - #If referenceFileNamesList and forms are lists of 1 then create a list of the single MSReference object + #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referenceFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[0],referenceFormsList[0]) + if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1990,11 +1990,11 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - if '.csv' in referenceFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + if '.csv' in referencePatternsFileNamesList[0]: + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. - if '.tsv' in referenceFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referenceFormsList[0]) + if '.tsv' in referencePatternsFileNamesList[0]: + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referenceFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -2005,22 +2005,22 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[0].update_relative_standard_uncertainties() return ReferenceDataList #Otherwise we have multiple reference files and forms - #If just one form is used, make a list of forms that is the same length as referenceFileNamesList + #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList if len(referenceFormsList) == 1: - #Generate a copy of referenceFileNamesList to be overwritten with forms - listOfForms = copy.copy(referenceFileNamesList) + #Generate a copy of referencePatternsFileNamesList to be overwritten with forms + listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form - for i in range(len(referenceFileNamesList)): + for i in range(len(referencePatternsFileNamesList)): listOfForms[i] = referenceFormsList[0] - #If list of forms is the same length of referenceFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referenceFileNamesList): + #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index + elif len(referenceFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms listOfForms = referenceFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list - for i in range(len(referenceFileNamesList)): - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referenceFileNamesList[i],listOfForms[i]) + for i in range(len(referencePatternsFileNamesList)): + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[i],listOfForms[i]) ReferenceDataList.append(MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)) #save each global variable into the class objects ReferenceDataList[i].ExportAtEachStep = G.ExportAtEachStep @@ -2041,10 +2041,10 @@ def GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_O ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - if '.csv'in referenceFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) - if '.tsv'in referenceFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referenceFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referenceFormsList[i]) + if '.csv'in referencePatternsFileNamesList[0]: + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + if '.tsv'in referencePatternsFileNamesList[0]: + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referenceFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -2402,7 +2402,7 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file @@ -2424,28 +2424,28 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): G.oldReferenceFileName = [] G.nextRefFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list #record the old file names G.oldReferenceFileName.append(RefName) #construct the file names for the current run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations - referenceFileNameTemp = G.referenceFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + referenceFileNameTemp = G.referencePatternsFileNamesList[RefIndex][:-18] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #copy the experimental and reference files into new names for this iterative run shutil.copy(RefName, referenceFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.referenceFileNamesList[RefIndex] = referenceFileNameTemp + G.referencePatternsFileNamesList[RefIndex] = referenceFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2472,19 +2472,19 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] G.oldReferenceFileName = [] - for RefIndex, RefName in enumerate(G.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list G.oldReferenceFileName.append(RefName) #construct the file names for the first run of the program - G.referenceFileNamesList[RefIndex] = G.referenceFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referenceFileNamesList[RefIndex][-4:] + G.referencePatternsFileNamesList[RefIndex] = G.referencePatternsFileNamesList[RefIndex][:-4] + str(G.iterationSuffix) + G.referencePatternsFileNamesList[RefIndex][-4:] #construct file names for the second run of the program G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2514,7 +2514,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list #Export current Reference Data #Reference data is trimmed prior to this function - ExportXYYYData(G.referenceFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') + ExportXYYYData(G.referencePatternsFileNamesList[RefObjectIndex], RefObject.provided_reference_patterns, RefObject.molecules, abscissaHeader = 'M/Z') #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported @@ -2620,7 +2620,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file G.nextUserInputModule.collectedFileName = G.nextExpFileName - G.nextUserInputModule.referenceFileNamesList = G.nextRefFileName + G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules #Updating the selected masses for the next user input file @@ -2660,12 +2660,12 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): str(iterationDirectoryName), str(G.nextUserInputModule.collectedFileName)) shutil.copy(copyFromPath, os.getcwd()) - for RefIndex, RefName in enumerate(G.nextUserInputModule.referenceFileNamesList): #a list + for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.referenceFileNamesList[RefIndex])) + str(G.nextUserInputModule.referencePatternsFileNamesList[RefIndex])) shutil.copy(copyFromPath, os.getcwd()) #returning to the parent directory os.chdir('..') @@ -2693,7 +2693,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referenceFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### @@ -5966,7 +5966,7 @@ def PopulateLogFile(): filename6 = 'LogFile.txt' #the log file is printed here f6 = open(filename6,'a') f6.write('\n') - f6.write('referenceFileName = %s \n'%(G.referenceFileNamesList)) + f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referenceFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen @@ -6212,16 +6212,16 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Read in the molecules used before parsing the user input file - G.referenceFileNamesList = parse.listCast(G.referenceFileNamesList) + G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) G.referenceFormsList = parse.listCast(G.referenceFormsList) [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, - mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(G.referenceFileNamesList[0], G.referenceFormsList[0]) + mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(G.referencePatternsFileNamesList[0], G.referenceFormsList[0]) G.moleculesNames = molecules @@ -6249,20 +6249,20 @@ def main(): #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names - AllMoleculesReferenceFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list - for referenceFileNameIndex in range(len(G.referenceFileNamesList)): #Loop through the reference file names list - AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referenceFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory + AllMoleculesreferencePatternsFileNamesList = [] #Initialize AllMoleculesReferenceDataList as an empty list + for referenceFileNameIndex in range(len(G.referencePatternsFileNamesList)): #Loop through the reference file names list + AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory - AllMoleculesReferenceFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name + AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename - AllMoleculesReferenceFileNamesList = copy.copy(G.referenceFileNamesList) + AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesReferenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder global PreparingAllMoleculesReferenceDataList; PreparingAllMoleculesReferenceDataList = False #initializing this flag for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): @@ -6302,7 +6302,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referenceFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): @@ -6310,14 +6310,14 @@ def main(): G.collectedFileUncertainties = int(G.collectedFileUncertainties) #Prints a warning if the user has more reference files than specified time ranges - if len(G.referencePatternTimeRanges) > 0 and (len(G.referenceFileNamesList) > len(G.referencePatternTimeRanges)): + if len(G.referencePatternTimeRanges) > 0 and (len(G.referencePatternsFileNamesList) > len(G.referencePatternTimeRanges)): print("WARNING: There are more reference files given than time ranges") #save global variable into the class objects ExperimentData.ExportAtEachStep = G.ExportAtEachStep #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referenceFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/UnitTests/ConcentrationFinder/test_1.py b/UnitTests/ConcentrationFinder/test_1.py index 26d5abe09..da65bbf8c 100644 --- a/UnitTests/ConcentrationFinder/test_1.py +++ b/UnitTests/ConcentrationFinder/test_1.py @@ -23,7 +23,7 @@ #Replace the global variables being pointed to in MSRESOLVE #This reference file has two molecules: Acetaldehyde and Acetaldehyde_easy_to_ionize #They are identical with the exceptions that Acetaldehyde has an ionization factor of 1 and signal peaks at m29 and m29.2 are 9999 and 0, respectively, and Acetaldehyde_easy_to_ionize has an ionization factor of 2 and signal peaks at m29 and m29.2 are 0 and 9999, respectively. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_test_1.csv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_1.csv'] #Use the truncated reference data that contains only m29 and m29.2 with signals of 1 for each time for both mass fragments MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.concentrationFinder = 'yes' #Turn on concentrationFinder diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py index d4e8951b8..92593777a 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py index ebd3798cc..5594e4f4a 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ConcentrationFinder/test_2.py b/UnitTests/ConcentrationFinder/test_2.py index 66f1ce362..e0e8eaddc 100644 --- a/UnitTests/ConcentrationFinder/test_2.py +++ b/UnitTests/ConcentrationFinder/test_2.py @@ -23,7 +23,7 @@ #Replace the global variables being pointed to in MSRESOLVE #This reference file has two molecules: Acetaldehyde and Acetaldehyde_easy_to_ionize #They are identical with the exceptions that Acetaldehyde has an ionization factor of 1 and signal peaks at m29 and m29.2 are 9999 and 0, respectively, and Acetaldehyde_easy_to_ionize has an ionization factor of 2 and signal peaks at m29 and m29.2 are 0 and 9999, respectively. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_test_2.csv','AcetaldehydeNISTRefMixed2_test_2.csv'] #List the reference file twice +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_2.csv','AcetaldehydeNISTRefMixed2_test_2.csv'] #List the reference file twice MSRESOLVE.G.referencePatternTimeRanges = [[1,4],[5,8]] #Give time ranges for each reference file #Use the truncated reference data that contains only m29 and m29.2 with signals of 1 for each time for both mass fragments MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated2.csv' diff --git a/UnitTests/ConcentrationFinder/test_3.py b/UnitTests/ConcentrationFinder/test_3.py index d300a3287..77ff7202c 100644 --- a/UnitTests/ConcentrationFinder/test_3.py +++ b/UnitTests/ConcentrationFinder/test_3.py @@ -24,7 +24,7 @@ #This reference file has three molecules: Acetaldehyde, Acetaldehyde_easy_to_ionize, and Acetaldehyde_copy #Acetaldehdye and Acetaldehyde_easy_to_ionize are identical with the exceptions that Acetaldehyde has an ionization factor of 1 and signal peaks at m29 and m29.2 are 9999 and 0, respectively, and Acetaldehyde_easy_to_ionize has an ionization factor of 2 and signal peaks at m29 and m29.2 are 0 and 9999, respectively. #Acetaldehyde and Acetaldheyde_copy are identical except Acetaldehyde has a signal of 9999 at m29 and 0 at m29.3. Acetaldehyde_copy is the opposite having a signal of 0 at m29 and 9999 at m29.3. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_test_3.csv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_3.csv'] #Use the truncated reference data that contains only m29 and m29.2 with signals of 1 for each time for both mass fragments MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated3.csv' MSRESOLVE.G.concentrationFinder = 'yes' #Turn on concentrationFinder diff --git a/UnitTests/ConcentrationFinder/test_4.py b/UnitTests/ConcentrationFinder/test_4.py index 3382cf220..4a8a71082 100644 --- a/UnitTests/ConcentrationFinder/test_4.py +++ b/UnitTests/ConcentrationFinder/test_4.py @@ -23,7 +23,7 @@ #Replace the global variables being pointed to in MSRESOLVE #This reference file has two molecules: Acetaldehyde and Acetaldehyde_easy_to_ionize #They are identical with the exceptions that Acetaldehyde has an ionization factor of 1 and signal peaks at m29 and m29.2 are 9999 and 0, respectively, and Acetaldehyde_easy_to_ionize has an ionization factor of 2 and signal peaks at m29 and m29.2 are 0 and 9999, respectively. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_test_2.csv','AcetaldehydeNISTRefMixed2_test_2.csv'] #List the reference file twice +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_2.csv','AcetaldehydeNISTRefMixed2_test_2.csv'] #List the reference file twice MSRESOLVE.G.referencePatternTimeRanges = [[1,1],[8,8]] #Give time ranges for each reference file (Every point that is not at 1 or 8 will need to be interpolated) #Use the truncated reference data that contains only 8 points with a signal of 1 for m29 MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated2.csv' diff --git a/UnitTests/ExtractReferencePatternFromData/test_1_input.py b/UnitTests/ExtractReferencePatternFromData/test_1_input.py index 705cf3cf8..85c7e3c2a 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_1_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_1_input.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_2_input.py b/UnitTests/ExtractReferencePatternFromData/test_2_input.py index 67e3fbb3e..86948aa68 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_2_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_2_input.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_3_input.py b/UnitTests/ExtractReferencePatternFromData/test_3_input.py index 9a3743ee4..577aec81c 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_3_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_3_input.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_4_input.py b/UnitTests/ExtractReferencePatternFromData/test_4_input.py index 836a60c8e..b4cd1144e 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_4_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_4_input.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_5_input.py b/UnitTests/ExtractReferencePatternFromData/test_5_input.py index da82644a6..90f81e9ba 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_5_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_5_input.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_6_input.py b/UnitTests/ExtractReferencePatternFromData/test_6_input.py index 7e70f0e0a..dc10ebac2 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_6_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_6_input.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index afb40a259..b7eb8d9d0 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IonizationFactors/test_1.py b/UnitTests/IonizationFactors/test_1.py index 2e1b0cc60..642b9add8 100644 --- a/UnitTests/IonizationFactors/test_1.py +++ b/UnitTests/IonizationFactors/test_1.py @@ -21,7 +21,7 @@ suffix = ut.returnDigitFromFilename(__file__) #This replaces the globals variables being pointed to in MSRESOLVE -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefKnownFactors.csv'] #Overwrite with desired reference file +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefKnownFactors.csv'] #Overwrite with desired reference file MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' diff --git a/UnitTests/IonizationFactors/test_2.py b/UnitTests/IonizationFactors/test_2.py index 8b5a2c390..dc28d3e67 100644 --- a/UnitTests/IonizationFactors/test_2.py +++ b/UnitTests/IonizationFactors/test_2.py @@ -23,7 +23,7 @@ ##First Test input - First reference file #This replaces the globals variables being pointed to in MSRESOLVE -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefMatchingMolecule.csv'] #Overwrite with desired reference file +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMatchingMolecule.csv'] #Overwrite with desired reference file MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' diff --git a/UnitTests/IonizationFactors/test_3.py b/UnitTests/IonizationFactors/test_3.py index 6dc094048..6f5a7f581 100644 --- a/UnitTests/IonizationFactors/test_3.py +++ b/UnitTests/IonizationFactors/test_3.py @@ -22,7 +22,7 @@ ##First Test input - First reference file #This replaces the globals variables being pointed to in MSRESOLVE -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefKnownTypes.csv'] #Overwrite with desired reference file +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefKnownTypes.csv'] #Overwrite with desired reference file MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' diff --git a/UnitTests/IonizationFactors/test_4.py b/UnitTests/IonizationFactors/test_4.py index d26e52e28..9d29faa0c 100644 --- a/UnitTests/IonizationFactors/test_4.py +++ b/UnitTests/IonizationFactors/test_4.py @@ -22,7 +22,7 @@ ##First Test input - First reference file #This replaces the globals variables being pointed to in MSRESOLVE -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeNISTRefDefault.csv'] #Overwrite with desired reference file +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefDefault.csv'] #Overwrite with desired reference file MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' diff --git a/UnitTests/IterativeAnalysis/_iter_1/UserInput_iter_1.py b/UnitTests/IterativeAnalysis/_iter_1/UserInput_iter_1.py index 1b657bf1a..5d9bd393c 100644 --- a/UnitTests/IterativeAnalysis/_iter_1/UserInput_iter_1.py +++ b/UnitTests/IterativeAnalysis/_iter_1/UserInput_iter_1.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated.csv' referencePatternTimeRanges = [] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = '' iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysis/_iter_2/UserInput_iter_2.py b/UnitTests/IterativeAnalysis/_iter_2/UserInput_iter_2.py index 4164fad2b..4083f6235 100644 --- a/UnitTests/IterativeAnalysis/_iter_2/UserInput_iter_2.py +++ b/UnitTests/IterativeAnalysis/_iter_2/UserInput_iter_2.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_1.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.2700946000000002 iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['(E) 2-Butenal (Crotonaldehyde'] chosenMassFragments = [39] diff --git a/UnitTests/IterativeAnalysis/_iter_3/UserInput_iter_3.py b/UnitTests/IterativeAnalysis/_iter_3/UserInput_iter_3.py index 596e6efe8..05df4af9f 100644 --- a/UnitTests/IterativeAnalysis/_iter_3/UserInput_iter_3.py +++ b/UnitTests/IterativeAnalysis/_iter_3/UserInput_iter_3.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_2.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.28897450000000013 iterationNumber = 2 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethanol'] chosenMassFragments = [31] diff --git a/UnitTests/IterativeAnalysis/_iter_4/UserInput_iter_4.py b/UnitTests/IterativeAnalysis/_iter_4/UserInput_iter_4.py index d040b4013..88c707016 100644 --- a/UnitTests/IterativeAnalysis/_iter_4/UserInput_iter_4.py +++ b/UnitTests/IterativeAnalysis/_iter_4/UserInput_iter_4.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_3.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.33806340000000024 iterationNumber = 3 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['H2O'] chosenMassFragments = [18] diff --git a/UnitTests/IterativeAnalysis/_iter_5/UserInput_iter_5.py b/UnitTests/IterativeAnalysis/_iter_5/UserInput_iter_5.py index 7f483dd7f..3bcd3005e 100644 --- a/UnitTests/IterativeAnalysis/_iter_5/UserInput_iter_5.py +++ b/UnitTests/IterativeAnalysis/_iter_5/UserInput_iter_5.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_4.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.29744729999999997 iterationNumber = 4 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Acetaldehyde'] chosenMassFragments = [41] diff --git a/UnitTests/IterativeAnalysis/_iter_6/UserInput_iter_6.py b/UnitTests/IterativeAnalysis/_iter_6/UserInput_iter_6.py index 54f38d0d1..fe2bb624b 100644 --- a/UnitTests/IterativeAnalysis/_iter_6/UserInput_iter_6.py +++ b/UnitTests/IterativeAnalysis/_iter_6/UserInput_iter_6.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_5.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.31938140000000015 iterationNumber = 5 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethylene (Ethene)'] chosenMassFragments = [27] diff --git a/UnitTests/IterativeAnalysis/_iter_7/UserInput_iter_7.py b/UnitTests/IterativeAnalysis/_iter_7/UserInput_iter_7.py index 8ca12820f..16c7e47d2 100644 --- a/UnitTests/IterativeAnalysis/_iter_7/UserInput_iter_7.py +++ b/UnitTests/IterativeAnalysis/_iter_7/UserInput_iter_7.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_6.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.2832543999999997 iterationNumber = 6 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['CO', 'CO2', 'H2'] chosenMassFragments = [2, 28, 44] diff --git a/UnitTests/IterativeAnalysis/_iter_8/UserInput_iter_8.py b/UnitTests/IterativeAnalysis/_iter_8/UserInput_iter_8.py index 27484c82d..4b3ccce0b 100644 --- a/UnitTests/IterativeAnalysis/_iter_8/UserInput_iter_8.py +++ b/UnitTests/IterativeAnalysis/_iter_8/UserInput_iter_8.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_7.csv' referencePatternTimeRanges = [] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = 0.5683270000000009 iterationNumber = 7 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py index 0dd86e636..7c45ac4b8 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.tsv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.tsv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py index 00c23dd58..87d5b9a60 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_1/UserInput_iter_1.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_1/UserInput_iter_1.py index bf08c75bd..28da6e597 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_1/UserInput_iter_1.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_1/UserInput_iter_1.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated.csv' referencePatternTimeRanges = [] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = '' iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_2/UserInput_iter_2.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_2/UserInput_iter_2.py index c734fc546..c82d56261 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_2/UserInput_iter_2.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_2/UserInput_iter_2.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_1.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.25305359999999943 iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['(E) 2-Butenal (Crotonaldehyde'] chosenMassFragments = [39] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_3/UserInput_iter_3.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_3/UserInput_iter_3.py index 85279a353..11879fa0c 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_3/UserInput_iter_3.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_3/UserInput_iter_3.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_2.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.21749119999999955 iterationNumber = 2 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethanol'] chosenMassFragments = [31] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_4/UserInput_iter_4.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_4/UserInput_iter_4.py index 68bf88f34..3110dd8fc 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_4/UserInput_iter_4.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_4/UserInput_iter_4.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_3.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.19979480000000027 iterationNumber = 3 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['H2O'] chosenMassFragments = [18] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_5/UserInput_iter_5.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_5/UserInput_iter_5.py index 0a4e7eff8..a08a78c83 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_5/UserInput_iter_5.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_5/UserInput_iter_5.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_4.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.23163160000000005 iterationNumber = 4 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Acetaldehyde'] chosenMassFragments = [41] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_6/UserInput_iter_6.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_6/UserInput_iter_6.py index f11923252..2140e5586 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_6/UserInput_iter_6.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_6/UserInput_iter_6.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_5.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.22055640000000043 iterationNumber = 5 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethylene (Ethene)'] chosenMassFragments = [27] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_7/UserInput_iter_7.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_7/UserInput_iter_7.py index a853d53ae..3cd9012a0 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_7/UserInput_iter_7.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_7/UserInput_iter_7.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_6.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.22843590000000003 iterationNumber = 6 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['CO', 'CO2', 'H2'] chosenMassFragments = [2, 28, 44] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_8/UserInput_iter_8.py b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_8/UserInput_iter_8.py index d812937b5..9642500ab 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/_iter_8/UserInput_iter_8.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/_iter_8/UserInput_iter_8.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_7.csv' referencePatternTimeRanges = [] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = 0.4921106000000002 iterationNumber = 7 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py index 1dbc58bc0..2a47b6ed6 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py index 456a8d314..be31fc2fc 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_1/UserInput_iter_1.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_1/UserInput_iter_1.py index 4b5e7b704..f74aca864 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_1/UserInput_iter_1.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_1/UserInput_iter_1.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv', 'AcetaldehydeNISTRefMixed2Edit.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv', 'AcetaldehydeNISTRefMixed2Edit.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = '' iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_2/UserInput_iter_2.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_2/UserInput_iter_2.py index a540c05de..26859b4db 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_2/UserInput_iter_2.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_2/UserInput_iter_2.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_1.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_1.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_1.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.21222889999999994 iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['(E) 2-Butenal (Crotonaldehyde'] chosenMassFragments = [39] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_3/UserInput_iter_3.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_3/UserInput_iter_3.py index e4145c3b9..35e5f1648 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_3/UserInput_iter_3.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_3/UserInput_iter_3.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_2.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_2.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.25337740000000064 iterationNumber = 2 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethanol'] chosenMassFragments = [31] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_4/UserInput_iter_4.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_4/UserInput_iter_4.py index c2bde4cb2..8aeae6000 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_4/UserInput_iter_4.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_4/UserInput_iter_4.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_3.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_3.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_3.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.21332720000000016 iterationNumber = 3 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['H2O'] chosenMassFragments = [18] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_5/UserInput_iter_5.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_5/UserInput_iter_5.py index af18aa96c..4f35f2c8d 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_5/UserInput_iter_5.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_5/UserInput_iter_5.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_4.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_4.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_4.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.2195286000000003 iterationNumber = 4 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Acetaldehyde'] chosenMassFragments = [41] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_6/UserInput_iter_6.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_6/UserInput_iter_6.py index e9094529a..d455b4417 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_6/UserInput_iter_6.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_6/UserInput_iter_6.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_5.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_5.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_5.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.20479350000000007 iterationNumber = 5 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethylene (Ethene)'] chosenMassFragments = [27] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_7/UserInput_iter_7.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_7/UserInput_iter_7.py index c19aa1c68..7f49b586f 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_7/UserInput_iter_7.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_7/UserInput_iter_7.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_6.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_6.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_6.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.3251596999999995 iterationNumber = 6 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['CO', 'CO2', 'H2'] chosenMassFragments = [2, 28, 44] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_8/UserInput_iter_8.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_8/UserInput_iter_8.py index a3311c0b4..caaec2101 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_8/UserInput_iter_8.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/_iter_8/UserInput_iter_8.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_7.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_7.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_7.csv' referencePatternTimeRanges = [[176, 200], [250, 400]] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = 0.6123443999999996 iterationNumber = 7 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py index 1f93f892f..e30c12e1d 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,200],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py index 4f6733dfc..55f178b03 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,200],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_1/UserInput_iter_1.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_1/UserInput_iter_1.py index d7f07109c..c421bfd6d 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_1/UserInput_iter_1.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_1/UserInput_iter_1.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv', 'AcetaldehydeNISTRefMixed2Edit.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv', 'AcetaldehydeNISTRefMixed2Edit.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = '' iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_2/UserInput_iter_2.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_2/UserInput_iter_2.py index 2c785bbac..a215fd561 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_2/UserInput_iter_2.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_2/UserInput_iter_2.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_1.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_1.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_1.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.26504939999999966 iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['(E) 2-Butenal (Crotonaldehyde'] chosenMassFragments = [39] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_3/UserInput_iter_3.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_3/UserInput_iter_3.py index bee15bb03..3c0a0c655 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_3/UserInput_iter_3.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_3/UserInput_iter_3.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_2.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_2.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.22017280000000028 iterationNumber = 2 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethanol'] chosenMassFragments = [31] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_4/UserInput_iter_4.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_4/UserInput_iter_4.py index 5c5b31a55..6577cf457 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_4/UserInput_iter_4.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_4/UserInput_iter_4.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_3.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_3.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_3.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.2981669999999994 iterationNumber = 3 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['H2O'] chosenMassFragments = [18] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_5/UserInput_iter_5.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_5/UserInput_iter_5.py index d10710a46..bfa8ca068 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_5/UserInput_iter_5.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_5/UserInput_iter_5.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_4.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_4.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_4.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.22669989999999984 iterationNumber = 4 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Acetaldehyde'] chosenMassFragments = [41] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_6/UserInput_iter_6.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_6/UserInput_iter_6.py index 884203c45..ac7131878 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_6/UserInput_iter_6.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_6/UserInput_iter_6.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_5.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_5.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_5.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.2669712999999998 iterationNumber = 5 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethylene (Ethene)'] chosenMassFragments = [27] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_7/UserInput_iter_7.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_7/UserInput_iter_7.py index 3b5e79169..90ee8f903 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_7/UserInput_iter_7.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_7/UserInput_iter_7.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_6.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_6.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_6.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.24958249999999982 iterationNumber = 6 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['CO', 'CO2', 'H2'] chosenMassFragments = [2, 28, 44] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_8/UserInput_iter_8.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_8/UserInput_iter_8.py index 347bc4c0b..81f89bf33 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_8/UserInput_iter_8.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/_iter_8/UserInput_iter_8.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_7.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv', 'AcetaldehydeNISTRefMixed2Edit_unused_iter_7.csv'] referenceFormsList = ['xyyy', 'xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_7.csv' referencePatternTimeRanges = [[176, 250], [250, 400]] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = 0.5310279000000007 iterationNumber = 7 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py index e633eb5aa..268222d78 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,250],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py index 4b53e814d..d065accf5 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,250],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_1/UserInput_iter_1.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_1/UserInput_iter_1.py index 6d2c26581..0c90c7359 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_1/UserInput_iter_1.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_1/UserInput_iter_1.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated.csv' referencePatternTimeRanges = [] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = '' iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_2/UserInput_iter_2.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_2/UserInput_iter_2.py index e85db67c2..94c0096ab 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_2/UserInput_iter_2.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_2/UserInput_iter_2.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_1.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_1.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.2758489000000002 iterationNumber = 1 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['H2O'] chosenMassFragments = [18] diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_3/UserInput_iter_3.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_3/UserInput_iter_3.py index 72c64f41f..39387920c 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_3/UserInput_iter_3.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_3/UserInput_iter_3.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_2.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_2.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.21335589999999982 iterationNumber = 2 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['H2'] chosenMassFragments = [2] diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_4/UserInput_iter_4.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_4/UserInput_iter_4.py index 80aaaff36..a594a2d00 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_4/UserInput_iter_4.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_4/UserInput_iter_4.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_3.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_3.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.26022700000000043 iterationNumber = 3 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['(E) 2-Butenal (Crotonaldehyde'] chosenMassFragments = [39] diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_5/UserInput_iter_5.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_5/UserInput_iter_5.py index 78541e4f1..0f0fad3b8 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_5/UserInput_iter_5.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_5/UserInput_iter_5.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_4.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_4.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.2105448000000001 iterationNumber = 4 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Ethanol'] chosenMassFragments = [31] diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_6/UserInput_iter_6.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_6/UserInput_iter_6.py index 2ce2eca32..a2628045e 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_6/UserInput_iter_6.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_6/UserInput_iter_6.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_5.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_5.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.25773820000000036 iterationNumber = 5 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['Acetaldehyde'] chosenMassFragments = [41] diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_7/UserInput_iter_7.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_7/UserInput_iter_7.py index 5acd1fbfc..1a820cbfa 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_7/UserInput_iter_7.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_7/UserInput_iter_7.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_6.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_6.csv' referencePatternTimeRanges = [] @@ -119,6 +119,6 @@ timeSinceLastCheckpoint = 0.22400719999999996 iterationNumber = 6 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] chosenMoleculesNames = ['CO', 'CO2','Ethylene (Ethene)'] chosenMassFragments = [27, 28, 44] diff --git a/UnitTests/IterativeAnalysisScaleRawData/_iter_8/UserInput_iter_8.py b/UnitTests/IterativeAnalysisScaleRawData/_iter_8/UserInput_iter_8.py index 18fba89f8..fe8a97184 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/_iter_8/UserInput_iter_8.py +++ b/UnitTests/IterativeAnalysisScaleRawData/_iter_8/UserInput_iter_8.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv'] +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_unused_iter_7.csv'] referenceFormsList = ['xyyy'] collectedFileName = '2-CrotAcetExp#2Truncated_remaining_iter_7.csv' referencePatternTimeRanges = [] @@ -119,4 +119,4 @@ timeSinceLastCheckpoint = 0.6084944999999999 iterationNumber = 7 -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','tuningCorrectPatternInternalVsExternal','referenceFileStandardTuningAndForm','createMixedTuningPattern','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations','referenceFileUncertainties','collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties','referenceCorrectionCoefficientsIonizationUncertainties','answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','implicitSLScorrection','implicitSLSRecursion','finalOptimization','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py index 7e8cc7c73..9aacffd99 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information +referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py index 892a4b1fd..a190b36ea 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index 7e2fe3606..93e1a1c4f 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py index 7d3bcd96d..151dbecc6 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py index 039bab41e..fd2973d77 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py index 368ae1347..2a911dff0 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[300,303],[306,309]] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ReferencePatternTimeChooser/test_2_input.py b/UnitTests/ReferencePatternTimeChooser/test_2_input.py index 423d18772..2169adca4 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_2_input.py +++ b/UnitTests/ReferencePatternTimeChooser/test_2_input.py @@ -6,7 +6,7 @@ #USER INPUT FILE #//Input Files// -referenceFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information +referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[300,303],[306,309]] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/TuningCorrector/test_1.py b/UnitTests/TuningCorrector/test_1.py index 971d5e68f..ce6036463 100644 --- a/UnitTests/TuningCorrector/test_1.py +++ b/UnitTests/TuningCorrector/test_1.py @@ -22,7 +22,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = False diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff index 6eaa01e94..8c05360d5 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff @@ -22,7 +22,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff index da04b764f..16e1f739f 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff @@ -22,7 +22,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff index 6eaa01e94..8c05360d5 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff @@ -22,7 +22,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_10.py b/UnitTests/TuningCorrector/test_10.py index 4f81a5f7b..008375e45 100644 --- a/UnitTests/TuningCorrector/test_10.py +++ b/UnitTests/TuningCorrector/test_10.py @@ -22,7 +22,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff index 6eaa01e94..8c05360d5 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff @@ -22,7 +22,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff index 72c7fc0ca..e0cd814ed 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff @@ -22,7 +22,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff index 72c7fc0ca..e0cd814ed 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff @@ -22,7 +22,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_11.py b/UnitTests/TuningCorrector/test_11.py index 80b4b777c..7fd23eedc 100644 --- a/UnitTests/TuningCorrector/test_11.py +++ b/UnitTests/TuningCorrector/test_11.py @@ -22,7 +22,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_2.py b/UnitTests/TuningCorrector/test_2.py index e54d0967d..facb7e58f 100644 --- a/UnitTests/TuningCorrector/test_2.py +++ b/UnitTests/TuningCorrector/test_2.py @@ -22,7 +22,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = False diff --git a/UnitTests/TuningCorrector/test_3.py b/UnitTests/TuningCorrector/test_3.py index 33fbe4e82..47916aaba 100644 --- a/UnitTests/TuningCorrector/test_3.py +++ b/UnitTests/TuningCorrector/test_3.py @@ -22,11 +22,11 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = False -MSRESOLVE.G.referenceFileNamesList[0] = 'ReferenceLiterature.tsv' +MSRESOLVE.G.referencePatternsFileNamesList[0] = 'ReferenceLiterature.tsv' MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceCollected.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuningAndForm =['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_4.py b/UnitTests/TuningCorrector/test_4.py index da9bb7b5e..179f3a120 100644 --- a/UnitTests/TuningCorrector/test_4.py +++ b/UnitTests/TuningCorrector/test_4.py @@ -22,7 +22,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'External' MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True diff --git a/UnitTests/TuningCorrector/test_5.py b/UnitTests/TuningCorrector/test_5.py index cfff0c208..33abc09de 100644 --- a/UnitTests/TuningCorrector/test_5.py +++ b/UnitTests/TuningCorrector/test_5.py @@ -22,7 +22,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_6.py b/UnitTests/TuningCorrector/test_6.py index d47645afc..b82e604ed 100644 --- a/UnitTests/TuningCorrector/test_6.py +++ b/UnitTests/TuningCorrector/test_6.py @@ -22,7 +22,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileStandardTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_7.py b/UnitTests/TuningCorrector/test_7.py index a8bbf318d..cd0440250 100644 --- a/UnitTests/TuningCorrector/test_7.py +++ b/UnitTests/TuningCorrector/test_7.py @@ -23,7 +23,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.measuredReferenceYorN = 'yes' MSRESOLVE.G.createMixedTuningPattern = True diff --git a/UnitTests/TuningCorrector/test_8.py b/UnitTests/TuningCorrector/test_8.py index 7c7e01491..c9daaadea 100644 --- a/UnitTests/TuningCorrector/test_8.py +++ b/UnitTests/TuningCorrector/test_8.py @@ -21,7 +21,7 @@ suffix = ut.returnDigitFromFilename(__file__) -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasured.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.measuredReferenceYorN = 'yes' diff --git a/UnitTests/TuningCorrector/test_9.py b/UnitTests/TuningCorrector/test_9.py index 3634d1fc8..f4a051f68 100644 --- a/UnitTests/TuningCorrector/test_9.py +++ b/UnitTests/TuningCorrector/test_9.py @@ -21,7 +21,7 @@ suffix = ut.returnDigitFromFilename(__file__) -MSRESOLVE.G.referenceFileNamesList = ['AcetaldehydeMeasuredShortened.tsv'] +MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasuredShortened.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. diff --git a/UnitTests/TuningCorrectorGasMixture/0-README.txt b/UnitTests/TuningCorrectorGasMixture/0-README.txt index 7b9fef02a..d94255113 100644 --- a/UnitTests/TuningCorrectorGasMixture/0-README.txt +++ b/UnitTests/TuningCorrectorGasMixture/0-README.txt @@ -10,7 +10,7 @@ Proc Doc type things: -- First added at line 5351 if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: -- Now make a reference object from LiteratureReference.tsv so that simulated signals can be made. - -- GenerateReferenceDataList(referenceFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): + -- GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): -- Need to be careful because "ReferenceInputPreProcessing" is being used. diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index 73050260f..6bfc1e72d 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index cd8c47351..fd331d6fd 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index 71229e2e6..357498791 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index 3f8f329b7..4c7e43c2f 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index 770c30e56..54d994a4f 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYXY.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYXY.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyxy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index 52610d7a8..a781c4457 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYYY.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYYY.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index d67212fd0..734164e32 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index 7e3c591c3..5d93c38c0 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index 51ad1e9df..41b4cf05b 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['reference_measured_EthyleneExtracted.csv'] +referencePatternsFileNamesList = ['reference_measured_EthyleneExtracted.csv'] referenceFormsList = 'xyyy' collectedFileName = 'Ethylene.csv' referencePatternTimeRanges = [] @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index 2eda4e3f7..bfa6a5220 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -1,4 +1,4 @@ -referenceFileNamesList = ['reference_measured_EthyleneExtracted.csv'] +referencePatternsFileNamesList = ['reference_measured_EthyleneExtracted.csv'] referenceFormsList = 'xyyy' collectedFileName = 'Ethylene.csv' referencePatternTimeRanges = [] @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index 44bdc278a..bfd4ff7fe 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index 995911149..9156004f7 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index 16e002822..c61c74794 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index 4ef91f562..b5480da21 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index f32896ee3..4b1e2b2ba 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index 5e1ea2bb1..cf71eb5de 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index af1ad32db..53f326cf3 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index 9e66b01ff..a24083888 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index 23e38d878..94cd6057b 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index f1c7f5a96..07d3a2570 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index d1e354676..36d2c4957 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index 57017006f..392029684 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index ce41d0486..2b22eb654 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index 90161cb77..d9a55a41f 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index 99c5557d5..9ead98c60 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index 9d95f5b11..f62b35f61 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index ac1d9443a..afb5c88f7 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index 7a99fa106..68bec484b 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index 74cad6af7..2eacadbc8 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -16,7 +16,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index eb5029457..238947a58 100644 --- a/UserInput.py +++ b/UserInput.py @@ -13,7 +13,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container -UserChoices['inputFiles']['referenceFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. +UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referenceFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index bf38cf476..7cb566a83 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -8,11 +8,11 @@ ''' def parseUserInput(currentUserInput): #Input Files - currentUserInput.referenceFileNamesList = parse.listCast(currentUserInput.referenceFileNamesList) #referenceFileName needs to be a list - currentUserInput.referenceFileNamesList = parse.stripListOfStrings(currentUserInput.referenceFileNamesList) + currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list + currentUserInput.referencePatternsFileNamesList = parse.stripListOfStrings(currentUserInput.referencePatternsFileNamesList) currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list currentUserInput.referenceFormsList = parse.stripListOfStrings(currentUserInput.referenceFormsList) - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referenceFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string currentUserInput.collectedFileName = currentUserInput.collectedFileName.strip() @@ -228,10 +228,10 @@ def parseUserInput(currentUserInput): if currentUserInput.TSC_List_Type == 'MultipleReferencePatterns': #If using multiple reference patterns then the user must input 1 value to use for each reference file or a value for each reference file #Then parallelize these variables to have the same length as number of reference patterns - currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referenceFileNamesList)) - currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referenceFileNamesList)) + currentUserInput.moleculesTSC_List = parse.parallelVectorize(currentUserInput.moleculesTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeSignalTSC_List = parse.parallelVectorize(currentUserInput.moleculeSignalTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.massNumberTSC_List = parse.parallelVectorize(currentUserInput.massNumberTSC_List,len(currentUserInput.referencePatternsFileNamesList)) + currentUserInput.moleculeConcentrationTSC_List = parse.parallelVectorize(currentUserInput.moleculeConcentrationTSC_List,len(currentUserInput.referencePatternsFileNamesList)) #NOTE: vectorizing these lists for 'SeparateMoleculesFactors' occurs in RatioFinder #Output Files @@ -291,27 +291,27 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #Will make sure that any referenceFileStandardTuning and referenceFileExistingTuning filenames have the same extension as the original reference pattern, and exit if that condition is not met. #First get the regular reference filename extension. - if '.csv' in UserChoices['inputFiles']['referenceFileNamesList'][0]: + if '.csv' in UserChoices['inputFiles']['referencePatternsFileNamesList'][0]: referenceFileExtension = 'csv' - if '.tsv' in UserChoices['inputFiles']['referenceFileNamesList'][0]: + if '.tsv' in UserChoices['inputFiles']['referencePatternsFileNamesList'][0]: referenceFileExtension = 'tsv' #Make sure all of the reference files match each other: - for referenceFileName in UserChoices['inputFiles']['referenceFileNamesList']: + for referenceFileName in UserChoices['inputFiles']['referencePatternsFileNamesList']: if referenceFileExtension not in referenceFileName: - print("ERROR: All filenamese in referenceFileNamesList must have the same extension."); sys.exit() + print("ERROR: All filenamese in referencePatternsFileNamesList must have the same extension."); sys.exit() if len (UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm']) > 0: if referenceFileExtension not in UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'][0]: - print("ERROR: All filenamese in referenceFileNamesList and referenceFileStandardTuningAndForm must have the same extension."); sys.exit() + print("ERROR: All filenamese in referencePatternsFileNamesList and referenceFileStandardTuningAndForm must have the same extension."); sys.exit() if len (UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm']) > 0: if referenceFileExtension not in UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'][0]: - print("ERROR: All filenamese in referenceFileNamesList and referenceFileExistingTuningAndForm must have the same extension."); sys.exit() + print("ERROR: All filenamese in referencePatternsFileNamesList and referenceFileExistingTuningAndForm must have the same extension."); sys.exit() #Filling settings variables dictionary so that variables can be populated from it. This is basically a mapping. See user input file for details. #The original variable names were single variables. Now, we are using a dictionary type structure (right side of equal signs) so they are being mapped to the single variables (left side of equal sign) #TODO: Consider if G.iterativeAnalysis = True or False should be changed to G.IterativeAnalysis_On or something like that, but will break backwards compatibility unless special care is taken. #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} - SettingsVDictionary['referenceFileNamesList'] = UserChoices['inputFiles']['referenceFileNamesList'] + SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] From a64be3c28b1d2836e3cc3cb3b018f72887a72844 Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 11:03:24 -0400 Subject: [PATCH 2/9] switching to referencePatternsFormsList referenceFormsList to referencePatternsFormsList --- DefaultUserInput.py | 4 +- ExampleAnalysis/DefaultUserInput.py | 4 +- ExampleAnalysis/MSRESOLVE.py | 30 +- ExampleAnalysis/UserInput.py | 4 +- ExampleAnalysis/userInputValidityFunctions.py | 6 +- .../DefaultUserInput.py | 4 +- ExampleReferenceExtraction/MSRESOLVE.py | 30 +- ExampleReferenceExtraction/UserInput.py | 4 +- .../userInputValidityFunctions.py | 6 +- ExampleTuningCorrectorGasMixture/0-README.txt | 2 +- .../DefaultUserInput.py | 4 +- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 42 +- .../MSRESOLVEBad1.py | 32 +- .../MSRESOLVEPrevious.py | 42 +- ExampleTuningCorrectorGasMixture/UserInput.py | 4 +- .../userInputValidityFunctions.py | 8 +- MSRESOLVE.py | 50 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../Exported1DataSmoother.csv | 957 ------------------ .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../test_3_input.py | 2 +- .../test_4_input.py | 2 +- .../test_5_input.py | 2 +- .../test_6_input.py | 2 +- .../test_1_Input_Brute_Finisher.py | 4 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/NegativeAnalyzer/test_1_Input.py | 4 +- .../test_1_inputA.py | 2 +- .../test_1_inputB.py | 2 +- .../test_1_inputC.py | 2 +- .../test_2_input.py | 2 +- .../TuningCorrectorGasMixture/0-README.txt | 2 +- .../UserInputGasMixture.py | 4 +- .../UserInputGasMixture2.py | 4 +- .../UserInputGasMixture3.py | 4 +- .../UserInputGasMixture4.py | 4 +- .../XYXYReferencePattern/test_1_inputXYXY.py | 4 +- .../XYXYReferencePattern/test_1_inputXYYY.py | 4 +- .../implicitSLScorrection/test_1_Input.py | 4 +- .../implicitSLScorrection/test_2_Input.py | 4 +- .../test_1_UserInput.py | 4 +- .../test_2_UserInput.py | 4 +- UnitTests/slsCommon/test_1_Input.py | 4 +- .../test_1_Input.py | 4 +- .../test_2_Input.py | 4 +- UnitTests/uncertainties/test_10_Input.py | 4 +- UnitTests/uncertainties/test_11_Input.py | 4 +- UnitTests/uncertainties/test_12_Input.py | 4 +- UnitTests/uncertainties/test_13_Input.py | 4 +- UnitTests/uncertainties/test_14_Input.py | 4 +- UnitTests/uncertainties/test_15_Input.py | 4 +- UnitTests/uncertainties/test_16_Input.py | 4 +- UnitTests/uncertainties/test_1_Input.py | 4 +- UnitTests/uncertainties/test_2_Input.py | 4 +- UnitTests/uncertainties/test_3_Input.py | 4 +- UnitTests/uncertainties/test_4_Input.py | 4 +- UnitTests/uncertainties/test_5_Input.py | 4 +- UnitTests/uncertainties/test_6_Input.py | 4 +- UnitTests/uncertainties/test_7_Input.py | 4 +- UnitTests/uncertainties/test_8_Input.py | 4 +- UnitTests/uncertainties/test_9_Input.py | 4 +- UserInput.py | 4 +- userInputValidityFunctions.py | 8 +- 74 files changed, 229 insertions(+), 1186 deletions(-) delete mode 100644 UnitTests/ExtractReferencePatternFromData/Exported1DataSmoother.csv diff --git a/DefaultUserInput.py b/DefaultUserInput.py index 238947a58..5868e7c9b 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index 26c183b39..d9aa238c6 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index 1cbca7872..6f5be3974 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -1253,17 +1253,17 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): - #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string +def GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): + #referencePatternsFormsList can take values of 'xyyy' or 'xyxy' and must be a string ##If referencePatternsFileNamesList is a string or if form is a string then make them lists if isinstance(referencePatternsFileNamesList,str): referencePatternsFileNamesList = [referencePatternsFileNamesList] - if isinstance(referenceFormsList,str): - referenceFormsList = [referenceFormsList] + if isinstance(referencePatternsFormsList,str): + referencePatternsFormsList = [referencePatternsFormsList] #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) + if len(referencePatternsFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referencePatternsFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1284,7 +1284,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1292,16 +1292,16 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, return ReferenceDataList #Otherwise we have multiple reference files and forms #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList - if len(referenceFormsList) == 1: + if len(referencePatternsFormsList) == 1: #Generate a copy of referencePatternsFileNamesList to be overwritten with forms listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form for i in range(len(referencePatternsFileNamesList)): - listOfForms[i] = referenceFormsList[0] + listOfForms[i] = referencePatternsFormsList[0] #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referencePatternsFileNamesList): + elif len(referencePatternsFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms - listOfForms = referenceFormsList + listOfForms = referencePatternsFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list @@ -1327,7 +1327,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -4938,7 +4938,7 @@ def PopulateLogFile(): f6 = open(filename6,'a') f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) - f6.write('form = %s \n'%(G.referenceFormsList)) + f6.write('form = %s \n'%(G.referencePatternsFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) @@ -5122,7 +5122,7 @@ def main(): #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' @@ -5168,7 +5168,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index 50b14c7c5..64d0def89 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index 4838e1370..7c8079c4f 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -9,8 +9,8 @@ def parseUserInput(currentUserInput): #Input Files currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list - currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referencePatternsFormsList = parse.listCast(currentUserInput.referencePatternsFormsList) #form needs to be a list + currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string @@ -249,7 +249,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] - SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] + SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index 26c183b39..d9aa238c6 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index 1cbca7872..6f5be3974 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -1253,17 +1253,17 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): - #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string +def GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): + #referencePatternsFormsList can take values of 'xyyy' or 'xyxy' and must be a string ##If referencePatternsFileNamesList is a string or if form is a string then make them lists if isinstance(referencePatternsFileNamesList,str): referencePatternsFileNamesList = [referencePatternsFileNamesList] - if isinstance(referenceFormsList,str): - referenceFormsList = [referenceFormsList] + if isinstance(referencePatternsFormsList,str): + referencePatternsFormsList = [referencePatternsFormsList] #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) + if len(referencePatternsFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referencePatternsFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1284,7 +1284,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1292,16 +1292,16 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, return ReferenceDataList #Otherwise we have multiple reference files and forms #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList - if len(referenceFormsList) == 1: + if len(referencePatternsFormsList) == 1: #Generate a copy of referencePatternsFileNamesList to be overwritten with forms listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form for i in range(len(referencePatternsFileNamesList)): - listOfForms[i] = referenceFormsList[0] + listOfForms[i] = referencePatternsFormsList[0] #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referencePatternsFileNamesList): + elif len(referencePatternsFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms - listOfForms = referenceFormsList + listOfForms = referencePatternsFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list @@ -1327,7 +1327,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -4938,7 +4938,7 @@ def PopulateLogFile(): f6 = open(filename6,'a') f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) - f6.write('form = %s \n'%(G.referenceFormsList)) + f6.write('form = %s \n'%(G.referencePatternsFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) @@ -5122,7 +5122,7 @@ def main(): #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' @@ -5168,7 +5168,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index 173055c3b..0242cd874 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExistingReferencePatterns.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index 4838e1370..7c8079c4f 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -9,8 +9,8 @@ def parseUserInput(currentUserInput): #Input Files currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list - currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referencePatternsFormsList = parse.listCast(currentUserInput.referencePatternsFormsList) #form needs to be a list + currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string @@ -249,7 +249,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] - SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] + SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] diff --git a/ExampleTuningCorrectorGasMixture/0-README.txt b/ExampleTuningCorrectorGasMixture/0-README.txt index d9228906f..797416260 100644 --- a/ExampleTuningCorrectorGasMixture/0-README.txt +++ b/ExampleTuningCorrectorGasMixture/0-README.txt @@ -11,7 +11,7 @@ Proc Doc type things: -- First added at line 5351 if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: -- Now make a reference object from LiteratureReference.csv so that simulated signals can be made. - -- GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): + -- GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): -- Need to be careful because "ReferenceInputPreProcessing" is being used. diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index 207a438c3..a4c9d793a 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index c68f4f612..7a420920a 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -507,7 +507,7 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien if measuredReferenceYorN =='yes': print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -570,7 +570,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu ReferenceDataExistingTuning = createReferenceDataObject ( G.referenceFileDesiredTuningAndForm[0],G.referenceFileDesiredTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternOriginalTuning.csv') if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. - referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. print("line 1489", referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) @@ -617,8 +617,8 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm referenceFileExistingTuningAndForm = G.referenceFileExistingTuningAndForm if referenceFileDesiredTuningAndForm == []: - print("line 622", G.referenceFormsList) - referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + print("line 622", G.referencePatternsFormsList) + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referencePatternsFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternExternal.csv') @@ -789,7 +789,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"] if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients @@ -1645,17 +1645,17 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): - #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string +def GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): + #referencePatternsFormsList can take values of 'xyyy' or 'xyxy' and must be a string ##If referencePatternsFileNamesList is a string or if form is a string then make them lists if isinstance(referencePatternsFileNamesList,str): referencePatternsFileNamesList = [referencePatternsFileNamesList] - if isinstance(referenceFormsList,str): - referenceFormsList = [referenceFormsList] + if isinstance(referencePatternsFormsList,str): + referencePatternsFormsList = [referencePatternsFormsList] #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) + if len(referencePatternsFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referencePatternsFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1676,7 +1676,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1688,16 +1688,16 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, return ReferenceDataList #Otherwise we have multiple reference files and forms #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList - if len(referenceFormsList) == 1: + if len(referencePatternsFormsList) == 1: #Generate a copy of referencePatternsFileNamesList to be overwritten with forms listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form for i in range(len(referencePatternsFileNamesList)): - listOfForms[i] = referenceFormsList[0] + listOfForms[i] = referencePatternsFormsList[0] #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referencePatternsFileNamesList): + elif len(referencePatternsFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms - listOfForms = referenceFormsList + listOfForms = referencePatternsFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list @@ -1723,7 +1723,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -5518,7 +5518,7 @@ def PopulateLogFile(): f6 = open(filename6,'a') f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) - f6.write('form = %s \n'%(G.referenceFormsList)) + f6.write('form = %s \n'%(G.referencePatternsFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) @@ -5690,7 +5690,7 @@ def main(): #Read in the molecules used before parsing the user input file G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) - G.referenceFormsList = parse.listCast(G.referenceFormsList) + G.referencePatternsFormsList = parse.listCast(G.referencePatternsFormsList) G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #If a tuning correction is going to be done, we'll make a mixed reference pattern. #G.moleculesNamesExtended needs to be populated before the first tuning correction and before parsing of userinput. @@ -5721,7 +5721,7 @@ def main(): #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' @@ -5759,7 +5759,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index d8a907b32..36ac5263f 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -509,7 +509,7 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -1520,17 +1520,17 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): - #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string +def GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): + #referencePatternsFormsList can take values of 'xyyy' or 'xyxy' and must be a string ##If referencePatternsFileNamesList is a string or if form is a string then make them lists if isinstance(referencePatternsFileNamesList,str): referencePatternsFileNamesList = [referencePatternsFileNamesList] - if isinstance(referenceFormsList,str): - referenceFormsList = [referenceFormsList] + if isinstance(referencePatternsFormsList,str): + referencePatternsFormsList = [referencePatternsFormsList] #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) + if len(referencePatternsFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referencePatternsFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1551,7 +1551,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1563,16 +1563,16 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, return ReferenceDataList #Otherwise we have multiple reference files and forms #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList - if len(referenceFormsList) == 1: + if len(referencePatternsFormsList) == 1: #Generate a copy of referencePatternsFileNamesList to be overwritten with forms listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form for i in range(len(referencePatternsFileNamesList)): - listOfForms[i] = referenceFormsList[0] + listOfForms[i] = referencePatternsFormsList[0] #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referencePatternsFileNamesList): + elif len(referencePatternsFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms - listOfForms = referenceFormsList + listOfForms = referencePatternsFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list @@ -1598,7 +1598,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -5383,7 +5383,7 @@ def PopulateLogFile(): f6 = open(filename6,'a') f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) - f6.write('form = %s \n'%(G.referenceFormsList)) + f6.write('form = %s \n'%(G.referencePatternsFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) @@ -5567,7 +5567,7 @@ def main(): #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' @@ -5611,7 +5611,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index ebc144c52..34dba473a 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -510,7 +510,7 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -576,7 +576,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternOriginalTuning.csv') if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!! TODO: NEED TO MAKE ExportedReferencePatternDesiredTuning FOR CASE OF THIS IF STATEMENT") - referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. print("line 1489", referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) @@ -624,8 +624,8 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm referenceFileExistingTuningAndForm = G.referenceFileExistingTuningAndForm if referenceFileDesiredTuningAndForm == []: - print("line 622", G.referenceFormsList) - referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + print("line 622", G.referencePatternsFormsList) + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referencePatternsFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) ReferenceDataExistingTuning.exportReferencePattern('ExportedReferencePatternExternal.csv') @@ -796,7 +796,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"] if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients = numpy.zeros(3) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients @@ -1651,17 +1651,17 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): - #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string +def GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): + #referencePatternsFormsList can take values of 'xyyy' or 'xyxy' and must be a string ##If referencePatternsFileNamesList is a string or if form is a string then make them lists if isinstance(referencePatternsFileNamesList,str): referencePatternsFileNamesList = [referencePatternsFileNamesList] - if isinstance(referenceFormsList,str): - referenceFormsList = [referenceFormsList] + if isinstance(referencePatternsFormsList,str): + referencePatternsFormsList = [referencePatternsFormsList] #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) + if len(referencePatternsFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referencePatternsFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1682,7 +1682,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[0].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -1694,16 +1694,16 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, return ReferenceDataList #Otherwise we have multiple reference files and forms #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList - if len(referenceFormsList) == 1: + if len(referencePatternsFormsList) == 1: #Generate a copy of referencePatternsFileNamesList to be overwritten with forms listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form for i in range(len(referencePatternsFileNamesList)): - listOfForms[i] = referenceFormsList[0] + listOfForms[i] = referencePatternsFormsList[0] #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referencePatternsFileNamesList): + elif len(referencePatternsFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms - listOfForms = referenceFormsList + listOfForms = referencePatternsFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list @@ -1729,7 +1729,7 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, ReferenceDataList[i].absolute_standard_uncertainties = absolute_standard_uncertainties #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -5522,7 +5522,7 @@ def PopulateLogFile(): f6 = open(filename6,'a') f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) - f6.write('form = %s \n'%(G.referenceFormsList)) + f6.write('form = %s \n'%(G.referencePatternsFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) @@ -5693,7 +5693,7 @@ def main(): #Read in the molecules used before parsing the user input file G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) - G.referenceFormsList = parse.listCast(G.referenceFormsList) + G.referencePatternsFormsList = parse.listCast(G.referencePatternsFormsList) G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #If a tuning correction is going to be done, we'll make a mixed reference pattern. #G.moleculesNamesExtended needs to be populated before the first tuning correction and before parsing of userinput. @@ -5724,7 +5724,7 @@ def main(): #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): AllMoleculesReferenceDataList[referenceObjectIndex].ExportAtEachStep = 'no' @@ -5762,7 +5762,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index c59d9d717..3c87af198 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index 6f846ade5..8f3f94c4d 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -10,9 +10,9 @@ def parseUserInput(currentUserInput): #Input Files currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list currentUserInput.referencePatternsFileNamesList = parse.stripListOfStrings(currentUserInput.referencePatternsFileNamesList) - currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list - currentUserInput.referenceFormsList = parse.stripListOfStrings(currentUserInput.referenceFormsList) - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referencePatternsFormsList = parse.listCast(currentUserInput.referencePatternsFormsList) #form needs to be a list + currentUserInput.referencePatternsFormsList = parse.stripListOfStrings(currentUserInput.referencePatternsFormsList) + currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string currentUserInput.collectedFileName = currentUserInput.collectedFileName.strip() @@ -275,7 +275,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] - SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] + SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index dd76dfca0..7f8dc1d64 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -524,9 +524,9 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien if measuredReferenceYorN =='yes': if len(referenceFileDesiredTuningAndForm) == 0:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. if '.csv' in G.referencePatternsFileNamesList[0]: - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. if '.tsv' in G.referencePatternsFileNamesList[0]: - referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.tsv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.tsv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients G.referenceCorrectionCoefficients = referenceCorrectionCoefficients #TODO: Maybe this logic should be changed, since it will result in an exporting of the last coefficients used, whether a person is doing forward tuning or reverse tuning. @@ -612,7 +612,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu if len(referenceFileDesiredTuningAndForm) == 0:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. resetReferenceFileDesiredTuningAndForm = True if ReferenceDataExistingTuning.referenceFileNameExtension =='csv': - referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. if ReferenceDataExistingTuning.referenceFileNameExtension =='tsv': referenceFileDesiredTuningAndForm = [ "ExportedReferencePatternOriginalAnalysis.tsv","xyyy" ] abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) @@ -659,7 +659,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileExistingTuningAndForm = G.referenceFileStandardTuningAndForm if len(referenceFileDesiredTuningAndForm) == 0: #Use the original reference pattern if blank. resetReferenceFileDesiredTuningAndForm = True - referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referencePatternsFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) if ReferenceDataExistingTuning.referenceFileNameExtension == 'csv': @@ -716,7 +716,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu referenceFileExistingTuningAndForm = G.referenceFileStandardTuningAndForm if len(referenceFileDesiredTuningAndForm) == 0: #Use the original reference pattern if blank. resetReferenceFileDesiredTuningAndForm = True - referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referencePatternsFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. #We don't use the function GenerateReferenceDataList because that function does more than just making a reference object. ReferenceDataExistingTuning = createReferenceDataObject ( referenceFileExistingTuningAndForm[0],referenceFileExistingTuningAndForm[1], AllMID_ObjectsDict=G.AllMID_ObjectsDict) if ReferenceDataExistingTuning.referenceFileNameExtension == 'csv': @@ -1419,7 +1419,7 @@ def CorrectionValuesObtain(ReferenceData): #NEED AN IF STATEMENT TO DETERMINE THESE COEFFICENTS FROM GAS MIXTURE IF USING THAT. if str(G.referenceFileStandardTuningAndForm[0]).lower() != 'gaxmixture': if len(G.referenceFileDesiredTuningAndForm) == 0: #Use the original reference pattern if blank. - referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referenceFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referenceFormsList. + referenceFileDesiredTuningAndForm = [G.referencePatternsFileNamesList[0], G.referencePatternsFormsList[0]] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. else: referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm abcCoefficients, abcCoefficients_covmat = ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm=referenceFileDesiredTuningAndForm, ReferencePatternDesiredTuning_FileNameAndForm = G.referenceFileStandardTuningAndForm, exportCoefficients=False) #We will separately export the coefficents for this usage. @@ -1959,17 +1959,17 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): on the referenceFileName and the corresponding form It allows MSRESOLVE to be backwards compatible with previous user input files ''' -def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): - #referenceFormsList can take values of 'xyyy' or 'xyxy' and must be a string +def GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): + #referencePatternsFormsList can take values of 'xyyy' or 'xyxy' and must be a string ##If referencePatternsFileNamesList is a string or if form is a string then make them lists if isinstance(referencePatternsFileNamesList,str): referencePatternsFileNamesList = [referencePatternsFileNamesList] - if isinstance(referenceFormsList,str): - referenceFormsList = [referenceFormsList] + if isinstance(referencePatternsFormsList,str): + referencePatternsFormsList = [referencePatternsFormsList] #If referencePatternsFileNamesList and forms are lists of 1 then create a list of the single MSReference object #This allows MSRESOLVE to be backwards compatible with previous user input files while still incorporating the reference pattern time chooser feature - if len(referenceFormsList) == 1 and len(referencePatternsFileNamesList) == 1: - [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referenceFormsList[0]) + if len(referencePatternsFormsList) == 1 and len(referencePatternsFileNamesList) == 1: + [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(referencePatternsFileNamesList[0],referencePatternsFormsList[0]) ReferenceDataList = [MSReference(provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName=referenceFileName, form=form, AllMID_ObjectsDict=AllMID_ObjectsDict)] #save each global variable into the class objects ReferenceDataList[0].ExportAtEachStep = G.ExportAtEachStep @@ -1991,10 +1991,10 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): if '.csv' in referencePatternsFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. if '.tsv' in referencePatternsFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referenceFormsList[0]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referencePatternsFormsList[0]) ReferenceDataList[0].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[0].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[0].absolute_standard_uncertainties[:,1:] = 100*ReferenceDataList[0].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -2006,16 +2006,16 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, return ReferenceDataList #Otherwise we have multiple reference files and forms #If just one form is used, make a list of forms that is the same length as referencePatternsFileNamesList - if len(referenceFormsList) == 1: + if len(referencePatternsFormsList) == 1: #Generate a copy of referencePatternsFileNamesList to be overwritten with forms listOfForms = copy.copy(referencePatternsFileNamesList) #replace each value with the given form for i in range(len(referencePatternsFileNamesList)): - listOfForms[i] = referenceFormsList[0] + listOfForms[i] = referencePatternsFormsList[0] #If list of forms is the same length of referencePatternsFileNamesList then each form should correspond to the referenceFile of the same index - elif len(referenceFormsList) == len(referencePatternsFileNamesList): + elif len(referencePatternsFormsList) == len(referencePatternsFileNamesList): #So just set listOfForms equal to forms - listOfForms = referenceFormsList + listOfForms = referencePatternsFormsList #Initialize ReferenceDataList so it can be appended to ReferenceDataList = [] #For loop to generate each MSReferenceObject and append it to a list @@ -2042,9 +2042,9 @@ def GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList, #We can't convert to relative uncertainties yet because the file may not be standardized yet. if type(G.referenceFileUncertainties) == type('string'): if '.csv'in referencePatternsFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.csv",referencePatternsFormsList[i]) if '.tsv'in referencePatternsFileNamesList[0]: - provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referenceFormsList[i]) + provided_reference_patterns_absolute_uncertainties, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form = readReferenceFile(referencePatternsFileNamesList[0][:-4]+"_absolute_uncertainties.tsv",referencePatternsFormsList[i]) ReferenceDataList[i].absolute_standard_uncertainties = provided_reference_patterns_absolute_uncertainties #Just initializing the variable before filling it properly. maximum_absolute_intensities = numpy.amax(ReferenceDataList[i].provided_reference_patterns[:,1:], axis = 0) #Find the maximum intensity for each molecule. ReferenceDataList[i].absolute_standard_uncertainties[:,1:] = ReferenceDataList[i].absolute_standard_uncertainties[:,1:]/maximum_absolute_intensities @@ -5967,7 +5967,7 @@ def PopulateLogFile(): f6 = open(filename6,'a') f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) - f6.write('form = %s \n'%(G.referenceFormsList)) + f6.write('form = %s \n'%(G.referencePatternsFormsList)) f6.write('collectedFileName = %s \n'%(G.collectedFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) @@ -6217,11 +6217,11 @@ def main(): #Read in the molecules used before parsing the user input file G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) - G.referenceFormsList = parse.listCast(G.referenceFormsList) + G.referencePatternsFormsList = parse.listCast(G.referencePatternsFormsList) [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, - mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(G.referencePatternsFileNamesList[0], G.referenceFormsList[0]) + mass_fragment_numbers_monitored, referenceFileName, form]=readReferenceFile(G.referencePatternsFileNamesList[0], G.referencePatternsFormsList[0]) G.moleculesNames = molecules @@ -6262,7 +6262,7 @@ def main(): #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder global PreparingAllMoleculesReferenceDataList; PreparingAllMoleculesReferenceDataList = False #initializing this flag for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): @@ -6302,7 +6302,7 @@ def main(): resultsObjects = {} [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) - ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referenceFormsList,G.AllMID_ObjectsDict) + ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. if type(G.collectedFileUncertainties) != type(None): diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py index 92593777a..1989a4bd4 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py index 5594e4f4a..e60bef772 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/Exported1DataSmoother.csv b/UnitTests/ExtractReferencePatternFromData/Exported1DataSmoother.csv deleted file mode 100644 index 37353fe53..000000000 --- a/UnitTests/ExtractReferencePatternFromData/Exported1DataSmoother.csv +++ /dev/null @@ -1,957 +0,0 @@ -Temp,m2,m18,m26,m27,m28,m29,m31,m39,m41,m44,m45,m56,m57,m70 -1.768480999999999881e+02,1.264518349936488262e+00,1.975837889848244822e-01,1.434966953747456309e-01,1.484318964229909277e-01,4.148103293985883511e+00,2.812681495016242650e-01,5.568628553450519214e-02,4.079210467697833020e-02,6.069668464663791063e-02,1.269845799761352367e+00,2.706084837745692528e-02,1.104064086299079428e-02,7.325183238521576490e-03,6.784902435499479134e-03 -1.768944999999999936e+02,1.264553503674088919e+00,1.977258653965595081e-01,1.440627790123940599e-01,1.488054576335078316e-01,4.150421393268473480e+00,2.870067581047202054e-01,5.572909100277870231e-02,4.082885900027874437e-02,6.098770617258009175e-02,1.273745550068063892e+00,2.717254936896495998e-02,1.101471380112947762e-02,7.305144943131003377e-03,6.796311401227043969e-03 -1.768788000000000125e+02,1.264541608982702625e+00,1.976777921279337380e-01,1.438712377815520860e-01,1.486790586894322086e-01,4.149637036399150603e+00,2.850650306247963783e-01,5.571460725597066066e-02,4.081642273140340116e-02,6.088923552694902597e-02,1.272426022485838359e+00,2.713475399037285074e-02,1.102348653542305212e-02,7.311925142217887141e-03,6.792451039978712746e-03 -1.767940999999999860e+02,1.264477438259108188e+00,1.974184414366845775e-01,1.428378911412755414e-01,1.479971484624755806e-01,4.145405506027694642e+00,2.745895963859581457e-01,5.563646882573863861e-02,4.074933024899943246e-02,6.035799580179102009e-02,1.265307297249231411e+00,2.693085153389163100e-02,1.107081459877766461e-02,7.348503668501982222e-03,6.771624759868269394e-03 -1.767974000000000103e+02,1.264479938417170324e+00,1.974285460090709488e-01,1.428781513999877184e-01,1.480237163933961764e-01,4.145570370847362796e+00,2.749977301874757529e-01,5.563951318016327474e-02,4.075194424182040920e-02,6.037869345342072869e-02,1.265584650180528570e+00,2.693879578544289277e-02,1.106897064825734800e-02,7.347078531114270561e-03,6.772436173379074720e-03 -1.768505000000000109e+02,1.264520168233260744e+00,1.975911377647418532e-01,1.435259755629001432e-01,1.484512185545694418e-01,4.148223195672914088e+00,2.815649740845458382e-01,5.568849961045038710e-02,4.079400576266631329e-02,6.071173748418678962e-02,1.270047510984115391e+00,2.706662601494880249e-02,1.103929980806692135e-02,7.324146774966872053e-03,6.785492554416426569e-03 -1.769009000000000071e+02,1.264558352465482205e+00,1.977454621430057569e-01,1.441408595141386861e-01,1.488569833177171287e-01,4.150741131100556203e+00,2.877982903258349268e-01,5.573499520529917595e-02,4.083392856211329192e-02,6.102784707271036169e-02,1.274283446662094477e+00,2.718795640227644750e-02,1.101113765466583960e-02,7.302381040318495220e-03,6.797885051672225565e-03 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-8.954148999999999887e+02,1.264845917583060420e+00,6.413226688354599636e-01,2.322323369287359052e-01,2.796581792423784019e-01,6.002520386220966842e+00,9.863469560910220757e-01,9.736672393574280493e-02,8.295958957034577086e-02,1.367490888772117386e-01,2.429155786433740971e+00,7.102822192057836603e-02,2.001213391533629427e-02,1.325922367425155790e-02,1.721148303095584864e-02 -8.955733999999999924e+02,1.264381989437278087e+00,6.414798544451336682e-01,2.321260166826237814e-01,2.796526691615406901e-01,6.000092778798787663e+00,9.857917495956214360e-01,9.742095240903875242e-02,8.285136577371687849e-02,1.367470304548355775e-01,2.428804620638823852e+00,7.104002541677145732e-02,1.992594022693289224e-02,1.330296054808943751e-02,1.718636027047418247e-02 -8.958460000000000036e+02,1.263703010132975368e+00,6.417220597830692874e-01,2.317810278023795800e-01,2.795218898818745412e-01,5.996896142736702018e+00,9.848564973090017105e-01,9.732748046656208851e-02,8.252570327644204173e-02,1.368706741838798258e-01,2.428001634898695471e+00,7.090578992003720993e-02,1.964212353660271804e-02,1.353718335998057784e-02,1.716663684982019933e-02 -8.962631000000000085e+02,1.262409986617272217e+00,6.421527763515315623e-01,2.315996438486093156e-01,2.795810121973546503e-01,5.989913874935137272e+00,9.833835302461753081e-01,9.758352232370776091e-02,8.232559324746918650e-02,1.367880654499032400e-01,2.427198320443285873e+00,7.103064408108555883e-02,1.949758523966027557e-02,1.355577634429902881e-02,1.708627164768208861e-02 -8.968424999999999727e+02,1.260714554047217328e+00,6.427545787216484285e-01,2.313250521798811965e-01,2.796511666990695311e-01,5.980269146856990403e+00,9.813710284733816458e-01,9.789132543865657066e-02,8.203898210682397663e-02,1.366924600821942670e-01,2.426163424645626066e+00,7.118326114943587801e-02,1.927969932352285864e-02,1.359666401643924716e-02,1.698900448369482924e-02 -8.973544000000000551e+02,1.259410678464227384e+00,6.432982713880557313e-01,2.312642291620748136e-01,2.797424997765226018e-01,5.972044578722609742e+00,9.799498895806215693e-01,9.810962446031440409e-02,8.180316038793328248e-02,1.365415819332568836e-01,2.425619934628423291e+00,7.133726435271767197e-02,1.901238307646546666e-02,1.362281288675806779e-02,1.699263158855417524e-02 -8.978215000000000146e+02,1.259279505450707548e+00,6.436677318272308046e-01,2.310723130004069259e-01,2.796469887368397966e-01,5.964234635183020217e+00,9.783750753358955166e-01,9.808575535493302411e-02,8.163558711417850944e-02,1.365803289108484253e-01,2.424995085248153437e+00,7.131351536634582267e-02,1.870259487883685345e-02,1.380936914917990643e-02,1.699045420941695458e-02 -8.980511000000000195e+02,1.258943977078142762e+00,6.439720683117489131e-01,2.311966828512329597e-01,2.793606245690953838e-01,5.959799731098456732e+00,9.776903896075266331e-01,9.837171240199071853e-02,8.150887675826584688e-02,1.362870227829454106e-01,2.424243225167198368e+00,7.160145146368374069e-02,1.845671567924744849e-02,1.374131590569495354e-02,1.710106427445454158e-02 -8.982355000000000018e+02,1.257326304312681664e+00,6.442596342517403762e-01,2.308719422744022198e-01,2.797323754483566072e-01,5.956902451411149713e+00,9.768226165175879494e-01,9.805158132509955715e-02,8.149845968018054609e-02,1.363717779404714503e-01,2.423055541869500118e+00,7.131704058935053880e-02,1.840773808266693568e-02,1.405289254456093540e-02,1.692312881467517016e-02 -8.983982999999999493e+02,1.255186200700246779e+00,6.442807287700709207e-01,2.306712147732140061e-01,2.794940972027586956e-01,5.952270824498679502e+00,9.749419452646286288e-01,9.822019656039829294e-02,8.122131739149329732e-02,1.364250994386312366e-01,2.421997914100632698e+00,7.124665000729664410e-02,1.840990888552163085e-02,1.396263686920423686e-02,1.691549888488413922e-02 -8.982911000000000286e+02,1.257179192850018001e+00,6.443214654812281506e-01,2.308514393367586126e-01,2.797364976247718182e-01,5.955960710328431773e+00,9.766346967874341978e-01,9.805363030313801742e-02,8.147816016151721019e-02,1.363584841727937258e-01,2.422909158726373580e+00,7.131948502398338663e-02,1.837180615728828403e-02,1.407525629917349974e-02,1.691914773711489239e-02 -8.982509000000000015e+02,1.257285557612591198e+00,6.442767601678214273e-01,2.308662634031843908e-01,2.797335172022558103e-01,5.956641609456584163e+00,9.767705668081569925e-01,9.805214884779366036e-02,8.149283715162991548e-02,1.363680958537405730e-01,2.423014996898202433e+00,7.131771764498626154e-02,1.839778571484618208e-02,1.405908682191764347e-02,1.692202614211350820e-02 -8.982922999999999547e+02,1.257176017782478450e+00,6.443227999681953033e-01,2.308509968273130819e-01,2.797365865926081385e-01,5.955940384981323277e+00,9.766306409659204490e-01,9.805367452568561348e-02,8.147772204240938398e-02,1.363581972569445633e-01,2.422905999377960917e+00,7.131953778156538415e-02,1.837103064810741149e-02,1.407573897013636444e-02,1.691906181457762670e-02 -8.983718000000000075e+02,1.256013235141860029e+00,6.446801658628461551e-01,2.309346708321368125e-01,2.794695092871548603e-01,5.953851291388030376e+00,9.759580175417239545e-01,9.852252778519399179e-02,8.115224644119067854e-02,1.358645657585654254e-01,2.422287691334434889e+00,7.151068567913083929e-02,1.821650530433094328e-02,1.393549878189603852e-02,1.722297604938938242e-02 -8.985057000000000471e+02,1.253904479309452924e+00,6.452451562933287921e-01,2.309974564140704623e-01,2.792325662071010739e-01,5.946594351129824929e+00,9.748692594288597135e-01,9.836139641348634610e-02,8.072755226178618404e-02,1.361911263770382297e-01,2.422550954874044038e+00,7.133113449562364372e-02,1.814595106923311274e-02,1.390729369273741023e-02,1.740910623694402748e-02 -8.988812000000000353e+02,1.252580995316760593e+00,6.445072136726439638e-01,2.310093821276996695e-01,2.800129275034027865e-01,5.934976146538538444e+00,9.713519737373799146e-01,9.833296716066095011e-02,8.103273501016161617e-02,1.364315475366371655e-01,2.419540176681604926e+00,7.129097806921971814e-02,1.855962525389795448e-02,1.373426654352166536e-02,1.707737073697238039e-02 -8.992589000000000397e+02,1.251206373869863331e+00,6.459619010940477191e-01,2.310826362296379832e-01,2.784083473171740097e-01,5.926183115086377740e+00,9.710971711189495537e-01,9.806330685005763825e-02,7.981563437409355810e-02,1.362688818040159178e-01,2.416750975140211644e+00,7.132598644343780825e-02,1.763087217067149659e-02,1.390473683223170109e-02,1.858556305133862718e-02 -8.995299999999999727e+02,1.250025018773428087e+00,6.463466168339336848e-01,2.310660576550237766e-01,2.782213760265311864e-01,5.919717920603687844e+00,9.698775414656042315e-01,9.806394966109470424e-02,7.952794588186606894e-02,1.362254552794791851e-01,2.415511743248862864e+00,7.133253427788935341e-02,1.743449768195326488e-02,1.393694212564899892e-02,1.882027539888908585e-02 -8.999246000000000549e+02,1.251814604693597399e+00,6.442989951689016559e-01,2.320662523544515521e-01,2.789274398539851041e-01,5.911273418800409019e+00,9.647912692824540670e-01,9.722746266120008141e-02,8.038776597413355152e-02,1.363633087173544700e-01,2.413937924649784961e+00,7.198596686747266160e-02,1.790275184433198774e-02,1.363945499820761950e-02,1.763338017134466473e-02 diff --git a/UnitTests/ExtractReferencePatternFromData/test_1_input.py b/UnitTests/ExtractReferencePatternFromData/test_1_input.py index 85c7e3c2a..a7c09315d 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_1_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_1_input.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_2_input.py b/UnitTests/ExtractReferencePatternFromData/test_2_input.py index 86948aa68..9a7ae3984 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_2_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_2_input.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_3_input.py b/UnitTests/ExtractReferencePatternFromData/test_3_input.py index 577aec81c..e873bc989 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_3_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_3_input.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_4_input.py b/UnitTests/ExtractReferencePatternFromData/test_4_input.py index b4cd1144e..0a67d2661 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_4_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_4_input.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_5_input.py b/UnitTests/ExtractReferencePatternFromData/test_5_input.py index 90f81e9ba..920c17a86 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_5_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_5_input.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ExtractReferencePatternFromData/test_6_input.py b/UnitTests/ExtractReferencePatternFromData/test_6_input.py index dc10ebac2..b7c9ef68d 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_6_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_6_input.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index b7eb8d9d0..3c2136d8a 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -18,7 +18,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py index 7c45ac4b8..52241f887 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.tsv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py index 87d5b9a60..0a13557b0 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py index 2a47b6ed6..c29656079 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py index be31fc2fc..9dce43a1a 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py index e30c12e1d..9b002dd1f 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,200],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py index 55f178b03..681448b5b 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,200],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py index 268222d78..0187f53c4 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,250],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py index d065accf5..29a7dd9f0 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,250],[250,400]] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py index 9aacffd99..f8f64123b 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py index a190b36ea..3d9073480 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -referenceFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index 93e1a1c4f..f01b58995 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py index 151dbecc6..c21974440 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information -referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py index fd2973d77..122c887d3 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information -referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py index 2a911dff0..0f511c37f 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information -referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[300,303],[306,309]] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/ReferencePatternTimeChooser/test_2_input.py b/UnitTests/ReferencePatternTimeChooser/test_2_input.py index 2169adca4..70f8e7d4e 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_2_input.py +++ b/UnitTests/ReferencePatternTimeChooser/test_2_input.py @@ -7,7 +7,7 @@ #USER INPUT FILE #//Input Files// referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information -referenceFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' +referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[300,303],[306,309]] collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data diff --git a/UnitTests/TuningCorrectorGasMixture/0-README.txt b/UnitTests/TuningCorrectorGasMixture/0-README.txt index d94255113..18022092a 100644 --- a/UnitTests/TuningCorrectorGasMixture/0-README.txt +++ b/UnitTests/TuningCorrectorGasMixture/0-README.txt @@ -10,7 +10,7 @@ Proc Doc type things: -- First added at line 5351 if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: -- Now make a reference object from LiteratureReference.tsv so that simulated signals can be made. - -- GenerateReferenceDataList(referencePatternsFileNamesList,referenceFormsList,AllMID_ObjectsDict={}): + -- GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): -- Need to be careful because "ReferenceInputPreProcessing" is being used. diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index 6bfc1e72d..555f9d237 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index fd331d6fd..4644f3d2e 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index 357498791..fc00529a0 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index 4c7e43c2f..e9fba6ca5 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index 54d994a4f..21df4500a 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYXY.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyxy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyxy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index a781c4457..4ef6ad488 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYYY.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index 734164e32..2665cbf0e 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index 5d93c38c0..41da1289f 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index 41b4cf05b..cc4f1106c 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -1,5 +1,5 @@ referencePatternsFileNamesList = ['reference_measured_EthyleneExtracted.csv'] -referenceFormsList = 'xyyy' +referencePatternsFormsList = 'xyyy' collectedFileName = 'Ethylene.csv' referencePatternTimeRanges = [] ionizationDataFileName = '181017ProvidedIonizationData.csv' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index bfa6a5220..09d4e1b43 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -1,5 +1,5 @@ referencePatternsFileNamesList = ['reference_measured_EthyleneExtracted.csv'] -referenceFormsList = 'xyyy' +referencePatternsFormsList = 'xyyy' collectedFileName = 'Ethylene.csv' referencePatternTimeRanges = [] ionizationDataFileName = '181017ProvidedIonizationData.csv' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index bfd4ff7fe..21629dd8a 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index 9156004f7..11642d399 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index c61c74794..516be48b6 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index b5480da21..a205753be 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index 4b1e2b2ba..14ae23a4d 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index cf71eb5de..fbd51a273 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index 53f326cf3..cff8025ea 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index a24083888..4c1b7504e 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index 94cd6057b..55433d5d1 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index 07d3a2570..2f2f622cd 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index 36d2c4957..92a170024 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index 392029684..f6625399d 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index 2b22eb654..54f2c8404 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index d9a55a41f..342e36412 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index 9ead98c60..968ce7863 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index f62b35f61..9610107e3 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index afb5c88f7..c523ebec3 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index 68bec484b..efbe03d4a 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index 2eacadbc8..5c04226bf 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -17,7 +17,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index 238947a58..5868e7c9b 100644 --- a/UserInput.py +++ b/UserInput.py @@ -14,7 +14,7 @@ #//Input Files// UserChoices['inputFiles'] = {} #initialize the inputFiles container UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. -UserChoices['inputFiles']['referenceFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) +UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referenceFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index 7cb566a83..fdccbe333 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -10,9 +10,9 @@ def parseUserInput(currentUserInput): #Input Files currentUserInput.referencePatternsFileNamesList = parse.listCast(currentUserInput.referencePatternsFileNamesList) #referenceFileName needs to be a list currentUserInput.referencePatternsFileNamesList = parse.stripListOfStrings(currentUserInput.referencePatternsFileNamesList) - currentUserInput.referenceFormsList = parse.listCast(currentUserInput.referenceFormsList) #form needs to be a list - currentUserInput.referenceFormsList = parse.stripListOfStrings(currentUserInput.referenceFormsList) - currentUserInput.referenceFormsList = parse.parallelVectorize(currentUserInput.referenceFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName + currentUserInput.referencePatternsFormsList = parse.listCast(currentUserInput.referencePatternsFormsList) #form needs to be a list + currentUserInput.referencePatternsFormsList = parse.stripListOfStrings(currentUserInput.referencePatternsFormsList) + currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string currentUserInput.collectedFileName = currentUserInput.collectedFileName.strip() @@ -312,7 +312,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t #Also to consider if other variables should change to have names like G.specificMolecules_chosenMoleculesNames. Probably not necessary since we have the dictionaries. SettingsVDictionary = {} SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] - SettingsVDictionary['referenceFormsList'] = UserChoices['inputFiles']['referenceFormsList'] + SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] From c708cf9a05bb81426d6e3e3eac1d3daa078f914b Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 11:12:33 -0400 Subject: [PATCH 3/9] changing to dataToAnalyzeFileName collectedFileName to dataToAnalyzeFileName --- DefaultUserInput.py | 6 +- ExampleAnalysis/DefaultUserInput.py | 6 +- ExampleAnalysis/LogFile.txt | 2 +- ExampleAnalysis/MSRESOLVE.py | 68 +++++++++---------- ExampleAnalysis/UserInput.py | 6 +- ExampleAnalysis/userInputValidityFunctions.py | 6 +- .../DefaultUserInput.py | 6 +- ExampleReferenceExtraction/LogFile.txt | 2 +- ExampleReferenceExtraction/MSRESOLVE.py | 68 +++++++++---------- ExampleReferenceExtraction/UserInput.py | 6 +- .../userInputValidityFunctions.py | 6 +- .../DefaultUserInput.py | 6 +- ExampleTuningCorrectorGasMixture/LogFile.txt | 2 +- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 68 +++++++++---------- .../MSRESOLVEBad1.py | 68 +++++++++---------- .../MSRESOLVEPrevious.py | 68 +++++++++---------- ExampleTuningCorrectorGasMixture/UserInput.py | 6 +- .../userInputValidityFunctions.py | 8 +-- MSRESOLVE.py | 68 +++++++++---------- .../DefaultUserInput.py | 4 +- Todo/SLS Common vs. Unique Bug/MSRESOLVE.py | 54 +++++++-------- Todo/SLS Common vs. Unique Bug/UserInput.py | 6 +- UnitTests/ConcentrationFinder/test_1.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/ConcentrationFinder/test_2.py | 2 +- UnitTests/ConcentrationFinder/test_3.py | 2 +- UnitTests/ConcentrationFinder/test_4.py | 2 +- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../test_3_input.py | 2 +- .../test_4_input.py | 2 +- .../test_5_input.py | 2 +- .../test_6_input.py | 2 +- .../test_1_Input_Brute_Finisher.py | 6 +- UnitTests/IonizationFactors/test_1.py | 2 +- UnitTests/IonizationFactors/test_2.py | 2 +- UnitTests/IonizationFactors/test_3.py | 2 +- UnitTests/IonizationFactors/test_4.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/NegativeAnalyzer/test_1_Input.py | 6 +- .../test_1_inputA.py | 2 +- .../test_1_inputB.py | 2 +- .../test_1_inputC.py | 2 +- .../test_2_input.py | 2 +- .../UserInputGasMixture.py | 6 +- .../UserInputGasMixture2.py | 6 +- .../UserInputGasMixture3.py | 6 +- .../UserInputGasMixture4.py | 6 +- .../XYXYReferencePattern/test_1_inputXYXY.py | 6 +- .../XYXYReferencePattern/test_1_inputXYYY.py | 6 +- .../test_1_input.py | 4 +- .../test_2_input.py | 4 +- .../implicitSLScorrection/test_1_Input.py | 6 +- .../implicitSLScorrection/test_2_Input.py | 6 +- .../test_1_UserInput.py | 6 +- .../test_2_UserInput.py | 6 +- UnitTests/slsCommon/test_1_Input.py | 6 +- .../test_1_Input.py | 6 +- .../test_2_Input.py | 6 +- UnitTests/uncertainties/test_10_Input.py | 6 +- UnitTests/uncertainties/test_11_Input.py | 6 +- UnitTests/uncertainties/test_12_Input.py | 6 +- UnitTests/uncertainties/test_13_Input.py | 6 +- UnitTests/uncertainties/test_14_Input.py | 6 +- UnitTests/uncertainties/test_15_Input.py | 6 +- UnitTests/uncertainties/test_16_Input.py | 6 +- UnitTests/uncertainties/test_1_Input.py | 6 +- UnitTests/uncertainties/test_2_Input.py | 6 +- UnitTests/uncertainties/test_3_Input.py | 6 +- UnitTests/uncertainties/test_4_Input.py | 6 +- UnitTests/uncertainties/test_5_Input.py | 6 +- UnitTests/uncertainties/test_6_Input.py | 6 +- UnitTests/uncertainties/test_7_Input.py | 6 +- UnitTests/uncertainties/test_8_Input.py | 6 +- UnitTests/uncertainties/test_9_Input.py | 6 +- UserInput.py | 6 +- userInputValidityFunctions.py | 8 +-- 87 files changed, 404 insertions(+), 404 deletions(-) diff --git a/DefaultUserInput.py b/DefaultUserInput.py index 5868e7c9b..8ec4f0f10 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index d9aa238c6..66a9b50d0 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/LogFile.txt b/ExampleAnalysis/LogFile.txt index 3bd7ef164..123cf8695 100644 --- a/ExampleAnalysis/LogFile.txt +++ b/ExampleAnalysis/LogFile.txt @@ -2,7 +2,7 @@ Thu May 21 16:26:45 2020 referenceFileName = ['ExtractedReferencePattern.csv'] form = ['xyyy'] -collectedFileName = Collected_Reference.csv +dataToAnalyzeFileName = Collected_Reference.csv linearBaselineCorrectionSemiAutomatic = yes selection = ['linear'] massesToBackgroundCorrect = [12.0 13.0 14.0 15.0 16.0 17.0 21.0 22.0 24.0 25.0 26.0 27.0 28.0 29.0 diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index 6f5be3974..fa8a61927 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -1658,24 +1658,24 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations - collectedFileNameTemp = str(G.collectedFileName)[:-21] + str(G.iterationSuffix) + str(G.collectedFileName)[-4:] + dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] #copy the experimental and reference files into new names for this iterative run - shutil.copy(G.collectedFileName, collectedFileNameTemp) + shutil.copy(G.dataToAnalyzeFileName, dataToAnalyzeFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.collectedFileName = collectedFileNameTemp + G.dataToAnalyzeFileName = dataToAnalyzeFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + str('_remaining') + G.collectedFileName[-11:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] #naming for reference files G.oldReferenceFileName = [] @@ -1698,10 +1698,10 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -1720,12 +1720,12 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program - G.collectedFileName = G.collectedFileName[:-4] + str(G.iterationSuffix) + G.collectedFileName[-4:] + G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] G.oldReferenceFileName = [] for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list @@ -1736,11 +1736,11 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -1774,7 +1774,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported - ExportXYYYData(G.collectedFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, + ExportXYYYData(G.dataToAnalyzeFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, abscissaHeader = ExperimentData.abscissaHeader, dataType = 'preProcessed', rowIndex = ExperimentData.times) for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list @@ -1875,7 +1875,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file - G.nextUserInputModule.collectedFileName = G.nextExpFileName + G.nextUserInputModule.dataToAnalyzeFileName = G.nextExpFileName G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules @@ -1914,7 +1914,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): #copy the experimental signals to the next iteration copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.collectedFileName)) + str(G.nextUserInputModule.dataToAnalyzeFileName)) shutil.copy(copyFromPath, os.getcwd()) for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder @@ -1949,17 +1949,17 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### #These functions read in the experimental data file and the reference file. The #returned variables can then be used to initialize the respective classes. -def readDataFile(collectedFileName): +def readDataFile(dataToAnalyzeFileName): #read the csv file into a dataframe. dataFrame means "dataframe" and is a pandas object. - dataFrame = pandas.read_csv('%s' %collectedFileName, header=None) + dataFrame = pandas.read_csv('%s' %dataToAnalyzeFileName, header=None) ''' generate mass fragment list''' #select only the 2nd row down, all columns except for the first. #"iloc" is a pandas dataframe function. All it does is select a portion of the data. @@ -2003,7 +2003,7 @@ def readDataFile(collectedFileName): rawCollectedData = numpy.vstack((rawCollectedData,rawCollectedData)) - return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #readReferenceFile is a helper function that reads the reference file in a certain form and returns the #variables and data that are used to initialize the class. It can read files both in XYYY and XYXY form. @@ -2267,10 +2267,10 @@ def getMoleculesFromReferenceData(ReferenceFileName): ''' getMassFragmentsFromCollectedData is a function that takes in the collected filename and returns the mass fragments present in the data ''' -def getMassFragmentsFromCollectedData(CollectedFileName): +def getMassFragmentsFromCollectedData(dataToAnalyzeFileName): #Read the csv file #TODO CHange to use numpy.gen_from_text instead of pandas - DataInfo = pandas.read_csv(CollectedFileName,header=0) + DataInfo = pandas.read_csv(dataToAnalyzeFileName,header=0) #Convert the data into an array DataInfoArray = numpy.array(DataInfo) #Get the names of mass fragments in collected data @@ -2340,9 +2340,9 @@ class MSData (object): #self.mass_fragment_numbers , 1D and must be integers #self.rawCollectedData, a 2D array of the signals. - def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName=None): + def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName=None): - self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.collectedFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.dataToAnalyzeFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #class object variable created to allow class to be used separately from the program. self.ExportAtEachStep = '' @@ -4939,7 +4939,7 @@ def PopulateLogFile(): f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referencePatternsFormsList)) - f6.write('collectedFileName = %s \n'%(G.collectedFileName )) + f6.write('dataToAnalyzeFileName = %s \n'%(G.dataToAnalyzeFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) f6.write('timeRangeStart = %s \n'%(G.timeRangeStart)) @@ -5104,7 +5104,7 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Save an MSReference object containing all molecules and an MSData object containing all mass fragments @@ -5114,14 +5114,14 @@ def main(): AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name - AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory + AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.dataToAnalyzeFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) - AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) + AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.dataToAnalyzeFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) - AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) + AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): @@ -5132,7 +5132,7 @@ def main(): G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments - G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) + G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.dataToAnalyzeFileName) #beforeParsedGDict this will be needed for iterative. This actually contains "UserChoices" when that's available, but we won't use that. beforeParsedGDict = {} @@ -5166,8 +5166,8 @@ def main(): global currentReferenceData global resultsObjects resultsObjects = {} - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) - ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(G.dataToAnalyzeFileName) + ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. @@ -5186,7 +5186,7 @@ def main(): #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index 64d0def89..42bc27c9c 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index 7c8079c4f..e68c930d6 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -12,7 +12,7 @@ def parseUserInput(currentUserInput): currentUserInput.referencePatternsFormsList = parse.listCast(currentUserInput.referencePatternsFormsList) #form needs to be a list currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list - parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string + parse.strCheck(currentUserInput.dataToAnalyzeFileName,'dataToAnalyzeFileName') #dataToAnalyzeFileName must be a string #preProcessing, dataAnalysis, dataSimulation, grapher @@ -251,7 +251,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] - SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] + SettingsVDictionary['dataToAnalyzeFileName'] = UserChoices['inputFiles']['dataToAnalyzeFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] SettingsVDictionary['preProcessing'] = UserChoices['preProcessing']['on'] @@ -270,7 +270,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['oldCollectedFileName'] = UserChoices['iterativeAnalysis']['oldCollectedFileName'] + SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index d9aa238c6..66a9b50d0 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/LogFile.txt b/ExampleReferenceExtraction/LogFile.txt index 56d6904fb..45b96f9ae 100644 --- a/ExampleReferenceExtraction/LogFile.txt +++ b/ExampleReferenceExtraction/LogFile.txt @@ -2,7 +2,7 @@ Thu May 21 20:37:44 2020 referenceFileName = ['ExistingReferencePatterns.csv'] form = ['xyyy'] -collectedFileName = Collected_Reference.csv +dataToAnalyzeFileName = Collected_Reference.csv linearBaselineCorrectionSemiAutomatic = yes selection = ['linear'] massesToBackgroundCorrect = [12.0 13.0 14.0 15.0 16.0 17.0 21.0 22.0 24.0 25.0 26.0 27.0 28.0 29.0 diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index 6f5be3974..fa8a61927 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -1658,24 +1658,24 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations - collectedFileNameTemp = str(G.collectedFileName)[:-21] + str(G.iterationSuffix) + str(G.collectedFileName)[-4:] + dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] #copy the experimental and reference files into new names for this iterative run - shutil.copy(G.collectedFileName, collectedFileNameTemp) + shutil.copy(G.dataToAnalyzeFileName, dataToAnalyzeFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.collectedFileName = collectedFileNameTemp + G.dataToAnalyzeFileName = dataToAnalyzeFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + str('_remaining') + G.collectedFileName[-11:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] #naming for reference files G.oldReferenceFileName = [] @@ -1698,10 +1698,10 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -1720,12 +1720,12 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program - G.collectedFileName = G.collectedFileName[:-4] + str(G.iterationSuffix) + G.collectedFileName[-4:] + G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] G.oldReferenceFileName = [] for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list @@ -1736,11 +1736,11 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -1774,7 +1774,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported - ExportXYYYData(G.collectedFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, + ExportXYYYData(G.dataToAnalyzeFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, abscissaHeader = ExperimentData.abscissaHeader, dataType = 'preProcessed', rowIndex = ExperimentData.times) for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list @@ -1875,7 +1875,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file - G.nextUserInputModule.collectedFileName = G.nextExpFileName + G.nextUserInputModule.dataToAnalyzeFileName = G.nextExpFileName G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules @@ -1914,7 +1914,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): #copy the experimental signals to the next iteration copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.collectedFileName)) + str(G.nextUserInputModule.dataToAnalyzeFileName)) shutil.copy(copyFromPath, os.getcwd()) for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder @@ -1949,17 +1949,17 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### #These functions read in the experimental data file and the reference file. The #returned variables can then be used to initialize the respective classes. -def readDataFile(collectedFileName): +def readDataFile(dataToAnalyzeFileName): #read the csv file into a dataframe. dataFrame means "dataframe" and is a pandas object. - dataFrame = pandas.read_csv('%s' %collectedFileName, header=None) + dataFrame = pandas.read_csv('%s' %dataToAnalyzeFileName, header=None) ''' generate mass fragment list''' #select only the 2nd row down, all columns except for the first. #"iloc" is a pandas dataframe function. All it does is select a portion of the data. @@ -2003,7 +2003,7 @@ def readDataFile(collectedFileName): rawCollectedData = numpy.vstack((rawCollectedData,rawCollectedData)) - return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #readReferenceFile is a helper function that reads the reference file in a certain form and returns the #variables and data that are used to initialize the class. It can read files both in XYYY and XYXY form. @@ -2267,10 +2267,10 @@ def getMoleculesFromReferenceData(ReferenceFileName): ''' getMassFragmentsFromCollectedData is a function that takes in the collected filename and returns the mass fragments present in the data ''' -def getMassFragmentsFromCollectedData(CollectedFileName): +def getMassFragmentsFromCollectedData(dataToAnalyzeFileName): #Read the csv file #TODO CHange to use numpy.gen_from_text instead of pandas - DataInfo = pandas.read_csv(CollectedFileName,header=0) + DataInfo = pandas.read_csv(dataToAnalyzeFileName,header=0) #Convert the data into an array DataInfoArray = numpy.array(DataInfo) #Get the names of mass fragments in collected data @@ -2340,9 +2340,9 @@ class MSData (object): #self.mass_fragment_numbers , 1D and must be integers #self.rawCollectedData, a 2D array of the signals. - def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName=None): + def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName=None): - self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.collectedFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.dataToAnalyzeFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #class object variable created to allow class to be used separately from the program. self.ExportAtEachStep = '' @@ -4939,7 +4939,7 @@ def PopulateLogFile(): f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referencePatternsFormsList)) - f6.write('collectedFileName = %s \n'%(G.collectedFileName )) + f6.write('dataToAnalyzeFileName = %s \n'%(G.dataToAnalyzeFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) f6.write('timeRangeStart = %s \n'%(G.timeRangeStart)) @@ -5104,7 +5104,7 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Save an MSReference object containing all molecules and an MSData object containing all mass fragments @@ -5114,14 +5114,14 @@ def main(): AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name - AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory + AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.dataToAnalyzeFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) - AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) + AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.dataToAnalyzeFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) - AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) + AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): @@ -5132,7 +5132,7 @@ def main(): G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments - G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) + G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.dataToAnalyzeFileName) #beforeParsedGDict this will be needed for iterative. This actually contains "UserChoices" when that's available, but we won't use that. beforeParsedGDict = {} @@ -5166,8 +5166,8 @@ def main(): global currentReferenceData global resultsObjects resultsObjects = {} - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) - ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(G.dataToAnalyzeFileName) + ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. @@ -5186,7 +5186,7 @@ def main(): #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index 0242cd874..794e2d2c6 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExistingReferencePatterns.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = 'Collected_Reference.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index 7c8079c4f..e68c930d6 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -12,7 +12,7 @@ def parseUserInput(currentUserInput): currentUserInput.referencePatternsFormsList = parse.listCast(currentUserInput.referencePatternsFormsList) #form needs to be a list currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list - parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string + parse.strCheck(currentUserInput.dataToAnalyzeFileName,'dataToAnalyzeFileName') #dataToAnalyzeFileName must be a string #preProcessing, dataAnalysis, dataSimulation, grapher @@ -251,7 +251,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] - SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] + SettingsVDictionary['dataToAnalyzeFileName'] = UserChoices['inputFiles']['dataToAnalyzeFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] SettingsVDictionary['preProcessing'] = UserChoices['preProcessing']['on'] @@ -270,7 +270,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['oldCollectedFileName'] = UserChoices['iterativeAnalysis']['oldCollectedFileName'] + SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index a4c9d793a..74c3edfde 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/LogFile.txt b/ExampleTuningCorrectorGasMixture/LogFile.txt index e9f57d4fa..9ed6787bc 100644 --- a/ExampleTuningCorrectorGasMixture/LogFile.txt +++ b/ExampleTuningCorrectorGasMixture/LogFile.txt @@ -2,7 +2,7 @@ Sat Sep 25 20:00:41 2021 referenceFileName = ['ExtractedReferencePattern.csv'] form = ['xyyy'] -collectedFileName = Collected_Data.csv +dataToAnalyzeFileName = Collected_Data.csv timeRangeLimit = yes timeRangeStart = 176.0 timeRangeFinish = 900.0 diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index 7a420920a..f15b19e19 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -2079,24 +2079,24 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations - collectedFileNameTemp = str(G.collectedFileName)[:-21] + str(G.iterationSuffix) + str(G.collectedFileName)[-4:] + dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] #copy the experimental and reference files into new names for this iterative run - shutil.copy(G.collectedFileName, collectedFileNameTemp) + shutil.copy(G.dataToAnalyzeFileName, dataToAnalyzeFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.collectedFileName = collectedFileNameTemp + G.dataToAnalyzeFileName = dataToAnalyzeFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + str('_remaining') + G.collectedFileName[-11:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] #naming for reference files G.oldReferenceFileName = [] @@ -2119,10 +2119,10 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2141,12 +2141,12 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program - G.collectedFileName = G.collectedFileName[:-4] + str(G.iterationSuffix) + G.collectedFileName[-4:] + G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] G.oldReferenceFileName = [] for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list @@ -2157,11 +2157,11 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2195,7 +2195,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported - ExportXYYYData(G.collectedFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, + ExportXYYYData(G.dataToAnalyzeFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, abscissaHeader = ExperimentData.abscissaHeader, dataType = 'preProcessed', rowIndex = ExperimentData.times) for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list @@ -2296,7 +2296,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file - G.nextUserInputModule.collectedFileName = G.nextExpFileName + G.nextUserInputModule.dataToAnalyzeFileName = G.nextExpFileName G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules @@ -2335,7 +2335,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): #copy the experimental signals to the next iteration copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.collectedFileName)) + str(G.nextUserInputModule.dataToAnalyzeFileName)) shutil.copy(copyFromPath, os.getcwd()) for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder @@ -2370,17 +2370,17 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### #These functions read in the experimental data file and the reference file. The #returned variables can then be used to initialize the respective classes. -def readDataFile(collectedFileName): +def readDataFile(dataToAnalyzeFileName): #read the csv file into a dataframe. dataFrame means "dataframe" and is a pandas object. - dataFrame = pandas.read_csv('%s' %collectedFileName, header=None) + dataFrame = pandas.read_csv('%s' %dataToAnalyzeFileName, header=None) ''' generate mass fragment list''' #select only the 2nd row down, all columns except for the first. #"iloc" is a pandas dataframe function. All it does is select a portion of the data. @@ -2423,7 +2423,7 @@ def readDataFile(collectedFileName): rawCollectedData = numpy.vstack((rawCollectedData,rawCollectedData)) - return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #readReferenceFile is a helper function that reads the reference file in a certain form and returns the #variables and data that are used to initialize the class. It can read files both in XYYY and XYXY form. @@ -2693,10 +2693,10 @@ def getMoleculesFromReferenceData(ReferenceFileName): ''' getMassFragmentsFromCollectedData is a function that takes in the collected filename and returns the mass fragments present in the data ''' -def getMassFragmentsFromCollectedData(CollectedFileName): +def getMassFragmentsFromCollectedData(dataToAnalyzeFileName): #Read the csv file #TODO CHange to use numpy.gen_from_text instead of pandas - DataInfo = pandas.read_csv(CollectedFileName,header=0) + DataInfo = pandas.read_csv(dataToAnalyzeFileName,header=0) #Convert the data into an array DataInfoArray = numpy.array(DataInfo) #Get the names of mass fragments in collected data @@ -2767,9 +2767,9 @@ class MSData (object): #self.mass_fragment_numbers , 1D and must be integers #self.rawCollectedData, a 2D array of the signals. - def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName=None): + def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName=None): - self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.collectedFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.dataToAnalyzeFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #class object variable created to allow class to be used separately from the program. self.ExportAtEachStep = '' @@ -5519,7 +5519,7 @@ def PopulateLogFile(): f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referencePatternsFormsList)) - f6.write('collectedFileName = %s \n'%(G.collectedFileName )) + f6.write('dataToAnalyzeFileName = %s \n'%(G.dataToAnalyzeFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) f6.write('timeRangeStart = %s \n'%(G.timeRangeStart)) @@ -5685,7 +5685,7 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Read in the molecules used before parsing the user input file @@ -5704,7 +5704,7 @@ def main(): moleculesToAddToReferencePattern.append(moleculeName) G.moleculesNamesExtended = list(G.moleculesNames) + list(moleculesToAddToReferencePattern) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments - G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) + G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.dataToAnalyzeFileName) #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names @@ -5713,14 +5713,14 @@ def main(): AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name - AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory + AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.dataToAnalyzeFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) - AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) + AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.dataToAnalyzeFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) - AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) + AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): @@ -5757,8 +5757,8 @@ def main(): global currentReferenceData global resultsObjects resultsObjects = {} - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) - ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(G.dataToAnalyzeFileName) + ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. @@ -5774,7 +5774,7 @@ def main(): #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index 36ac5263f..cfc3bb1a4 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -1951,24 +1951,24 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations - collectedFileNameTemp = str(G.collectedFileName)[:-21] + str(G.iterationSuffix) + str(G.collectedFileName)[-4:] + dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] #copy the experimental and reference files into new names for this iterative run - shutil.copy(G.collectedFileName, collectedFileNameTemp) + shutil.copy(G.dataToAnalyzeFileName, dataToAnalyzeFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.collectedFileName = collectedFileNameTemp + G.dataToAnalyzeFileName = dataToAnalyzeFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + str('_remaining') + G.collectedFileName[-11:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] #naming for reference files G.oldReferenceFileName = [] @@ -1991,10 +1991,10 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2013,12 +2013,12 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program - G.collectedFileName = G.collectedFileName[:-4] + str(G.iterationSuffix) + G.collectedFileName[-4:] + G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] G.oldReferenceFileName = [] for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list @@ -2029,11 +2029,11 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2067,7 +2067,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported - ExportXYYYData(G.collectedFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, + ExportXYYYData(G.dataToAnalyzeFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, abscissaHeader = ExperimentData.abscissaHeader, dataType = 'preProcessed', rowIndex = ExperimentData.times) for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list @@ -2168,7 +2168,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file - G.nextUserInputModule.collectedFileName = G.nextExpFileName + G.nextUserInputModule.dataToAnalyzeFileName = G.nextExpFileName G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules @@ -2207,7 +2207,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): #copy the experimental signals to the next iteration copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.collectedFileName)) + str(G.nextUserInputModule.dataToAnalyzeFileName)) shutil.copy(copyFromPath, os.getcwd()) for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder @@ -2242,17 +2242,17 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### #These functions read in the experimental data file and the reference file. The #returned variables can then be used to initialize the respective classes. -def readDataFile(collectedFileName): +def readDataFile(dataToAnalyzeFileName): #read the csv file into a dataframe. dataFrame means "dataframe" and is a pandas object. - dataFrame = pandas.read_csv('%s' %collectedFileName, header=None) + dataFrame = pandas.read_csv('%s' %dataToAnalyzeFileName, header=None) ''' generate mass fragment list''' #select only the 2nd row down, all columns except for the first. #"iloc" is a pandas dataframe function. All it does is select a portion of the data. @@ -2295,7 +2295,7 @@ def readDataFile(collectedFileName): rawCollectedData = numpy.vstack((rawCollectedData,rawCollectedData)) - return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #readReferenceFile is a helper function that reads the reference file in a certain form and returns the #variables and data that are used to initialize the class. It can read files both in XYYY and XYXY form. @@ -2561,10 +2561,10 @@ def getMoleculesFromReferenceData(ReferenceFileName): ''' getMassFragmentsFromCollectedData is a function that takes in the collected filename and returns the mass fragments present in the data ''' -def getMassFragmentsFromCollectedData(CollectedFileName): +def getMassFragmentsFromCollectedData(dataToAnalyzeFileName): #Read the csv file #TODO CHange to use numpy.gen_from_text instead of pandas - DataInfo = pandas.read_csv(CollectedFileName,header=0) + DataInfo = pandas.read_csv(dataToAnalyzeFileName,header=0) #Convert the data into an array DataInfoArray = numpy.array(DataInfo) #Get the names of mass fragments in collected data @@ -2635,9 +2635,9 @@ class MSData (object): #self.mass_fragment_numbers , 1D and must be integers #self.rawCollectedData, a 2D array of the signals. - def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName=None): + def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName=None): - self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.collectedFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.dataToAnalyzeFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #class object variable created to allow class to be used separately from the program. self.ExportAtEachStep = '' @@ -5384,7 +5384,7 @@ def PopulateLogFile(): f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referencePatternsFormsList)) - f6.write('collectedFileName = %s \n'%(G.collectedFileName )) + f6.write('dataToAnalyzeFileName = %s \n'%(G.dataToAnalyzeFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) f6.write('timeRangeStart = %s \n'%(G.timeRangeStart)) @@ -5549,7 +5549,7 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Save an MSReference object containing all molecules and an MSData object containing all mass fragments @@ -5559,14 +5559,14 @@ def main(): AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name - AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory + AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.dataToAnalyzeFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) - AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) + AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.dataToAnalyzeFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) - AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) + AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): @@ -5577,7 +5577,7 @@ def main(): G.referencePatternsFileNamesList = parse.listCast(G.referencePatternsFileNamesList) G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments - G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) + G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.dataToAnalyzeFileName) #beforeParsedGDict this will be needed for iterative. This actually contains "UserChoices" when that's available, but we won't use that. beforeParsedGDict = {} @@ -5609,8 +5609,8 @@ def main(): global currentReferenceData global resultsObjects resultsObjects = {} - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) - ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(G.dataToAnalyzeFileName) + ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. @@ -5626,7 +5626,7 @@ def main(): #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index 34dba473a..d2a092185 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -2082,24 +2082,24 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations - collectedFileNameTemp = str(G.collectedFileName)[:-21] + str(G.iterationSuffix) + str(G.collectedFileName)[-4:] + dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] #copy the experimental and reference files into new names for this iterative run - shutil.copy(G.collectedFileName, collectedFileNameTemp) + shutil.copy(G.dataToAnalyzeFileName, dataToAnalyzeFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.collectedFileName = collectedFileNameTemp + G.dataToAnalyzeFileName = dataToAnalyzeFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + str('_remaining') + G.collectedFileName[-11:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] #naming for reference files G.oldReferenceFileName = [] @@ -2122,10 +2122,10 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2144,12 +2144,12 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program - G.collectedFileName = G.collectedFileName[:-4] + str(G.iterationSuffix) + G.collectedFileName[-4:] + G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] G.oldReferenceFileName = [] for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list @@ -2160,11 +2160,11 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2198,7 +2198,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported - ExportXYYYData(G.collectedFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, + ExportXYYYData(G.dataToAnalyzeFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, abscissaHeader = ExperimentData.abscissaHeader, dataType = 'preProcessed', rowIndex = ExperimentData.times) for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list @@ -2299,7 +2299,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file - G.nextUserInputModule.collectedFileName = G.nextExpFileName + G.nextUserInputModule.dataToAnalyzeFileName = G.nextExpFileName G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules @@ -2338,7 +2338,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): #copy the experimental signals to the next iteration copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.collectedFileName)) + str(G.nextUserInputModule.dataToAnalyzeFileName)) shutil.copy(copyFromPath, os.getcwd()) for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder @@ -2373,17 +2373,17 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### #These functions read in the experimental data file and the reference file. The #returned variables can then be used to initialize the respective classes. -def readDataFile(collectedFileName): +def readDataFile(dataToAnalyzeFileName): #read the csv file into a dataframe. dataFrame means "dataframe" and is a pandas object. - dataFrame = pandas.read_csv('%s' %collectedFileName, header=None) + dataFrame = pandas.read_csv('%s' %dataToAnalyzeFileName, header=None) ''' generate mass fragment list''' #select only the 2nd row down, all columns except for the first. #"iloc" is a pandas dataframe function. All it does is select a portion of the data. @@ -2426,7 +2426,7 @@ def readDataFile(collectedFileName): rawCollectedData = numpy.vstack((rawCollectedData,rawCollectedData)) - return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #readReferenceFile is a helper function that reads the reference file in a certain form and returns the #variables and data that are used to initialize the class. It can read files both in XYYY and XYXY form. @@ -2696,10 +2696,10 @@ def getMoleculesFromReferenceData(ReferenceFileName): ''' getMassFragmentsFromCollectedData is a function that takes in the collected filename and returns the mass fragments present in the data ''' -def getMassFragmentsFromCollectedData(CollectedFileName): +def getMassFragmentsFromCollectedData(dataToAnalyzeFileName): #Read the csv file #TODO CHange to use numpy.gen_from_text instead of pandas - DataInfo = pandas.read_csv(CollectedFileName,header=0) + DataInfo = pandas.read_csv(dataToAnalyzeFileName,header=0) #Convert the data into an array DataInfoArray = numpy.array(DataInfo) #Get the names of mass fragments in collected data @@ -2770,9 +2770,9 @@ class MSData (object): #self.mass_fragment_numbers , 1D and must be integers #self.rawCollectedData, a 2D array of the signals. - def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName=None): + def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName=None): - self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.collectedFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.dataToAnalyzeFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #class object variable created to allow class to be used separately from the program. self.ExportAtEachStep = '' @@ -5523,7 +5523,7 @@ def PopulateLogFile(): f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referencePatternsFormsList)) - f6.write('collectedFileName = %s \n'%(G.collectedFileName )) + f6.write('dataToAnalyzeFileName = %s \n'%(G.dataToAnalyzeFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) f6.write('timeRangeStart = %s \n'%(G.timeRangeStart)) @@ -5688,7 +5688,7 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Read in the molecules used before parsing the user input file @@ -5707,7 +5707,7 @@ def main(): moleculesToAddToReferencePattern.append(moleculeName) G.moleculesNamesExtended = list(G.moleculesNames) + list(moleculesToAddToReferencePattern) #We are reading the experimental data in and this must be before user input processing so we have the mass fragments - G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) + G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.dataToAnalyzeFileName) #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names @@ -5716,14 +5716,14 @@ def main(): AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name - AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory + AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.dataToAnalyzeFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) - AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) + AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.dataToAnalyzeFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) - AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) + AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder for referenceObjectIndex in range(len(AllMoleculesReferenceDataList)): @@ -5760,8 +5760,8 @@ def main(): global currentReferenceData global resultsObjects resultsObjects = {} - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) - ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(G.dataToAnalyzeFileName) + ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. @@ -5777,7 +5777,7 @@ def main(): #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index 3c87af198..562fc90ed 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index 8f3f94c4d..9df4c4815 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -14,8 +14,8 @@ def parseUserInput(currentUserInput): currentUserInput.referencePatternsFormsList = parse.stripListOfStrings(currentUserInput.referencePatternsFormsList) currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list - parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string - currentUserInput.collectedFileName = currentUserInput.collectedFileName.strip() + parse.strCheck(currentUserInput.dataToAnalyzeFileName,'dataToAnalyzeFileName') #dataToAnalyzeFileName must be a string + currentUserInput.dataToAnalyzeFileName = currentUserInput.dataToAnalyzeFileName.strip() #preProcessing, dataAnalysis, dataSimulation, grapher @@ -277,7 +277,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] - SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] + SettingsVDictionary['dataToAnalyzeFileName'] = UserChoices['inputFiles']['dataToAnalyzeFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] SettingsVDictionary['preProcessing'] = UserChoices['preProcessing']['on'] @@ -296,7 +296,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['oldCollectedFileName'] = UserChoices['iterativeAnalysis']['oldCollectedFileName'] + SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index 7f8dc1d64..1517a25b7 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -2402,24 +2402,24 @@ def IterativeDirectoryChange(iterativeAnalysis, iterationNumber): os.chdir(iterationDirectoryName) #this will be changed back at the end of the program def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterativeDirectoryChange(iterativeAnalysis, iterationNumber) #naming for collected file #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations - collectedFileNameTemp = str(G.collectedFileName)[:-21] + str(G.iterationSuffix) + str(G.collectedFileName)[-4:] + dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] #copy the experimental and reference files into new names for this iterative run - shutil.copy(G.collectedFileName, collectedFileNameTemp) + shutil.copy(G.dataToAnalyzeFileName, dataToAnalyzeFileNameTemp) #change the globals to reflect the renaming of the ref and exp files - G.collectedFileName = collectedFileNameTemp + G.dataToAnalyzeFileName = dataToAnalyzeFileNameTemp #construct file names for the next run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + str('_remaining') + G.collectedFileName[-11:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] #naming for reference files G.oldReferenceFileName = [] @@ -2442,10 +2442,10 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -2464,12 +2464,12 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program - G.collectedFileName = G.collectedFileName[:-4] + str(G.iterationSuffix) + G.collectedFileName[-4:] + G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program #TODO FIXME, This syntax with -11 will not allow iterative to be compatible with more than 9 iterations - G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] G.oldReferenceFileName = [] for RefIndex, RefName in enumerate(G.referencePatternsFileNamesList): #a list @@ -2480,11 +2480,11 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referencePatternsFileNamesList,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): - #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber + #implied arguments: G.dataSimulation, G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMoleculesNames, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -2518,7 +2518,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported - ExportXYYYData(G.collectedFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, + ExportXYYYData(G.dataToAnalyzeFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, abscissaHeader = ExperimentData.abscissaHeader, dataType = 'preProcessed', rowIndex = ExperimentData.times) for RefObjectIndex, RefObject in enumerate(ReferenceDataList): #a list @@ -2619,7 +2619,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.__var_list__ = G.__var_list__ #save the new file name for the next user input file - G.nextUserInputModule.collectedFileName = G.nextExpFileName + G.nextUserInputModule.dataToAnalyzeFileName = G.nextExpFileName G.nextUserInputModule.referencePatternsFileNamesList = G.nextRefFileName #updating the selected molecules for the next user input file G.nextUserInputModule.chosenMoleculesNames = G.unusedMolecules @@ -2658,7 +2658,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): #copy the experimental signals to the next iteration copyFromPath = os.path.join(os.curdir, os.pardir, str(iterationDirectoryName), - str(G.nextUserInputModule.collectedFileName)) + str(G.nextUserInputModule.dataToAnalyzeFileName)) shutil.copy(copyFromPath, os.getcwd()) for RefIndex, RefName in enumerate(G.nextUserInputModule.referencePatternsFileNamesList): #a list #copy the next reference file from the previous iteration folder to the next iteration folder @@ -2693,15 +2693,15 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment exportSimulatedSignalsSoFar(G.simulatedSignalsOutputName,iterationDirectoryName,G.iterationNumber) #subtract 1 from the iteration number since the iteration number has already been changed IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy) return None - #implied returns: G.referencePatternsFileNamesList, G.collectedFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix + #implied returns: G.referencePatternsFileNamesList, G.dataToAnalyzeFileName, G.nextRefFileName, G.chosenMoleculesNames, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### #These functions read in the experimental data file and the reference file. The #returned variables can then be used to initialize the respective classes. -def readDataFile(collectedFileName): +def readDataFile(dataToAnalyzeFileName): #read the csv file into a dataframe. dataFrame means "dataframe" and is a pandas object. - dataFrame = pandas.read_csv('%s' %collectedFileName, header=None) + dataFrame = pandas.read_csv('%s' %dataToAnalyzeFileName, header=None) ''' generate mass fragment list''' #select only the 2nd row down, all columns except for the first. #"iloc" is a pandas dataframe function. All it does is select a portion of the data. @@ -2744,7 +2744,7 @@ def readDataFile(collectedFileName): rawCollectedData = numpy.vstack((rawCollectedData,rawCollectedData)) - return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #readReferenceFile is a helper function that reads the reference file in a certain form and returns the #variables and data that are used to initialize the class. It can read files both in XYYY and XYXY form. @@ -3065,10 +3065,10 @@ def FromXYXYtoXYYY(provided_reference_patterns): ''' getMassFragmentsFromCollectedData is a function that takes in the collected filename and returns the mass fragments present in the data ''' -def getMassFragmentsFromCollectedData(CollectedFileName): +def getMassFragmentsFromCollectedData(dataToAnalyzeFileName): #Read the csv file #TODO CHange to use numpy.gen_from_text instead of pandas - DataInfo = pandas.read_csv(CollectedFileName,header=0) + DataInfo = pandas.read_csv(dataToAnalyzeFileName,header=0) #Convert the data into an array DataInfoArray = numpy.array(DataInfo) #Get the names of mass fragments in collected data @@ -3142,9 +3142,9 @@ class MSData (object): #self.mass_fragment_numbers , 1D and must be integers #self.rawCollectedData, a 2D array of the signals. - def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName=None): + def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName=None): - self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.collectedFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.dataToAnalyzeFileName=mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #class object variable created to allow class to be used separately from the program. self.ExportAtEachStep = '' @@ -5968,7 +5968,7 @@ def PopulateLogFile(): f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referencePatternsFileNamesList)) f6.write('form = %s \n'%(G.referencePatternsFormsList)) - f6.write('collectedFileName = %s \n'%(G.collectedFileName )) + f6.write('dataToAnalyzeFileName = %s \n'%(G.dataToAnalyzeFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) f6.write('timeRangeStart = %s \n'%(G.timeRangeStart)) @@ -6212,7 +6212,7 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #This function also changes the working directory #Read in the molecules used before parsing the user input file @@ -6245,7 +6245,7 @@ def main(): #We are reading the experimental data in and this must be before user input processing so we have the mass fragments - G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.collectedFileName) + G.exp_mass_fragment_numbers = getMassFragmentsFromCollectedData(G.dataToAnalyzeFileName) #Save an MSReference object containing all molecules and an MSData object containing all mass fragments if G.iterativeAnalysis and G.iterationNumber != 1: #If using iterative and not on the first iteration we will need to remove _iter_x from the file names @@ -6254,14 +6254,14 @@ def main(): AllMoleculesReferenceFileName = remove_iter_fromFileName(G.referencePatternsFileNamesList[referenceFileNameIndex]) #Remove the _iter_ from the name so the program has the original filename to access from the parent directory AllMoleculesReferenceDataFilePath = os.path.normpath(os.path.join(os.curdir, os.pardir,AllMoleculesReferenceFileName)) #This function will get the path of the reference file from the parent directory AllMoleculesreferencePatternsFileNamesList.append(AllMoleculesReferenceDataFilePath) #Append the path to the list and the program will read the reference file from the path name - AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.collectedFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory + AllMassFragmentsExperimentDataFileName = remove_iter_fromFileName(G.dataToAnalyzeFileName) #Remove _iter_ from the data filename so the program has the original filename to access from the parent directory AllMassFragmentsExperimentDataFileNamePath = os.path.normpath(os.path.join(os.curdir, os.pardir, AllMassFragmentsExperimentDataFileName)) #This function will get the path of the data file from the parent directory else: #Otherwise not running iterative or in the first iteration, just copy the filename AllMoleculesreferencePatternsFileNamesList = copy.copy(G.referencePatternsFileNamesList) - AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.collectedFileName) + AllMassFragmentsExperimentDataFileNamePath = copy.copy(G.dataToAnalyzeFileName) #Create the MSReference and MSData objects containing all molecules and all mass fragments, respectively - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) - AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(AllMassFragmentsExperimentDataFileNamePath) + AllMassFragmentsExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) AllMoleculesReferenceDataList = GenerateReferenceDataList(AllMoleculesreferencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) #Then prepare AllMoleculesReferenceDataList to get reciprocal_matching_correction_values, this value is fed into RatioFinder global PreparingAllMoleculesReferenceDataList; PreparingAllMoleculesReferenceDataList = False #initializing this flag @@ -6300,8 +6300,8 @@ def main(): global currentReferenceData global resultsObjects resultsObjects = {} - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) - ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(G.dataToAnalyzeFileName) + ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) ReferenceDataList = GenerateReferenceDataList(G.referencePatternsFileNamesList,G.referencePatternsFormsList,G.AllMID_ObjectsDict) ExperimentData.provided_mass_fragment_numbers = ExperimentData.mass_fragment_numbers #This is where the experimental uncertainties object first gets populated, but it does get modified later as masses are removed and time-points are removed. @@ -6317,7 +6317,7 @@ def main(): #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referencePatternsFileNamesList and G.collectedFileName + #implied arguments for the following function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py index 29131b46e..1700c898d 100644 --- a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py +++ b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py @@ -8,7 +8,7 @@ #//Input Files// referenceFileName = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information form = 'xyyy' #form is either 'xyyy' or 'xyxy' -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data exportSuffix = '' #Iterative Analysis @@ -235,7 +235,7 @@ timeSinceLastCheckpoint = '' -__var_list__ = ['referenceFileName','form','collectedFileName','iterativeAnalysis','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish', +__var_list__ = ['referenceFileName','form','dataToAnalyzeFileName','iterativeAnalysis','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish', 'specificMolecules','chosenMolecules','specificMassFragments','chosenMassFragments', 'moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes', 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', diff --git a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py index 3b0d4b66f..237de9dd1 100644 --- a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py +++ b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py @@ -1131,7 +1131,7 @@ def SpecificIterationName(iterativeAnalysis, iterationNumber): return iterationDirectoryName def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber, iterate = False): - #implied arguments for this function are G.referenceFileName and G.collectedFileName + #implied arguments for this function are G.referenceFileName and G.dataToAnalyzeFileName if iterate: iterationNumber += 1 G.iterationNumber = iterationNumber @@ -1148,29 +1148,29 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber, iterate = if not iterate: #record the old file names G.oldReferenceFileName = G.referenceFileName - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program referenceFileNameTemp = G.referenceFileName[:-18] + str(G.iterationSuffix) + G.referenceFileName[-4:] - collectedFileNameTemp = G.collectedFileName[:-21] + str(G.iterationSuffix) + G.collectedFileName[-4:] + dataToAnalyzeFileNameTemp = G.dataToAnalyzeFileName[:-21] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #copy the experimental and reference files into new names for this iterative run shutil.copy(G.referenceFileName, referenceFileNameTemp) - shutil.copy(G.collectedFileName, collectedFileNameTemp) + shutil.copy(G.dataToAnalyzeFileName, dataToAnalyzeFileNameTemp) #change the globals to reflect the renaming of the ref and exp files G.referenceFileName = referenceFileNameTemp - G.collectedFileName = collectedFileNameTemp + G.dataToAnalyzeFileName = dataToAnalyzeFileNameTemp #construct file names for the next run of the program G.nextRefFileName = G.referenceFileName[:-11] + str('_unused') + G.referenceFileName[-11:] - G.nextExpFileName = G.collectedFileName[:-11] + str('_remaining') + G.collectedFileName[-11:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileName,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referenceFileName,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): - #implied arguments for this function are G.referenceFileName and G.collectedFileName + #implied arguments for this function are G.referenceFileName and G.dataToAnalyzeFileName #this global value is set so that each export statement can label the output files correctly G.iterationNumber = iterationNumber @@ -1190,22 +1190,22 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #record the old file names G.oldReferenceFileName = G.referenceFileName - G.oldcollectedFileName = G.collectedFileName + G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.referenceFileName = G.referenceFileName[:-4] + str(G.iterationSuffix) + G.referenceFileName[-4:] - G.collectedFileName = G.collectedFileName[:-4] + str(G.iterationSuffix) + G.collectedFileName[-4:] + G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program G.nextRefFileName = G.referenceFileName[:-11] + '_unused_iter_1' + G.referenceFileName[-4:] - G.nextExpFileName = G.collectedFileName[:-11] + '_remaining_iter_1' + G.collectedFileName[-4:] + G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] return None - #implied returns: G.oldReferenceFileName, G.oldcollectedFileName, G.referenceFileName,G.collectedFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referenceFileName,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ReferenceData, ReferenceDataFullCopy): - #implied arguments: G.dataSimulation, G.referenceFileName, G.collectedFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMolecules, G.iterationNumber + #implied arguments: G.dataSimulation, G.referenceFileName, G.dataToAnalyzeFileName, G.nextRefFileName, G.oldReferenceFileName, G.chosenMolecules, G.iterationNumber #override data simulation to yes if it was not selected if G.dataSimulation != 'yes': print("Iterative analysis cannot find the remaining signals in the experiment without signal simulation being run.") @@ -1231,7 +1231,7 @@ def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecule #Export current Experimental Data #Experimental data is trimmed prior to this function, but it still needs to be exported - ExportXYYYData(G.collectedFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, + ExportXYYYData(G.dataToAnalyzeFileName, ExperimentData.workingData, ExperimentData.mass_fragment_numbers, abscissaHeader = ExperimentData.abscissaHeader, dataType = 'preProcessed', rowIndex = ExperimentData.times) #export reference data for next iteration @@ -1262,7 +1262,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber, iterate = True) #save the new file name for the next user input file - G.collectedFileName = G.nextExpFileName + G.dataToAnalyzeFileName = G.nextExpFileName G.referenceFileName = G.nextRefFileName #updating the selected molecules for the next user input file G.chosenMolecules = G.unusedMolecules @@ -1277,7 +1277,7 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment if not G.iterativeAnalysis == True: iterationDirectoryName = '%s_iter_%s' %(G.iterativeAnalysis, str(G.iterationNumber - 1)) #copy the experimental signals to the next iteration - shutil.copy("..\%s\%s" %(iterationDirectoryName, G.collectedFileName), os.getcwd()) + shutil.copy("..\%s\%s" %(iterationDirectoryName, G.dataToAnalyzeFileName), os.getcwd()) #copy the next reference file from the previous iteration folder to the next iteration folder shutil.copy("..\%s\%s" %(iterationDirectoryName, G.referenceFileName), os.getcwd()) @@ -1289,17 +1289,17 @@ def IterativeAnalysisPostProcessing(ExperimentData, simulateddata, mass_fragment DataFunctions.AppendColumnsToCSV(G.TotalConcentrationsOutputName, concdata, moleculeConcLabels, times, ["Time"]) return None - #implied returns: G.referenceFileName, G.collectedFileName, G.nextRefFileName, G.chosenMolecules, G.iterationSuffix + #implied returns: G.referenceFileName, G.dataToAnalyzeFileName, G.nextRefFileName, G.chosenMolecules, G.iterationSuffix ############################################################################### ######################### Functions to read data files ####################### ############################################################################### #These functions read in the experimental data file and the reference file. The #returned variables can then be used to initialize the respective classes. -def readDataFile(collectedFileName): +def readDataFile(dataToAnalyzeFileName): #read the csv file into a dataframe. dataFrame means "dataframe" and is a pandas object. - dataFrame = pandas.read_csv('%s' %collectedFileName, header=None) + dataFrame = pandas.read_csv('%s' %dataToAnalyzeFileName, header=None) ''' generate mass fragment list''' #select only the 2nd row down, all columns except for the first. #"iloc" is a pandas dataframe function. All it does is select a portion of the data. @@ -1341,7 +1341,7 @@ def readDataFile(collectedFileName): rawCollectedData = numpy.vstack((rawCollectedData,rawCollectedData)) - return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName + return mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName #readReferenceFile is a helper function that reads the reference file in a certain form and returns the #variables and data that are used to initialize the class. It can read files both in XYYY and XYXY form. @@ -1502,9 +1502,9 @@ class MSData (object): #self.mass_fragment_numbers , 1D and must be integers #self.rawCollectedData, a 2D array of the signals. - def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName=None): + def __init__(self, mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName=None): - [self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.collectedFileName]=[mass_fragment_numbers, abscissaHeader, times, rawCollectedData, collectedFileName] + [self.mass_fragment_numbers, self.abscissaHeader, self.times, self.rawCollectedData, self.dataToAnalyzeFileName]=[mass_fragment_numbers, abscissaHeader, times, rawCollectedData, dataToAnalyzeFileName] '''create data set to work on''' @@ -3022,7 +3022,7 @@ def PopulateLogFile(): f6.write('\n') f6.write('referenceFileName = %s \n'%(G.referenceFileName)) f6.write('form = %s \n'%(G.form)) - f6.write('collectedFileName = %s \n'%(G.collectedFileName )) + f6.write('dataToAnalyzeFileName = %s \n'%(G.dataToAnalyzeFileName )) if G.timeRangeLimit == 'yes':#some of the lines in the backgroundinput file don't need to be printed unless a selection is made, so the if statements here make that happen f6.write('timeRangeLimit = %s \n'%(G.timeRangeLimit)) f6.write('timeRangeStart = %s \n'%(G.timeRangeStart)) @@ -3139,7 +3139,7 @@ def main(): #if this is not the first iterative run, then the required files are all stored in the highest iteration directory if G.iterativeAnalysis and G.iterationNumber != 1: - #implied arguments for this function are G.referenceFileName and G.collectedFileName + #implied arguments for this function are G.referenceFileName and G.dataToAnalyzeFileName IterationDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) #initalize the data classes with the data from given Excel files @@ -3148,8 +3148,8 @@ def main(): global ExperimentData global currentReferenceData - [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_collectedFileName]=readDataFile(G.collectedFileName) - ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, collectedFileName=exp_collectedFileName) + [exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, exp_dataToAnalyzeFileName]=readDataFile(G.dataToAnalyzeFileName) + ExperimentData = MSData(exp_mass_fragment_numbers, exp_abscissaHeader, exp_times, exp_rawCollectedData, dataToAnalyzeFileName=exp_dataToAnalyzeFileName) ReferenceDataList = GenerateReferenceDataList(G.referenceFileName,G.form) currentReferenceData = ReferenceDataList[0] #Prints a warning if the user has more reference files than specified time ranges @@ -3158,7 +3158,7 @@ def main(): #if this is the first iterative run, then the reference and experimental files need to have been imported before the iteration can begin if G.iterativeAnalysis and G.iterationNumber == 1 : - #implied arguments for the following function are G.referenceFileName and G.collectedFileName + #implied arguments for the following function are G.referenceFileName and G.dataToAnalyzeFileName IterationFirstDirectoryPreparation(G.iterativeAnalysis, G.iterationNumber) # Skip preProcessing all together if we are loading analyzed data diff --git a/Todo/SLS Common vs. Unique Bug/UserInput.py b/Todo/SLS Common vs. Unique Bug/UserInput.py index adc33e67c..9250f20f4 100644 --- a/Todo/SLS Common vs. Unique Bug/UserInput.py +++ b/Todo/SLS Common vs. Unique Bug/UserInput.py @@ -9,7 +9,7 @@ referenceFileName = '180710ReferenceFile14thiteration.csv' #enter the file name of the file containing reference information form = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '180710MassSpecSSITKAData.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '180710MassSpecSSITKAData.csv' #enter the file name with raw mass spectrometer data #Iterative Analysis #Options are True, False, or '' @@ -238,11 +238,11 @@ iterationSuffix= '' unusedMolecules ='' oldReferenceFileName = '' -oldCollectedFileName ='' +olddataToAnalyzeFileName ='' nextRefFileName = '' nextExpFileName = '' -__var_list__ = ['referenceFileName','form','collectedFileName','referencePatternTimeRanges','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish', +__var_list__ = ['referenceFileName','form','dataToAnalyzeFileName','referencePatternTimeRanges','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish', 'specificMolecules','chosenMolecules','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes', 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', diff --git a/UnitTests/ConcentrationFinder/test_1.py b/UnitTests/ConcentrationFinder/test_1.py index da65bbf8c..13e71815c 100644 --- a/UnitTests/ConcentrationFinder/test_1.py +++ b/UnitTests/ConcentrationFinder/test_1.py @@ -25,7 +25,7 @@ #They are identical with the exceptions that Acetaldehyde has an ionization factor of 1 and signal peaks at m29 and m29.2 are 9999 and 0, respectively, and Acetaldehyde_easy_to_ionize has an ionization factor of 2 and signal peaks at m29 and m29.2 are 0 and 9999, respectively. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_1.csv'] #Use the truncated reference data that contains only m29 and m29.2 with signals of 1 for each time for both mass fragments -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.concentrationFinder = 'yes' #Turn on concentrationFinder MSRESOLVE.G.TSC_List_Type = 'SeparateMolecularFactors' #Use factors for separate molecules rather than numerous reference files MSRESOLVE.G.moleculesTSC_List = ['Acetaldehyde'] #Using the 'known' concentration values for Acetaldehyde with SeparateMoleculesFactors, concentrationFinder will calculate a conversion factor based on this info and apply to it the scaled concentration of itself and Acetaldehyde_easy_to_ionize diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py index 1989a4bd4..0bf404a2e 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py index e60bef772..df94c3107 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/ConcentrationFinder/test_2.py b/UnitTests/ConcentrationFinder/test_2.py index e0e8eaddc..52e6ededd 100644 --- a/UnitTests/ConcentrationFinder/test_2.py +++ b/UnitTests/ConcentrationFinder/test_2.py @@ -26,7 +26,7 @@ MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_2.csv','AcetaldehydeNISTRefMixed2_test_2.csv'] #List the reference file twice MSRESOLVE.G.referencePatternTimeRanges = [[1,4],[5,8]] #Give time ranges for each reference file #Use the truncated reference data that contains only m29 and m29.2 with signals of 1 for each time for both mass fragments -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated2.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated2.csv' MSRESOLVE.G.concentrationFinder = 'yes' #Turn on concentrationFinder MSRESOLVE.G.TSC_List_Type = 'MultipleReferencePatterns' #Use factors for numerous reference files MSRESOLVE.G.moleculesTSC_List = ['Acetaldehyde','Acetaldehyde'] diff --git a/UnitTests/ConcentrationFinder/test_3.py b/UnitTests/ConcentrationFinder/test_3.py index 77ff7202c..7a62cfa2f 100644 --- a/UnitTests/ConcentrationFinder/test_3.py +++ b/UnitTests/ConcentrationFinder/test_3.py @@ -26,7 +26,7 @@ #Acetaldehyde and Acetaldheyde_copy are identical except Acetaldehyde has a signal of 9999 at m29 and 0 at m29.3. Acetaldehyde_copy is the opposite having a signal of 0 at m29 and 9999 at m29.3. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_3.csv'] #Use the truncated reference data that contains only m29 and m29.2 with signals of 1 for each time for both mass fragments -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated3.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated3.csv' MSRESOLVE.G.concentrationFinder = 'yes' #Turn on concentrationFinder MSRESOLVE.G.TSC_List_Type = 'SeparateMolecularFactors' #Use factors for separate molecules rather than numerous reference files MSRESOLVE.G.moleculesTSC_List = ['Acetaldehyde','Acetaldehyde_Easy_To_Ionize'] #the conversion factor for both molecules are determined based on the known concentrations at a particular signal for both molecules diff --git a/UnitTests/ConcentrationFinder/test_4.py b/UnitTests/ConcentrationFinder/test_4.py index 4a8a71082..e98d2b8c4 100644 --- a/UnitTests/ConcentrationFinder/test_4.py +++ b/UnitTests/ConcentrationFinder/test_4.py @@ -26,7 +26,7 @@ MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2_test_2.csv','AcetaldehydeNISTRefMixed2_test_2.csv'] #List the reference file twice MSRESOLVE.G.referencePatternTimeRanges = [[1,1],[8,8]] #Give time ranges for each reference file (Every point that is not at 1 or 8 will need to be interpolated) #Use the truncated reference data that contains only 8 points with a signal of 1 for m29 -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated2.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated2.csv' MSRESOLVE.G.concentrationFinder = 'yes' #Turn on concentrationFinder MSRESOLVE.G.TSC_List_Type = 'MultipleReferencePatterns' #Use factors for numerous reference files MSRESOLVE.G.moleculesTSC_List = ['Acetaldehyde','Acetaldehyde'] #Use the same molecule diff --git a/UnitTests/ExtractReferencePatternFromData/test_1_input.py b/UnitTests/ExtractReferencePatternFromData/test_1_input.py index a7c09315d..feee12907 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_1_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_1_input.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data #Iterative Analysis #Options are True, False, or '' diff --git a/UnitTests/ExtractReferencePatternFromData/test_2_input.py b/UnitTests/ExtractReferencePatternFromData/test_2_input.py index 9a7ae3984..968b63552 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_2_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_2_input.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data #Iterative Analysis #Options are True, False, or '' diff --git a/UnitTests/ExtractReferencePatternFromData/test_3_input.py b/UnitTests/ExtractReferencePatternFromData/test_3_input.py index e873bc989..cd5a036be 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_3_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_3_input.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data #Iterative Analysis #Options are True, False, or '' diff --git a/UnitTests/ExtractReferencePatternFromData/test_4_input.py b/UnitTests/ExtractReferencePatternFromData/test_4_input.py index 0a67d2661..7768c0c0a 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_4_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_4_input.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data iterativeAnalysis = False iterationNumber = None diff --git a/UnitTests/ExtractReferencePatternFromData/test_5_input.py b/UnitTests/ExtractReferencePatternFromData/test_5_input.py index 920c17a86..e74564a6e 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_5_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_5_input.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data iterativeAnalysis = False iterationNumber = None diff --git a/UnitTests/ExtractReferencePatternFromData/test_6_input.py b/UnitTests/ExtractReferencePatternFromData/test_6_input.py index b7c9ef68d..9e300ebb5 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_6_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_6_input.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data iterativeAnalysis = False iterationNumber = None diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index 3c2136d8a..a888b2545 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -20,7 +20,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -35,7 +35,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IonizationFactors/test_1.py b/UnitTests/IonizationFactors/test_1.py index 642b9add8..664965db6 100644 --- a/UnitTests/IonizationFactors/test_1.py +++ b/UnitTests/IonizationFactors/test_1.py @@ -22,7 +22,7 @@ #This replaces the globals variables being pointed to in MSRESOLVE MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefKnownFactors.csv'] #Overwrite with desired reference file -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' MSRESOLVE.G.exportAtEachStep = 'no' diff --git a/UnitTests/IonizationFactors/test_2.py b/UnitTests/IonizationFactors/test_2.py index dc28d3e67..11223cace 100644 --- a/UnitTests/IonizationFactors/test_2.py +++ b/UnitTests/IonizationFactors/test_2.py @@ -24,7 +24,7 @@ ##First Test input - First reference file #This replaces the globals variables being pointed to in MSRESOLVE MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefMatchingMolecule.csv'] #Overwrite with desired reference file -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' MSRESOLVE.G.exportAtEachStep = 'no' diff --git a/UnitTests/IonizationFactors/test_3.py b/UnitTests/IonizationFactors/test_3.py index 6f5a7f581..321e0e02d 100644 --- a/UnitTests/IonizationFactors/test_3.py +++ b/UnitTests/IonizationFactors/test_3.py @@ -23,7 +23,7 @@ ##First Test input - First reference file #This replaces the globals variables being pointed to in MSRESOLVE MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefKnownTypes.csv'] #Overwrite with desired reference file -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' MSRESOLVE.G.exportAtEachStep = 'no' diff --git a/UnitTests/IonizationFactors/test_4.py b/UnitTests/IonizationFactors/test_4.py index 9d29faa0c..fee703d23 100644 --- a/UnitTests/IonizationFactors/test_4.py +++ b/UnitTests/IonizationFactors/test_4.py @@ -23,7 +23,7 @@ ##First Test input - First reference file #This replaces the globals variables being pointed to in MSRESOLVE MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeNISTRefDefault.csv'] #Overwrite with desired reference file -MSRESOLVE.G.collectedFileName = '2-CrotAcetExp#2Truncated.csv' +MSRESOLVE.G.dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' MSRESOLVE.G.ionizationDataFileName = 'ProvidedIonizationDataExample.csv' MSRESOLVE.G.grapher = 'no' MSRESOLVE.G.exportAtEachStep = 'no' diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py index 52241f887..1601ad01c 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.tsv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py index 0a13557b0..e460daf62 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py index c29656079..43888640b 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py index 9dce43a1a..1159842fc 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py index 9b002dd1f..dfa0829fb 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,200],[250,400]] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py index 681448b5b..735ad205c 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,200],[250,400]] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py index 0187f53c4..3ea8e3cb9 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,250],[250,400]] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py index 29a7dd9f0..724980392 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[176,250],[250,400]] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py index f8f64123b..c5387b5c8 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py index 3d9073480..c15d28ec4 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2Truncated.csv' #enter the file name with raw mass spectrometer data ionizationDataFileName = '_ProvidedIonizationData.csv' diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index f01b58995..576125240 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py index c21974440..d0e49befd 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data iterationNumber = None diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py index 122c887d3..5b6509d5f 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data iterationNumber = None diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py index 0f511c37f..f0d1b370c 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[300,303],[306,309]] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data iterationNumber = None diff --git a/UnitTests/ReferencePatternTimeChooser/test_2_input.py b/UnitTests/ReferencePatternTimeChooser/test_2_input.py index 70f8e7d4e..72f7f90e7 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_2_input.py +++ b/UnitTests/ReferencePatternTimeChooser/test_2_input.py @@ -9,7 +9,7 @@ referencePatternsFileNamesList = ['AcetaldehydeNISTRefMixed2.csv','AcetaldehydeNISTRefMixed2Edit.csv'] #enter the file name of the file containing reference information referencePatternsFormsList = ['xyyy'] #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [[300,303],[306,309]] -collectedFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data iterationNumber = None diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index 555f9d237..aee1b1bb7 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.tsv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index 4644f3d2e..af110502f 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.tsv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index fc00529a0..0640e68c6 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.tsv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index e9fba6ca5..5ff3bc441 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ExtractedReferencePattern.tsv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = 'Collected_Data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.tsv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index 21df4500a..f14fb50dc 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYXY.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyxy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index 4ef6ad488..cf29741d7 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2XYYY.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py index e01da6084..16a8acf36 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py @@ -9,7 +9,7 @@ referenceFileNameList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information form = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2ExclusionTest.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2ExclusionTest.csv' #enter the file name with raw mass spectrometer data #Iterative Analysis #Options are True, False, or '' @@ -238,7 +238,7 @@ iterationSuffix= '' unusedMolecules ='' oldReferenceFileName = '' -oldCollectedFileName ='' +olddataToAnalyzeFileName ='' nextRefFileName = '' nextExpFileName = '' iterationNumber = None diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py index a5c3ef77f..c611af474 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py @@ -9,7 +9,7 @@ referenceFileNameList = 'AcetaldehydeNISTRefMixed2.csv' #enter the file name of the file containing reference information form = 'xyyy' #form is either 'xyyy' or 'xyxy' referencePatternTimeRanges = [] #Leave empty if not using reference pattern time chooser [] -collectedFileName = '2-CrotAcetExp#2ExclusionTest.csv' #enter the file name with raw mass spectrometer data +dataToAnalyzeFileName = '2-CrotAcetExp#2ExclusionTest.csv' #enter the file name with raw mass spectrometer data #Iterative Analysis #Options are True, False, or '' @@ -239,7 +239,7 @@ iterationSuffix= '' unusedMolecules ='' oldReferenceFileName = '' -oldCollectedFileName ='' +olddataToAnalyzeFileName ='' nextRefFileName = '' nextExpFileName = '' iterationNumber = None diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index 2665cbf0e..56d6ad985 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index 41da1289f..f073b8c4c 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index cc4f1106c..d9750b4dd 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -1,6 +1,6 @@ referencePatternsFileNamesList = ['reference_measured_EthyleneExtracted.csv'] referencePatternsFormsList = 'xyyy' -collectedFileName = 'Ethylene.csv' +dataToAnalyzeFileName = 'Ethylene.csv' referencePatternTimeRanges = [] ionizationDataFileName = '181017ProvidedIonizationData.csv' iterativeAnalysis = False @@ -8,7 +8,7 @@ iterationSuffix = '' unusedMolecules = '' oldReferenceFileName = [] -oldCollectedFileName = '' +olddataToAnalyzeFileName = '' nextRefFileName = [] nextExpFileName = '' preProcessing = 'yes' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','olddataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index 09d4e1b43..7bdf8894e 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -1,6 +1,6 @@ referencePatternsFileNamesList = ['reference_measured_EthyleneExtracted.csv'] referencePatternsFormsList = 'xyyy' -collectedFileName = 'Ethylene.csv' +dataToAnalyzeFileName = 'Ethylene.csv' referencePatternTimeRanges = [] ionizationDataFileName = '181017ProvidedIonizationData.csv' iterativeAnalysis = False @@ -8,7 +8,7 @@ iterationSuffix = '' unusedMolecules = '' oldReferenceFileName = [] -oldCollectedFileName = '' +olddataToAnalyzeFileName = '' nextRefFileName = [] nextExpFileName = '' preProcessing = 'yes' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldCollectedFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','olddataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index 21629dd8a..186e2a3da 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index 11642d399..96aaaaaea 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index 516be48b6..b1b2da614 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index a205753be..d084be9e4 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index 14ae23a4d..021fda4f4 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index fbd51a273..cb8ed8390 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index cff8025ea..7aecea9a4 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index 4c1b7504e..d3fc958a4 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index 55433d5d1..082f9d586 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index 2f2f622cd..4589aa8b7 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index 92a170024..333b0148e 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index f6625399d..ca89dc848 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index 54f2c8404..41ec04b64 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index 342e36412..bba604cdc 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index 968ce7863..c6b5eed93 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index 9610107e3..3e45b5da4 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index c523ebec3..465db3b3e 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index efbe03d4a..92c89827b 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index 5c04226bf..a5bab86a3 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -19,7 +19,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['ConvertedSpectra.csv'] #enter the file name of the file containing reference information UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '20190817A-integer-data.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index 5868e7c9b..8ec4f0f10 100644 --- a/UserInput.py +++ b/UserInput.py @@ -16,7 +16,7 @@ UserChoices['inputFiles']['referencePatternsFileNamesList'] = ['AcetaldehydeNISTRefMixed2.tsv'] #enter the file name of the file containing reference information. tsv is tab-separated, csv is comma separated. tsv supports commas in molecule names. UserChoices['inputFiles']['referencePatternsFormsList'] = 'xyyy' #form is either 'xyyy' or 'xyxy' (if using reference pattern time chooser enter as list with forms for each individual reference file ['xyyy','xyyy','xyyy']) UserChoices['inputFiles']['referencePatternTimeRanges'] = [] #Leave empty if not using reference pattern time chooser [] -UserChoices['inputFiles']['collectedFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data +UserChoices['inputFiles']['dataToAnalyzeFileName'] = '2-CrotAcetExp#2.csv' #enter the file name with raw mass spectrometer data UserChoices['inputFiles']['ionizationDataFileName'] = '181017ProvidedIonizationData.csv' #the name of the file containing the ionization data @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['oldCollectedFileName'] ='' +UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','collectedFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldCollectedFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index fdccbe333..167276579 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -14,8 +14,8 @@ def parseUserInput(currentUserInput): currentUserInput.referencePatternsFormsList = parse.stripListOfStrings(currentUserInput.referencePatternsFormsList) currentUserInput.referencePatternsFormsList = parse.parallelVectorize(currentUserInput.referencePatternsFormsList,len(currentUserInput.referencePatternsFileNamesList)) #form needs to be a list of the same length as referenceFileName currentUserInput.referencePatternTimeRanges = parse.listCast(currentUserInput.referencePatternTimeRanges) #RefPatternTimeRanges needs to be a list - parse.strCheck(currentUserInput.collectedFileName,'collectedFileName') #collectedFileName must be a string - currentUserInput.collectedFileName = currentUserInput.collectedFileName.strip() + parse.strCheck(currentUserInput.dataToAnalyzeFileName,'dataToAnalyzeFileName') #dataToAnalyzeFileName must be a string + currentUserInput.dataToAnalyzeFileName = currentUserInput.dataToAnalyzeFileName.strip() #preProcessing, dataAnalysis, dataSimulation, grapher @@ -314,7 +314,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['referencePatternsFileNamesList'] = UserChoices['inputFiles']['referencePatternsFileNamesList'] SettingsVDictionary['referencePatternsFormsList'] = UserChoices['inputFiles']['referencePatternsFormsList'] SettingsVDictionary['referencePatternTimeRanges'] = UserChoices['inputFiles']['referencePatternTimeRanges'] - SettingsVDictionary['collectedFileName'] = UserChoices['inputFiles']['collectedFileName'] + SettingsVDictionary['dataToAnalyzeFileName'] = UserChoices['inputFiles']['dataToAnalyzeFileName'] SettingsVDictionary['ionizationDataFileName'] = UserChoices['inputFiles']['ionizationDataFileName'] SettingsVDictionary['preProcessing'] = UserChoices['preProcessing']['on'] @@ -333,7 +333,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['oldCollectedFileName'] = UserChoices['iterativeAnalysis']['oldCollectedFileName'] + SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] From a60c19dd7faf07a257a692dffb4795cbff39073a Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 11:37:03 -0400 Subject: [PATCH 4/9] oldDataToAnalyzeFileName capitalization fix --- DefaultUserInput.py | 4 ++-- ExampleAnalysis/DefaultUserInput.py | 4 ++-- ExampleAnalysis/MSRESOLVE.py | 8 ++++---- ExampleAnalysis/UserInput.py | 4 ++-- ExampleAnalysis/userInputValidityFunctions.py | 2 +- ExampleReferenceExtraction/DefaultUserInput.py | 4 ++-- ExampleReferenceExtraction/MSRESOLVE.py | 8 ++++---- ExampleReferenceExtraction/UserInput.py | 4 ++-- ExampleReferenceExtraction/userInputValidityFunctions.py | 2 +- ExampleTuningCorrectorGasMixture/DefaultUserInput.py | 4 ++-- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 8 ++++---- ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py | 8 ++++---- ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py | 8 ++++---- ExampleTuningCorrectorGasMixture/UserInput.py | 4 ++-- .../userInputValidityFunctions.py | 2 +- MSRESOLVE.py | 8 ++++---- Todo/SLS Common vs. Unique Bug/MSRESOLVE.py | 8 ++++---- Todo/SLS Common vs. Unique Bug/UserInput.py | 4 ++-- UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py | 4 ++-- UnitTests/NegativeAnalyzer/test_1_Input.py | 4 ++-- .../TuningCorrectorGasMixture/UserInputGasMixture.py | 4 ++-- .../TuningCorrectorGasMixture/UserInputGasMixture2.py | 4 ++-- .../TuningCorrectorGasMixture/UserInputGasMixture3.py | 4 ++-- .../TuningCorrectorGasMixture/UserInputGasMixture4.py | 4 ++-- UnitTests/XYXYReferencePattern/test_1_inputXYXY.py | 4 ++-- UnitTests/XYXYReferencePattern/test_1_inputXYYY.py | 4 ++-- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- UnitTests/implicitSLScorrection/test_1_Input.py | 4 ++-- UnitTests/implicitSLScorrection/test_2_Input.py | 4 ++-- .../test_1_UserInput.py | 4 ++-- .../test_2_UserInput.py | 4 ++-- UnitTests/slsCommon/test_1_Input.py | 4 ++-- .../slsUniquePositiveConcentrationsOnly/test_1_Input.py | 4 ++-- .../slsUniquePositiveConcentrationsOnly/test_2_Input.py | 4 ++-- UnitTests/uncertainties/test_10_Input.py | 4 ++-- UnitTests/uncertainties/test_11_Input.py | 4 ++-- UnitTests/uncertainties/test_12_Input.py | 4 ++-- UnitTests/uncertainties/test_13_Input.py | 4 ++-- UnitTests/uncertainties/test_14_Input.py | 4 ++-- UnitTests/uncertainties/test_15_Input.py | 4 ++-- UnitTests/uncertainties/test_16_Input.py | 4 ++-- UnitTests/uncertainties/test_1_Input.py | 4 ++-- UnitTests/uncertainties/test_2_Input.py | 4 ++-- UnitTests/uncertainties/test_3_Input.py | 4 ++-- UnitTests/uncertainties/test_4_Input.py | 4 ++-- UnitTests/uncertainties/test_5_Input.py | 4 ++-- UnitTests/uncertainties/test_6_Input.py | 4 ++-- UnitTests/uncertainties/test_7_Input.py | 4 ++-- UnitTests/uncertainties/test_8_Input.py | 4 ++-- UnitTests/uncertainties/test_9_Input.py | 4 ++-- UserInput.py | 4 ++-- userInputValidityFunctions.py | 2 +- 53 files changed, 114 insertions(+), 114 deletions(-) diff --git a/DefaultUserInput.py b/DefaultUserInput.py index 8ec4f0f10..1b2b6e729 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index 66a9b50d0..17f961c3c 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index fa8a61927..1fb829cc0 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -1663,7 +1663,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #naming for collected file #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] @@ -1698,7 +1698,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName @@ -1720,7 +1720,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program @@ -1736,7 +1736,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index 42bc27c9c..a5755f0a9 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index e68c930d6..37e7bb09f 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -270,7 +270,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] + SettingsVDictionary['oldDataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index 66a9b50d0..17f961c3c 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index fa8a61927..1fb829cc0 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -1663,7 +1663,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #naming for collected file #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] @@ -1698,7 +1698,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName @@ -1720,7 +1720,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program @@ -1736,7 +1736,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index 794e2d2c6..f0693978e 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index e68c930d6..37e7bb09f 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -270,7 +270,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] + SettingsVDictionary['oldDataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index 74c3edfde..d9687cfec 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index f15b19e19..d55df876a 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -2084,7 +2084,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #naming for collected file #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] @@ -2119,7 +2119,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName @@ -2141,7 +2141,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program @@ -2157,7 +2157,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index cfc3bb1a4..aa25f1eb0 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -1956,7 +1956,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #naming for collected file #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] @@ -1991,7 +1991,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName @@ -2013,7 +2013,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program @@ -2029,7 +2029,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index d2a092185..e0e16b8c7 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -2087,7 +2087,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #naming for collected file #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] @@ -2122,7 +2122,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName @@ -2144,7 +2144,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program @@ -2160,7 +2160,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index 562fc90ed..b367b52fe 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index 9df4c4815..1a69f0148 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -296,7 +296,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] + SettingsVDictionary['oldDataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index 1517a25b7..c528979d6 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -2407,7 +2407,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #naming for collected file #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program #TODO FIXME, This syntax with -21 will not allow iterative to be compatible with more than 9 iterations dataToAnalyzeFileNameTemp = str(G.dataToAnalyzeFileName)[:-21] + str(G.iterationSuffix) + str(G.dataToAnalyzeFileName)[-4:] @@ -2442,7 +2442,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber): #TODO FIXME, This syntax with -18 will not allow iterative to be compatible with more than 9 iterations G.nextRefFileName.append(RefName[:-18] + '_unused_iter_%s' %G.iterationNumber + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #implied arguments for this function are G.referencePatternsFileNamesList and G.dataToAnalyzeFileName @@ -2464,7 +2464,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): AppendListToFile("__var_list__", G.__var_list__, "UserInput_iter_1.py", float('Inf')) #record the old file names - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] #construct file names for the second run of the program @@ -2480,7 +2480,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextRefFileName.append(RefName[:-4] + '_unused_iter_1' + RefName[-4:]) return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referencePatternsFileNamesList,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ExperimentDataFullCopy, ReferenceDataList, ReferenceDataListFullCopy): diff --git a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py index 237de9dd1..69c594162 100644 --- a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py +++ b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py @@ -1148,7 +1148,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber, iterate = if not iterate: #record the old file names G.oldReferenceFileName = G.referenceFileName - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the current run of the program referenceFileNameTemp = G.referenceFileName[:-18] + str(G.iterationSuffix) + G.referenceFileName[-4:] @@ -1167,7 +1167,7 @@ def IterationDirectoryPreparation(iterativeAnalysis, iterationNumber, iterate = G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + str('_remaining') + G.dataToAnalyzeFileName[-11:] return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referenceFileName,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referenceFileName,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #implied arguments for this function are G.referenceFileName and G.dataToAnalyzeFileName @@ -1190,7 +1190,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): #record the old file names G.oldReferenceFileName = G.referenceFileName - G.olddataToAnalyzeFileName = G.dataToAnalyzeFileName + G.oldDataToAnalyzeFileName = G.dataToAnalyzeFileName #construct the file names for the first run of the program G.referenceFileName = G.referenceFileName[:-4] + str(G.iterationSuffix) + G.referenceFileName[-4:] G.dataToAnalyzeFileName = G.dataToAnalyzeFileName[:-4] + str(G.iterationSuffix) + G.dataToAnalyzeFileName[-4:] @@ -1201,7 +1201,7 @@ def IterationFirstDirectoryPreparation(iterativeAnalysis,iterationNumber): G.nextExpFileName = G.dataToAnalyzeFileName[:-11] + '_remaining_iter_1' + G.dataToAnalyzeFileName[-4:] return None - #implied returns: G.oldReferenceFileName, G.olddataToAnalyzeFileName, G.referenceFileName,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber + #implied returns: G.oldReferenceFileName, G.oldDataToAnalyzeFileName, G.referenceFileName,G.dataToAnalyzeFileName, G.nextRefFileName, G. nextExpFileName, G.iterationNumber #The IterativeAnalysisDirectory and Variable Population function is used to shrink the size of the program analysis and redirect the output. def IADirandVarPopulation(iterativeAnalysis, chosenMassFragments, chosenMolecules, ExperimentData, ReferenceData, ReferenceDataFullCopy): diff --git a/Todo/SLS Common vs. Unique Bug/UserInput.py b/Todo/SLS Common vs. Unique Bug/UserInput.py index 9250f20f4..4a13133c6 100644 --- a/Todo/SLS Common vs. Unique Bug/UserInput.py +++ b/Todo/SLS Common vs. Unique Bug/UserInput.py @@ -238,11 +238,11 @@ iterationSuffix= '' unusedMolecules ='' oldReferenceFileName = '' -olddataToAnalyzeFileName ='' +oldDataToAnalyzeFileName ='' nextRefFileName = '' nextExpFileName = '' -__var_list__ = ['referenceFileName','form','dataToAnalyzeFileName','referencePatternTimeRanges','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish', +__var_list__ = ['referenceFileName','form','dataToAnalyzeFileName','referencePatternTimeRanges','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish', 'specificMolecules','chosenMolecules','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes', 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index a888b2545..096a71edb 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -35,7 +35,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index 576125240..1065efc7d 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index aee1b1bb7..ba163067c 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index af110502f..7e702da79 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index 0640e68c6..01537571e 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index 5ff3bc441..52851ea9a 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index f14fb50dc..b8925bd64 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index cf29741d7..099e81607 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py index 16a8acf36..4de5ca783 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py @@ -238,7 +238,7 @@ iterationSuffix= '' unusedMolecules ='' oldReferenceFileName = '' -olddataToAnalyzeFileName ='' +oldDataToAnalyzeFileName ='' nextRefFileName = '' nextExpFileName = '' iterationNumber = None diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py index c611af474..638b983b2 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py @@ -239,7 +239,7 @@ iterationSuffix= '' unusedMolecules ='' oldReferenceFileName = '' -olddataToAnalyzeFileName ='' +oldDataToAnalyzeFileName ='' nextRefFileName = '' nextExpFileName = '' iterationNumber = None diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index 56d6ad985..96fe4e4b8 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index f073b8c4c..fdcb0c6a7 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index d9750b4dd..c96740b97 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -8,7 +8,7 @@ iterationSuffix = '' unusedMolecules = '' oldReferenceFileName = [] -olddataToAnalyzeFileName = '' +oldDataToAnalyzeFileName = '' nextRefFileName = [] nextExpFileName = '' preProcessing = 'yes' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','olddataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index 7bdf8894e..52b168b21 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -8,7 +8,7 @@ iterationSuffix = '' unusedMolecules = '' oldReferenceFileName = [] -olddataToAnalyzeFileName = '' +oldDataToAnalyzeFileName = '' nextRefFileName = [] nextExpFileName = '' preProcessing = 'yes' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','olddataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index 186e2a3da..4af66537c 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index 96aaaaaea..dfbb8ae36 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index b1b2da614..df44c8d82 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index d084be9e4..db95f74a7 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index 021fda4f4..3260fd6b3 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index cb8ed8390..5cf29ab53 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index 7aecea9a4..87eaa3667 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index d3fc958a4..261149d2a 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index 082f9d586..4a49b5c8f 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index 4589aa8b7..19fa86ace 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index 333b0148e..79c289b68 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index ca89dc848..b29749b3b 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index 41ec04b64..fb82a3c07 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index bba604cdc..4a8b6b194 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index c6b5eed93..d950d2713 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index 3e45b5da4..f2fdfc5a9 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index 465db3b3e..b39f37253 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index 92c89827b..b617a0cc4 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index a5bab86a3..4966663eb 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -34,7 +34,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index 8ec4f0f10..1b2b6e729 100644 --- a/UserInput.py +++ b/UserInput.py @@ -31,7 +31,7 @@ UserChoices['iterativeAnalysis']['iterationSuffix'] = '' UserChoices['iterativeAnalysis']['unusedMolecules'] ='' UserChoices['iterativeAnalysis']['oldReferenceFileName'] = [] -UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] ='' +UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] ='' UserChoices['iterativeAnalysis']['nextRefFileName'] = [] UserChoices['iterativeAnalysis']['nextExpFileName'] = '' UserChoices['iterativeAnalysis']['iterationNumber'] = None #just initializing. @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'olddataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index 167276579..c78c5ac4f 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -333,7 +333,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['iterationSuffix'] = UserChoices['iterativeAnalysis']['iterationSuffix'] SettingsVDictionary['unusedMolecules'] = UserChoices['iterativeAnalysis']['unusedMolecules'] SettingsVDictionary['oldReferenceFileName'] = UserChoices['iterativeAnalysis']['oldReferenceFileName'] - SettingsVDictionary['olddataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['olddataToAnalyzeFileName'] + SettingsVDictionary['oldDataToAnalyzeFileName'] = UserChoices['iterativeAnalysis']['oldDataToAnalyzeFileName'] SettingsVDictionary['nextRefFileName'] = UserChoices['iterativeAnalysis']['nextRefFileName'] SettingsVDictionary['nextExpFileName'] = UserChoices['iterativeAnalysis']['nextExpFileName'] SettingsVDictionary['iterationNumber'] = UserChoices['iterativeAnalysis']['iterationNumber'] From 563b22f3e169b62af994ca93e58e0934e274fdc9 Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 11:58:25 -0400 Subject: [PATCH 5/9] Update 190930TuningCorrectorInstructions.docx --- .../190930TuningCorrectorInstructions.docx | Bin 21114 -> 22041 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/Documentation/190930TuningCorrectorInstructions.docx b/Documentation/190930TuningCorrectorInstructions.docx index d01a7ca217162d1b5cdc3b71b8d3cc0c4a95fa05..e01cd771ca303f1c6c1648957c10c2788671e73a 100644 GIT binary patch delta 15314 zcmaKTb986HvTkhKwrx*r+s?$+B){1H#hlo-Cz{x{Z6_1GIp^Ga&w2N)_4eB9Tispt zb=4oetM{(z{ig^tqYAX{01A$uamQ3w;2q@sDjl>qxwx%vpn~V_{jn*-ER}Ql6f`afHaA$yoh3*PLKVh zVUipN7uQqL^8J;W*b3D3dMJ`O)N#5E{we0RUxnjoptIHL8sOZcF`Z7~K2VP@p8x!0 zcSvak0JQ&k2E5(hP4eI|S{kOafsn~>F&r1RTFrCh^tN}&OR6~@QDL(KFr;KSWSAvq zFW55W-xEFCWA<(-r(GCc?TMtwnPql-OYpZkM|F@K9ukq(cs$Z>*uXHDrPR0;yW?$f zHjGK;iap95!1g>rAjl8e6_oppmG3A`n?a>F0I(>=&7d-Ch^pf|2b(0fSqaITB(PZt 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Subject: [PATCH 6/9] UserChoices['measuredReferenceYorN'] --> 'tuningCorrection' --- DefaultUserInput.py | 30 +++---- ExampleAnalysis/DefaultUserInput.py | 16 ++-- ExampleAnalysis/MSRESOLVE.py | 10 +-- ExampleAnalysis/UserInput.py | 16 ++-- ExampleAnalysis/userInputValidityFunctions.py | 12 +-- .../DefaultUserInput.py | 16 ++-- ExampleReferenceExtraction/MSRESOLVE.py | 10 +-- ExampleReferenceExtraction/UserInput.py | 16 ++-- .../userInputValidityFunctions.py | 12 +-- ExampleTuningCorrectorGasMixture/0-README.txt | 2 +- .../DefaultUserInput.py | 16 ++-- ExampleTuningCorrectorGasMixture/LogFile.txt | 2 +- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 32 ++++---- .../MSRESOLVEBad1.py | 24 +++--- .../MSRESOLVEPrevious.py | 28 +++---- ExampleTuningCorrectorGasMixture/UserInput.py | 22 +++--- .../userInputValidityFunctions.py | 32 ++++---- MSRESOLVE.py | 42 +++++----- .../DefaultUserInput.py | 4 +- Todo/SLS Common vs. Unique Bug/MSRESOLVE.py | 10 +-- Todo/SLS Common vs. Unique Bug/UserInput.py | 4 +- .../bestMassFragChooser.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../test_3_input.py | 2 +- .../test_4_input.py | 2 +- .../test_5_input.py | 2 +- .../test_6_input.py | 2 +- .../test_1_Input_Brute_Finisher.py | 14 ++-- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/NegativeAnalyzer/test_1_Input.py | 14 ++-- .../test_1_inputA.py | 2 +- .../test_1_inputB.py | 2 +- .../test_1_inputC.py | 2 +- .../test_2_input.py | 2 +- UnitTests/TuningCorrector/test_1.py | 2 +- .../test_10 Manual SLS/1/test_10.turnedOff | 2 +- .../test_10 Manual SLS/1/test_5.turnedOff | 2 +- .../test_10 Manual SLS/4/test_10.turnedOff | 2 +- UnitTests/TuningCorrector/test_10.py | 2 +- .../1/test_10.turnedOff | 2 +- .../1/test_11.turnedOff | 2 +- .../4/test_11.turnedOff | 2 +- UnitTests/TuningCorrector/test_11.py | 2 +- UnitTests/TuningCorrector/test_2.py | 2 +- UnitTests/TuningCorrector/test_3.py | 2 +- UnitTests/TuningCorrector/test_4.py | 2 +- UnitTests/TuningCorrector/test_5.py | 2 +- UnitTests/TuningCorrector/test_6.py | 2 +- UnitTests/TuningCorrector/test_7.py | 2 +- UnitTests/TuningCorrector/test_8.py | 2 +- UnitTests/TuningCorrector/test_9.py | 2 +- .../TuningCorrectorGasMixture/0-README.txt | 2 +- .../UserInputGasMixture.py | 22 +++--- .../UserInputGasMixture2.py | 26 +++---- .../UserInputGasMixture3.py | 26 +++---- .../UserInputGasMixture4.py | 26 +++---- .../XYXYReferencePattern/test_1_inputXYXY.py | 28 +++---- .../XYXYReferencePattern/test_1_inputXYYY.py | 28 +++---- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../implicitSLScorrection/test_1_Input.py | 14 ++-- .../implicitSLScorrection/test_2_Input.py | 14 ++-- .../test_1_UserInput.py | 4 +- .../test_2_UserInput.py | 4 +- UnitTests/slsCommon/test_1_Input.py | 14 ++-- .../test_1_Input.py | 14 ++-- .../test_2_Input.py | 14 ++-- UnitTests/uncertainties/test_10_Input.py | 14 ++-- UnitTests/uncertainties/test_11_Input.py | 14 ++-- UnitTests/uncertainties/test_12_Input.py | 14 ++-- UnitTests/uncertainties/test_13_Input.py | 14 ++-- UnitTests/uncertainties/test_14_Input.py | 20 ++--- UnitTests/uncertainties/test_15_Input.py | 20 ++--- UnitTests/uncertainties/test_16_Input.py | 18 ++--- UnitTests/uncertainties/test_1_Input.py | 14 ++-- UnitTests/uncertainties/test_2_Input.py | 14 ++-- UnitTests/uncertainties/test_3_Input.py | 14 ++-- UnitTests/uncertainties/test_4_Input.py | 14 ++-- UnitTests/uncertainties/test_5_Input.py | 14 ++-- UnitTests/uncertainties/test_6_Input.py | 14 ++-- UnitTests/uncertainties/test_7_Input.py | 14 ++-- UnitTests/uncertainties/test_8_Input.py | 14 ++-- UnitTests/uncertainties/test_9_Input.py | 14 ++-- UserInput.py | 30 +++---- userInputValidityFunctions.py | 78 +++++++++---------- 97 files changed, 526 insertions(+), 526 deletions(-) diff --git a/DefaultUserInput.py b/DefaultUserInput.py index 1b2b6e729..37c79b79d 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -150,24 +150,24 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['tuningCorrectPatternInternalVsExternal'] = 'External' #the options are 'External' or 'Internal'. Typically, External with createMixedTuningPattern is used. With "External", the existing pattern is assumed to be an External pattern and is tuning corrected. With "Internal" the existing pattern is assumed to be an Internal pattern, and the analysis pattern is changed to match the tuning of the desired pattern. Another use of 'Internal' when applying reference Coefficients manually to the Reference Analysis pattern. As of Nov 2021, if "External" is used, then at least one of referenceFileStandardTuningAndForm and referenceFileExistingTuningAndForm must be filled. -UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = [] #optional: Provides tuningCorrectionIntensity feature. Must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be pattern tuning corrected. Normally should be empty list, []. Otherwise, must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Normally should be empty, list, []. Otherwise, must include csv file and form. Example: ['OriginalRef.csv', 'xyyy'] . -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided (along with filling the next two variables). -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". - -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['tuningCorrectPatternInternalVsExternal'] = 'External' #the options are 'External' or 'Internal'. Typically, External with createMixedTuningPattern is used. With "External", the existing pattern is assumed to be an External pattern and is tuning corrected. With "Internal" the existing pattern is assumed to be an Internal pattern, and the analysis pattern is changed to match the tuning of the desired pattern. Another use of 'Internal' when applying reference Coefficients manually to the Reference Analysis pattern. As of Nov 2021, if "External" is used, then at least one of referenceFileStandardTuningAndForm and referenceFileExistingTuningAndForm must be filled. +UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = [] #optional: Provides tuningCorrectionIntensity feature. Must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be pattern tuning corrected. Normally should be empty list, []. Otherwise, must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Normally should be empty, list, []. Otherwise, must include csv file and form. Example: ['OriginalRef.csv', 'xyyy'] . +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided (along with filling the next two variables). +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". + +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index 17f961c3c..3fe20f588 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -150,17 +150,17 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index 1fb829cc0..43f460727 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -482,8 +482,8 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi #this function either creates or gets the three coefficients for the polynomial correction (Tuning Correction) and calculates #the correction factor for the relative intensities of each mass fragment, outputting a corrected set #of relative intensities -def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm,measuredReferenceYorN): - if measuredReferenceYorN =='yes': +def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm,tuningCorrection): + if tuningCorrection =='yes': abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients referenceCorrectionCoefficients_cov = abcCoefficients_cov @@ -1196,7 +1196,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): ReferenceData.standardized_reference_patterns, ReferenceData.standardized_reference_patterns_tuning_uncertainties = TuningCorrector(ReferenceData.standardized_reference_patterns, G.referenceCorrectionCoefficients,G.referenceCorrectionCoefficients_cov, G.referenceFileDesiredTuningAndForm, G.referenceFileExistingTuningAndForm, - G.measuredReferenceYorN) + G.tuningCorrection) #Now check if uncertainties already exist, and if they do then the two uncertainties need to be combined. Else, made equal. try: ReferenceData.absolute_standard_uncertainties = (ReferenceData.absolute_standard_uncertainties**2 + ReferenceData.standardized_reference_patterns_tuning_uncertainties**2)**0.5 @@ -4948,8 +4948,8 @@ def PopulateLogFile(): f6.write('backgroundMassFragment = %s \n'%(G.backgroundMassFragment)) f6.write('backgroundSlopes = %s \n'%(G.backgroundSlopes)) f6.write('backgroundIntercepts = %s \n'%(G.backgroundIntercepts)) - if G.measuredReferenceYorN == 'yes': - f6.write('measuredReferenceYorN = %s \n'%G.measuredReferenceYorN) + if G.tuningCorrection == 'yes': + f6.write('tuningCorrection = %s \n'%G.tuningCorrection) f6.write('referenceCorrectionCoefficientA = %s \n'%(G.referenceCorrectionCoefficients[0])) f6.write('referenceCorrectionCoefficientB = %s \n'%(G.referenceCorrectionCoefficients[1])) f6.write('referenceCorrectionCoefficientC = %s \n'%(G.referenceCorrectionCoefficients[2])) diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index a5755f0a9..f3115930f 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -150,17 +150,17 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index 37e7bb09f..de557484e 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -106,7 +106,7 @@ def parseUserInput(currentUserInput): currentUserInput.scaleRawDataFactor = float(currentUserInput.scaleRawDataFactor) #scaleRawDataFactor is a float #Reference Correction Changer - parse.strCheck(currentUserInput.measuredReferenceYorN,'measuredReferenceYorN') + parse.strCheck(currentUserInput.tuningCorrection,'tuningCorrection') #The below two variables are no longer strings. They are now lists with two elements, each of which are strings. TODO: Change their names to referenceFileExistingTuningAndForm and referenceFileDesiredTuningAndForm #parse.strCheck(currentUserInput.referenceFileExistingTuningAndForm,'referenceFileExistingTuningAndForm') #parse.strCheck(currentUserInput.referenceFileDesiredTuningAndForm,'referenceFileDesiredTuningAndForm') @@ -312,12 +312,12 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['scaleRawDataOption'] = UserChoices['scaleRawDataYorN']['scaleRawDataOption'] SettingsVDictionary['scaleRawDataFactor'] = UserChoices['scaleRawDataYorN']['scaleRawDataFactor'] - SettingsVDictionary['measuredReferenceYorN'] = UserChoices['measuredReferenceYorN']['on'] - SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] - SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] - SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] + SettingsVDictionary['tuningCorrection'] = UserChoices['tuningCorrection']['on'] + SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] + SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] + SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] try: - SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] + SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] except: SettingsVDictionary['referenceCorrectionCoefficients_cov'] = [0,0,0] #TODO: This is to keep some old unit tests running. Ideally they should be fixed. SettingsVDictionary['extractReferencePatternFromDataOption'] = UserChoices['extractReferencePatternFromDataOption']['on'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index 17f961c3c..3fe20f588 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -150,17 +150,17 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index 1fb829cc0..43f460727 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -482,8 +482,8 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi #this function either creates or gets the three coefficients for the polynomial correction (Tuning Correction) and calculates #the correction factor for the relative intensities of each mass fragment, outputting a corrected set #of relative intensities -def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm,measuredReferenceYorN): - if measuredReferenceYorN =='yes': +def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm,tuningCorrection): + if tuningCorrection =='yes': abcCoefficients, abcCoefficients_cov = ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm) referenceCorrectionCoefficients[0],referenceCorrectionCoefficients[1],referenceCorrectionCoefficients[2]= abcCoefficients referenceCorrectionCoefficients_cov = abcCoefficients_cov @@ -1196,7 +1196,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): ReferenceData.standardized_reference_patterns, ReferenceData.standardized_reference_patterns_tuning_uncertainties = TuningCorrector(ReferenceData.standardized_reference_patterns, G.referenceCorrectionCoefficients,G.referenceCorrectionCoefficients_cov, G.referenceFileDesiredTuningAndForm, G.referenceFileExistingTuningAndForm, - G.measuredReferenceYorN) + G.tuningCorrection) #Now check if uncertainties already exist, and if they do then the two uncertainties need to be combined. Else, made equal. try: ReferenceData.absolute_standard_uncertainties = (ReferenceData.absolute_standard_uncertainties**2 + ReferenceData.standardized_reference_patterns_tuning_uncertainties**2)**0.5 @@ -4948,8 +4948,8 @@ def PopulateLogFile(): f6.write('backgroundMassFragment = %s \n'%(G.backgroundMassFragment)) f6.write('backgroundSlopes = %s \n'%(G.backgroundSlopes)) f6.write('backgroundIntercepts = %s \n'%(G.backgroundIntercepts)) - if G.measuredReferenceYorN == 'yes': - f6.write('measuredReferenceYorN = %s \n'%G.measuredReferenceYorN) + if G.tuningCorrection == 'yes': + f6.write('tuningCorrection = %s \n'%G.tuningCorrection) f6.write('referenceCorrectionCoefficientA = %s \n'%(G.referenceCorrectionCoefficients[0])) f6.write('referenceCorrectionCoefficientB = %s \n'%(G.referenceCorrectionCoefficients[1])) f6.write('referenceCorrectionCoefficientC = %s \n'%(G.referenceCorrectionCoefficients[2])) diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index f0693978e..d3670a93e 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -150,17 +150,17 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index 37e7bb09f..de557484e 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -106,7 +106,7 @@ def parseUserInput(currentUserInput): currentUserInput.scaleRawDataFactor = float(currentUserInput.scaleRawDataFactor) #scaleRawDataFactor is a float #Reference Correction Changer - parse.strCheck(currentUserInput.measuredReferenceYorN,'measuredReferenceYorN') + parse.strCheck(currentUserInput.tuningCorrection,'tuningCorrection') #The below two variables are no longer strings. They are now lists with two elements, each of which are strings. TODO: Change their names to referenceFileExistingTuningAndForm and referenceFileDesiredTuningAndForm #parse.strCheck(currentUserInput.referenceFileExistingTuningAndForm,'referenceFileExistingTuningAndForm') #parse.strCheck(currentUserInput.referenceFileDesiredTuningAndForm,'referenceFileDesiredTuningAndForm') @@ -312,12 +312,12 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['scaleRawDataOption'] = UserChoices['scaleRawDataYorN']['scaleRawDataOption'] SettingsVDictionary['scaleRawDataFactor'] = UserChoices['scaleRawDataYorN']['scaleRawDataFactor'] - SettingsVDictionary['measuredReferenceYorN'] = UserChoices['measuredReferenceYorN']['on'] - SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] - SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] - SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] + SettingsVDictionary['tuningCorrection'] = UserChoices['tuningCorrection']['on'] + SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] + SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] + SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] try: - SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] + SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] except: SettingsVDictionary['referenceCorrectionCoefficients_cov'] = [0,0,0] #TODO: This is to keep some old unit tests running. Ideally they should be fixed. SettingsVDictionary['extractReferencePatternFromDataOption'] = UserChoices['extractReferencePatternFromDataOption']['on'] diff --git a/ExampleTuningCorrectorGasMixture/0-README.txt b/ExampleTuningCorrectorGasMixture/0-README.txt index 797416260..f278bd2e7 100644 --- a/ExampleTuningCorrectorGasMixture/0-README.txt +++ b/ExampleTuningCorrectorGasMixture/0-README.txt @@ -9,7 +9,7 @@ The reference pattern listed for analysis has internally collected spectra which Proc Doc type things: -- First added at line 5351 - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) > 0: -- Now make a reference object from LiteratureReference.csv so that simulated signals can be made. -- GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): -- Need to be careful because "ReferenceInputPreProcessing" is being used. diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index d9687cfec..87853e0d0 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -150,17 +150,17 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =['ReferenceCollected.csv','xyyy'] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =['ReferenceLiterature.csv','xyyy'] +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/LogFile.txt b/ExampleTuningCorrectorGasMixture/LogFile.txt index 9ed6787bc..8119c5a0c 100644 --- a/ExampleTuningCorrectorGasMixture/LogFile.txt +++ b/ExampleTuningCorrectorGasMixture/LogFile.txt @@ -6,7 +6,7 @@ dataToAnalyzeFileName = Collected_Data.csv timeRangeLimit = yes timeRangeStart = 176.0 timeRangeFinish = 900.0 -measuredReferenceYorN = yes +tuningCorrection = yes referenceCorrectionCoefficientA = -0.006486881698506962 referenceCorrectionCoefficientB = 0.25062935187812 referenceCorrectionCoefficientC = -0.9533139758788823 diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index d55df876a..c9a15ab78 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -499,12 +499,12 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa #this function either creates or gets the three coefficients for the polynomial correction (Tuning Correction) and calculates #the correction factor for the relative intensities of each mass fragment, outputting a corrected set #of relative intensities -def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,measuredReferenceYorN="no"): +def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,tuningCorrection="no"): #Tuning corrector is designed to work with standardized_reference_patterns, so first we make sure standardize the data. referenceDataArrayWithAbscissa=StandardizeReferencePattern(referenceDataArrayWithAbscissa) if type(referenceCorrectionCoefficients) == type({}):#check if it's a dictionary. If it is, we need to make it a list. referenceCorrectionCoefficients = [referenceCorrectionCoefficients['A'],referenceCorrectionCoefficients['B'],referenceCorrectionCoefficients['C']] - if measuredReferenceYorN =='yes': + if tuningCorrection =='yes': print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. @@ -558,11 +558,11 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu G.referenceCorrectionCoefficients_cov = None #Wanted to do something like "if list(G.referenceCorrectionCoefficients) != [0,0,1]:" but can't do it out here. Can do it inside function. - if G.measuredReferenceYorN =='no': + if G.tuningCorrection =='no': G.createMixedTuningPattern = False #override the mixed tuning pattern choice if there is no measured reference. if G.createMixedTuningPattern == False: - if G.measuredReferenceYorN =='yes': #in this case, we are going to apply the external tuning to the current pattern. + if G.tuningCorrection =='yes': #in this case, we are going to apply the external tuning to the current pattern. print("line 520!!!!!") referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm @@ -612,7 +612,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu if G.createMixedTuningPattern== True: #in this case, we are going to apply the current tuning to the external pattern, and also create a mixed pattern. So the ReferenceData pointer will point to a mixed pattern by the end of this if statement. print("line 619!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!") - if G.measuredReferenceYorN =='yes': + if G.tuningCorrection =='yes': #First read in the existing tuning patterns. referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm referenceFileExistingTuningAndForm = G.referenceFileExistingTuningAndForm @@ -754,9 +754,9 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there for moleculeIndex,moleculeName in enumerate(ReferenceDataExistingTuning.molecules): desiredConcentrationIndex = moleculeIndex #Take the concentration if it's named: - if moleculeName in G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']: - currentConcentrationIndex = list(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) - knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] + if moleculeName in G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']: + currentConcentrationIndex = list(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) + knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] else: #else set it to zero. knownConcentrationsArray[desiredConcentrationIndex] = 0 #The first item in the concentrations array is supposed to be the time. We will simply put the integer "1" there, since we will have one point. @@ -783,7 +783,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there TuningCorrectorGasMixtureSimulatedHypotheticalReferenceDataObject.exportReferencePattern("TuningCorrectorGasMixtureSimulatedHypotheticalReferenceData.csv") print('line 646') - if G.measuredReferenceYorN =='yes': + if G.tuningCorrection =='yes': #we are using specific files for obtaining the tuning correction coefficients in the case of GasMixtureTuningCorrector referenceFileExistingTuningAndForm=["TuningCorrectorGasMixtureSimulatedHypotheticalReferenceData.csv","XYYY"] referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"] @@ -1615,7 +1615,7 @@ def ImportAnalyzedData(concentrationsOutputName): ''' def ReferenceInputPreProcessing(ReferenceData, verbose=True): #We will skip the regular createReferencePatternWithTuningCorrection if using the gas mixture feature. - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) == 0: + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) == 0: ReferenceData = createReferencePatternWithTuningCorrection(ReferenceData, verbose=verbose) #TODO: the minimal reference value can cause inaccuracies if interpolating between multiple reference patterns if one pattern has a value rounded to 0 and the other does not #TODO: option 1: this issue can be fixed by moving this to after interpolation @@ -5528,8 +5528,8 @@ def PopulateLogFile(): f6.write('backgroundMassFragment = %s \n'%(G.backgroundMassFragment)) f6.write('backgroundSlopes = %s \n'%(G.backgroundSlopes)) f6.write('backgroundIntercepts = %s \n'%(G.backgroundIntercepts)) - if G.measuredReferenceYorN == 'yes': - f6.write('measuredReferenceYorN = %s \n'%G.measuredReferenceYorN) + if G.tuningCorrection == 'yes': + f6.write('tuningCorrection = %s \n'%G.tuningCorrection) f6.write('referenceCorrectionCoefficientA = %s \n'%(G.referenceCorrectionCoefficients[0])) f6.write('referenceCorrectionCoefficientB = %s \n'%(G.referenceCorrectionCoefficients[1])) f6.write('referenceCorrectionCoefficientC = %s \n'%(G.referenceCorrectionCoefficients[2])) @@ -5636,7 +5636,7 @@ def main(): if name.startswith("Exported") and name.endswith(".csv"): print("Previous run Exported file detected. Deleting file", name) os.remove(name) - print("Line 5500!!!!!", G.measuredReferenceYorN) + print("Line 5500!!!!!", G.tuningCorrection) # #The below try statement is to check the user input dictionary's existence. Older MSRESOLVE did not use a dictionary. # for now, these types of lines are at the bottom of the UserInput and DefaultUserInput files. I'm considering keeping there permanently and then deleting these commented out lines. #from userInputValidityFunctions import parseUserInput, userInputValidityCheck, settingsCompatibilityCheck, #settingsDependenciesCheck,populateModuleVariablesFromDictionary,populateModuleVariablesFromNestedDictionary @@ -5694,7 +5694,7 @@ def main(): G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #If a tuning correction is going to be done, we'll make a mixed reference pattern. #G.moleculesNamesExtended needs to be populated before the first tuning correction and before parsing of userinput. - if str(G.measuredReferenceYorN).lower() == 'yes': + if str(G.tuningCorrection).lower() == 'yes': G.moleculesNamesExistingTuning = getMoleculesFromReferenceData(G.referenceFileExistingTuningAndForm[0]) moleculesToAddToReferencePattern = [] for moleculeName in list(G.moleculesNamesExistingTuning): @@ -5845,8 +5845,8 @@ def main(): #This codeblock is for the TuningCorrectorGasMixture feature. It should be before the prototypicalReferenceData is created. #A measured gas mixture spectrum is compared to a simulated gas mixture spectrum, and the tuning correction is then made accordingly. - if G.measuredReferenceYorN == 'yes': - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: + if G.tuningCorrection == 'yes': + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) > 0: ReferenceDataList = tuningCorrectorGasMixture(ReferenceDataList, G) #Creating prototypicalReferenceData which will be interrogated later for which molecules and masses to expect in the ReferenceDataObjects. prototypicalReferenceData = copy.deepcopy(ReferenceDataList[0]) diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index aa25f1eb0..b877ccf7e 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -500,12 +500,12 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa #this function either creates or gets the three coefficients for the polynomial correction (Tuning Correction) and calculates #the correction factor for the relative intensities of each mass fragment, outputting a corrected set #of relative intensities -def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm,measuredReferenceYorN): +def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm,tuningCorrection): #Tuning corrector is designed to work with standardized_reference_patterns, so first we make sure standardize the data. referenceDataArrayWithAbscissa=StandardizeReferencePattern(referenceDataArrayWithAbscissa) if type(referenceCorrectionCoefficients) == type({}):#check if it's a dictionary. If it is, we need to make it a list. referenceCorrectionCoefficients = [referenceCorrectionCoefficients['A'],referenceCorrectionCoefficients['B'],referenceCorrectionCoefficients['C']] - if measuredReferenceYorN =='yes': + if tuningCorrection =='yes': print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") @@ -600,9 +600,9 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there for moleculeIndex,moleculeName in enumerate(ReferenceDataExistingTuning.molecules): desiredConcentrationIndex = moleculeIndex #Take the concentration if it's named: - if moleculeName in G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']: - currentConcentrationIndex = list(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) - knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] + if moleculeName in G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']: + currentConcentrationIndex = list(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) + knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] else: #else set it to zero. knownConcentrationsArray[desiredConcentrationIndex] = 0 #The first item in the concentrations array is supposed to be the time. We will simply put the integer "1" there, since we will have one point. @@ -630,7 +630,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there print('line 646') ReferenceDataExistingTuningAfterCorrection = copy.deepcopy(ReferenceDataExistingTuning) #just initializing here, then actual tuning correction occurs in next lines. #Tuning corrector does not operate on a ReferenceData object, it operates on standardized reference patterns. - ReferenceDataExistingTuningAfterCorrection.standardized_reference_patterns, ReferenceDataExistingTuningAfterCorrection.standardized_reference_patterns_tuning_uncertainties = TuningCorrector(ReferenceDataExistingTuning.standardized_reference_patterns, G.referenceCorrectionCoefficients, G.referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=["TuningCorrectorGasMixtureSimulatedHypotheticalReferenceData.csv","XYYY"], referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"], measuredReferenceYorN =G.measuredReferenceYorN) + ReferenceDataExistingTuningAfterCorrection.standardized_reference_patterns, ReferenceDataExistingTuningAfterCorrection.standardized_reference_patterns_tuning_uncertainties = TuningCorrector(ReferenceDataExistingTuning.standardized_reference_patterns, G.referenceCorrectionCoefficients, G.referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=["TuningCorrectorGasMixtureSimulatedHypotheticalReferenceData.csv","XYYY"], referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"], tuningCorrection =G.tuningCorrection) # TuningCorrectorGasMixtureCorrectedReferenceDataObject = MSReference(ReferenceDataExistingTuning.standardized_reference_patterns, electronnumbers=ReferenceDataExistingTuning.electronnumbers, molecules=ReferenceDataExistingTuning.molecules, molecularWeights=ReferenceDataExistingTuning.molecularWeights, SourceOfFragmentationPatterns=ReferenceDataExistingTuning.SourceOfFragmentationPatterns, sourceOfIonizationData=ReferenceDataExistingTuning.sourceOfIonizationData, relativeIonizationEfficiencies=ReferenceDataExistingTuning.relativeIonizationEfficiencies, moleculeIonizationType=ReferenceDataExistingTuning.moleculeIonizationType) ReferenceDataExistingTuningAfterCorrection.addSuffixToSourceOfFragmentationPatterns("_TuningCorrected") @@ -1448,7 +1448,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True): if type(G.referenceFileUncertainties) != type(None): ReferenceData.update_relative_standard_uncertainties() #Skip much of the function if using tuningCorrectorGasMixtureMoleculeNames - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) == 0: + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) == 0: if verbose: print('beginning TuningCorrector') if G.referenceFileExistingTuningAndForm == []: #Mkae the current reference data the Existing Tuning pattern. @@ -1464,7 +1464,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True): ReferenceData.standardized_reference_patterns, ReferenceData.standardized_reference_patterns_tuning_uncertainties = TuningCorrector(ReferenceData.standardized_reference_patterns, G.referenceCorrectionCoefficients,G.referenceCorrectionCoefficients_cov, G.referenceFileExistingTuningAndForm, G.referenceFileDesiredTuningAndForm, - G.measuredReferenceYorN) + G.tuningCorrection) ReferenceData.ExportCollector('TuningCorrector', use_provided_reference_patterns=False) #TuningCorrector un-standardizes the patterns, so the patterns have to be standardized again. ReferenceData.standardized_reference_patterns=StandardizeReferencePattern(ReferenceData.standardized_reference_patterns,len(ReferenceData.molecules)) @@ -5393,8 +5393,8 @@ def PopulateLogFile(): f6.write('backgroundMassFragment = %s \n'%(G.backgroundMassFragment)) f6.write('backgroundSlopes = %s \n'%(G.backgroundSlopes)) f6.write('backgroundIntercepts = %s \n'%(G.backgroundIntercepts)) - if G.measuredReferenceYorN == 'yes': - f6.write('measuredReferenceYorN = %s \n'%G.measuredReferenceYorN) + if G.tuningCorrection == 'yes': + f6.write('tuningCorrection = %s \n'%G.tuningCorrection) f6.write('referenceCorrectionCoefficientA = %s \n'%(G.referenceCorrectionCoefficients[0])) f6.write('referenceCorrectionCoefficientB = %s \n'%(G.referenceCorrectionCoefficients[1])) f6.write('referenceCorrectionCoefficientC = %s \n'%(G.referenceCorrectionCoefficients[2])) @@ -5697,8 +5697,8 @@ def main(): #This codeblock is for the TuningCorrectorGasMixture feature. It should be before the prototypicalReferenceData is created. #A measured gas mixture spectrum is compared to a simulated gas mixture spectrum, and the tuning correction is then made accordingly. - if G.UserChoices['measuredReferenceYorN']['on'] == 'yes': - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: + if G.UserChoices['tuningCorrection']['on'] == 'yes': + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) > 0: ReferenceDataList = tuningCorrectorGasMixture(ReferenceDataList, G) #Creating prototypicalReferenceData which will be interrogated later for which molecules and masses to expect in the ReferenceDataObjects. prototypicalReferenceData = copy.deepcopy(ReferenceDataList[0]) diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index e0e16b8c7..5550e7fae 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -500,13 +500,13 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa #this function either creates or gets the three coefficients for the polynomial correction (Tuning Correction) and calculates #the correction factor for the relative intensities of each mass fragment, outputting a corrected set #of relative intensities -def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,measuredReferenceYorN="no"): +def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,tuningCorrection="no"): #Tuning corrector is designed to work with standardized_reference_patterns, so first we make sure standardize the data. referenceDataArrayWithAbscissa=StandardizeReferencePattern(referenceDataArrayWithAbscissa) if type(referenceCorrectionCoefficients) == type({}):#check if it's a dictionary. If it is, we need to make it a list. referenceCorrectionCoefficients = [referenceCorrectionCoefficients['A'],referenceCorrectionCoefficients['B'],referenceCorrectionCoefficients['C']] - if measuredReferenceYorN =='yes': + if tuningCorrection =='yes': print("line 520!!!!!") if referenceFileDesiredTuningAndForm == []:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. print("line 522!!!!!") @@ -563,11 +563,11 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu G.referenceCorrectionCoefficients_cov = None #Wanted to do something like "if list(G.referenceCorrectionCoefficients) != [0,0,1]:" but can't do it out here. Can do it inside function. - if G.measuredReferenceYorN =='no': + if G.tuningCorrection =='no': G.createMixedTuningPattern = False #override the mixed tuning pattern choice if there is no measured reference. if G.createMixedTuningPattern == False: - if G.measuredReferenceYorN =='yes': #in this case, we are going to apply the external tuning to the current pattern. + if G.tuningCorrection =='yes': #in this case, we are going to apply the external tuning to the current pattern. print("line 520!!!!!") referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm @@ -619,7 +619,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu if G.createMixedTuningPattern== True: #in this case, we are going to apply the current tuning to the external pattern, and also create a mixed pattern. So the ReferenceData pointer will point to a mixed pattern by the end of this if statement. print("line 619!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!") - if G.measuredReferenceYorN =='yes': + if G.tuningCorrection =='yes': #First read in the existing tuning patterns. referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm referenceFileExistingTuningAndForm = G.referenceFileExistingTuningAndForm @@ -761,9 +761,9 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there for moleculeIndex,moleculeName in enumerate(ReferenceDataExistingTuning.molecules): desiredConcentrationIndex = moleculeIndex #Take the concentration if it's named: - if moleculeName in G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']: - currentConcentrationIndex = list(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) - knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] + if moleculeName in G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']: + currentConcentrationIndex = list(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) + knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] else: #else set it to zero. knownConcentrationsArray[desiredConcentrationIndex] = 0 #The first item in the concentrations array is supposed to be the time. We will simply put the integer "1" there, since we will have one point. @@ -790,7 +790,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there TuningCorrectorGasMixtureSimulatedHypotheticalReferenceDataObject.exportReferencePattern("TuningCorrectorGasMixtureSimulatedHypotheticalReferenceData.csv") print('line 646') - if G.measuredReferenceYorN =='yes': + if G.tuningCorrection =='yes': #we are using specific files for obtaining the tuning correction coefficients in the case of GasMixtureTuningCorrector referenceFileExistingTuningAndForm=["TuningCorrectorGasMixtureSimulatedHypotheticalReferenceData.csv","XYYY"] referenceFileDesiredTuningAndForm=["TuningCorrectorGasMixtureMeasuredHypotheticalReferenceData.csv", "XYYY"] @@ -5532,8 +5532,8 @@ def PopulateLogFile(): f6.write('backgroundMassFragment = %s \n'%(G.backgroundMassFragment)) f6.write('backgroundSlopes = %s \n'%(G.backgroundSlopes)) f6.write('backgroundIntercepts = %s \n'%(G.backgroundIntercepts)) - if G.measuredReferenceYorN == 'yes': - f6.write('measuredReferenceYorN = %s \n'%G.measuredReferenceYorN) + if G.tuningCorrection == 'yes': + f6.write('tuningCorrection = %s \n'%G.tuningCorrection) f6.write('referenceCorrectionCoefficientA = %s \n'%(G.referenceCorrectionCoefficients[0])) f6.write('referenceCorrectionCoefficientB = %s \n'%(G.referenceCorrectionCoefficients[1])) f6.write('referenceCorrectionCoefficientC = %s \n'%(G.referenceCorrectionCoefficients[2])) @@ -5697,7 +5697,7 @@ def main(): G.moleculesNames = getMoleculesFromReferenceData(G.referencePatternsFileNamesList[0]) #If a tuning correction is going to be done, we'll make a mixed reference pattern. #G.moleculesNamesExtended needs to be populated before the first tuning correction and before parsing of userinput. - if str(G.measuredReferenceYorN).lower() == 'yes': + if str(G.tuningCorrection).lower() == 'yes': G.moleculesNamesExistingTuning = getMoleculesFromReferenceData(G.referenceFileExistingTuningAndForm[0]) moleculesToAddToReferencePattern = [] for moleculeName in list(G.moleculesNamesExistingTuning): @@ -5848,8 +5848,8 @@ def main(): #This codeblock is for the TuningCorrectorGasMixture feature. It should be before the prototypicalReferenceData is created. #A measured gas mixture spectrum is compared to a simulated gas mixture spectrum, and the tuning correction is then made accordingly. - if G.measuredReferenceYorN == 'yes': - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: + if G.tuningCorrection == 'yes': + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) > 0: ReferenceDataList = tuningCorrectorGasMixture(ReferenceDataList, G) #Creating prototypicalReferenceData which will be interrogated later for which molecules and masses to expect in the ReferenceDataObjects. prototypicalReferenceData = copy.deepcopy(ReferenceDataList[0]) diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index b367b52fe..f327a3713 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -150,20 +150,20 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = ['LiteratureReference.csv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = ['LiteratureReference.csv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index 1a69f0148..16dbe89bc 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -52,16 +52,16 @@ def parseUserInput(currentUserInput): if currentUserInput.specificMolecules == 'yes': #if yes, use the user's chosen moleclues chosenMoleculesForParsing = copy.deepcopy(currentUserInput.chosenMoleculesNames) #If using specificMolecules, make sure all selected molecules are in the reference data - if currentUserInput.measuredReferenceYorN == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. + if currentUserInput.tuningCorrection == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. parse.compareElementsBetweenLists(currentUserInput.chosenMoleculesNames,currentUserInput.moleculesNames,'chosenMolecules','Molecules from Reference Data') - if currentUserInput.measuredReferenceYorN == 'yes':#If using a making a reference pattern, check the extended moleculesNames list. + if currentUserInput.tuningCorrection == 'yes':#If using a making a reference pattern, check the extended moleculesNames list. currentUserInput.moleculesNamesExtended = parse.stripListOfStrings(currentUserInput.moleculesNamesExtended) parse.compareElementsBetweenLists(currentUserInput.chosenMoleculesNames,currentUserInput.moleculesNamesExtended,'chosenMolecules','Molecules from Reference Data') elif currentUserInput.specificMolecules == 'no': #Otherwise use all molecules - if currentUserInput.measuredReferenceYorN == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. + if currentUserInput.tuningCorrection == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. currentUserInput.moleculesNames = parse.stripListOfStrings(list(currentUserInput.moleculesNames)) chosenMoleculesForParsing = copy.deepcopy(currentUserInput.moleculesNames) - if currentUserInput.measuredReferenceYorN == 'yes':#If using a making a reference pattern, check the extended moleculesNames list. + if currentUserInput.tuningCorrection == 'yes':#If using a making a reference pattern, check the extended moleculesNames list. currentUserInput.moleculesNamesExtended = parse.stripListOfStrings(currentUserInput.moleculesNamesExtended) chosenMoleculesForParsing = copy.deepcopy(currentUserInput.moleculesNamesExtended) @@ -122,7 +122,7 @@ def parseUserInput(currentUserInput): currentUserInput.scaleRawDataFactor = float(currentUserInput.scaleRawDataFactor) #scaleRawDataFactor is a float #Reference Correction Changer - parse.strCheck(currentUserInput.measuredReferenceYorN,'measuredReferenceYorN') + parse.strCheck(currentUserInput.tuningCorrection,'tuningCorrection') #The below two variables are no longer strings. They are now lists with two elements, each of which are strings. TODO: Change their names to referenceFileExistingTuningAndForm and referenceFileDesiredTuningAndForm #parse.strCheck(currentUserInput.referenceFileExistingTuningAndForm,'referenceFileExistingTuningAndForm') #parse.strCheck(currentUserInput.referenceFileDesiredTuningAndForm,'referenceFileDesiredTuningAndForm') @@ -338,22 +338,22 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['scaleRawDataOption'] = UserChoices['scaleRawDataYorN']['scaleRawDataOption'] SettingsVDictionary['scaleRawDataFactor'] = UserChoices['scaleRawDataYorN']['scaleRawDataFactor'] - SettingsVDictionary['measuredReferenceYorN'] = UserChoices['measuredReferenceYorN']['on'] - if 'createMixedTuningPattern' not in UserChoices['measuredReferenceYorN']: - UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True - SettingsVDictionary['createMixedTuningPattern'] = UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] - SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] - SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] - SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] + SettingsVDictionary['tuningCorrection'] = UserChoices['tuningCorrection']['on'] + if 'createMixedTuningPattern' not in UserChoices['tuningCorrection']: + UserChoices['tuningCorrection']['createMixedTuningPattern'] = True + SettingsVDictionary['createMixedTuningPattern'] = UserChoices['tuningCorrection']['createMixedTuningPattern'] + SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] + SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] + SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] try: #to make sure old unit tests and analyses work. - #if 'tuningCorrectorGasMixtureMoleculeNames' in UserChoices['measuredReferenceYorN'].keys(): - SettingsVDictionary['tuningCorrectorGasMixtureMoleculeNames'] = UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] + #if 'tuningCorrectorGasMixtureMoleculeNames' in UserChoices['tuningCorrection'].keys(): + SettingsVDictionary['tuningCorrectorGasMixtureMoleculeNames'] = UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] except: #to make sure old unit tests work. SettingsVDictionary['tuningCorrectorGasMixtureMoleculeNames'] = [] - UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] = [] + UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] = [] try: - SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] + SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] except: SettingsVDictionary['referenceCorrectionCoefficients_cov'] = [0,0,0] #TODO: This is to keep some old unit tests running. Ideally they should be fixed. SettingsVDictionary['extractReferencePatternFromDataOption'] = UserChoices['extractReferencePatternFromDataOption']['on'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index c528979d6..a785a7bce 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -516,12 +516,12 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa #this function either creates or gets the three coefficients for the polynomial correction (Tuning Correction) and calculates #the correction factor for the relative intensities of each mass fragment, outputting a corrected set #of relative intensities -def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,measuredReferenceYorN="no"): +def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficients, referenceCorrectionCoefficients_cov, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,tuningCorrection="no"): #Tuning corrector is designed to work with standardized_reference_patterns, so first we make sure standardize the data. referenceDataArrayWithAbscissa=StandardizeReferencePattern(referenceDataArrayWithAbscissa) if type(referenceCorrectionCoefficients) == type({}):#check if it's a dictionary. If it is, we need to make it a list. referenceCorrectionCoefficients = [referenceCorrectionCoefficients['A'],referenceCorrectionCoefficients['B'],referenceCorrectionCoefficients['C']] - if measuredReferenceYorN =='yes': + if tuningCorrection =='yes': if len(referenceFileDesiredTuningAndForm) == 0:#TODO: this isn't very good logic, but it allows automatic population of referenceFileDesiredTuningAndForm. The problem is it is reading from file again instead of using the already made ReferenceData object. ABCDetermination and possibly TuningCorrector should be changed so that it can take *either* a ReferenceData object **or** a ReferenceData filename. The function can check if it is receiving a string, and if it's not receiving a string it can assume it's receiving an object. if '.csv' in G.referencePatternsFileNamesList[0]: referenceFileDesiredTuningAndForm = [ "ExportedDesiredTuningReferencePattern.csv","xyyy" ] #Take the first item from G.referencePatternsFileNamesList and from G.referencePatternsFormsList. @@ -560,8 +560,8 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien '''Makes a mixed reference pattern from two reference patterns, including tuning correction.''' def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, returnMixedPattern=False): - #If tuning corrector is off (as of Nov 2021, variable measuredReferenceYorN), then we return ReferenceData unchanged. - if G.measuredReferenceYorN =='no': + #If tuning corrector is off (as of Nov 2021, variable tuningCorrection), then we return ReferenceData unchanged. + if G.tuningCorrection =='no': return ReferenceData @@ -587,7 +587,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu G.referenceCorrectionCoefficients_cov = None #Wanted to do something like "if list(G.referenceCorrectionCoefficients) != [0,0,1]:" but can't do it out here. Can do it inside function. - if G.measuredReferenceYorN =='no': + if G.tuningCorrection =='no': G.createMixedTuningPattern = False #override the mixed tuning pattern choice if there is no measured reference. resetReferenceFileDesiredTuningAndForm = False #initializing. At end, will reset G.referenceFileDesiredTuningAndForm if it was originally blank. @@ -708,7 +708,7 @@ def createReferencePatternWithTuningCorrection(ReferenceData, verbose=True, retu ReferenceData.ExportCollector('StandardizeReferencePattern_relative_standard_uncertainties', export_relative_uncertainties= True) elif ((G.createMixedTuningPattern== True) and (G.tuningCorrectPatternInternalVsExternal =='External')): #in this case, we are going to apply the current tuning to the external pattern, and also create a mixed pattern. So the ReferenceData pointer will point to a mixed pattern by the end of this if statement. - if G.measuredReferenceYorN =='yes': + if G.tuningCorrection =='yes': #First read in the existing tuning patterns. referenceFileDesiredTuningAndForm = G.referenceFileDesiredTuningAndForm referenceFileExistingTuningAndForm = G.referenceFileExistingTuningAndForm @@ -881,9 +881,9 @@ def tuningCorrectorGasMixture(ReferenceDataList, G, ExperimentData=None): #makin for moleculeIndex,moleculeName in enumerate(ReferenceDataExistingTuning.molecules): desiredConcentrationIndex = moleculeIndex #Take the concentration if it's named: - if moleculeName in G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']: - currentConcentrationIndex = list(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) - knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] + if moleculeName in G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']: + currentConcentrationIndex = list(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']).index(moleculeName) + knownConcentrationsArray[desiredConcentrationIndex] = G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'][currentConcentrationIndex] else: #else set it to zero. knownConcentrationsArray[desiredConcentrationIndex] = 0 #The first item in the concentrations array is supposed to be the time. We will simply put the integer "1" there, since we will have one point. @@ -911,9 +911,9 @@ def tuningCorrectorGasMixture(ReferenceDataList, G, ExperimentData=None): #makin if ReferenceDataTuningCorrectorGasMixtureSimulatedHypothetical.referenceFileNameExtension == 'tsv': ReferenceDataTuningCorrectorGasMixtureSimulatedHypothetical.exportReferencePattern("ExportedReferencePatternGasMixtureSimulatedHypothetical.tsv") - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals']) == 0: #if the length is zero, we will populate this with the max and min of the times. - G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [ min(ExperimentData.times), max(ExperimentData.times)] - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals']) == 2: #We assume in this case that we have a pair of times. + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals']) == 0: #if the length is zero, we will populate this with the max and min of the times. + G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [ min(ExperimentData.times), max(ExperimentData.times)] + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals']) == 2: #We assume in this case that we have a pair of times. ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical = copy.deepcopy(ReferenceDataTuningCorrectorGasMixtureSimulatedHypothetical) #just initializing. ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.SourceOfFragmentationPatterns = ["measured"] #Get the mass fragments we need. @@ -929,14 +929,14 @@ def tuningCorrectorGasMixture(ReferenceDataList, G, ExperimentData=None): #makin ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.provided_reference_patterns[:,1:] = numpy.ones(numpy.shape(ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.provided_reference_patterns[:,1:])) ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.provided_mass_fragments = ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.provided_reference_patterns[:,0] #note that the last two arguments need to be further nested. - ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.standardized_reference_patterns,ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical_uncertainties = ExtractReferencePatternFromData(ExperimentData=ExperimentData, referenceData=ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical,rpcChosenMolecules=["GasMixture"],rpcChosenMoleculesMF=[commonMF],rpcTimeRanges=[G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals']]) + ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.standardized_reference_patterns,ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical_uncertainties = ExtractReferencePatternFromData(ExperimentData=ExperimentData, referenceData=ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical,rpcChosenMolecules=["GasMixture"],rpcChosenMoleculesMF=[commonMF],rpcTimeRanges=[G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals']]) if ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.referenceFileNameExtension == 'csv': ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.exportReferencePattern("ExportedReferencePatternGasMixtureMeasuredHypothetical.csv") if ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.referenceFileNameExtension == 'tsv': ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.exportReferencePattern("ExportedReferencePatternGasMixtureMeasuredHypothetical.tsv") - if G.measuredReferenceYorN =='yes': + if G.tuningCorrection =='yes': #we are using specific files for obtaining the tuning correction coefficients in the case of GasMixtureTuningCorrector if ReferenceDataTuningCorrectorGasMixtureMeasuredHypothetical.referenceFileNameExtension == 'csv': referenceFileExistingTuningAndForm=["ExportedReferencePatternGasMixtureSimulatedHypothetical.csv","XYYY"] @@ -1463,7 +1463,7 @@ def CorrectionValuesObtain(ReferenceData): listOfMoleculesToRemove.append(moleculeName) ReferenceDataStandardTuning = ReferenceDataStandardTuning.removeMolecules(listOfMoleculesToRemove) #Now have to convert the original reference data for anlaysis to standard tuning to make the mixed pattern. - referenceDataArrayWithAbscissa, referenceDataArrayWithAbscissa_tuning_uncertainties = TuningCorrector(ReferenceDataOriginalStandardTuning.standardized_reference_patterns,abcCoefficients, abcCoefficients_covmat, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,measuredReferenceYorN="no") + referenceDataArrayWithAbscissa, referenceDataArrayWithAbscissa_tuning_uncertainties = TuningCorrector(ReferenceDataOriginalStandardTuning.standardized_reference_patterns,abcCoefficients, abcCoefficients_covmat, referenceFileExistingTuningAndForm=None,referenceFileDesiredTuningAndForm=None,tuningCorrection="no") #TuningCorrector un-standardizes the patterns, so the patterns have to be standardized again. ReferenceDataOriginalStandardTuning.standardized_reference_patterns = StandardizeReferencePattern(referenceDataArrayWithAbscissa) ReferenceDataOriginalStandardTuning.standardized_reference_patterns_tuning_uncertainties = referenceDataArrayWithAbscissa_tuning_uncertainties @@ -1926,7 +1926,7 @@ def ImportAnalyzedData(concentrationsOutputName): def ReferenceInputPreProcessing(ReferenceData, verbose=True): #We will skip the regular createReferencePatternWithTuningCorrection if using the gas mixture feature. try: - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) == 0: + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) == 0: ReferenceData = createReferencePatternWithTuningCorrection(ReferenceData, verbose=verbose) except: #This try and except is so that iterative can work correctly. ReferenceData = createReferencePatternWithTuningCorrection(ReferenceData, verbose=verbose) @@ -5977,8 +5977,8 @@ def PopulateLogFile(): f6.write('backgroundMassFragment = %s \n'%(G.backgroundMassFragment)) f6.write('backgroundSlopes = %s \n'%(G.backgroundSlopes)) f6.write('backgroundIntercepts = %s \n'%(G.backgroundIntercepts)) - if G.measuredReferenceYorN == 'yes': - f6.write('measuredReferenceYorN = %s \n'%G.measuredReferenceYorN) + if G.tuningCorrection == 'yes': + f6.write('tuningCorrection = %s \n'%G.tuningCorrection) f6.write('referenceCorrectionCoefficientA = %s \n'%(G.referenceCorrectionCoefficients[0])) f6.write('referenceCorrectionCoefficientB = %s \n'%(G.referenceCorrectionCoefficients[1])) f6.write('referenceCorrectionCoefficientC = %s \n'%(G.referenceCorrectionCoefficients[2])) @@ -6227,7 +6227,7 @@ def main(): #If a tuning correction is going to be done, and if requested, we'll make a mixed reference pattern. #G.moleculesNamesExtended needs to be populated before the first tuning correction and before parsing of userinput. - if str(G.measuredReferenceYorN).lower() == 'yes': + if str(G.tuningCorrection).lower() == 'yes': if G.createMixedTuningPattern == True: if len(G.referenceFileExistingTuningAndForm) == 0: G.referenceFileExistingTuningAndForm = G.referenceFileStandardTuningAndForm #Use the standard tuning file if blank. @@ -6388,8 +6388,8 @@ def main(): #This codeblock is for the TuningCorrectorGasMixture feature. It should be before the prototypicalReferenceData is created. #A measured gas mixture spectrum is compared to a simulated gas mixture spectrum, and the tuning correction is then made accordingly. - if G.measuredReferenceYorN == 'yes': - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: + if G.tuningCorrection == 'yes': + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) > 0: ReferenceDataList = tuningCorrectorGasMixture(ReferenceDataList, G, ExperimentData) #Creating prototypicalReferenceData which will be interrogated later for which molecules and masses to expect in the ReferenceDataObjects. prototypicalReferenceData = copy.deepcopy(ReferenceDataList[0]) diff --git a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py index 1700c898d..b3bf186e7 100644 --- a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py +++ b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py @@ -119,7 +119,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} @@ -239,7 +239,7 @@ 'specificMolecules','chosenMolecules','specificMassFragments','chosenMassFragments', 'moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes', 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', - 'measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', + 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', 'rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', diff --git a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py index 69c594162..482cfa3ea 100644 --- a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py +++ b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py @@ -341,9 +341,9 @@ def ABCDetermination(ReferencePatternMeasured, ReferencePatternLiterature): #this function either creates or gets the three coefficients for the polynomial correction and calculates #the correction factor for the relative intensities of each mass fragment, outputting a corrected set #of relative intensities -def CorrectionValueCorrector(reference,referenceCorrectionCoefficients,referenceFileDesiredTuningAndForm,referenceFileExistingTuningAndForm,measuredReferenceYorN): +def CorrectionValueCorrector(reference,referenceCorrectionCoefficients,referenceFileDesiredTuningAndForm,referenceFileExistingTuningAndForm,tuningCorrection): - if measuredReferenceYorN =='yes': + if tuningCorrection =='yes': (referenceCorrectionCoefficients['A'],referenceCorrectionCoefficients['B'],referenceCorrectionCoefficients['C'])=ABCDetermination(referenceFileExistingTuningAndForm,referenceFileDesiredTuningAndForm ) referenceabscissa = reference[:,0] #gets arrays of just data and abscissa @@ -925,7 +925,7 @@ def ReferenceInputPreProcessing(ReferenceData): print('beginning CorrectionValueCorrector') ReferenceData.standardized_reference_intensities = CorrectionValueCorrector(ReferenceData.standardized_reference_intensities, G.referenceCorrectionCoefficients, G.referenceFileDesiredTuningAndForm, G.referenceFileExistingTuningAndForm, - G.measuredReferenceYorN) + G.tuningCorrection) ReferenceData.ExportCollector('CorrectionValueCorrector') if G.minimalReferenceValue == 'yes': @@ -3031,8 +3031,8 @@ def PopulateLogFile(): f6.write('backgroundMassFragment = %s \n'%(G.backgroundMassFragment)) f6.write('backgroundSlopes = %s \n'%(G.backgroundSlopes)) f6.write('backgroundIntercepts = %s \n'%(G.backgroundIntercepts)) - if G.measuredReferenceYorN == 'yes': - f6.write('measuredReferenceYorN = %s \n'%G.measuredReferenceYorN) + if G.tuningCorrection == 'yes': + f6.write('tuningCorrection = %s \n'%G.tuningCorrection) f6.write('referenceCorrectionCoefficientA = %s \n'%(G.referenceCorrectionCoefficients['A'])) f6.write('referenceCorrectionCoefficientB = %s \n'%(G.referenceCorrectionCoefficients['B'])) f6.write('referenceCorrectionCoefficientC = %s \n'%(G.referenceCorrectionCoefficients['C'])) diff --git a/Todo/SLS Common vs. Unique Bug/UserInput.py b/Todo/SLS Common vs. Unique Bug/UserInput.py index 4a13133c6..98dfb3b3a 100644 --- a/Todo/SLS Common vs. Unique Bug/UserInput.py +++ b/Todo/SLS Common vs. Unique Bug/UserInput.py @@ -119,7 +119,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} @@ -246,7 +246,7 @@ 'specificMolecules','chosenMolecules','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes', 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', - 'measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', + 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', 'rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', diff --git a/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py b/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py index f61e630e2..92d068b1f 100644 --- a/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py +++ b/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py @@ -117,7 +117,7 @@ def bestMassFragChooser(chosenMolecules, G.referenceCorrectionCoefficients = [G.referenceCorrectionCoefficients['A'],G.referenceCorrectionCoefficients['B'],G.referenceCorrectionCoefficients['C']] truncatedReferenceData.standardized_reference_patterns, ReferenceData.standardized_reference_patterns_tuning_uncertainties = MSRESOLVE.TuningCorrector( truncatedReferenceData.standardized_reference_patterns, G.referenceCorrectionCoefficients, G.referenceCorrectionCoefficients_cov, - G.referenceFileDesiredTuningAndForm, G.referenceFileExistingTuningAndForm, G.measuredReferenceYorN) + G.referenceFileDesiredTuningAndForm, G.referenceFileExistingTuningAndForm, G.tuningCorrection) #Removing entire rows of data for mass fragments with all reference #intensities below the threshold. diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py index 0bf404a2e..a1116967e 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py index df94c3107..5ba22ddc4 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ExtractReferencePatternFromData/test_1_input.py b/UnitTests/ExtractReferencePatternFromData/test_1_input.py index feee12907..b48855a13 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_1_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_1_input.py @@ -119,7 +119,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ExtractReferencePatternFromData/test_2_input.py b/UnitTests/ExtractReferencePatternFromData/test_2_input.py index 968b63552..c5571a270 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_2_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_2_input.py @@ -119,7 +119,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ExtractReferencePatternFromData/test_3_input.py b/UnitTests/ExtractReferencePatternFromData/test_3_input.py index cd5a036be..7634d9894 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_3_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_3_input.py @@ -119,7 +119,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ExtractReferencePatternFromData/test_4_input.py b/UnitTests/ExtractReferencePatternFromData/test_4_input.py index 7768c0c0a..df6051ec7 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_4_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_4_input.py @@ -108,7 +108,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ExtractReferencePatternFromData/test_5_input.py b/UnitTests/ExtractReferencePatternFromData/test_5_input.py index e74564a6e..17ec09e37 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_5_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_5_input.py @@ -108,7 +108,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ExtractReferencePatternFromData/test_6_input.py b/UnitTests/ExtractReferencePatternFromData/test_6_input.py index 9e300ebb5..7a028974e 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_6_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_6_input.py @@ -108,7 +108,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index 096a71edb..f32e0ccfa 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -154,15 +154,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py index 1601ad01c..20c5dc719 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py index e460daf62..4621aa373 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py index 43888640b..2c3b7549e 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py index 1159842fc..d2a430841 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py index dfa0829fb..0d5bc16f1 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py index 735ad205c..162bd340f 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py index 3ea8e3cb9..695f5aef7 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py index 724980392..0188bfd74 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py index c5387b5c8..f0a7b12a4 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py index c15d28ec4..19a561ea0 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py @@ -121,7 +121,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index 1065efc7d..97dc9e56a 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py index d0e49befd..90bb280cd 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py @@ -108,7 +108,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py index 5b6509d5f..7e820d87c 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py @@ -108,7 +108,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py index f0d1b370c..4ebd79be2 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py @@ -108,7 +108,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/ReferencePatternTimeChooser/test_2_input.py b/UnitTests/ReferencePatternTimeChooser/test_2_input.py index 72f7f90e7..3e6831b3c 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_2_input.py +++ b/UnitTests/ReferencePatternTimeChooser/test_2_input.py @@ -108,7 +108,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/TuningCorrector/test_1.py b/UnitTests/TuningCorrector/test_1.py index ce6036463..ac8817032 100644 --- a/UnitTests/TuningCorrector/test_1.py +++ b/UnitTests/TuningCorrector/test_1.py @@ -24,7 +24,7 @@ #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = False MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceCollected.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuningAndForm =['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff index 8c05360d5..3c6221ec9 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff @@ -23,7 +23,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuning =[] diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff index 16e1f739f..86482b118 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff @@ -23,7 +23,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuning =[] diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff index 8c05360d5..3c6221ec9 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff @@ -23,7 +23,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuning =[] diff --git a/UnitTests/TuningCorrector/test_10.py b/UnitTests/TuningCorrector/test_10.py index 008375e45..b3dad9d9d 100644 --- a/UnitTests/TuningCorrector/test_10.py +++ b/UnitTests/TuningCorrector/test_10.py @@ -23,7 +23,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuningAndForm =[] diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff index 8c05360d5..3c6221ec9 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff @@ -23,7 +23,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuning =[] diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff index e0cd814ed..9b9c6e39b 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff @@ -23,7 +23,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuning =[] diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff index e0cd814ed..9b9c6e39b 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff @@ -23,7 +23,7 @@ suffix = ut.returnDigitFromFilename(__file__) #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuning = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuning =[] diff --git a/UnitTests/TuningCorrector/test_11.py b/UnitTests/TuningCorrector/test_11.py index 7fd23eedc..d2473e1ab 100644 --- a/UnitTests/TuningCorrector/test_11.py +++ b/UnitTests/TuningCorrector/test_11.py @@ -23,7 +23,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuningAndForm =[] diff --git a/UnitTests/TuningCorrector/test_2.py b/UnitTests/TuningCorrector/test_2.py index facb7e58f..f0890937f 100644 --- a/UnitTests/TuningCorrector/test_2.py +++ b/UnitTests/TuningCorrector/test_2.py @@ -24,7 +24,7 @@ #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = False MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceCollected.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuningAndForm =['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_3.py b/UnitTests/TuningCorrector/test_3.py index 47916aaba..5b27abd36 100644 --- a/UnitTests/TuningCorrector/test_3.py +++ b/UnitTests/TuningCorrector/test_3.py @@ -24,7 +24,7 @@ #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = False MSRESOLVE.G.referencePatternsFileNamesList[0] = 'ReferenceLiterature.tsv' MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceCollected.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_4.py b/UnitTests/TuningCorrector/test_4.py index 179f3a120..6b9af1293 100644 --- a/UnitTests/TuningCorrector/test_4.py +++ b/UnitTests/TuningCorrector/test_4.py @@ -24,7 +24,7 @@ #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'External' -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuningAndForm =['ReferenceCollected.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_5.py b/UnitTests/TuningCorrector/test_5.py index 33abc09de..5a4ea0629 100644 --- a/UnitTests/TuningCorrector/test_5.py +++ b/UnitTests/TuningCorrector/test_5.py @@ -23,7 +23,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileDesiredTuningAndForm =[] diff --git a/UnitTests/TuningCorrector/test_6.py b/UnitTests/TuningCorrector/test_6.py index b82e604ed..c2fd683c7 100644 --- a/UnitTests/TuningCorrector/test_6.py +++ b/UnitTests/TuningCorrector/test_6.py @@ -23,7 +23,7 @@ #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileStandardTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileExistingTuningAndForm = [] diff --git a/UnitTests/TuningCorrector/test_7.py b/UnitTests/TuningCorrector/test_7.py index cd0440250..e2d3e5e22 100644 --- a/UnitTests/TuningCorrector/test_7.py +++ b/UnitTests/TuningCorrector/test_7.py @@ -25,7 +25,7 @@ #Need to change the "direct variable" version rather than the dictionary version. MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileStandardTuningAndForm = [] MSRESOLVE.G.referenceFileExistingTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] diff --git a/UnitTests/TuningCorrector/test_8.py b/UnitTests/TuningCorrector/test_8.py index c9daaadea..92b21bcf5 100644 --- a/UnitTests/TuningCorrector/test_8.py +++ b/UnitTests/TuningCorrector/test_8.py @@ -24,7 +24,7 @@ MSRESOLVE.G.referencePatternsFileNamesList = ['AcetaldehydeMeasured.tsv'] #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = True MSRESOLVE.G.referenceFileStandardTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileExistingTuningAndForm = [] diff --git a/UnitTests/TuningCorrector/test_9.py b/UnitTests/TuningCorrector/test_9.py index f4a051f68..09c30a446 100644 --- a/UnitTests/TuningCorrector/test_9.py +++ b/UnitTests/TuningCorrector/test_9.py @@ -25,7 +25,7 @@ MSRESOLVE.G.tuningCorrectPatternInternalVsExternal = 'Internal' #We can use the default user input, which is already in MSRESOLVE.G. #Need to change the "direct variable" version rather than the dictionary version. -MSRESOLVE.G.measuredReferenceYorN = 'yes' +MSRESOLVE.G.tuningCorrection = 'yes' MSRESOLVE.G.createMixedTuningPattern = False MSRESOLVE.G.referenceFileStandardTuningAndForm = ['ReferenceLiterature.tsv','xyyy'] MSRESOLVE.G.referenceFileExistingTuningAndForm = [] diff --git a/UnitTests/TuningCorrectorGasMixture/0-README.txt b/UnitTests/TuningCorrectorGasMixture/0-README.txt index 18022092a..da4e5d14c 100644 --- a/UnitTests/TuningCorrectorGasMixture/0-README.txt +++ b/UnitTests/TuningCorrectorGasMixture/0-README.txt @@ -8,7 +8,7 @@ This is in the file TuningCorrectorGasMixtureHypotheticalReferenceMeasuredSignal Proc Doc type things: -- First added at line 5351 - if len(G.UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames']) > 0: + if len(G.UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames']) > 0: -- Now make a reference object from LiteratureReference.tsv so that simulated signals can be made. -- GenerateReferenceDataList(referencePatternsFileNamesList,referencePatternsFormsList,AllMID_ObjectsDict={}): -- Need to be careful because "ReferenceInputPreProcessing" is being used. diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index ba163067c..65e5a2553 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -150,20 +150,20 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index 7e702da79..a523ebe35 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -150,22 +150,22 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = [] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = [] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index 01537571e..ae6676a9d 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -150,22 +150,22 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = [] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = [] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index 52851ea9a..2f7c14a7f 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -150,22 +150,22 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = [] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = ['LiteratureReference.tsv','xyyy'] #This is the pattern that will be changed. Typically this is NIST patterns. +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = [] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #normally to be left blank. #This is what the pattern will look more like after everything is done. Typically, this is a measured pattern. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #left blank to extract from the full dataset. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =['ethane', 'ethene', 'ethyne'] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[10, 2, 1] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index b8925bd64..339202a67 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -150,23 +150,23 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = [] #optional: provides tuningCorrectionIntensity feature. Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be changed. Should be blank by default. -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Should be blank by default. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". - -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = [] #optional: provides tuningCorrectionIntensity feature. Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be changed. Should be blank by default. +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Should be blank by default. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". + +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index 099e81607..1c6b663a0 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -150,23 +150,23 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = [] #optional: provides tuningCorrectionIntensity feature. Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be changed. Should be blank by default. -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Should be blank by default. -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". - -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = [] #optional: provides tuningCorrectionIntensity feature. Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be changed. Should be blank by default. +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Should be blank by default. +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". + +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py index 4de5ca783..bd5ccb28a 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py @@ -119,7 +119,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py index 638b983b2..e0d87cdc3 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py @@ -119,7 +119,7 @@ #//Reference Correction Coefficients// #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -measuredReferenceYorN='no' +tuningCorrection='no' referenceFileExistingTuningAndForm='AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm ='AcetaldehydeOnlyNISTRef.csv' referenceCorrectionCoefficients = {'A': 0.0, 'B': 0.0, 'C': 1.0} diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index 96fe4e4b8..2f4fd64be 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index fdcb0c6a7..40f615598 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index c96740b97..ba9f9b29d 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -48,7 +48,7 @@ maxPermutations = 100001 scaleRawDataOption = 'manual' scaleRawDataFactor = 1 -measuredReferenceYorN = 'no' +tuningCorrection = 'no' referenceFileStandardTuningAndForm =[] referenceFileExistingTuningAndForm = 'AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm = 'AcetaldehydeOnlyNISTRef.csv' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index 52b168b21..e6b78ae37 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -48,7 +48,7 @@ maxPermutations = 100001 scaleRawDataOption = 'manual' scaleRawDataFactor = 1 -measuredReferenceYorN = 'no' +tuningCorrection = 'no' referenceFileStandardTuningAndForm = [] referenceFileExistingTuningAndForm = 'AcetaldehydeMeasuredRef.csv' referenceFileDesiredTuningAndForm = 'AcetaldehydeOnlyNISTRef.csv' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index 4af66537c..63eda409a 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index dfbb8ae36..1d525e93b 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index df44c8d82..df4b1b629 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index db95f74a7..0aaeb526d 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index 3260fd6b3..731d9d403 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index 5cf29ab53..9d665a6c7 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index 87eaa3667..32397c161 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index 261149d2a..0d8098bbc 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -153,19 +153,19 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -#UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +#UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['tuningCorrectPatternInternalVsExternal'] = 'Internal' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =[] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] = 'AcetaldehydeOnlyNISTRef.csv' #This will be ignored in test_14.py -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = False -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = [0.00041154151447065387, -0.0200083957021084, 1.2192131558273835] +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['tuningCorrectPatternInternalVsExternal'] = 'Internal' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =[] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] = 'AcetaldehydeOnlyNISTRef.csv' #This will be ignored in test_14.py +UserChoices['tuningCorrection']['createMixedTuningPattern'] = False +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = [0.00041154151447065387, -0.0200083957021084, 1.2192131558273835] #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [[1.6745077041967374e-07, -1.2256016522854983e-05, 0.00020694004752915527], [-1.225601652285498e-05, 0.0009248854589718302, -0.016160488458714865], [0.0002069400475291552, -0.016160488458714862, 0.2955588432116031]] +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [[1.6745077041967374e-07, -1.2256016522854983e-05, 0.00020694004752915527], [-1.225601652285498e-05, 0.0009248854589718302, -0.016160488458714865], [0.0002069400475291552, -0.016160488458714862, 0.2955588432116031]] #//Reference Pattern Changer // (rpc) UserChoices['extractReferencePatternFromDataOption'] = {} #initialize the extractReferencePatternFromDataOption container @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index 4a49b5c8f..cdf5f520a 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -153,19 +153,19 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -#UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +#UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['tuningCorrectPatternInternalVsExternal'] = 'Internal' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =[] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' #this will be ignored in test_15.py -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = False -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = [0.00041154151447065387, -0.0200083957021084, 1.2192131558273835] +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['tuningCorrectPatternInternalVsExternal'] = 'Internal' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =[] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' #this will be ignored in test_15.py +UserChoices['tuningCorrection']['createMixedTuningPattern'] = False +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = [0.00041154151447065387, -0.0200083957021084, 1.2192131558273835] #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #no cov. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #no cov. #//Reference Pattern Changer // (rpc) UserChoices['extractReferencePatternFromDataOption'] = {} #initialize the extractReferencePatternFromDataOption container @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index 19fa86ace..60810fd77 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -153,18 +153,18 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -#UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +#UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='yes' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = [] #['ReferenceExternal.csv', 'xyxy'] -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] = [] -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = [0.00041154151447065387, -0.0200083957021084, 1.2192131558273835] +UserChoices['tuningCorrection']['on'] ='yes' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = [] #['ReferenceExternal.csv', 'xyxy'] +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] = [] +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = [0.00041154151447065387, -0.0200083957021084, 1.2192131558273835] #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [[1.6745077041967374e-07, -1.2256016522854983e-05, 0.00020694004752915527], [-1.225601652285498e-05, 0.0009248854589718302, -0.016160488458714865], [0.0002069400475291552, -0.016160488458714862, 0.2955588432116031]] +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [[1.6745077041967374e-07, -1.2256016522854983e-05, 0.00020694004752915527], [-1.225601652285498e-05, 0.0009248854589718302, -0.016160488458714865], [0.0002069400475291552, -0.016160488458714862, 0.2955588432116031]] #//Reference Pattern Changer // (rpc) UserChoices['extractReferencePatternFromDataOption'] = {} #initialize the extractReferencePatternFromDataOption container @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index 79c289b68..ed56a5597 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index b29749b3b..18ea74224 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index fb82a3c07..8e39035a8 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index 4a8b6b194..f6b103dc7 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index d950d2713..690757bd7 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index f2fdfc5a9..8b42ac58a 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index b39f37253..6ddd63c20 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index b617a0cc4..e9c4ea617 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index 4966663eb..ba0528799 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -153,15 +153,15 @@ #Note that 1 is the default and will make no alteration to the data #//Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] ='AcetaldehydeMeasuredRef.csv' +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] ='AcetaldehydeOnlyNISTRef.csv' +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten (Ashi thinks it will generate a new reference pattern) +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0 #//Reference Pattern Changer // (rpc) @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index 1b2b6e729..37c79b79d 100644 --- a/UserInput.py +++ b/UserInput.py @@ -150,24 +150,24 @@ #Note that 1 is the default and will make no alteration to the data #//Tuning Corrector - Reference Correction Coefficients// -UserChoices['measuredReferenceYorN'] = {} #initialize the measuredReferenceYorN container +UserChoices['tuningCorrection'] = {} #initialize the tuningCorrection container #TODO Reference Correction Coefficients feature should be upgraded to enable separate coefficients for each molecule to allow mixing and matching of reference patterns #TODO This can be tested by looking at the exported reference file and comparing it to the existing reference file #To change reference data based on mass dependent 2nd degree polynomial fit, input polynomial below. If you do not wish to use this function, simply leave as default -UserChoices['measuredReferenceYorN']['on'] ='no' -UserChoices['measuredReferenceYorN']['tuningCorrectPatternInternalVsExternal'] = 'External' #the options are 'External' or 'Internal'. Typically, External with createMixedTuningPattern is used. With "External", the existing pattern is assumed to be an External pattern and is tuning corrected. With "Internal" the existing pattern is assumed to be an Internal pattern, and the analysis pattern is changed to match the tuning of the desired pattern. Another use of 'Internal' when applying reference Coefficients manually to the Reference Analysis pattern. As of Nov 2021, if "External" is used, then at least one of referenceFileStandardTuningAndForm and referenceFileExistingTuningAndForm must be filled. -UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = [] #optional: Provides tuningCorrectionIntensity feature. Must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. -UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. -UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be pattern tuning corrected. Normally should be empty list, []. Otherwise, must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . -UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Normally should be empty, list, []. Otherwise, must include csv file and form. Example: ['OriginalRef.csv', 'xyyy'] . -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided (along with filling the next two variables). -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided -UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". - -#The reference correction coefficients are always used. If measuredReferenceYorN is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} +UserChoices['tuningCorrection']['on'] ='no' +UserChoices['tuningCorrection']['tuningCorrectPatternInternalVsExternal'] = 'External' #the options are 'External' or 'Internal'. Typically, External with createMixedTuningPattern is used. With "External", the existing pattern is assumed to be an External pattern and is tuning corrected. With "Internal" the existing pattern is assumed to be an Internal pattern, and the analysis pattern is changed to match the tuning of the desired pattern. Another use of 'Internal' when applying reference Coefficients manually to the Reference Analysis pattern. As of Nov 2021, if "External" is used, then at least one of referenceFileStandardTuningAndForm and referenceFileExistingTuningAndForm must be filled. +UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = [] #optional: Provides tuningCorrectionIntensity feature. Must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True. +UserChoices['tuningCorrection']['createMixedTuningPattern'] = True #Users should normally never change this. If True, the external pattern gets changed, and a mixed reference pattern gets changded. If False, the *internal* pattern gets changed. +UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] =[] #This is the pattern that will be pattern tuning corrected. Normally should be empty list, []. Otherwise, must include csv file and form. Example: ['NISTRef.csv', 'xyyy'] . +UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] =[] #This is what the pattern will look more like after everything is done. Normally should be empty, list, []. Otherwise, must include csv file and form. Example: ['OriginalRef.csv', 'xyyy'] . +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum molecule names must be provided (along with filling the next two variables). +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureConcentrations'] =[] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum concetrations must be provided +UserChoices['tuningCorrection']['tuningCorrectorGasMixtureSignals'] = [] #Optional: Special case, When using tuning corrector with a measured gas mixture spectrum, tuningCorrectorGasMixtureSignals must be provided or will be used to extract from the data. Leaving this unchanged will take the average of all of the data. If a pair of times is provided, that will be used to extract from the measured data. Alternatively, a single filename with an MSRESOLVE reference file and molecule name "GaxMixture". + +#The reference correction coefficients are always used. If tuningCorrection is 'yes' then the coefficients are overwritten and a new reference pattern is also generated to look more like the "Literature" case. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] = {'A': 0.0, 'B': 0.0, 'C': 1.0} #default is 'A': 0.0, 'B': 0.0, 'C': 1.0. Used as.... Factor = A*X^2 + B*X + C, so A=0,B=0,C=1.0 means the final factor is 1.0 and independent of molecular weight. -UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. +UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] = [0,0,0] #Covariance for reference correction coefficients for tuning corrector. Default is 0,0,0. Can be 9 x 9 covariance. #//Reference Pattern Changer // (rpc) @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','measuredReferenceYorN', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index c78c5ac4f..fada716a3 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -53,18 +53,18 @@ def parseUserInput(currentUserInput): if currentUserInput.specificMolecules == 'yes': #if yes, use the user's chosen moleclues chosenMoleculesForParsing = copy.deepcopy(currentUserInput.chosenMoleculesNames) #If using specificMolecules, make sure all selected molecules are in the reference data - if currentUserInput.measuredReferenceYorN == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. + if currentUserInput.tuningCorrection == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. parse.compareElementsBetweenLists(currentUserInput.chosenMoleculesNames,currentUserInput.moleculesNames,'chosenMolecules','Molecules from Reference Data') - if (currentUserInput.measuredReferenceYorN == 'yes') and (currentUserInput.createMixedTuningPattern == True):#If using a making a mixed reference pattern, check the extended moleculesNames list. + if (currentUserInput.tuningCorrection == 'yes') and (currentUserInput.createMixedTuningPattern == True):#If using a making a mixed reference pattern, check the extended moleculesNames list. currentUserInput.moleculesNamesExtended = parse.stripListOfStrings(currentUserInput.moleculesNamesExtended) parse.compareElementsBetweenLists(currentUserInput.chosenMoleculesNames,currentUserInput.moleculesNamesExtended,'chosenMolecules','Molecules from Reference Data') elif currentUserInput.specificMolecules == 'no': #Otherwise use all molecules - if currentUserInput.measuredReferenceYorN == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. + if currentUserInput.tuningCorrection == 'no': #If not making a mixed reference pattern, then use the regular moleculesNames object for comparison. currentUserInput.moleculesNames = parse.stripListOfStrings(list(currentUserInput.moleculesNames)) chosenMoleculesForParsing = copy.deepcopy(currentUserInput.moleculesNames) - if (currentUserInput.measuredReferenceYorN == 'yes') and (currentUserInput.createMixedTuningPattern == False):#If using tuning corrector and not making a mixed reference pattern, then we make the same chosenMoleculesForParsing as the normal case. + if (currentUserInput.tuningCorrection == 'yes') and (currentUserInput.createMixedTuningPattern == False):#If using tuning corrector and not making a mixed reference pattern, then we make the same chosenMoleculesForParsing as the normal case. chosenMoleculesForParsing = copy.deepcopy(currentUserInput.moleculesNames) - if (currentUserInput.measuredReferenceYorN == 'yes') and (currentUserInput.createMixedTuningPattern == True):#If using a making a mixed reference pattern, check the extended moleculesNames list. + if (currentUserInput.tuningCorrection == 'yes') and (currentUserInput.createMixedTuningPattern == True):#If using a making a mixed reference pattern, check the extended moleculesNames list. currentUserInput.moleculesNamesExtended = parse.stripListOfStrings(currentUserInput.moleculesNamesExtended) chosenMoleculesForParsing = copy.deepcopy(currentUserInput.moleculesNamesExtended) @@ -127,7 +127,7 @@ def parseUserInput(currentUserInput): currentUserInput.scaleRawDataFactor = float(currentUserInput.scaleRawDataFactor) #scaleRawDataFactor is a float #Reference Correction Changer - parse.strCheck(currentUserInput.measuredReferenceYorN,'measuredReferenceYorN') + parse.strCheck(currentUserInput.tuningCorrection,'tuningCorrection') #The below two variables are no longer strings. They are now lists with two elements, each of which are strings. TODO: Change their names to referenceFileExistingTuningAndForm and referenceFileDesiredTuningAndForm #parse.strCheck(currentUserInput.referenceFileExistingTuningAndForm,'referenceFileExistingTuningAndForm') #parse.strCheck(currentUserInput.referenceFileDesiredTuningAndForm,'referenceFileDesiredTuningAndForm') @@ -276,17 +276,17 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t UserChoices['dataAnalysisMethods']['implicitSLScorrection'] = False print("Incompatible choice detected: implicitSLScorrection only works with sls unique. forcing implicitSLScorrection to False.") - if UserChoices['measuredReferenceYorN']['on'] == 'no': #forcing the standard and external reference files to blank if measuredReferenceYorN is not on. - UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = [] - UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = [] + if UserChoices['tuningCorrection']['on'] == 'no': #forcing the standard and external reference files to blank if tuningCorrection is not on. + UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = [] + UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = [] - if 'referenceFileStandardTuningAndForm' not in UserChoices['measuredReferenceYorN']: - UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] = [] #set to default if not present, for backwards compatibility, to make sure old unit tests and analyses work. - if 'referenceFileExistingTuningAndForm' not in UserChoices['measuredReferenceYorN']: - UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] = [] #set to default if not present, for backwards compatibility, to make sure old unit tests and analyses work. + if 'referenceFileStandardTuningAndForm' not in UserChoices['tuningCorrection']: + UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] = [] #set to default if not present, for backwards compatibility, to make sure old unit tests and analyses work. + if 'referenceFileExistingTuningAndForm' not in UserChoices['tuningCorrection']: + UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] = [] #set to default if not present, for backwards compatibility, to make sure old unit tests and analyses work. - if ((UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] == []) and (UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] == [])): #This If statement sets createMixedTuningPattern to False if referenceFileStandardTuningAndForm pattern and referenceFileExistingTuningAndForm are both populated with a blank list. - UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = False + if ((UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] == []) and (UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] == [])): #This If statement sets createMixedTuningPattern to False if referenceFileStandardTuningAndForm pattern and referenceFileExistingTuningAndForm are both populated with a blank list. + UserChoices['tuningCorrection']['createMixedTuningPattern'] = False print("No Standard or External tuning pattern. Forcing createMixedTuningPattern to False.") #Will make sure that any referenceFileStandardTuning and referenceFileExistingTuning filenames have the same extension as the original reference pattern, and exit if that condition is not met. @@ -299,11 +299,11 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t for referenceFileName in UserChoices['inputFiles']['referencePatternsFileNamesList']: if referenceFileExtension not in referenceFileName: print("ERROR: All filenamese in referencePatternsFileNamesList must have the same extension."); sys.exit() - if len (UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm']) > 0: - if referenceFileExtension not in UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'][0]: + if len (UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm']) > 0: + if referenceFileExtension not in UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'][0]: print("ERROR: All filenamese in referencePatternsFileNamesList and referenceFileStandardTuningAndForm must have the same extension."); sys.exit() - if len (UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm']) > 0: - if referenceFileExtension not in UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'][0]: + if len (UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm']) > 0: + if referenceFileExtension not in UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'][0]: print("ERROR: All filenamese in referencePatternsFileNamesList and referenceFileExistingTuningAndForm must have the same extension."); sys.exit() #Filling settings variables dictionary so that variables can be populated from it. This is basically a mapping. See user input file for details. @@ -375,47 +375,47 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['scaleRawDataOption'] = UserChoices['scaleRawDataYorN']['scaleRawDataOption'] SettingsVDictionary['scaleRawDataFactor'] = UserChoices['scaleRawDataYorN']['scaleRawDataFactor'] - SettingsVDictionary['measuredReferenceYorN'] = UserChoices['measuredReferenceYorN']['on'] + SettingsVDictionary['tuningCorrection'] = UserChoices['tuningCorrection']['on'] - SettingsVDictionary['referenceFileStandardTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] - SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] + SettingsVDictionary['referenceFileStandardTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] + SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] - if 'tuningCorrectPatternInternalVsExternal' in UserChoices['measuredReferenceYorN']: - SettingsVDictionary['tuningCorrectPatternInternalVsExternal'] = UserChoices['measuredReferenceYorN']['tuningCorrectPatternInternalVsExternal'] - #if UserChoices['measuredReferenceYorN']['tuningCorrectPatternInternalVsExternal'].lower() == 'internal': #Create a warning if internal & createMixedTuningPattern are both chosen. - #if 'createMixedTuningPattern' in UserChoices['measuredReferenceYorN']: - #if UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] == True: + if 'tuningCorrectPatternInternalVsExternal' in UserChoices['tuningCorrection']: + SettingsVDictionary['tuningCorrectPatternInternalVsExternal'] = UserChoices['tuningCorrection']['tuningCorrectPatternInternalVsExternal'] + #if UserChoices['tuningCorrection']['tuningCorrectPatternInternalVsExternal'].lower() == 'internal': #Create a warning if internal & createMixedTuningPattern are both chosen. + #if 'createMixedTuningPattern' in UserChoices['tuningCorrection']: + #if UserChoices['tuningCorrection']['createMixedTuningPattern'] == True: #print("Warning: createMixedTuningPattern is on and tuningCorrectPatternInternalVsExternal is set to internal. This is not the typical set of choices.") else: #If not provided, then populate with the default for backwards compatibility. SettingsVDictionary['tuningCorrectPatternInternalVsExternal'] = 'External' - if 'createMixedTuningPattern' not in UserChoices['measuredReferenceYorN']: - UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] = True - SettingsVDictionary['createMixedTuningPattern'] = UserChoices['measuredReferenceYorN']['createMixedTuningPattern'] - SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileExistingTuningAndForm'] - SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileDesiredTuningAndForm'] - SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients'] + if 'createMixedTuningPattern' not in UserChoices['tuningCorrection']: + UserChoices['tuningCorrection']['createMixedTuningPattern'] = True + SettingsVDictionary['createMixedTuningPattern'] = UserChoices['tuningCorrection']['createMixedTuningPattern'] + SettingsVDictionary['referenceFileExistingTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileExistingTuningAndForm'] + SettingsVDictionary['referenceFileDesiredTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileDesiredTuningAndForm'] + SettingsVDictionary['referenceCorrectionCoefficients'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients'] if 'implicitSLSRecursion' not in UserChoices['dataAnalysisMethods']: #This variable is a work in progress. This if statement is to prevent errors thats created by old Unit Test. UserChoices['dataAnalysisMethods']['implicitSLSRecursion'] = 0 SettingsVDictionary['implicitSLSRecursion'] = UserChoices['dataAnalysisMethods']['implicitSLSRecursion'] #to make sure old unit tests and analyses work. - if 'referenceFileStandardTuningAndForm' in UserChoices['measuredReferenceYorN']: - SettingsVDictionary['referenceFileStandardTuningAndForm'] = UserChoices['measuredReferenceYorN']['referenceFileStandardTuningAndForm'] + if 'referenceFileStandardTuningAndForm' in UserChoices['tuningCorrection']: + SettingsVDictionary['referenceFileStandardTuningAndForm'] = UserChoices['tuningCorrection']['referenceFileStandardTuningAndForm'] else: SettingsVDictionary['referenceFileStandardTuningAndForm'] = [] try: #to make sure old unit tests and analyses work. - #if 'tuningCorrectorGasMixtureMoleculeNames' in UserChoices['measuredReferenceYorN'].keys(): - SettingsVDictionary['tuningCorrectorGasMixtureMoleculeNames'] = UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] + #if 'tuningCorrectorGasMixtureMoleculeNames' in UserChoices['tuningCorrection'].keys(): + SettingsVDictionary['tuningCorrectorGasMixtureMoleculeNames'] = UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] except: #to make sure old unit tests work. SettingsVDictionary['tuningCorrectorGasMixtureMoleculeNames'] = [] - UserChoices['measuredReferenceYorN']['tuningCorrectorGasMixtureMoleculeNames'] = [] + UserChoices['tuningCorrection']['tuningCorrectorGasMixtureMoleculeNames'] = [] try: - SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['measuredReferenceYorN']['referenceCorrectionCoefficients_cov'] + SettingsVDictionary['referenceCorrectionCoefficients_cov'] = UserChoices['tuningCorrection']['referenceCorrectionCoefficients_cov'] except: SettingsVDictionary['referenceCorrectionCoefficients_cov'] = [0,0,0] #TODO: This is to keep some old unit tests running. Ideally they should be fixed. SettingsVDictionary['extractReferencePatternFromDataOption'] = UserChoices['extractReferencePatternFromDataOption']['on'] From 72f41e6fb1073eeee8fab33fe56c1e9c35ddde9e Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 12:25:19 -0400 Subject: [PATCH 7/9] minimalReferenceValue --> applyReferenceMassFragmentsThresholds --- DefaultUserInput.py | 10 +++---- ExampleAnalysis/DefaultUserInput.py | 10 +++---- ExampleAnalysis/LogFile.txt | 2 +- ExampleAnalysis/MSRESOLVE.py | 22 +++++++------- ExampleAnalysis/UserInput.py | 10 +++---- ExampleAnalysis/userInputValidityFunctions.py | 10 +++---- .../DefaultUserInput.py | 10 +++---- ExampleReferenceExtraction/MSRESOLVE.py | 22 +++++++------- ExampleReferenceExtraction/UserInput.py | 10 +++---- .../userInputValidityFunctions.py | 10 +++---- .../DefaultUserInput.py | 10 +++---- ExampleTuningCorrectorGasMixture/LogFile.txt | 2 +- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 26 ++++++++-------- .../MSRESOLVEBad1.py | 26 ++++++++-------- .../MSRESOLVEPrevious.py | 26 ++++++++-------- ExampleTuningCorrectorGasMixture/UserInput.py | 10 +++---- .../userInputValidityFunctions.py | 10 +++---- MSRESOLVE.py | 30 +++++++++---------- README.txt | 2 +- .../DefaultUserInput.py | 4 +-- Todo/SLS Common vs. Unique Bug/MSRESOLVE.py | 8 ++--- Todo/SLS Common vs. Unique Bug/UserInput.py | 4 +-- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../test_3_input.py | 2 +- .../test_4_input.py | 2 +- .../test_5_input.py | 2 +- .../test_6_input.py | 2 +- .../test_1_Input_Brute_Finisher.py | 10 +++---- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/NegativeAnalyzer/test_1_Input.py | 10 +++---- .../test_1_inputA.py | 2 +- .../test_1_inputB.py | 2 +- .../test_1_inputC.py | 2 +- .../test_2_input.py | 2 +- UnitTests/TuningCorrector/test_1.py | 4 +-- .../test_10 Manual SLS/1/test_10.turnedOff | 4 +-- .../test_10 Manual SLS/1/test_5.turnedOff | 4 +-- .../test_10 Manual SLS/4/test_10.turnedOff | 4 +-- UnitTests/TuningCorrector/test_10.py | 4 +-- .../1/test_10.turnedOff | 4 +-- .../1/test_11.turnedOff | 4 +-- .../4/test_11.turnedOff | 4 +-- UnitTests/TuningCorrector/test_11.py | 4 +-- UnitTests/TuningCorrector/test_2.py | 4 +-- UnitTests/TuningCorrector/test_3.py | 4 +-- UnitTests/TuningCorrector/test_4.py | 4 +-- UnitTests/TuningCorrector/test_5.py | 4 +-- UnitTests/TuningCorrector/test_6.py | 4 +-- UnitTests/TuningCorrector/test_7.py | 4 +-- UnitTests/TuningCorrector/test_8.py | 4 +-- UnitTests/TuningCorrector/test_9.py | 4 +-- .../UserInputGasMixture.py | 10 +++---- .../UserInputGasMixture2.py | 10 +++---- .../UserInputGasMixture3.py | 10 +++---- .../UserInputGasMixture4.py | 10 +++---- .../XYXYReferencePattern/test_1_inputXYXY.py | 10 +++---- .../XYXYReferencePattern/test_1_inputXYYY.py | 10 +++---- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../implicitSLScorrection/test_1_Input.py | 10 +++---- .../implicitSLScorrection/test_2_Input.py | 10 +++---- .../test_1_UserInput.py | 4 +-- .../test_2_UserInput.py | 4 +-- UnitTests/slsCommon/test_1_Input.py | 10 +++---- .../test_1_Input.py | 10 +++---- .../test_2_Input.py | 10 +++---- UnitTests/uncertainties/test_10_Input.py | 10 +++---- UnitTests/uncertainties/test_11_Input.py | 10 +++---- UnitTests/uncertainties/test_12_Input.py | 10 +++---- UnitTests/uncertainties/test_13_Input.py | 10 +++---- UnitTests/uncertainties/test_14_Input.py | 10 +++---- UnitTests/uncertainties/test_15_Input.py | 10 +++---- UnitTests/uncertainties/test_16_Input.py | 10 +++---- UnitTests/uncertainties/test_1_Input.py | 10 +++---- UnitTests/uncertainties/test_2_Input.py | 10 +++---- UnitTests/uncertainties/test_3_Input.py | 10 +++---- UnitTests/uncertainties/test_4_Input.py | 10 +++---- UnitTests/uncertainties/test_5_Input.py | 10 +++---- UnitTests/uncertainties/test_6_Input.py | 10 +++---- UnitTests/uncertainties/test_7_Input.py | 10 +++---- UnitTests/uncertainties/test_8_Input.py | 10 +++---- UnitTests/uncertainties/test_9_Input.py | 10 +++---- UserInput.py | 10 +++---- userInputValidityFunctions.py | 12 ++++---- 96 files changed, 355 insertions(+), 355 deletions(-) diff --git a/DefaultUserInput.py b/DefaultUserInput.py index 37c79b79d..99d0b507a 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -186,11 +186,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] #typical values are between 5 and 50. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This setting causes MSRESOLVE to favor larger intensity reference peaks (above the number provided) during solving. +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #typical values are between 5 and 50. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This setting causes MSRESOLVE to favor larger intensity reference peaks (above the number provided) during solving. #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index 3fe20f588..c41cab466 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -179,11 +179,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/LogFile.txt b/ExampleAnalysis/LogFile.txt index 123cf8695..e00d433ab 100644 --- a/ExampleAnalysis/LogFile.txt +++ b/ExampleAnalysis/LogFile.txt @@ -9,7 +9,7 @@ massesToBackgroundCorrect = [12.0 13.0 14.0 15.0 16.0 17.0 21.0 22.0 24.0 25.0 2 30.0] earlyBaselineTimes = [[850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870]] lateBaselineTimes = [[1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070]] -minimalReferenceValue = yes +applyReferenceMassFragmentsThresholds = yes referenceValueThreshold = [1.01, 1.01, 1.01] referenceSignificantFragmentThresholds = [20.0, 20.0, 20.0] answer = sls diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index 43f460727..51ef66d5a 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -381,7 +381,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ''' - if G.minimalReferenceValue !='yes': + if G.applyReferenceMassFragmentsThresholds !='yes': print("Warning: The ABCDetermination will occur without threshold filtering, since that setting is off.") #For simplicity, we will put the items into temporary items, then into dictionaries that we can then access. @@ -390,7 +390,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternMeasuredDict['molecules']=molecules ReferencePatternMeasuredDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternMeasuredDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternMeasuredDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternMeasuredDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternMeasuredDict['provided_reference_patterns'],G.referenceValueThreshold) ReferencePatternLiteratureDict = {} @@ -398,7 +398,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternLiteratureDict['molecules']=molecules ReferencePatternLiteratureDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternLiteratureDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternLiteratureDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternLiteratureDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternLiteratureDict['provided_reference_patterns'],G.referenceValueThreshold) ''' @@ -1228,7 +1228,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): #TODO: the minimal reference value can cause inaccuracies if interpolating between multiple reference patterns if one pattern has a value rounded to 0 and the other does not #TODO: option 1: this issue can be fixed by moving this to after interpolation #TODO: option 2: Or we can below assign to preprocessed_reference_pattern rather than standardized_reference_patterns and then use that in data analysis (Note that interpolate would continue to use standardized_reference_patterns as well as preprocess the output) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) @@ -2654,7 +2654,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for minimalReferenceValue feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -3449,7 +3449,7 @@ def SLSUniqueFragments(molecules,monitored_reference_intensities,reciprocal_matc chosenMolecule = None tuplesOfUniqueFragmentsList = [] - if G.minimalReferenceValue == "yes": #We only will do some filtering things if it's requested. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only will do some filtering things if it's requested. #Before going forward, we're going to make a variable called remaining_referenceSignificantFragmentThresholds, using a function. def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFragmentThresholds, molecules_unedited, remaining_molecules_SLS): remaining_referenceSignificantFragmentThresholds = list(copy.deepcopy(referenceSignificantFragmentThresholds)) @@ -3489,12 +3489,12 @@ def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFra #consideredMolecule = remaining_molecules_SLS[moleculeIndexOfUniqueIntensity] #This is for debugging purposes, this can be printed. #For debugging, also print remaining_reference_intensities_SLS and massFragmentIndex_i. #However, now we have a few lines of code to check if we are above the referenceSignificantFragmentThresholds. - if G.minimalReferenceValue == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. if (max(remaining_reference_intensities_SLS[massFragmentIndex_i]) < remaining_referenceSignificantFragmentThresholds[moleculeIndexOfUniqueIntensity]): #This allows separate referenceSignificantFragmentThresholds for each molecule. significantFragment = False #Set to false if the fragment is too small. else: significantFragment = True #This means the fragment is greater than or equal to the threshold for significance. - if G.minimalReferenceValue != "yes": #if the option is not selected, then all fragments are considered significant. + if G.applyReferenceMassFragmentsThresholds != "yes": #if the option is not selected, then all fragments are considered significant. significantFragment = True if significantFragment == True: #now make a tuple with the unique standardized intensity in the front so we can sort by that @@ -4375,7 +4375,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['minimalReferenceValue']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -4992,8 +4992,8 @@ def PopulateLogFile(): f6.write('rpcMoleculesToChange = %s \n'%(G.rpcMoleculesToChange)) f6.write('rpcMoleculesToChangeMF = %s \n'%(G.rpcMoleculesToChangeMF)) f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) - if G.minimalReferenceValue == 'yes': - f6.write('minimalReferenceValue = %s \n'%(G.minimalReferenceValue)) + if G.applyReferenceMassFragmentsThresholds == 'yes': + f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index f3115930f..f19a4fa88 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -179,11 +179,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [1.01] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [20.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [1.01] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [20.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index de557484e..5fd98e453 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -123,8 +123,8 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.rpcMoleculesToChange,chosenMoleculesForParsing,'rpcMoleculesToChange','chosenMolecules') #Reference Mass Fragmentation Threshold - parse.strCheck(currentUserInput.minimalReferenceValue,'minimalReferenceValue') - if currentUserInput.minimalReferenceValue == 'yes': #If using reference mass fragmentation threshold + parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') + if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) @@ -325,9 +325,9 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcTimeRanges'] = UserChoices['extractReferencePatternFromDataOption']['rpcTimeRanges'] SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] - SettingsVDictionary['minimalReferenceValue'] = UserChoices['minimalReferenceValue']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['minimalReferenceValue']['referenceValueThreshold'] - SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] + SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] + SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on'] SettingsVDictionary['massesToLowerBoundThresholdFilter'] = UserChoices['lowerBoundThresholdChooser']['massesToLowerBoundThresholdFilter'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index 3fe20f588..c41cab466 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -179,11 +179,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index 43f460727..51ef66d5a 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -381,7 +381,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ''' - if G.minimalReferenceValue !='yes': + if G.applyReferenceMassFragmentsThresholds !='yes': print("Warning: The ABCDetermination will occur without threshold filtering, since that setting is off.") #For simplicity, we will put the items into temporary items, then into dictionaries that we can then access. @@ -390,7 +390,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternMeasuredDict['molecules']=molecules ReferencePatternMeasuredDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternMeasuredDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternMeasuredDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternMeasuredDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternMeasuredDict['provided_reference_patterns'],G.referenceValueThreshold) ReferencePatternLiteratureDict = {} @@ -398,7 +398,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternLiteratureDict['molecules']=molecules ReferencePatternLiteratureDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternLiteratureDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternLiteratureDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternLiteratureDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternLiteratureDict['provided_reference_patterns'],G.referenceValueThreshold) ''' @@ -1228,7 +1228,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): #TODO: the minimal reference value can cause inaccuracies if interpolating between multiple reference patterns if one pattern has a value rounded to 0 and the other does not #TODO: option 1: this issue can be fixed by moving this to after interpolation #TODO: option 2: Or we can below assign to preprocessed_reference_pattern rather than standardized_reference_patterns and then use that in data analysis (Note that interpolate would continue to use standardized_reference_patterns as well as preprocess the output) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) @@ -2654,7 +2654,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for minimalReferenceValue feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -3449,7 +3449,7 @@ def SLSUniqueFragments(molecules,monitored_reference_intensities,reciprocal_matc chosenMolecule = None tuplesOfUniqueFragmentsList = [] - if G.minimalReferenceValue == "yes": #We only will do some filtering things if it's requested. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only will do some filtering things if it's requested. #Before going forward, we're going to make a variable called remaining_referenceSignificantFragmentThresholds, using a function. def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFragmentThresholds, molecules_unedited, remaining_molecules_SLS): remaining_referenceSignificantFragmentThresholds = list(copy.deepcopy(referenceSignificantFragmentThresholds)) @@ -3489,12 +3489,12 @@ def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFra #consideredMolecule = remaining_molecules_SLS[moleculeIndexOfUniqueIntensity] #This is for debugging purposes, this can be printed. #For debugging, also print remaining_reference_intensities_SLS and massFragmentIndex_i. #However, now we have a few lines of code to check if we are above the referenceSignificantFragmentThresholds. - if G.minimalReferenceValue == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. if (max(remaining_reference_intensities_SLS[massFragmentIndex_i]) < remaining_referenceSignificantFragmentThresholds[moleculeIndexOfUniqueIntensity]): #This allows separate referenceSignificantFragmentThresholds for each molecule. significantFragment = False #Set to false if the fragment is too small. else: significantFragment = True #This means the fragment is greater than or equal to the threshold for significance. - if G.minimalReferenceValue != "yes": #if the option is not selected, then all fragments are considered significant. + if G.applyReferenceMassFragmentsThresholds != "yes": #if the option is not selected, then all fragments are considered significant. significantFragment = True if significantFragment == True: #now make a tuple with the unique standardized intensity in the front so we can sort by that @@ -4375,7 +4375,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['minimalReferenceValue']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -4992,8 +4992,8 @@ def PopulateLogFile(): f6.write('rpcMoleculesToChange = %s \n'%(G.rpcMoleculesToChange)) f6.write('rpcMoleculesToChangeMF = %s \n'%(G.rpcMoleculesToChangeMF)) f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) - if G.minimalReferenceValue == 'yes': - f6.write('minimalReferenceValue = %s \n'%(G.minimalReferenceValue)) + if G.applyReferenceMassFragmentsThresholds == 'yes': + f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index d3670a93e..8f21ad82a 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -179,11 +179,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index de557484e..5fd98e453 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -123,8 +123,8 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.rpcMoleculesToChange,chosenMoleculesForParsing,'rpcMoleculesToChange','chosenMolecules') #Reference Mass Fragmentation Threshold - parse.strCheck(currentUserInput.minimalReferenceValue,'minimalReferenceValue') - if currentUserInput.minimalReferenceValue == 'yes': #If using reference mass fragmentation threshold + parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') + if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) @@ -325,9 +325,9 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcTimeRanges'] = UserChoices['extractReferencePatternFromDataOption']['rpcTimeRanges'] SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] - SettingsVDictionary['minimalReferenceValue'] = UserChoices['minimalReferenceValue']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['minimalReferenceValue']['referenceValueThreshold'] - SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] + SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] + SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on'] SettingsVDictionary['massesToLowerBoundThresholdFilter'] = UserChoices['lowerBoundThresholdChooser']['massesToLowerBoundThresholdFilter'] diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index 87853e0d0..12dea2fa5 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -179,11 +179,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/LogFile.txt b/ExampleTuningCorrectorGasMixture/LogFile.txt index 8119c5a0c..221b5e802 100644 --- a/ExampleTuningCorrectorGasMixture/LogFile.txt +++ b/ExampleTuningCorrectorGasMixture/LogFile.txt @@ -12,7 +12,7 @@ referenceCorrectionCoefficientB = 0.25062935187812 referenceCorrectionCoefficientC = -0.9533139758788823 referenceCorrection_abcCoefficients = [-0.006486881698506962, 0.25062935187812, -0.9533139758788823] referenceCorrection_abcCoefficients_cov = [[6.210441332505573e-06, -0.00026708328912830614, 0.002613875252542956], [-0.0002670832891283059, 0.01155046014720452, -0.11397285273190337], [0.0026138752525429526, -0.11397285273190326, 1.140196952429929]] -minimalReferenceValue = yes +applyReferenceMassFragmentsThresholds = yes referenceValueThreshold = [2.0, 2.0, 2.0, 2.0] referenceSignificantFragmentThresholds = [6.0, 6.0, 6.0, 6.0] answer = sls diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index c9a15ab78..3f8d084ea 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -381,7 +381,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ''' - if G.minimalReferenceValue !='yes': + if G.applyReferenceMassFragmentsThresholds !='yes': print("Warning: The ABCDetermination will occur without threshold filtering, since that setting is off.") if G.extractReferencePatternFromDataOption == 'yes': @@ -393,7 +393,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['molecules']=molecules ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ReferencePatternDesiredTuningDict = {} @@ -401,7 +401,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['molecules']=molecules ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ''' @@ -865,7 +865,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there if ReferenceDataList[ReferenceDataIndex].ExportAtEachStep == 'yes': print("line 685", ReferenceDataList[ReferenceDataIndex].relativeIonizationEfficiencies) print("line 686", ReferenceDataList[ReferenceDataIndex].sourceOfIonizationData) - print(G.UserChoices['minimalReferenceValue']['referenceValueThreshold']) + print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']) ReferenceDataList[ReferenceDataIndex].ExportCollector('StandardizedReferencePattern', use_provided_reference_patterns=False) ReferenceDataList[ReferenceDataIndex].exportReferencePattern("TuningCorrectorMixedPattern.csv") @@ -1620,7 +1620,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): #TODO: the minimal reference value can cause inaccuracies if interpolating between multiple reference patterns if one pattern has a value rounded to 0 and the other does not #TODO: option 1: this issue can be fixed by moving this to after interpolation #TODO: option 2: Or we can below assign to preprocessed_reference_pattern rather than standardized_reference_patterns and then use that in data analysis (Note that interpolate would continue to use standardized_reference_patterns as well as preprocess the output) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) @@ -3232,7 +3232,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for minimalReferenceValue feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -4027,7 +4027,7 @@ def SLSUniqueFragments(molecules,monitored_reference_intensities,reciprocal_matc chosenMolecule = None tuplesOfUniqueFragmentsList = [] - if G.minimalReferenceValue == "yes": #We only will do some filtering things if it's requested. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only will do some filtering things if it's requested. #Before going forward, we're going to make a variable called remaining_referenceSignificantFragmentThresholds, using a function. def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFragmentThresholds, molecules_unedited, remaining_molecules_SLS): remaining_referenceSignificantFragmentThresholds = list(copy.deepcopy(referenceSignificantFragmentThresholds)) @@ -4067,12 +4067,12 @@ def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFra #consideredMolecule = remaining_molecules_SLS[moleculeIndexOfUniqueIntensity] #This is for debugging purposes, this can be printed. #For debugging, also print remaining_reference_intensities_SLS and massFragmentIndex_i. #However, now we have a few lines of code to check if we are above the referenceSignificantFragmentThresholds. - if G.minimalReferenceValue == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. if (max(remaining_reference_intensities_SLS[massFragmentIndex_i]) < remaining_referenceSignificantFragmentThresholds[moleculeIndexOfUniqueIntensity]): #This allows separate referenceSignificantFragmentThresholds for each molecule. significantFragment = False #Set to false if the fragment is too small. else: significantFragment = True #This means the fragment is greater than or equal to the threshold for significance. - if G.minimalReferenceValue != "yes": #if the option is not selected, then all fragments are considered significant. + if G.applyReferenceMassFragmentsThresholds != "yes": #if the option is not selected, then all fragments are considered significant. significantFragment = True if significantFragment == True: #now make a tuple with the unique standardized intensity in the front so we can sort by that @@ -4953,7 +4953,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['minimalReferenceValue']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -5572,8 +5572,8 @@ def PopulateLogFile(): f6.write('rpcMoleculesToChange = %s \n'%(G.rpcMoleculesToChange)) f6.write('rpcMoleculesToChangeMF = %s \n'%(G.rpcMoleculesToChangeMF)) f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) - if G.minimalReferenceValue == 'yes': - f6.write('minimalReferenceValue = %s \n'%(G.minimalReferenceValue)) + if G.applyReferenceMassFragmentsThresholds == 'yes': + f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': @@ -6098,7 +6098,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['minimalReferenceValue']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index b877ccf7e..f3428c978 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -381,7 +381,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ''' - if G.minimalReferenceValue !='yes': + if G.applyReferenceMassFragmentsThresholds !='yes': print("Warning: The ABCDetermination will occur without threshold filtering, since that setting is off.") if G.extractReferencePatternFromDataOption == 'yes': @@ -393,7 +393,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['molecules']=molecules ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ReferencePatternDesiredTuningDict = {} @@ -401,7 +401,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['molecules']=molecules ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ''' @@ -697,7 +697,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there if ReferenceDataList[ReferenceDataIndex].ExportAtEachStep == 'yes': print("line 685", ReferenceDataList[ReferenceDataIndex].relativeIonizationEfficiencies) print("line 686", ReferenceDataList[ReferenceDataIndex].sourceOfIonizationData) - print(G.UserChoices['minimalReferenceValue']['referenceValueThreshold']) + print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']) ReferenceDataList[ReferenceDataIndex].ExportCollector('StandardizedReferencePattern', use_provided_reference_patterns=False) ReferenceDataList[ReferenceDataIndex].exportReferencePattern("TuningCorrectorMixedPattern.csv") @@ -1495,7 +1495,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): #TODO: the minimal reference value can cause inaccuracies if interpolating between multiple reference patterns if one pattern has a value rounded to 0 and the other does not #TODO: option 1: this issue can be fixed by moving this to after interpolation #TODO: option 2: Or we can below assign to preprocessed_reference_pattern rather than standardized_reference_patterns and then use that in data analysis (Note that interpolate would continue to use standardized_reference_patterns as well as preprocess the output) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) @@ -3095,7 +3095,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for minimalReferenceValue feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -3890,7 +3890,7 @@ def SLSUniqueFragments(molecules,monitored_reference_intensities,reciprocal_matc chosenMolecule = None tuplesOfUniqueFragmentsList = [] - if G.minimalReferenceValue == "yes": #We only will do some filtering things if it's requested. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only will do some filtering things if it's requested. #Before going forward, we're going to make a variable called remaining_referenceSignificantFragmentThresholds, using a function. def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFragmentThresholds, molecules_unedited, remaining_molecules_SLS): remaining_referenceSignificantFragmentThresholds = list(copy.deepcopy(referenceSignificantFragmentThresholds)) @@ -3932,12 +3932,12 @@ def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFra #consideredMolecule = remaining_molecules_SLS[moleculeIndexOfUniqueIntensity] #This is for debugging purposes, this can be printed. #For debugging, also print remaining_reference_intensities_SLS and massFragmentIndex_i. #However, now we have a few lines of code to check if we are above the referenceSignificantFragmentThresholds. - if G.minimalReferenceValue == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. if (max(remaining_reference_intensities_SLS[massFragmentIndex_i]) < remaining_referenceSignificantFragmentThresholds[moleculeIndexOfUniqueIntensity]): #This allows separate referenceSignificantFragmentThresholds for each molecule. significantFragment = False #Set to false if the fragment is too small. else: significantFragment = True #This means the fragment is greater than or equal to the threshold for significance. - if G.minimalReferenceValue != "yes": #if the option is not selected, then all fragments are considered significant. + if G.applyReferenceMassFragmentsThresholds != "yes": #if the option is not selected, then all fragments are considered significant. significantFragment = True if significantFragment == True: #now make a tuple with the unique standardized intensity in the front so we can sort by that @@ -4818,7 +4818,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['minimalReferenceValue']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -5437,8 +5437,8 @@ def PopulateLogFile(): f6.write('rpcMoleculesToChange = %s \n'%(G.rpcMoleculesToChange)) f6.write('rpcMoleculesToChangeMF = %s \n'%(G.rpcMoleculesToChangeMF)) f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) - if G.minimalReferenceValue == 'yes': - f6.write('minimalReferenceValue = %s \n'%(G.minimalReferenceValue)) + if G.applyReferenceMassFragmentsThresholds == 'yes': + f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': @@ -5950,7 +5950,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['minimalReferenceValue']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index 5550e7fae..98e9b3517 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -381,7 +381,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ''' - if G.minimalReferenceValue !='yes': + if G.applyReferenceMassFragmentsThresholds !='yes': print("Warning: The ABCDetermination will occur without threshold filtering, since that setting is off.") if G.extractReferencePatternFromDataOption == 'yes': @@ -393,7 +393,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['molecules']=molecules ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ReferencePatternDesiredTuningDict = {} @@ -401,7 +401,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['molecules']=molecules ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ''' @@ -872,7 +872,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there if ReferenceDataList[ReferenceDataIndex].ExportAtEachStep == 'yes': print("line 685", ReferenceDataList[ReferenceDataIndex].relativeIonizationEfficiencies) print("line 686", ReferenceDataList[ReferenceDataIndex].sourceOfIonizationData) - print(G.UserChoices['minimalReferenceValue']['referenceValueThreshold']) + print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']) ReferenceDataList[ReferenceDataIndex].ExportCollector('StandardizedReferencePattern', use_provided_reference_patterns=False) ReferenceDataList[ReferenceDataIndex].exportReferencePattern("TuningCorrectorMixedPattern.csv") @@ -1626,7 +1626,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): #TODO: the minimal reference value can cause inaccuracies if interpolating between multiple reference patterns if one pattern has a value rounded to 0 and the other does not #TODO: option 1: this issue can be fixed by moving this to after interpolation #TODO: option 2: Or we can below assign to preprocessed_reference_pattern rather than standardized_reference_patterns and then use that in data analysis (Note that interpolate would continue to use standardized_reference_patterns as well as preprocess the output) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) @@ -3234,7 +3234,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for minimalReferenceValue feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -4029,7 +4029,7 @@ def SLSUniqueFragments(molecules,monitored_reference_intensities,reciprocal_matc chosenMolecule = None tuplesOfUniqueFragmentsList = [] - if G.minimalReferenceValue == "yes": #We only will do some filtering things if it's requested. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only will do some filtering things if it's requested. #Before going forward, we're going to make a variable called remaining_referenceSignificantFragmentThresholds, using a function. def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFragmentThresholds, molecules_unedited, remaining_molecules_SLS): remaining_referenceSignificantFragmentThresholds = list(copy.deepcopy(referenceSignificantFragmentThresholds)) @@ -4071,12 +4071,12 @@ def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFra #consideredMolecule = remaining_molecules_SLS[moleculeIndexOfUniqueIntensity] #This is for debugging purposes, this can be printed. #For debugging, also print remaining_reference_intensities_SLS and massFragmentIndex_i. #However, now we have a few lines of code to check if we are above the referenceSignificantFragmentThresholds. - if G.minimalReferenceValue == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. if (max(remaining_reference_intensities_SLS[massFragmentIndex_i]) < remaining_referenceSignificantFragmentThresholds[moleculeIndexOfUniqueIntensity]): #This allows separate referenceSignificantFragmentThresholds for each molecule. significantFragment = False #Set to false if the fragment is too small. else: significantFragment = True #This means the fragment is greater than or equal to the threshold for significance. - if G.minimalReferenceValue != "yes": #if the option is not selected, then all fragments are considered significant. + if G.applyReferenceMassFragmentsThresholds != "yes": #if the option is not selected, then all fragments are considered significant. significantFragment = True if significantFragment == True: #now make a tuple with the unique standardized intensity in the front so we can sort by that @@ -4957,7 +4957,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['minimalReferenceValue']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -5576,8 +5576,8 @@ def PopulateLogFile(): f6.write('rpcMoleculesToChange = %s \n'%(G.rpcMoleculesToChange)) f6.write('rpcMoleculesToChangeMF = %s \n'%(G.rpcMoleculesToChangeMF)) f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) - if G.minimalReferenceValue == 'yes': - f6.write('minimalReferenceValue = %s \n'%(G.minimalReferenceValue)) + if G.applyReferenceMassFragmentsThresholds == 'yes': + f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': @@ -6101,7 +6101,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['minimalReferenceValue']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index f327a3713..4eaf1afdc 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -182,11 +182,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index 16dbe89bc..2fdc34d8b 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -140,8 +140,8 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.rpcMoleculesToChange,chosenMoleculesForParsing,'rpcMoleculesToChange','chosenMolecules') #Reference Mass Fragmentation Threshold - parse.strCheck(currentUserInput.minimalReferenceValue,'minimalReferenceValue') - if currentUserInput.minimalReferenceValue == 'yes': #If using reference mass fragmentation threshold + parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') + if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) @@ -361,9 +361,9 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcTimeRanges'] = UserChoices['extractReferencePatternFromDataOption']['rpcTimeRanges'] SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] - SettingsVDictionary['minimalReferenceValue'] = UserChoices['minimalReferenceValue']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['minimalReferenceValue']['referenceValueThreshold'] - SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] + SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] + SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on'] SettingsVDictionary['massesToLowerBoundThresholdFilter'] = UserChoices['lowerBoundThresholdChooser']['massesToLowerBoundThresholdFilter'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index a785a7bce..307b0aa44 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -381,7 +381,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ''' - if G.minimalReferenceValue !='yes': + if G.applyReferenceMassFragmentsThresholds !='yes': print("Warning: The ABCDetermination will occur without threshold filtering, since that setting is off.") if G.extractReferencePatternFromDataOption == 'yes': @@ -393,7 +393,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['molecules']=molecules ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ReferencePatternDesiredTuningDict = {} @@ -401,7 +401,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['molecules']=molecules ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. - if G.minimalReferenceValue =='yes': + if G.applyReferenceMassFragmentsThresholds =='yes': ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) ''' @@ -1933,7 +1933,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): #TODO: the minimal reference value can cause inaccuracies if interpolating between multiple reference patterns if one pattern has a value rounded to 0 and the other does not #TODO: option 1: this issue can be fixed by moving this to after interpolation #TODO: option 2: Or we can below assign to preprocessed_reference_pattern rather than standardized_reference_patterns and then use that in data analysis (Note that interpolate would continue to use standardized_reference_patterns as well as preprocess the output) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) @@ -1943,7 +1943,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): #One could move this function prior to threshold filtering however then correction values would not be correctly calculated for interpolated reference patterns #We are not sure there are any other reasons we can't move this function call. However, there may be some care needed when using uncertainties. ReferenceData.correction_values, ReferenceData.correction_values_relative_uncertainties = CorrectionValuesObtain(ReferenceData) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. There is an implied return in global variable. G.currentReferenceDataUnfiltered.correction_values, G.currentReferenceDataUnfiltered.correction_values_relative_uncertainties = CorrectionValuesObtain(G.currentReferenceDataUnfiltered) @@ -2243,7 +2243,7 @@ def PrepareReferenceObjectsAndCorrectionValues(ReferenceData, massesOfInterest=[ # based on the massesOfInterest, which is typically the ExperimentData.mass_fragment_numbers if len(massesOfInterest) > 0: ReferenceData = Populate_reciprocal_matching_correction_values(massesOfInterest,ReferenceData) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #if implicitSLS correction is being used, we need to do it for the unfiltered reference pattern also. G.currentReferenceDataUnfiltered = Populate_reciprocal_matching_correction_values(massesOfInterest,G.currentReferenceDataUnfiltered) #Exports the matching correction value @@ -2257,7 +2257,7 @@ def PrepareReferenceObjectsAndCorrectionValues(ReferenceData, massesOfInterest=[ ## (monitored_reference_intensities) so that it can potentially be applied to other arrays ## like ReferenceData.standardized_reference_patterns ReferenceData = UnnecessaryMoleculesDeleter(ReferenceData) - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #if implicitSLS correction is being used, we need to do it for the unfiltered reference pattern also. G.currentReferenceDataUnfiltered = UnnecessaryMoleculesDeleter(G.currentReferenceDataUnfiltered) ReferenceData.ExportCollector('UnnecessaryMoleculesDeleter') @@ -3628,7 +3628,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if len(combinations) == 0:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for minimalReferenceValue feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -4431,7 +4431,7 @@ def SLSUniqueFragments(molecules,monitored_reference_intensities,reciprocal_matc chosenMolecule = None tuplesOfUniqueFragmentsList = [] - if G.minimalReferenceValue == "yes": #We only will do some filtering things if it's requested. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only will do some filtering things if it's requested. #Before going forward, we're going to make a variable called remaining_referenceSignificantFragmentThresholds, using a function. def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFragmentThresholds, molecules_unedited, remaining_molecules_SLS): remaining_referenceSignificantFragmentThresholds = list(copy.deepcopy(referenceSignificantFragmentThresholds)) @@ -4471,12 +4471,12 @@ def get_remaining_referenceSignificantFragmentThresholds(referenceSignificantFra #consideredMolecule = remaining_molecules_SLS[moleculeIndexOfUniqueIntensity] #This is for debugging purposes, this can be printed. #For debugging, also print remaining_reference_intensities_SLS and massFragmentIndex_i. #However, now we have a few lines of code to check if we are above the referenceSignificantFragmentThresholds. - if G.minimalReferenceValue == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. + if G.applyReferenceMassFragmentsThresholds == "yes": #We only check for the remaining_referenceSignificantFragmentThresholds if this option has been chosen. if (max(remaining_reference_intensities_SLS[massFragmentIndex_i]) < remaining_referenceSignificantFragmentThresholds[moleculeIndexOfUniqueIntensity]): #This allows separate referenceSignificantFragmentThresholds for each molecule. significantFragment = False #Set to false if the fragment is too small. else: significantFragment = True #This means the fragment is greater than or equal to the threshold for significance. - if G.minimalReferenceValue != "yes": #if the option is not selected, then all fragments are considered significant. + if G.applyReferenceMassFragmentsThresholds != "yes": #if the option is not selected, then all fragments are considered significant. significantFragment = True if significantFragment == True: #now make a tuple with the unique standardized intensity in the front so we can sort by that @@ -5400,7 +5400,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['minimalReferenceValue']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -6022,8 +6022,8 @@ def PopulateLogFile(): f6.write('rpcMoleculesToChange = %s \n'%(G.rpcMoleculesToChange)) f6.write('rpcMoleculesToChangeMF = %s \n'%(G.rpcMoleculesToChangeMF)) f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) - if G.minimalReferenceValue == 'yes': - f6.write('minimalReferenceValue = %s \n'%(G.minimalReferenceValue)) + if G.applyReferenceMassFragmentsThresholds == 'yes': + f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': @@ -6641,7 +6641,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['minimalReferenceValue']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/README.txt b/README.txt index 0e7f5ad62..f1a9cc8b2 100644 --- a/README.txt +++ b/README.txt @@ -17,7 +17,7 @@ Suggested Procedure for Solving Time Series Data of Mass Signals 2) Create an MSRESOLVE run with SLS Unique and see what masse MSRESOLVE chooses, with ExportedSLSUniqueMassesUsedInSolvingMolecules. 3) If unsatisfied, start narrowing things down with chosen masses. 4) Also start using some reference file threshold filtering . -a. UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [1.0] #this is what I am suggesting that you use. +a. UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [1.0] #this is what I am suggesting that you use. 5) If the application warrants doing so, include more sophisticated features of MSRESOLVE, such as mass spectrum tuning correction. diff --git a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py index b3bf186e7..c41b643f9 100644 --- a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py +++ b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py @@ -143,7 +143,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] @@ -240,7 +240,7 @@ 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', - 'rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', + 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', 'uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniquePrint','SLSUniqueExport','concentrationFinder','molecule','moleculeSignal','massNumber','moleculeConcentration', diff --git a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py index 482cfa3ea..0cbc13c86 100644 --- a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py +++ b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py @@ -928,7 +928,7 @@ def ReferenceInputPreProcessing(ReferenceData): G.tuningCorrection) ReferenceData.ExportCollector('CorrectionValueCorrector') - if G.minimalReferenceValue == 'yes': + if G.applyReferenceMassFragmentsThresholds == 'yes': ReferenceData.standardized_reference_intensities = ReferenceThreshold(ReferenceData.standardized_reference_intensities,G.referenceValueThreshold) ReferenceData.ExportCollector('ReferenceThreshold') @@ -1688,7 +1688,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for minimalReferenceValue feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,moleculenum]) @@ -3062,8 +3062,8 @@ def PopulateLogFile(): f6.write('rpcMoleculesToChange = %s \n'%(G.rpcMoleculesToChange)) f6.write('rpcMoleculesToChangeMF = %s \n'%(G.rpcMoleculesToChangeMF)) f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) - if G.minimalReferenceValue == 'yes': - f6.write('minimalReferenceValue = %s \n'%(G.minimalReferenceValue)) + if G.applyReferenceMassFragmentsThresholds == 'yes': + f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) diff --git a/Todo/SLS Common vs. Unique Bug/UserInput.py b/Todo/SLS Common vs. Unique Bug/UserInput.py index 98dfb3b3a..3c329a3ea 100644 --- a/Todo/SLS Common vs. Unique Bug/UserInput.py +++ b/Todo/SLS Common vs. Unique Bug/UserInput.py @@ -144,7 +144,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'yes' +applyReferenceMassFragmentsThresholds= 'yes' referenceValueThreshold = [4.9] @@ -247,7 +247,7 @@ 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', - 'rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', + 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', 'uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniquePrint','SLSUniqueExport','concentrationFinder','molecule','moleculeSignal','massNumber','moleculeConcentration', diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py index a1116967e..395e67cc1 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py index 5ba22ddc4..2a1cfc4f3 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ExtractReferencePatternFromData/test_1_input.py b/UnitTests/ExtractReferencePatternFromData/test_1_input.py index b48855a13..d6a9883de 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_1_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_1_input.py @@ -136,7 +136,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ExtractReferencePatternFromData/test_2_input.py b/UnitTests/ExtractReferencePatternFromData/test_2_input.py index c5571a270..1d487fd8c 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_2_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_2_input.py @@ -136,7 +136,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ExtractReferencePatternFromData/test_3_input.py b/UnitTests/ExtractReferencePatternFromData/test_3_input.py index 7634d9894..1f61d0062 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_3_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_3_input.py @@ -136,7 +136,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ExtractReferencePatternFromData/test_4_input.py b/UnitTests/ExtractReferencePatternFromData/test_4_input.py index df6051ec7..9a56aef68 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_4_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_4_input.py @@ -125,7 +125,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ExtractReferencePatternFromData/test_5_input.py b/UnitTests/ExtractReferencePatternFromData/test_5_input.py index 17ec09e37..d024bda2d 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_5_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_5_input.py @@ -125,7 +125,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ExtractReferencePatternFromData/test_6_input.py b/UnitTests/ExtractReferencePatternFromData/test_6_input.py index 7a028974e..1938b1ba5 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_6_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_6_input.py @@ -125,7 +125,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index f32e0ccfa..0222bead0 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -181,11 +181,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py index 20c5dc719..842e8b744 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'yes' +applyReferenceMassFragmentsThresholds= 'yes' referenceValueThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py index 4621aa373..fa79773a3 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'yes' +applyReferenceMassFragmentsThresholds= 'yes' referenceValueThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py index 2c3b7549e..73a0474f7 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py index d2a430841..c2533b488 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py index 0d5bc16f1..4d8a8ce56 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py index 162bd340f..4fdd24956 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py index 695f5aef7..2307cb619 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py index 0188bfd74..8b2530614 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py index f0a7b12a4..0b5924daf 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'yes' +applyReferenceMassFragmentsThresholds= 'yes' referenceValueThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py index 19a561ea0..f4e97ac88 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py @@ -146,7 +146,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'yes' +applyReferenceMassFragmentsThresholds= 'yes' referenceValueThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index 97dc9e56a..cf931662c 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py index 90bb280cd..8a980e1ec 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py @@ -133,7 +133,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py index 7e820d87c..3756af6b8 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py @@ -133,7 +133,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py index 4ebd79be2..e3d28f43d 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py @@ -133,7 +133,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/ReferencePatternTimeChooser/test_2_input.py b/UnitTests/ReferencePatternTimeChooser/test_2_input.py index 3e6831b3c..edb32d8fe 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_2_input.py +++ b/UnitTests/ReferencePatternTimeChooser/test_2_input.py @@ -133,7 +133,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/TuningCorrector/test_1.py b/UnitTests/TuningCorrector/test_1.py index ac8817032..ef21a9ac7 100644 --- a/UnitTests/TuningCorrector/test_1.py +++ b/UnitTests/TuningCorrector/test_1.py @@ -40,8 +40,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'no' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' MSRESOLVE.G.referenceValueThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff index 3c6221ec9..1ecc06292 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeStart = 176 #start time (-int) MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff index 86482b118..ad3b964b8 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeStart = 176 #start time (-int) MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'no' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' MSRESOLVE.G.referenceValueThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff index 3c6221ec9..1ecc06292 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeStart = 176 #start time (-int) MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_10.py b/UnitTests/TuningCorrector/test_10.py index b3dad9d9d..2b448a719 100644 --- a/UnitTests/TuningCorrector/test_10.py +++ b/UnitTests/TuningCorrector/test_10.py @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff index 3c6221ec9..1ecc06292 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeStart = 176 #start time (-int) MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff index 9b9c6e39b..4e4a2a8cc 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeStart = 176 #start time (-int) MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff index 9b9c6e39b..4e4a2a8cc 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeStart = 176 #start time (-int) MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_11.py b/UnitTests/TuningCorrector/test_11.py index d2473e1ab..1aa39e81c 100644 --- a/UnitTests/TuningCorrector/test_11.py +++ b/UnitTests/TuningCorrector/test_11.py @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_2.py b/UnitTests/TuningCorrector/test_2.py index f0890937f..378a8271b 100644 --- a/UnitTests/TuningCorrector/test_2.py +++ b/UnitTests/TuningCorrector/test_2.py @@ -40,8 +40,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_3.py b/UnitTests/TuningCorrector/test_3.py index 5b27abd36..de4a88e30 100644 --- a/UnitTests/TuningCorrector/test_3.py +++ b/UnitTests/TuningCorrector/test_3.py @@ -42,8 +42,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'no' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' MSRESOLVE.G.referenceValueThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_4.py b/UnitTests/TuningCorrector/test_4.py index 6b9af1293..dab06ff84 100644 --- a/UnitTests/TuningCorrector/test_4.py +++ b/UnitTests/TuningCorrector/test_4.py @@ -40,8 +40,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'no' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' MSRESOLVE.G.referenceValueThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_5.py b/UnitTests/TuningCorrector/test_5.py index 5a4ea0629..8b17dcabd 100644 --- a/UnitTests/TuningCorrector/test_5.py +++ b/UnitTests/TuningCorrector/test_5.py @@ -39,8 +39,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'no' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' MSRESOLVE.G.referenceValueThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_6.py b/UnitTests/TuningCorrector/test_6.py index c2fd683c7..650d5cc3e 100644 --- a/UnitTests/TuningCorrector/test_6.py +++ b/UnitTests/TuningCorrector/test_6.py @@ -40,8 +40,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'no' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' MSRESOLVE.G.referenceValueThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_7.py b/UnitTests/TuningCorrector/test_7.py index e2d3e5e22..a988b2fa9 100644 --- a/UnitTests/TuningCorrector/test_7.py +++ b/UnitTests/TuningCorrector/test_7.py @@ -42,8 +42,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_8.py b/UnitTests/TuningCorrector/test_8.py index 92b21bcf5..1d52d21e4 100644 --- a/UnitTests/TuningCorrector/test_8.py +++ b/UnitTests/TuningCorrector/test_8.py @@ -41,8 +41,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrector/test_9.py b/UnitTests/TuningCorrector/test_9.py index 09c30a446..49a46e2d0 100644 --- a/UnitTests/TuningCorrector/test_9.py +++ b/UnitTests/TuningCorrector/test_9.py @@ -42,8 +42,8 @@ MSRESOLVE.G.timeRangeFinish = 178 #start time (-int) MSRESOLVE.G.dataSmootherYorN = 'no' -#will use minimalReferenceValue (single value means it will be applied to all molecules) -MSRESOLVE.G.minimalReferenceValue= 'yes' +#will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) +MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' MSRESOLVE.G.referenceValueThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index 65e5a2553..50fbbca19 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -182,11 +182,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index a523ebe35..ab806210a 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -184,11 +184,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index ae6676a9d..d0fe5362d 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -184,11 +184,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index 2f7c14a7f..d8f5f55f4 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -184,11 +184,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index 339202a67..563abb13a 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -185,11 +185,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index 1c6b663a0..35da21ad2 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -185,11 +185,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py index bd5ccb28a..8b76fb85b 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py @@ -144,7 +144,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py index e0d87cdc3..75d037f6f 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py @@ -144,7 +144,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks -minimalReferenceValue= 'no' +applyReferenceMassFragmentsThresholds= 'no' referenceValueThreshold = [6.0] diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index 2f4fd64be..a1c2d1bce 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index 40f615598..f1efea640 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index ba9f9b29d..16cc8e2b3 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -57,7 +57,7 @@ rpcMoleculesToChange = ['Ethylene'] rpcMoleculesToChangeMF = [[2, 4, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 32, 44]] rpcTimeRanges = [[6745.0, 8000]] -minimalReferenceValue = 'yes' +applyReferenceMassFragmentsThresholds = 'yes' referenceValueThreshold = [1.0] referenceSignificantFragmentThresholds = [3.0] lowerBoundThresholdChooser = 'no' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index e6b78ae37..5b1fdfccb 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -57,7 +57,7 @@ rpcMoleculesToChange = ['Ethylene'] rpcMoleculesToChangeMF = [[2, 4, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 32, 44]] rpcTimeRanges = [[6745.0, 8000]] -minimalReferenceValue = 'yes' +applyReferenceMassFragmentsThresholds = 'yes' referenceValueThreshold = [1.0] referenceSignificantFragmentThresholds = [1.0, 3.0, 3.0] lowerBoundThresholdChooser = 'no' @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index 63eda409a..50b2ff9ce 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index 1d525e93b..c28bf2de0 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index df4b1b629..46b25035b 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index 0aaeb526d..fc517880c 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index 731d9d403..9b85f0a64 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [0.1] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index 9d665a6c7..5c2530f2b 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index 32397c161..68c082b3e 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [0.1] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index 0d8098bbc..fb46ac78d 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -183,11 +183,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [0.1] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [2.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index cdf5f520a..d86c7566f 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -183,11 +183,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [0.1] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [2.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index 60810fd77..947ddcebd 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -182,11 +182,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [0.1] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [2.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index ed56a5597..95cae1c3e 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index 18ea74224..3d2fc3b48 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index 8e39035a8..0577ba78e 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index f6b103dc7..4fb2c9755 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index 690757bd7..7c8a19bc0 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index 8b42ac58a..c4580b1bf 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index 6ddd63c20..d51595498 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index e9c4ea617..82c080cb2 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [2.0] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index ba0528799..51738bf02 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -180,11 +180,11 @@ ] #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'yes' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [0.5] -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [5.0] +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.5] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index 37c79b79d..99d0b507a 100644 --- a/UserInput.py +++ b/UserInput.py @@ -186,11 +186,11 @@ ] #Make sure every mass you listed was collected otherwise there will be an error. #//Reference Mass Fragmentation Threshold// -UserChoices['minimalReferenceValue'] = {} #initialize the minimalReferenceValue container +UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks -UserChoices['minimalReferenceValue']['on'] = 'no' -UserChoices['minimalReferenceValue']['referenceValueThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. -UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] = [6.0] #typical values are between 5 and 50. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This setting causes MSRESOLVE to favor larger intensity reference peaks (above the number provided) during solving. +UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' +UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. +UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #typical values are between 5 and 50. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This setting causes MSRESOLVE to favor larger intensity reference peaks (above the number provided) during solving. #//Data Threshold Filter// UserChoices['lowerBoundThresholdChooser'] = {} #initialize the lowerBoundThresholdChooser container @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','minimalReferenceValue','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index fada716a3..f638d35dd 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -145,8 +145,8 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.rpcMoleculesToChange,chosenMoleculesForParsing,'rpcMoleculesToChange','chosenMolecules') #Reference Mass Fragmentation Threshold - parse.strCheck(currentUserInput.minimalReferenceValue,'minimalReferenceValue') - if currentUserInput.minimalReferenceValue == 'yes': #If using reference mass fragmentation threshold + parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') + if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) @@ -268,7 +268,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t print("Incompatible choice detected: forcing SLSUniqueExport to no.") if 'implicitSLScorrection' in UserChoices['dataAnalysisMethods']: - if UserChoices['minimalReferenceValue']['on'] =='no': #Turn off SLS implicit if the mnimalReferenceValue is not being used. + if UserChoices['applyReferenceMassFragmentsThresholds']['on'] =='no': #Turn off SLS implicit if the mnimalReferenceValue is not being used. UserChoices['dataAnalysisMethods']['implicitSLScorrection'] = False if UserChoices['dataAnalysisMethods']['implicitSLScorrection'] == True: if (UserChoices['dataAnalysisMethods']['uniqueOrCommon'] != 'unique'): @@ -423,9 +423,9 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcTimeRanges'] = UserChoices['extractReferencePatternFromDataOption']['rpcTimeRanges'] SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] - SettingsVDictionary['minimalReferenceValue'] = UserChoices['minimalReferenceValue']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['minimalReferenceValue']['referenceValueThreshold'] - SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['minimalReferenceValue']['referenceSignificantFragmentThresholds'] + SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] + SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on'] SettingsVDictionary['massesToLowerBoundThresholdFilter'] = UserChoices['lowerBoundThresholdChooser']['massesToLowerBoundThresholdFilter'] From f1c2b0df1d6e412b03aa8f000904b5828ac6a653 Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 12:37:24 -0400 Subject: [PATCH 8/9] rawSignalThresholdMethod --> applyRawSignalThresholds --- DefaultUserInput.py | 16 ++++++++-------- ExampleAnalysis/DefaultUserInput.py | 16 ++++++++-------- ExampleAnalysis/MSRESOLVE.py | 10 +++++----- ExampleAnalysis/UserInput.py | 16 ++++++++-------- ExampleAnalysis/userInputValidityFunctions.py | 16 ++++++++-------- ExampleReferenceExtraction/DefaultUserInput.py | 16 ++++++++-------- ExampleReferenceExtraction/MSRESOLVE.py | 10 +++++----- ExampleReferenceExtraction/UserInput.py | 16 ++++++++-------- .../userInputValidityFunctions.py | 16 ++++++++-------- .../DefaultUserInput.py | 16 ++++++++-------- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 10 +++++----- .../MSRESOLVEBad1.py | 10 +++++----- .../MSRESOLVEPrevious.py | 10 +++++----- ExampleTuningCorrectorGasMixture/UserInput.py | 16 ++++++++-------- .../userInputValidityFunctions.py | 16 ++++++++-------- MSRESOLVE.py | 10 +++++----- .../DefaultUserInput.py | 4 ++-- Todo/SLS Common vs. Unique Bug/MSRESOLVE.py | 10 +++++----- Todo/SLS Common vs. Unique Bug/UserInput.py | 4 ++-- .../bestMassFragChooser.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../test_3_input.py | 2 +- .../test_4_input.py | 2 +- .../test_5_input.py | 2 +- .../test_6_input.py | 2 +- .../test_1_Input_Brute_Finisher.py | 16 ++++++++-------- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/NegativeAnalyzer/test_1_Input.py | 16 ++++++++-------- .../ReferencePatternTimeChooser/test_1_inputA.py | 2 +- .../ReferencePatternTimeChooser/test_1_inputB.py | 2 +- .../ReferencePatternTimeChooser/test_1_inputC.py | 2 +- .../ReferencePatternTimeChooser/test_2_input.py | 2 +- .../UserInputGasMixture.py | 16 ++++++++-------- .../UserInputGasMixture2.py | 16 ++++++++-------- .../UserInputGasMixture3.py | 16 ++++++++-------- .../UserInputGasMixture4.py | 16 ++++++++-------- .../XYXYReferencePattern/test_1_inputXYXY.py | 16 ++++++++-------- .../XYXYReferencePattern/test_1_inputXYYY.py | 16 ++++++++-------- .../test_1.py | 2 +- .../test_1_input.py | 2 +- .../test_2.py | 2 +- .../test_2_input.py | 2 +- UnitTests/implicitSLScorrection/test_1_Input.py | 16 ++++++++-------- UnitTests/implicitSLScorrection/test_2_Input.py | 16 ++++++++-------- .../test_1_UserInput.py | 4 ++-- .../test_2_UserInput.py | 4 ++-- UnitTests/slsCommon/test_1_Input.py | 16 ++++++++-------- .../test_1_Input.py | 16 ++++++++-------- .../test_2.py | 2 +- .../test_2_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_10_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_11_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_12_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_13_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_14_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_15_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_16_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_1_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_2_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_3_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_4_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_5_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_6_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_7_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_8_Input.py | 16 ++++++++-------- UnitTests/uncertainties/test_9_Input.py | 16 ++++++++-------- UserInput.py | 16 ++++++++-------- userInputValidityFunctions.py | 16 ++++++++-------- 80 files changed, 399 insertions(+), 399 deletions(-) diff --git a/DefaultUserInput.py b/DefaultUserInput.py index 99d0b507a..a3da682d4 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -218,18 +218,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index c41cab466..4b9384896 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -211,18 +211,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index 51ef66d5a..de95487ca 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -4169,7 +4169,7 @@ def RawSignalThresholdFilter (distinguished,reciprocal_matching_correction_value monitored_reference_intensities_copy = monitored_reference_intensities rawsignalsarray_copy = remaining_rawsignals_SLS summation = sum(rawsignalsarray_copy) - [rawSignalThresholdMethod,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList + [applyRawSignalThresholds,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList #this section of the code enables the function to eliminate from the raw signal array (for the purpose of this function only) #the highest value in the array, if it makes up over 90 percent of the raw signals present. This is useful because if one of #the signals does become this great then it will eliminate all the other signals present when it becomes very high @@ -5007,8 +5007,8 @@ def PopulateLogFile(): f6.write('dataSmootherTimeRadius = %s \n'%(G.dataSmootherTimeRadius)) f6.write('dataSmootherPointRadius = %s \n'%(G.dataSmootherPointRadius)) f6.write('dataSmootherHeadersToConfineTo = %s \n'%(G.dataSmootherHeadersToConfineTo)) - if G.rawSignalThresholdMethod == 'yes': - f6.write('rawSignalThresholdMethod = %s \n'%(G.rawSignalThresholdMethod)) + if G.applyRawSignalThresholds == 'yes': + f6.write('applyRawSignalThresholds = %s \n'%(G.applyRawSignalThresholds)) f6.write('rawSignalThresholdValue = %s \n'%(G.rawSignalThresholdValue)) f6.write('sensitivityThresholdValue = %s \n'%(G.sensitivityThresholdValue)) f6.write('rawSignalThresholdDivider = %s \n'%(G.rawSignalThresholdDivider)) @@ -5337,7 +5337,7 @@ def main(): G.csvFile, G.moleculesToRestrict, G.csvFileName,G.dataUpperBound, G.dataLowerBound, G.bruteIncrements, G.permutationNum] SLSChoices = [G.uniqueOrCommon, G.slsFinish, G.distinguished] - ThresholdList = [G.rawSignalThresholdMethod, G.rawSignalThresholdValue, G.sensitivityThresholdValue, + ThresholdList = [G.applyRawSignalThresholds, G.rawSignalThresholdValue, G.sensitivityThresholdValue, G.rawSignalThresholdDivider, G.rawSignalThresholdLimit, G.rawSignalThresholdLimitPercent] currentReferenceData = ReferenceDataList[0] #TODO this line is placeholder by charles to fix currentRefenceData issue until Alex has a better solution @@ -5414,7 +5414,7 @@ def main(): #TODO continued: I am putting some variables here to make that process easier by getting some of it done already, then only the user input file needs to be changed. #This feature is intended to remove molecules that have major fragments not observed. previously, it was done in a more complicated way. # now, to simplify things, is being used as a filter that simply sets standardized intensities in the reference patterns to zero. - G.excludeMoleculesIfSignificantFragmentNotObserved = G.rawSignalThresholdMethod + G.excludeMoleculesIfSignificantFragmentNotObserved = G.applyRawSignalThresholds G.minimumSignalRequired = G.rawSignalThresholdValue G.minimumStandardizedReferenceHeightToBeSignificant = G.sensitivityThresholdValue if G.excludeMoleculesIfSignificantFragmentNotObserved == 'yes': diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index f19a4fa88..38dd671ae 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -211,18 +211,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index 5fd98e453..b1e8772a3 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -156,9 +156,9 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.dataSmootherHeadersToConfineTo,chosenMassFragmentsForParsing,'dataSmootherHeadersToConfineTo','chosenMolecules') #Raw Signal Threshold - parse.strCheck(currentUserInput.rawSignalThresholdMethod,'rawSignalThresholdMethod') + parse.strCheck(currentUserInput.applyRawSignalThresholds,'applyRawSignalThresholds') parse.strCheck(currentUserInput.rawSignalThresholdLimit,'rawSignalThresholdLimit') - if currentUserInput.rawSignalThresholdMethod == 'yes': #If using rawSignalThresholdMethod + if currentUserInput.applyRawSignalThresholds == 'yes': #If using applyRawSignalThresholds #raw signal threshold value, sensitivity value, raw signal threshold divider, and raw signal threshold limit percent are all lists currentUserInput.rawSignalThresholdValue = parse.listCast(currentUserInput.rawSignalThresholdValue) currentUserInput.sensitivityThresholdValue = parse.listCast(currentUserInput.sensitivityThresholdValue) @@ -341,12 +341,12 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['dataSmootherHeadersToConfineTo'] = UserChoices['dataSmootherYorN']['dataSmootherHeadersToConfineTo'] SettingsVDictionary['polynomialOrder'] = UserChoices['dataSmootherYorN']['polynomialOrder'] - SettingsVDictionary['rawSignalThresholdMethod'] = UserChoices['rawSignalThresholdMethod']['on'] - SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] - SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] - SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] - SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] - SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] + SettingsVDictionary['applyRawSignalThresholds'] = UserChoices['applyRawSignalThresholds']['on'] + SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] + SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] + SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] + SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] + SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] SettingsVDictionary['calculateUncertaintiesInConcentrations'] = UserChoices['uncertainties']['calculateUncertaintiesInConcentrations'] SettingsVDictionary['referenceFileUncertainties'] = UserChoices['uncertainties']['referenceFileUncertainties'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index c41cab466..4b9384896 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -211,18 +211,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index 51ef66d5a..de95487ca 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -4169,7 +4169,7 @@ def RawSignalThresholdFilter (distinguished,reciprocal_matching_correction_value monitored_reference_intensities_copy = monitored_reference_intensities rawsignalsarray_copy = remaining_rawsignals_SLS summation = sum(rawsignalsarray_copy) - [rawSignalThresholdMethod,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList + [applyRawSignalThresholds,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList #this section of the code enables the function to eliminate from the raw signal array (for the purpose of this function only) #the highest value in the array, if it makes up over 90 percent of the raw signals present. This is useful because if one of #the signals does become this great then it will eliminate all the other signals present when it becomes very high @@ -5007,8 +5007,8 @@ def PopulateLogFile(): f6.write('dataSmootherTimeRadius = %s \n'%(G.dataSmootherTimeRadius)) f6.write('dataSmootherPointRadius = %s \n'%(G.dataSmootherPointRadius)) f6.write('dataSmootherHeadersToConfineTo = %s \n'%(G.dataSmootherHeadersToConfineTo)) - if G.rawSignalThresholdMethod == 'yes': - f6.write('rawSignalThresholdMethod = %s \n'%(G.rawSignalThresholdMethod)) + if G.applyRawSignalThresholds == 'yes': + f6.write('applyRawSignalThresholds = %s \n'%(G.applyRawSignalThresholds)) f6.write('rawSignalThresholdValue = %s \n'%(G.rawSignalThresholdValue)) f6.write('sensitivityThresholdValue = %s \n'%(G.sensitivityThresholdValue)) f6.write('rawSignalThresholdDivider = %s \n'%(G.rawSignalThresholdDivider)) @@ -5337,7 +5337,7 @@ def main(): G.csvFile, G.moleculesToRestrict, G.csvFileName,G.dataUpperBound, G.dataLowerBound, G.bruteIncrements, G.permutationNum] SLSChoices = [G.uniqueOrCommon, G.slsFinish, G.distinguished] - ThresholdList = [G.rawSignalThresholdMethod, G.rawSignalThresholdValue, G.sensitivityThresholdValue, + ThresholdList = [G.applyRawSignalThresholds, G.rawSignalThresholdValue, G.sensitivityThresholdValue, G.rawSignalThresholdDivider, G.rawSignalThresholdLimit, G.rawSignalThresholdLimitPercent] currentReferenceData = ReferenceDataList[0] #TODO this line is placeholder by charles to fix currentRefenceData issue until Alex has a better solution @@ -5414,7 +5414,7 @@ def main(): #TODO continued: I am putting some variables here to make that process easier by getting some of it done already, then only the user input file needs to be changed. #This feature is intended to remove molecules that have major fragments not observed. previously, it was done in a more complicated way. # now, to simplify things, is being used as a filter that simply sets standardized intensities in the reference patterns to zero. - G.excludeMoleculesIfSignificantFragmentNotObserved = G.rawSignalThresholdMethod + G.excludeMoleculesIfSignificantFragmentNotObserved = G.applyRawSignalThresholds G.minimumSignalRequired = G.rawSignalThresholdValue G.minimumStandardizedReferenceHeightToBeSignificant = G.sensitivityThresholdValue if G.excludeMoleculesIfSignificantFragmentNotObserved == 'yes': diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index 8f21ad82a..d41d870de 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -211,18 +211,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index 5fd98e453..b1e8772a3 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -156,9 +156,9 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.dataSmootherHeadersToConfineTo,chosenMassFragmentsForParsing,'dataSmootherHeadersToConfineTo','chosenMolecules') #Raw Signal Threshold - parse.strCheck(currentUserInput.rawSignalThresholdMethod,'rawSignalThresholdMethod') + parse.strCheck(currentUserInput.applyRawSignalThresholds,'applyRawSignalThresholds') parse.strCheck(currentUserInput.rawSignalThresholdLimit,'rawSignalThresholdLimit') - if currentUserInput.rawSignalThresholdMethod == 'yes': #If using rawSignalThresholdMethod + if currentUserInput.applyRawSignalThresholds == 'yes': #If using applyRawSignalThresholds #raw signal threshold value, sensitivity value, raw signal threshold divider, and raw signal threshold limit percent are all lists currentUserInput.rawSignalThresholdValue = parse.listCast(currentUserInput.rawSignalThresholdValue) currentUserInput.sensitivityThresholdValue = parse.listCast(currentUserInput.sensitivityThresholdValue) @@ -341,12 +341,12 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['dataSmootherHeadersToConfineTo'] = UserChoices['dataSmootherYorN']['dataSmootherHeadersToConfineTo'] SettingsVDictionary['polynomialOrder'] = UserChoices['dataSmootherYorN']['polynomialOrder'] - SettingsVDictionary['rawSignalThresholdMethod'] = UserChoices['rawSignalThresholdMethod']['on'] - SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] - SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] - SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] - SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] - SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] + SettingsVDictionary['applyRawSignalThresholds'] = UserChoices['applyRawSignalThresholds']['on'] + SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] + SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] + SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] + SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] + SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] SettingsVDictionary['calculateUncertaintiesInConcentrations'] = UserChoices['uncertainties']['calculateUncertaintiesInConcentrations'] SettingsVDictionary['referenceFileUncertainties'] = UserChoices['uncertainties']['referenceFileUncertainties'] diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index 12dea2fa5..c4155ed42 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -211,18 +211,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index 3f8d084ea..21b9b3476 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -4747,7 +4747,7 @@ def RawSignalThresholdFilter (distinguished,reciprocal_matching_correction_value monitored_reference_intensities_copy = monitored_reference_intensities rawsignalsarray_copy = remaining_rawsignals_SLS summation = sum(rawsignalsarray_copy) - [rawSignalThresholdMethod,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList + [applyRawSignalThresholds,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList #this section of the code enables the function to eliminate from the raw signal array (for the purpose of this function only) #the highest value in the array, if it makes up over 90 percent of the raw signals present. This is useful because if one of #the signals does become this great then it will eliminate all the other signals present when it becomes very high @@ -5587,8 +5587,8 @@ def PopulateLogFile(): f6.write('dataSmootherTimeRadius = %s \n'%(G.dataSmootherTimeRadius)) f6.write('dataSmootherPointRadius = %s \n'%(G.dataSmootherPointRadius)) f6.write('dataSmootherHeadersToConfineTo = %s \n'%(G.dataSmootherHeadersToConfineTo)) - if G.rawSignalThresholdMethod == 'yes': - f6.write('rawSignalThresholdMethod = %s \n'%(G.rawSignalThresholdMethod)) + if G.applyRawSignalThresholds == 'yes': + f6.write('applyRawSignalThresholds = %s \n'%(G.applyRawSignalThresholds)) f6.write('rawSignalThresholdValue = %s \n'%(G.rawSignalThresholdValue)) f6.write('sensitivityThresholdValue = %s \n'%(G.sensitivityThresholdValue)) f6.write('rawSignalThresholdDivider = %s \n'%(G.rawSignalThresholdDivider)) @@ -5947,7 +5947,7 @@ def main(): G.csvFile, G.moleculesToRestrict, G.csvFileName,G.dataUpperBound, G.dataLowerBound, G.bruteIncrements, G.permutationNum] SLSChoices = [G.uniqueOrCommon, G.slsFinish, G.distinguished] - ThresholdList = [G.rawSignalThresholdMethod, G.rawSignalThresholdValue, G.sensitivityThresholdValue, + ThresholdList = [G.applyRawSignalThresholds, G.rawSignalThresholdValue, G.sensitivityThresholdValue, G.rawSignalThresholdDivider, G.rawSignalThresholdLimit, G.rawSignalThresholdLimitPercent] currentReferenceData = ReferenceDataList[0] #TODO this line is placeholder by charles to fix currentRefenceData issue until Alex has a better solution @@ -6024,7 +6024,7 @@ def main(): #TODO continued: I am putting some variables here to make that process easier by getting some of it done already, then only the user input file needs to be changed. #This feature is intended to remove molecules that have major fragments not observed. previously, it was done in a more complicated way. # now, to simplify things, is being used as a filter that simply sets standardized intensities in the reference patterns to zero. - G.excludeMoleculesIfSignificantFragmentNotObserved = G.rawSignalThresholdMethod + G.excludeMoleculesIfSignificantFragmentNotObserved = G.applyRawSignalThresholds G.minimumSignalRequired = G.rawSignalThresholdValue G.minimumStandardizedReferenceHeightToBeSignificant = G.sensitivityThresholdValue if G.excludeMoleculesIfSignificantFragmentNotObserved == 'yes': diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index f3428c978..c1015c7be 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -4612,7 +4612,7 @@ def RawSignalThresholdFilter (distinguished,reciprocal_matching_correction_value monitored_reference_intensities_copy = monitored_reference_intensities rawsignalsarray_copy = remaining_rawsignals_SLS summation = sum(rawsignalsarray_copy) - [rawSignalThresholdMethod,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList + [applyRawSignalThresholds,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList #this section of the code enables the function to eliminate from the raw signal array (for the purpose of this function only) #the highest value in the array, if it makes up over 90 percent of the raw signals present. This is useful because if one of #the signals does become this great then it will eliminate all the other signals present when it becomes very high @@ -5452,8 +5452,8 @@ def PopulateLogFile(): f6.write('dataSmootherTimeRadius = %s \n'%(G.dataSmootherTimeRadius)) f6.write('dataSmootherPointRadius = %s \n'%(G.dataSmootherPointRadius)) f6.write('dataSmootherHeadersToConfineTo = %s \n'%(G.dataSmootherHeadersToConfineTo)) - if G.rawSignalThresholdMethod == 'yes': - f6.write('rawSignalThresholdMethod = %s \n'%(G.rawSignalThresholdMethod)) + if G.applyRawSignalThresholds == 'yes': + f6.write('applyRawSignalThresholds = %s \n'%(G.applyRawSignalThresholds)) f6.write('rawSignalThresholdValue = %s \n'%(G.rawSignalThresholdValue)) f6.write('sensitivityThresholdValue = %s \n'%(G.sensitivityThresholdValue)) f6.write('rawSignalThresholdDivider = %s \n'%(G.rawSignalThresholdDivider)) @@ -5799,7 +5799,7 @@ def main(): G.csvFile, G.moleculesToRestrict, G.csvFileName,G.dataUpperBound, G.dataLowerBound, G.bruteIncrements, G.permutationNum] SLSChoices = [G.uniqueOrCommon, G.slsFinish, G.distinguished] - ThresholdList = [G.rawSignalThresholdMethod, G.rawSignalThresholdValue, G.sensitivityThresholdValue, + ThresholdList = [G.applyRawSignalThresholds, G.rawSignalThresholdValue, G.sensitivityThresholdValue, G.rawSignalThresholdDivider, G.rawSignalThresholdLimit, G.rawSignalThresholdLimitPercent] currentReferenceData = ReferenceDataList[0] #TODO this line is placeholder by charles to fix currentRefenceData issue until Alex has a better solution @@ -5876,7 +5876,7 @@ def main(): #TODO continued: I am putting some variables here to make that process easier by getting some of it done already, then only the user input file needs to be changed. #This feature is intended to remove molecules that have major fragments not observed. previously, it was done in a more complicated way. # now, to simplify things, is being used as a filter that simply sets standardized intensities in the reference patterns to zero. - G.excludeMoleculesIfSignificantFragmentNotObserved = G.rawSignalThresholdMethod + G.excludeMoleculesIfSignificantFragmentNotObserved = G.applyRawSignalThresholds G.minimumSignalRequired = G.rawSignalThresholdValue G.minimumStandardizedReferenceHeightToBeSignificant = G.sensitivityThresholdValue if G.excludeMoleculesIfSignificantFragmentNotObserved == 'yes': diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index 98e9b3517..a2781e340 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -4751,7 +4751,7 @@ def RawSignalThresholdFilter (distinguished,reciprocal_matching_correction_value monitored_reference_intensities_copy = monitored_reference_intensities rawsignalsarray_copy = remaining_rawsignals_SLS summation = sum(rawsignalsarray_copy) - [rawSignalThresholdMethod,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList + [applyRawSignalThresholds,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList #this section of the code enables the function to eliminate from the raw signal array (for the purpose of this function only) #the highest value in the array, if it makes up over 90 percent of the raw signals present. This is useful because if one of #the signals does become this great then it will eliminate all the other signals present when it becomes very high @@ -5591,8 +5591,8 @@ def PopulateLogFile(): f6.write('dataSmootherTimeRadius = %s \n'%(G.dataSmootherTimeRadius)) f6.write('dataSmootherPointRadius = %s \n'%(G.dataSmootherPointRadius)) f6.write('dataSmootherHeadersToConfineTo = %s \n'%(G.dataSmootherHeadersToConfineTo)) - if G.rawSignalThresholdMethod == 'yes': - f6.write('rawSignalThresholdMethod = %s \n'%(G.rawSignalThresholdMethod)) + if G.applyRawSignalThresholds == 'yes': + f6.write('applyRawSignalThresholds = %s \n'%(G.applyRawSignalThresholds)) f6.write('rawSignalThresholdValue = %s \n'%(G.rawSignalThresholdValue)) f6.write('sensitivityThresholdValue = %s \n'%(G.sensitivityThresholdValue)) f6.write('rawSignalThresholdDivider = %s \n'%(G.rawSignalThresholdDivider)) @@ -5950,7 +5950,7 @@ def main(): G.csvFile, G.moleculesToRestrict, G.csvFileName,G.dataUpperBound, G.dataLowerBound, G.bruteIncrements, G.permutationNum] SLSChoices = [G.uniqueOrCommon, G.slsFinish, G.distinguished] - ThresholdList = [G.rawSignalThresholdMethod, G.rawSignalThresholdValue, G.sensitivityThresholdValue, + ThresholdList = [G.applyRawSignalThresholds, G.rawSignalThresholdValue, G.sensitivityThresholdValue, G.rawSignalThresholdDivider, G.rawSignalThresholdLimit, G.rawSignalThresholdLimitPercent] currentReferenceData = ReferenceDataList[0] #TODO this line is placeholder by charles to fix currentRefenceData issue until Alex has a better solution @@ -6027,7 +6027,7 @@ def main(): #TODO continued: I am putting some variables here to make that process easier by getting some of it done already, then only the user input file needs to be changed. #This feature is intended to remove molecules that have major fragments not observed. previously, it was done in a more complicated way. # now, to simplify things, is being used as a filter that simply sets standardized intensities in the reference patterns to zero. - G.excludeMoleculesIfSignificantFragmentNotObserved = G.rawSignalThresholdMethod + G.excludeMoleculesIfSignificantFragmentNotObserved = G.applyRawSignalThresholds G.minimumSignalRequired = G.rawSignalThresholdValue G.minimumStandardizedReferenceHeightToBeSignificant = G.sensitivityThresholdValue if G.excludeMoleculesIfSignificantFragmentNotObserved == 'yes': diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index 4eaf1afdc..4a4cbdc07 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -214,18 +214,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index 2fdc34d8b..eadde53dd 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -175,9 +175,9 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.dataSmootherHeadersToConfineTo,chosenMassFragmentsForParsing,'dataSmootherHeadersToConfineTo','chosenMolecules') #Raw Signal Threshold - parse.strCheck(currentUserInput.rawSignalThresholdMethod,'rawSignalThresholdMethod') + parse.strCheck(currentUserInput.applyRawSignalThresholds,'applyRawSignalThresholds') parse.strCheck(currentUserInput.rawSignalThresholdLimit,'rawSignalThresholdLimit') - if currentUserInput.rawSignalThresholdMethod == 'yes': #If using rawSignalThresholdMethod + if currentUserInput.applyRawSignalThresholds == 'yes': #If using applyRawSignalThresholds #raw signal threshold value, sensitivity value, raw signal threshold divider, and raw signal threshold limit percent are all lists currentUserInput.rawSignalThresholdValue = parse.listCast(currentUserInput.rawSignalThresholdValue) currentUserInput.sensitivityThresholdValue = parse.listCast(currentUserInput.sensitivityThresholdValue) @@ -377,12 +377,12 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['dataSmootherHeadersToConfineTo'] = UserChoices['dataSmootherYorN']['dataSmootherHeadersToConfineTo'] SettingsVDictionary['polynomialOrder'] = UserChoices['dataSmootherYorN']['polynomialOrder'] - SettingsVDictionary['rawSignalThresholdMethod'] = UserChoices['rawSignalThresholdMethod']['on'] - SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] - SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] - SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] - SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] - SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] + SettingsVDictionary['applyRawSignalThresholds'] = UserChoices['applyRawSignalThresholds']['on'] + SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] + SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] + SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] + SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] + SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] SettingsVDictionary['calculateUncertaintiesInConcentrations'] = UserChoices['uncertainties']['calculateUncertaintiesInConcentrations'] SettingsVDictionary['referenceFileUncertainties'] = UserChoices['uncertainties']['referenceFileUncertainties'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index 307b0aa44..af76fc14f 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -5194,7 +5194,7 @@ def RawSignalThresholdFilter (distinguished,reciprocal_matching_correction_value monitored_reference_intensities_copy = monitored_reference_intensities rawsignalsarray_copy = remaining_rawsignals_SLS summation = sum(rawsignalsarray_copy) - [rawSignalThresholdMethod,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList + [applyRawSignalThresholds,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList #this section of the code enables the function to eliminate from the raw signal array (for the purpose of this function only) #the highest value in the array, if it makes up over 90 percent of the raw signals present. This is useful because if one of #the signals does become this great then it will eliminate all the other signals present when it becomes very high @@ -6037,8 +6037,8 @@ def PopulateLogFile(): f6.write('dataSmootherTimeRadius = %s \n'%(G.dataSmootherTimeRadius)) f6.write('dataSmootherPointRadius = %s \n'%(G.dataSmootherPointRadius)) f6.write('dataSmootherHeadersToConfineTo = %s \n'%(G.dataSmootherHeadersToConfineTo)) - if G.rawSignalThresholdMethod == 'yes': - f6.write('rawSignalThresholdMethod = %s \n'%(G.rawSignalThresholdMethod)) + if G.applyRawSignalThresholds == 'yes': + f6.write('applyRawSignalThresholds = %s \n'%(G.applyRawSignalThresholds)) f6.write('rawSignalThresholdValue = %s \n'%(G.rawSignalThresholdValue)) f6.write('sensitivityThresholdValue = %s \n'%(G.sensitivityThresholdValue)) f6.write('rawSignalThresholdDivider = %s \n'%(G.rawSignalThresholdDivider)) @@ -6490,7 +6490,7 @@ def main(): G.csvFile, G.moleculesToRestrict, G.csvFileName,G.dataUpperBound, G.dataLowerBound, G.bruteIncrements, G.permutationNum] SLSChoices = [G.uniqueOrCommon, G.slsFinish, G.distinguished] - ThresholdList = [G.rawSignalThresholdMethod, G.rawSignalThresholdValue, G.sensitivityThresholdValue, + ThresholdList = [G.applyRawSignalThresholds, G.rawSignalThresholdValue, G.sensitivityThresholdValue, G.rawSignalThresholdDivider, G.rawSignalThresholdLimit, G.rawSignalThresholdLimitPercent] currentReferenceData = ReferenceDataList[0] #TODO this line is placeholder by charles to fix currentRefenceData issue until Alex has a better solution @@ -6567,7 +6567,7 @@ def main(): #TODO continued: I am putting some variables here to make that process easier by getting some of it done already, then only the user input file needs to be changed. #This feature is intended to remove molecules that have major fragments not observed. previously, it was done in a more complicated way. # now, to simplify things, is being used as a filter that simply sets standardized intensities in the reference patterns to zero. - G.excludeMoleculesIfSignificantFragmentNotObserved = G.rawSignalThresholdMethod + G.excludeMoleculesIfSignificantFragmentNotObserved = G.applyRawSignalThresholds G.minimumSignalRequired = G.rawSignalThresholdValue G.minimumStandardizedReferenceHeightToBeSignificant = G.sensitivityThresholdValue if G.excludeMoleculesIfSignificantFragmentNotObserved == 'yes': diff --git a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py index c41b643f9..00c441bda 100644 --- a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py +++ b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py @@ -176,7 +176,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] @@ -241,7 +241,7 @@ 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', - 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod', + 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', 'uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniquePrint','SLSUniqueExport','concentrationFinder','molecule','moleculeSignal','massNumber','moleculeConcentration', 'units','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName', diff --git a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py index 0cbc13c86..10158098b 100644 --- a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py +++ b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py @@ -2684,7 +2684,7 @@ def RawSignalThresholdFilter (distinguished,reciprocal_matching_correction_value monitored_reference_intensities_copy = monitored_reference_intensities rawsignalsarray_copy = remaining_rawsignals_SLS summation = sum(rawsignalsarray_copy) - [rawSignalThresholdMethod,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList + [applyRawSignalThresholds,rawSignalThresholdValue,sensitivityThresholdValue,rawSignalThresholdDivider,rawSignalThresholdLimit,rawSignalThresholdLimitPercent] = ThresholdList #this section of the code enables the function to eliminate from the raw signal array (for the purpose of this function only) #the highest value in the array, if it makes up over 90 percent of the raw signals present. This is useful because if one of #the signals does become this great then it will eliminate all the other signals present when it becomes very high @@ -3076,8 +3076,8 @@ def PopulateLogFile(): f6.write('dataSmootherTimeRadius = %s \n'%(G.dataSmootherTimeRadius)) f6.write('dataSmootherPointRadius = %s \n'%(G.dataSmootherPointRadius)) f6.write('dataSmootherHeadersToConfineTo = %s \n'%(G.dataSmootherHeadersToConfineTo)) - if G.rawSignalThresholdMethod == 'yes': - f6.write('rawSignalThresholdMethod = %s \n'%(G.rawSignalThresholdMethod)) + if G.applyRawSignalThresholds == 'yes': + f6.write('applyRawSignalThresholds = %s \n'%(G.applyRawSignalThresholds)) f6.write('rawSignalThresholdValue = %s \n'%(G.rawSignalThresholdValue)) f6.write('sensitivityThresholdValue = %s \n'%(G.sensitivityThresholdValue)) f6.write('rawSignalThresholdDivider = %s \n'%(G.rawSignalThresholdDivider)) @@ -3313,7 +3313,7 @@ def main(): G.csvFile, G.moleculesRange, G.csvFileName,G.dataUpperBound, G.dataLowerBound, G.increments, G.permutationNum] SLSChoices = [G.uniqueOrCommon, G.slsFinish, G.distinguished] - ThresholdList = [G.rawSignalThresholdMethod, G.rawSignalThresholdValue, G.sensitivityThresholdValue, + ThresholdList = [G.applyRawSignalThresholds, G.rawSignalThresholdValue, G.sensitivityThresholdValue, G.rawSignalThresholdDivider, G.rawSignalThresholdLimit, G.rawSignalThresholdLimitPercent] # Calculate a coefficient for doing a unit conversion on concentrations @@ -3335,7 +3335,7 @@ def main(): timeIndex,currentReferenceData.referenceabscissa)#gets the collected values that will be solved - if G.rawSignalThresholdMethod == 'yes':#user input, this function calls either sls or inverse, deletes thresholds + if G.applyRawSignalThresholds == 'yes':#user input, this function calls either sls or inverse, deletes thresholds solutions =RawSignalThresholdFilter(G.distinguished, currentReferenceData.reciprocal_matching_correction_values,rawsignalsarrayline, currentReferenceData.monitored_reference_intensities,currentReferenceData.molecules,timeIndex,ExperimentData.mass_fragment_numbers, ThresholdList,G.answer,ExperimentData.times[timeIndex],ExperimentData.conversionfactor,ExperimentData.datafromcsv, diff --git a/Todo/SLS Common vs. Unique Bug/UserInput.py b/Todo/SLS Common vs. Unique Bug/UserInput.py index 3c329a3ea..5ae342d86 100644 --- a/Todo/SLS Common vs. Unique Bug/UserInput.py +++ b/Todo/SLS Common vs. Unique Bug/UserInput.py @@ -177,7 +177,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] @@ -248,7 +248,7 @@ 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', - 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod', + 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', 'uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniquePrint','SLSUniqueExport','concentrationFinder','molecule','moleculeSignal','massNumber','moleculeConcentration', 'units','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName', diff --git a/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py b/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py index 92d068b1f..48c0b0b2c 100644 --- a/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py +++ b/UnitTests/BestMassFragmentChooser/bestMassFragChooser.py @@ -81,7 +81,7 @@ def bestMassFragChooser(chosenMolecules, G.uniqueOrCommon='unique' - G.excludeMoleculesIfSignificantFragmentNotObserved=G.rawSignalThresholdMethod + G.excludeMoleculesIfSignificantFragmentNotObserved=G.applyRawSignalThresholds #Initialize a ReferenceData class object [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py index 395e67cc1..bdfaab5d3 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py index 2a1cfc4f3..ba4fb9468 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ExtractReferencePatternFromData/test_1_input.py b/UnitTests/ExtractReferencePatternFromData/test_1_input.py index d6a9883de..a43723602 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_1_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_1_input.py @@ -169,7 +169,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ExtractReferencePatternFromData/test_2_input.py b/UnitTests/ExtractReferencePatternFromData/test_2_input.py index 1d487fd8c..92cc2c70b 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_2_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_2_input.py @@ -169,7 +169,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ExtractReferencePatternFromData/test_3_input.py b/UnitTests/ExtractReferencePatternFromData/test_3_input.py index 1f61d0062..145d8688c 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_3_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_3_input.py @@ -169,7 +169,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ExtractReferencePatternFromData/test_4_input.py b/UnitTests/ExtractReferencePatternFromData/test_4_input.py index 9a56aef68..31a6f42c1 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_4_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_4_input.py @@ -158,7 +158,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ExtractReferencePatternFromData/test_5_input.py b/UnitTests/ExtractReferencePatternFromData/test_5_input.py index d024bda2d..dee4d62e9 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_5_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_5_input.py @@ -158,7 +158,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ExtractReferencePatternFromData/test_6_input.py b/UnitTests/ExtractReferencePatternFromData/test_6_input.py index 1938b1ba5..aff4fa212 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_6_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_6_input.py @@ -158,7 +158,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index 0222bead0..777dbbead 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -213,18 +213,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Negative Analyzer// UserChoices['negativeAnalyzerYorN'] = {} #initialize the negativeAnalyzerYorN container @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py index 842e8b744..7757156bc 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py index fa79773a3..8e2d534e3 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py @@ -180,7 +180,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py index 73a0474f7..4b4c3a92f 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py index c2533b488..010990f44 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py index 4d8a8ce56..f23eadc25 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py index 4fdd24956..24136774d 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py index 2307cb619..2446a30fc 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py index 8b2530614..f73eacc0e 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -179,7 +179,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py index 0b5924daf..508e5eb3e 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py @@ -180,7 +180,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py index f4e97ac88..b1011220b 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py @@ -180,7 +180,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index cf931662c..6228c8bff 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Negative Analyzer// UserChoices['negativeAnalyzerYorN'] = {} #initialize the negativeAnalyzerYorN container @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py index 8a980e1ec..85bc8d3e5 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py @@ -166,7 +166,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py index 3756af6b8..01a5fcfd5 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py @@ -166,7 +166,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py index e3d28f43d..b79b27710 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py @@ -166,7 +166,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/ReferencePatternTimeChooser/test_2_input.py b/UnitTests/ReferencePatternTimeChooser/test_2_input.py index edb32d8fe..4a1971f0d 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_2_input.py +++ b/UnitTests/ReferencePatternTimeChooser/test_2_input.py @@ -166,7 +166,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [.0000001] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index 50fbbca19..5ed05dbb4 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -214,18 +214,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index ab806210a..41a3ee2d7 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -216,18 +216,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index d0fe5362d..f6d96eda8 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -216,18 +216,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index d8f5f55f4..6ee912f6b 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -216,18 +216,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index 563abb13a..071990e6a 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -217,18 +217,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index 35da21ad2..3192e55ab 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -217,18 +217,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1.py index e4601d021..87d0c9c37 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1.py @@ -17,7 +17,7 @@ import test_1_input MSRESOLVE.G = test_1_input -#this input file uses the rawSignalThresholdMethod,which excludes molecules if they have significant mass fragments +#this input file uses the applyRawSignalThresholds,which excludes molecules if they have significant mass fragments # that are not present above a particular signal threshold. # in this case, we set the signal threshold to be 0.02, and the significance to be at 1% for standardized reference patterns. # the mass 70 signal is always below 0.02 and a significant for both crotyl alcohol and 2-butenal (crotonaldehyde) diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py index 8b76fb85b..d30e11375 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py @@ -177,7 +177,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.02] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2.py index 768e2c267..e007af2cb 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2.py @@ -17,7 +17,7 @@ import test_2_input MSRESOLVE.G = test_2_input -#this input file uses the rawSignalThresholdMethod,which excludes molecules if they have significant mass fragments +#this input file uses the applyRawSignalThresholds,which excludes molecules if they have significant mass fragments # that are not present above a particular signal threshold. # in this case, we set the signal threshold to be 0.02, and the significance to be at 1% for standardized reference patterns. # the mass 70 signal is always below 0.02 and a significant for both crotyl alcohol and 2-butenal (crotonaldehyde) diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py index 75d037f6f..ffc039e2e 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py @@ -177,7 +177,7 @@ #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -rawSignalThresholdMethod = 'yes' +applyRawSignalThresholds = 'yes' rawSignalThresholdValue = [.02] sensitivityThresholdValue = [1] #this is the number in the Reference given, the relative intensity of the signal of the mass fragment rawSignalThresholdDivider = [] diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index a1c2d1bce..7d388354a 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index f1efea640..149b1d09e 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index 16cc8e2b3..c8895f668 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -70,7 +70,7 @@ dataSmootherPointRadius = 7.0 dataSmootherHeadersToConfineTo = [] polynomialOrder = 1 -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [1e-07] sensitivityThresholdValue = [0.05] rawSignalThresholdDivider = [] @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index 5b1fdfccb..3e1bb1eb8 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -70,7 +70,7 @@ dataSmootherPointRadius = 7.0 dataSmootherHeadersToConfineTo = [] polynomialOrder = 1 -rawSignalThresholdMethod = 'no' +applyRawSignalThresholds = 'no' rawSignalThresholdValue = [1e-07] sensitivityThresholdValue = [0.05] rawSignalThresholdDivider = [] @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index 50b2ff9ce..015976792 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Negative Analyzer// UserChoices['negativeAnalyzerYorN'] = {} #initialize the negativeAnalyzerYorN container @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index c28bf2de0..51e59a1df 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Negative Analyzer// UserChoices['negativeAnalyzerYorN'] = {} #initialize the negativeAnalyzerYorN container @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2.py index db795d642..a1747a0b6 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2.py @@ -17,7 +17,7 @@ import test_2_Input MSRESOLVE.G = test_2_Input -#this input file uses the rawSignalThresholdMethod,which excludes molecules if they have significant mass fragments +#this input file uses the applyRawSignalThresholds,which excludes molecules if they have significant mass fragments # that are not present above a particular signal threshold. # in this case, we set the signal threshold to be 0.02, and the significance to be at 1% for standardized reference patterns. # the mass 70 signal is always below 0.02 and a significant for both crotyl alcohol and 2-butenal (crotonaldehyde) diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index 46b25035b..1db6a126f 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Negative Analyzer// UserChoices['negativeAnalyzerYorN'] = {} #initialize the negativeAnalyzerYorN container @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index fc517880c..95dbdf233 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index 9b85f0a64..e26952415 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index 5c2530f2b..10785c7c4 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index 68c082b3e..746edccb8 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index fb46ac78d..e3551c139 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -215,18 +215,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index d86c7566f..9456cbe42 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -215,18 +215,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index 947ddcebd..702c0c0a8 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -214,18 +214,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index 95cae1c3e..bd198a2a6 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index 3d2fc3b48..622dfed2e 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index 0577ba78e..352b05cf7 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index 4fb2c9755..8f64d986c 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index 7c8a19bc0..3c91bc419 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index c4580b1bf..a1e402b70 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index d51595498..e10d88125 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index 82c080cb2..9809dc665 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index 51738bf02..f0ec8b86a 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -212,18 +212,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index 99d0b507a..a3da682d4 100644 --- a/UserInput.py +++ b/UserInput.py @@ -218,18 +218,18 @@ UserChoices['dataSmootherYorN']['polynomialOrder'] = 1 #During the local smoothing, a linear fit (or polynomial fit) is applied. #//Raw Signal Threshold// -UserChoices['rawSignalThresholdMethod'] = {} #initialize the rawSignalThresholdMethod container +UserChoices['applyRawSignalThresholds'] = {} #initialize the applyRawSignalThresholds container #To change the threshold at which raw signals are not longer relevant, change below (similar to above function, but for rows instead of columns) #We think the reference to the 'above function' in the previous line is referring to Data Threshold Filter #These signals get converted into 0. #WARNING: This function is highly complex and should be considered a work in progress. It cannot be confirmed to work properly (as of 7/18/17). -UserChoices['rawSignalThresholdMethod']['on'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] = [.0000001] -UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] = [] +UserChoices['applyRawSignalThresholds']['on'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] = [.0000001] +UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] = [1] #this is the number in the Reference given the relative intensity of the signal of the mass fragment +UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] = [] #Part of previous entry function, but this function enables the user to change the sum of raw signals, allowing molecules with very high concentrations not to affect previous funciton -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] = 'no' -UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] = [] +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] = 'no' +UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] = [] #//Uncertainties for Calculating Uncertainties in Concentrations// UserChoices['uncertainties'] = {} @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','rawSignalThresholdMethod','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index f638d35dd..34d9d7038 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -179,9 +179,9 @@ def parseUserInput(currentUserInput): parse.compareElementsBetweenLists(currentUserInput.dataSmootherHeadersToConfineTo,chosenMassFragmentsForParsing,'dataSmootherHeadersToConfineTo','chosenMolecules') #Raw Signal Threshold - parse.strCheck(currentUserInput.rawSignalThresholdMethod,'rawSignalThresholdMethod') + parse.strCheck(currentUserInput.applyRawSignalThresholds,'applyRawSignalThresholds') parse.strCheck(currentUserInput.rawSignalThresholdLimit,'rawSignalThresholdLimit') - if currentUserInput.rawSignalThresholdMethod == 'yes': #If using rawSignalThresholdMethod + if currentUserInput.applyRawSignalThresholds == 'yes': #If using applyRawSignalThresholds #raw signal threshold value, sensitivity value, raw signal threshold divider, and raw signal threshold limit percent are all lists currentUserInput.rawSignalThresholdValue = parse.listCast(currentUserInput.rawSignalThresholdValue) currentUserInput.sensitivityThresholdValue = parse.listCast(currentUserInput.sensitivityThresholdValue) @@ -439,12 +439,12 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['dataSmootherHeadersToConfineTo'] = UserChoices['dataSmootherYorN']['dataSmootherHeadersToConfineTo'] SettingsVDictionary['polynomialOrder'] = UserChoices['dataSmootherYorN']['polynomialOrder'] - SettingsVDictionary['rawSignalThresholdMethod'] = UserChoices['rawSignalThresholdMethod']['on'] - SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdValue'] - SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['rawSignalThresholdMethod']['sensitivityThresholdValue'] - SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdDivider'] - SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimit'] - SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['rawSignalThresholdMethod']['rawSignalThresholdLimitPercent'] + SettingsVDictionary['applyRawSignalThresholds'] = UserChoices['applyRawSignalThresholds']['on'] + SettingsVDictionary['rawSignalThresholdValue'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdValue'] + SettingsVDictionary['sensitivityThresholdValue'] = UserChoices['applyRawSignalThresholds']['sensitivityThresholdValue'] + SettingsVDictionary['rawSignalThresholdDivider'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdDivider'] + SettingsVDictionary['rawSignalThresholdLimit'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimit'] + SettingsVDictionary['rawSignalThresholdLimitPercent'] = UserChoices['applyRawSignalThresholds']['rawSignalThresholdLimitPercent'] SettingsVDictionary['calculateUncertaintiesInConcentrations'] = UserChoices['uncertainties']['calculateUncertaintiesInConcentrations'] SettingsVDictionary['referenceFileUncertainties'] = UserChoices['uncertainties']['referenceFileUncertainties'] From 9e0156fbdf4b2cfa483fa0ff4d85ae277af39198 Mon Sep 17 00:00:00 2001 From: AdityaSavara <39929571+AdityaSavara@users.noreply.github.com> Date: Sat, 23 Jul 2022 12:49:31 -0400 Subject: [PATCH 9/9] referenceValueThreshold --> referenceMassFragmentFilterThreshold --- DefaultUserInput.py | 4 +-- ExampleAnalysis/DefaultUserInput.py | 4 +-- ExampleAnalysis/LogFile.txt | 2 +- ExampleAnalysis/MSRESOLVE.py | 28 +++++++-------- ExampleAnalysis/UserInput.py | 4 +-- ExampleAnalysis/userInputValidityFunctions.py | 6 ++-- .../DefaultUserInput.py | 4 +-- ExampleReferenceExtraction/MSRESOLVE.py | 28 +++++++-------- ExampleReferenceExtraction/UserInput.py | 4 +-- .../userInputValidityFunctions.py | 6 ++-- .../DefaultUserInput.py | 4 +-- ExampleTuningCorrectorGasMixture/LogFile.txt | 2 +- ExampleTuningCorrectorGasMixture/MSRESOLVE.py | 36 +++++++++---------- .../MSRESOLVEBad1.py | 36 +++++++++---------- .../MSRESOLVEPrevious.py | 36 +++++++++---------- ExampleTuningCorrectorGasMixture/UserInput.py | 4 +-- .../userInputValidityFunctions.py | 6 ++-- MSRESOLVE.py | 36 +++++++++---------- README.txt | 2 +- .../DefaultUserInput.py | 4 +-- Todo/SLS Common vs. Unique Bug/MSRESOLVE.py | 10 +++--- Todo/SLS Common vs. Unique Bug/UserInput.py | 4 +-- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../test_3_input.py | 2 +- .../test_4_input.py | 2 +- .../test_5_input.py | 2 +- .../test_6_input.py | 2 +- .../test_1_Input_Brute_Finisher.py | 4 +-- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- .../test_1_initial_input_iterative.py | 2 +- .../test_1_initial_input_noniterative.py | 2 +- UnitTests/NegativeAnalyzer/test_1_Input.py | 4 +-- .../test_1_inputA.py | 2 +- .../test_1_inputB.py | 2 +- .../test_1_inputC.py | 2 +- .../test_2_input.py | 2 +- UnitTests/TuningCorrector/test_1.py | 2 +- .../test_10 Manual SLS/1/test_10.turnedOff | 2 +- .../test_10 Manual SLS/1/test_5.turnedOff | 2 +- .../test_10 Manual SLS/4/test_10.turnedOff | 2 +- UnitTests/TuningCorrector/test_10.py | 2 +- .../1/test_10.turnedOff | 2 +- .../1/test_11.turnedOff | 2 +- .../4/test_11.turnedOff | 2 +- UnitTests/TuningCorrector/test_11.py | 2 +- UnitTests/TuningCorrector/test_2.py | 2 +- UnitTests/TuningCorrector/test_3.py | 2 +- UnitTests/TuningCorrector/test_4.py | 2 +- UnitTests/TuningCorrector/test_5.py | 2 +- UnitTests/TuningCorrector/test_6.py | 2 +- UnitTests/TuningCorrector/test_7.py | 2 +- UnitTests/TuningCorrector/test_8.py | 2 +- UnitTests/TuningCorrector/test_9.py | 2 +- .../UserInputGasMixture.py | 4 +-- .../UserInputGasMixture2.py | 4 +-- .../UserInputGasMixture3.py | 4 +-- .../UserInputGasMixture4.py | 4 +-- .../XYXYReferencePattern/test_1_inputXYXY.py | 4 +-- .../XYXYReferencePattern/test_1_inputXYYY.py | 4 +-- .../test_1_input.py | 2 +- .../test_2_input.py | 2 +- .../implicitSLScorrection/test_1_Input.py | 4 +-- .../implicitSLScorrection/test_2_Input.py | 4 +-- .../test_1_UserInput.py | 4 +-- .../test_2_UserInput.py | 4 +-- UnitTests/slsCommon/test_1_Input.py | 4 +-- .../test_1_Input.py | 4 +-- .../test_2_Input.py | 4 +-- UnitTests/uncertainties/test_10_Input.py | 4 +-- UnitTests/uncertainties/test_11_Input.py | 4 +-- UnitTests/uncertainties/test_12_Input.py | 4 +-- UnitTests/uncertainties/test_13_Input.py | 4 +-- UnitTests/uncertainties/test_14_Input.py | 4 +-- UnitTests/uncertainties/test_15_Input.py | 4 +-- UnitTests/uncertainties/test_16_Input.py | 4 +-- UnitTests/uncertainties/test_1_Input.py | 4 +-- UnitTests/uncertainties/test_2_Input.py | 4 +-- UnitTests/uncertainties/test_3_Input.py | 4 +-- UnitTests/uncertainties/test_4_Input.py | 4 +-- UnitTests/uncertainties/test_5_Input.py | 4 +-- UnitTests/uncertainties/test_6_Input.py | 4 +-- UnitTests/uncertainties/test_7_Input.py | 4 +-- UnitTests/uncertainties/test_8_Input.py | 4 +-- UnitTests/uncertainties/test_9_Input.py | 4 +-- UserInput.py | 4 +-- userInputValidityFunctions.py | 6 ++-- 96 files changed, 243 insertions(+), 243 deletions(-) diff --git a/DefaultUserInput.py b/DefaultUserInput.py index a3da682d4..517fecf5f 100644 --- a/DefaultUserInput.py +++ b/DefaultUserInput.py @@ -189,7 +189,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #typical values are between 5 and 50. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This setting causes MSRESOLVE to favor larger intensity reference peaks (above the number provided) during solving. #//Data Threshold Filter// @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/ExampleAnalysis/DefaultUserInput.py b/ExampleAnalysis/DefaultUserInput.py index 4b9384896..677273ca7 100644 --- a/ExampleAnalysis/DefaultUserInput.py +++ b/ExampleAnalysis/DefaultUserInput.py @@ -182,7 +182,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/LogFile.txt b/ExampleAnalysis/LogFile.txt index e00d433ab..7f7fb6023 100644 --- a/ExampleAnalysis/LogFile.txt +++ b/ExampleAnalysis/LogFile.txt @@ -10,7 +10,7 @@ massesToBackgroundCorrect = [12.0 13.0 14.0 15.0 16.0 17.0 21.0 22.0 24.0 25.0 2 earlyBaselineTimes = [[850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870], [850, 870]] lateBaselineTimes = [[1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070], [1050, 1070]] applyReferenceMassFragmentsThresholds = yes -referenceValueThreshold = [1.01, 1.01, 1.01] +referenceMassFragmentFilterThreshold = [1.01, 1.01, 1.01] referenceSignificantFragmentThresholds = [20.0, 20.0, 20.0] answer = sls uniqueOrCommon = unique diff --git a/ExampleAnalysis/MSRESOLVE.py b/ExampleAnalysis/MSRESOLVE.py index de95487ca..d719b4d5b 100644 --- a/ExampleAnalysis/MSRESOLVE.py +++ b/ExampleAnalysis/MSRESOLVE.py @@ -391,7 +391,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternMeasuredDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternMeasuredDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternMeasuredDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternMeasuredDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternMeasuredDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternMeasuredDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternMeasuredDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ReferencePatternLiteratureDict = {} [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form] = readReferenceFile(*ReferencePatternLiteratureFileNameAndForm) @@ -399,7 +399,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternLiteratureDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternLiteratureDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternLiteratureDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternLiteratureDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternLiteratureDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternLiteratureDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternLiteratureDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ''' Step 3a: Truncate to the molecules which match. @@ -512,17 +512,17 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien #this function eliminates (neglects) reference intensities that are below a certain threshold. Useful for solving #data that is giving negatives or over emphasizing small mass fragments,by assuming no contribution from the molecule at that mass fragment. -def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceValueThreshold): +def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceMassFragmentFilterThreshold): referenceDataArray = referenceDataArrayWithAbscissa[:,1:] #all the data except the line of abscissa- mass fragment numbers for columncounter in range(len(referenceDataArray[0,:])):#goes through all columns in all rows in reference (this loop is one molecule at a time) for rowcounter in range(len(referenceDataArray[:,0])):#goes through all rows in references (one mass fragment at a time) - if len(referenceValueThreshold) == 1: #this is for if a single value was provided for referenceValueThreshold - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[0]: + if len(referenceMassFragmentFilterThreshold) == 1: #this is for if a single value was provided for referenceMassFragmentFilterThreshold + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[0]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero # (len(referenceDataArray[:,0])) #this is masses. # (len(referenceDataArray[0,:])) #this is molecules - else: #this is for if values of referenceValueThreshold were provided for each molecule. - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[columncounter]: + else: #this is for if values of referenceMassFragmentFilterThreshold were provided for each molecule. + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[columncounter]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero referenceDataArrayWithAbscissa[:,1:] = referenceDataArray #this puts changed referenceData back with mass fragment numbers return referenceDataArrayWithAbscissa @@ -1231,7 +1231,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. - ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) + ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceMassFragmentFilterThreshold) ReferenceData.ExportCollector('ReferenceThresholdFilter') #As the program is currently written, this function is called to act upon already threshold filtered standardized reference patterns which could cause innaccuracy. @@ -1897,7 +1897,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.scaleRawDataFactor = G.scaleRawDataFactor #Now going to overwrite parallelized variables with their original versions if they were set to length of chosen molecules. - delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceValueThreshold, referenceSignificantFragmentThresholds' + delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceMassFragmentFilterThreshold, referenceSignificantFragmentThresholds' listOfVariablesToUnparallelize = delimitedStringOfVariablesToUnparallelize.split(", ") #Note that we are using ", " as the delimeter, not just "," for variable in listOfVariablesToUnparallelize: G.nextUserInputModule.__dict__[variable]=G.beforeParsedGDict[variable] @@ -2654,7 +2654,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceMassFragmentFilterThreshold, such as referenceMassFragmentFilterThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -2917,7 +2917,7 @@ def InverseMethodDistinguished(monitored_reference_intensities,reciprocal_matchi try: numpy.linalg.det(reciprocal_matching_correction_values) except: - print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceValueThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") + print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceMassFragmentFilterThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") if numpy.linalg.det(reciprocal_matching_correction_values) != 0:#only solves if determinant is not equal to zero #Now we will solve with the inverse way, and also for uncertainties if that module is present. #The uncertainties module works well for matrix inverse, but not for dot product. So we make a custom function. @@ -4125,7 +4125,7 @@ def SLSMethod(molecules,monitored_reference_intensities,reciprocal_matching_corr except: pass except IndexError: - print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceValueThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") + print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceMassFragmentFilterThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") solutions = numpy.array([None]) #This is just creating a numpy array with an element that has a None object, so that the main function can know that SLSMethod failed. if len(uncertainties_dict) > 0: #Note: the indexing in the solutions must match the original indexing, or errors will occur. Now we take the "filled up" solutions and put everything together. uncertainties_dict['concentrations_relative_uncertainties_one_time'] = uncertainties_dict['concentrations_relative_uncertainties_one_time_after_finisher'].transpose()*1.0 @@ -4375,7 +4375,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -4994,7 +4994,7 @@ def PopulateLogFile(): f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) if G.applyReferenceMassFragmentsThresholds == 'yes': f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) - f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) + f6.write('referenceMassFragmentFilterThreshold = %s \n'%(G.referenceMassFragmentFilterThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) diff --git a/ExampleAnalysis/UserInput.py b/ExampleAnalysis/UserInput.py index 38dd671ae..a92a5decf 100644 --- a/ExampleAnalysis/UserInput.py +++ b/ExampleAnalysis/UserInput.py @@ -182,7 +182,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [1.01] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [1.01] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [20.0] #//Data Threshold Filter// @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleAnalysis/userInputValidityFunctions.py b/ExampleAnalysis/userInputValidityFunctions.py index b1e8772a3..51573dee3 100644 --- a/ExampleAnalysis/userInputValidityFunctions.py +++ b/ExampleAnalysis/userInputValidityFunctions.py @@ -125,9 +125,9 @@ def parseUserInput(currentUserInput): #Reference Mass Fragmentation Threshold parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold - currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list + currentUserInput.referenceMassFragmentFilterThreshold = parse.listCast(currentUserInput.referenceMassFragmentFilterThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules - currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) + currentUserInput.referenceMassFragmentFilterThreshold = parse.parallelVectorize(currentUserInput.referenceMassFragmentFilterThreshold,len(chosenMoleculesForParsing)) currentUserInput.referenceSignificantFragmentThresholds = parse.parallelVectorize(currentUserInput.referenceSignificantFragmentThresholds,len(chosenMoleculesForParsing)) #Data Threshold Filter @@ -326,7 +326,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceMassFragmentFilterThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on'] diff --git a/ExampleReferenceExtraction/DefaultUserInput.py b/ExampleReferenceExtraction/DefaultUserInput.py index 4b9384896..677273ca7 100644 --- a/ExampleReferenceExtraction/DefaultUserInput.py +++ b/ExampleReferenceExtraction/DefaultUserInput.py @@ -182,7 +182,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/MSRESOLVE.py b/ExampleReferenceExtraction/MSRESOLVE.py index de95487ca..d719b4d5b 100644 --- a/ExampleReferenceExtraction/MSRESOLVE.py +++ b/ExampleReferenceExtraction/MSRESOLVE.py @@ -391,7 +391,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternMeasuredDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternMeasuredDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternMeasuredDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternMeasuredDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternMeasuredDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternMeasuredDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternMeasuredDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ReferencePatternLiteratureDict = {} [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form] = readReferenceFile(*ReferencePatternLiteratureFileNameAndForm) @@ -399,7 +399,7 @@ def ABCDetermination(ReferencePatternMeasuredFileNameAndForm, ReferencePatternLi ReferencePatternLiteratureDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternLiteratureDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternLiteratureDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternLiteratureDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternLiteratureDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternLiteratureDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternLiteratureDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ''' Step 3a: Truncate to the molecules which match. @@ -512,17 +512,17 @@ def TuningCorrector(referenceDataArrayWithAbscissa,referenceCorrectionCoefficien #this function eliminates (neglects) reference intensities that are below a certain threshold. Useful for solving #data that is giving negatives or over emphasizing small mass fragments,by assuming no contribution from the molecule at that mass fragment. -def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceValueThreshold): +def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceMassFragmentFilterThreshold): referenceDataArray = referenceDataArrayWithAbscissa[:,1:] #all the data except the line of abscissa- mass fragment numbers for columncounter in range(len(referenceDataArray[0,:])):#goes through all columns in all rows in reference (this loop is one molecule at a time) for rowcounter in range(len(referenceDataArray[:,0])):#goes through all rows in references (one mass fragment at a time) - if len(referenceValueThreshold) == 1: #this is for if a single value was provided for referenceValueThreshold - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[0]: + if len(referenceMassFragmentFilterThreshold) == 1: #this is for if a single value was provided for referenceMassFragmentFilterThreshold + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[0]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero # (len(referenceDataArray[:,0])) #this is masses. # (len(referenceDataArray[0,:])) #this is molecules - else: #this is for if values of referenceValueThreshold were provided for each molecule. - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[columncounter]: + else: #this is for if values of referenceMassFragmentFilterThreshold were provided for each molecule. + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[columncounter]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero referenceDataArrayWithAbscissa[:,1:] = referenceDataArray #this puts changed referenceData back with mass fragment numbers return referenceDataArrayWithAbscissa @@ -1231,7 +1231,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. - ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) + ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceMassFragmentFilterThreshold) ReferenceData.ExportCollector('ReferenceThresholdFilter') #As the program is currently written, this function is called to act upon already threshold filtered standardized reference patterns which could cause innaccuracy. @@ -1897,7 +1897,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.scaleRawDataFactor = G.scaleRawDataFactor #Now going to overwrite parallelized variables with their original versions if they were set to length of chosen molecules. - delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceValueThreshold, referenceSignificantFragmentThresholds' + delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceMassFragmentFilterThreshold, referenceSignificantFragmentThresholds' listOfVariablesToUnparallelize = delimitedStringOfVariablesToUnparallelize.split(", ") #Note that we are using ", " as the delimeter, not just "," for variable in listOfVariablesToUnparallelize: G.nextUserInputModule.__dict__[variable]=G.beforeParsedGDict[variable] @@ -2654,7 +2654,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceMassFragmentFilterThreshold, such as referenceMassFragmentFilterThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -2917,7 +2917,7 @@ def InverseMethodDistinguished(monitored_reference_intensities,reciprocal_matchi try: numpy.linalg.det(reciprocal_matching_correction_values) except: - print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceValueThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") + print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceMassFragmentFilterThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") if numpy.linalg.det(reciprocal_matching_correction_values) != 0:#only solves if determinant is not equal to zero #Now we will solve with the inverse way, and also for uncertainties if that module is present. #The uncertainties module works well for matrix inverse, but not for dot product. So we make a custom function. @@ -4125,7 +4125,7 @@ def SLSMethod(molecules,monitored_reference_intensities,reciprocal_matching_corr except: pass except IndexError: - print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceValueThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") + print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceMassFragmentFilterThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") solutions = numpy.array([None]) #This is just creating a numpy array with an element that has a None object, so that the main function can know that SLSMethod failed. if len(uncertainties_dict) > 0: #Note: the indexing in the solutions must match the original indexing, or errors will occur. Now we take the "filled up" solutions and put everything together. uncertainties_dict['concentrations_relative_uncertainties_one_time'] = uncertainties_dict['concentrations_relative_uncertainties_one_time_after_finisher'].transpose()*1.0 @@ -4375,7 +4375,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -4994,7 +4994,7 @@ def PopulateLogFile(): f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) if G.applyReferenceMassFragmentsThresholds == 'yes': f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) - f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) + f6.write('referenceMassFragmentFilterThreshold = %s \n'%(G.referenceMassFragmentFilterThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) diff --git a/ExampleReferenceExtraction/UserInput.py b/ExampleReferenceExtraction/UserInput.py index d41d870de..c3240c761 100644 --- a/ExampleReferenceExtraction/UserInput.py +++ b/ExampleReferenceExtraction/UserInput.py @@ -182,7 +182,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleReferenceExtraction/userInputValidityFunctions.py b/ExampleReferenceExtraction/userInputValidityFunctions.py index b1e8772a3..51573dee3 100644 --- a/ExampleReferenceExtraction/userInputValidityFunctions.py +++ b/ExampleReferenceExtraction/userInputValidityFunctions.py @@ -125,9 +125,9 @@ def parseUserInput(currentUserInput): #Reference Mass Fragmentation Threshold parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold - currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list + currentUserInput.referenceMassFragmentFilterThreshold = parse.listCast(currentUserInput.referenceMassFragmentFilterThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules - currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) + currentUserInput.referenceMassFragmentFilterThreshold = parse.parallelVectorize(currentUserInput.referenceMassFragmentFilterThreshold,len(chosenMoleculesForParsing)) currentUserInput.referenceSignificantFragmentThresholds = parse.parallelVectorize(currentUserInput.referenceSignificantFragmentThresholds,len(chosenMoleculesForParsing)) #Data Threshold Filter @@ -326,7 +326,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceMassFragmentFilterThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on'] diff --git a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py index c4155ed42..4d6c92912 100644 --- a/ExampleTuningCorrectorGasMixture/DefaultUserInput.py +++ b/ExampleTuningCorrectorGasMixture/DefaultUserInput.py @@ -182,7 +182,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -294,4 +294,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/LogFile.txt b/ExampleTuningCorrectorGasMixture/LogFile.txt index 221b5e802..cb9f73354 100644 --- a/ExampleTuningCorrectorGasMixture/LogFile.txt +++ b/ExampleTuningCorrectorGasMixture/LogFile.txt @@ -13,7 +13,7 @@ referenceCorrectionCoefficientC = -0.9533139758788823 referenceCorrection_abcCoefficients = [-0.006486881698506962, 0.25062935187812, -0.9533139758788823] referenceCorrection_abcCoefficients_cov = [[6.210441332505573e-06, -0.00026708328912830614, 0.002613875252542956], [-0.0002670832891283059, 0.01155046014720452, -0.11397285273190337], [0.0026138752525429526, -0.11397285273190326, 1.140196952429929]] applyReferenceMassFragmentsThresholds = yes -referenceValueThreshold = [2.0, 2.0, 2.0, 2.0] +referenceMassFragmentFilterThreshold = [2.0, 2.0, 2.0, 2.0] referenceSignificantFragmentThresholds = [6.0, 6.0, 6.0, 6.0] answer = sls uniqueOrCommon = unique diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py index 21b9b3476..818764d80 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVE.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVE.py @@ -394,7 +394,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ReferencePatternDesiredTuningDict = {} [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form] = readReferenceFile(*ReferencePatternDesiredTuning_FileNameAndForm) @@ -402,7 +402,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ''' Step 3a: Truncate to the molecules which match. @@ -865,7 +865,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there if ReferenceDataList[ReferenceDataIndex].ExportAtEachStep == 'yes': print("line 685", ReferenceDataList[ReferenceDataIndex].relativeIonizationEfficiencies) print("line 686", ReferenceDataList[ReferenceDataIndex].sourceOfIonizationData) - print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']) + print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']) ReferenceDataList[ReferenceDataIndex].ExportCollector('StandardizedReferencePattern', use_provided_reference_patterns=False) ReferenceDataList[ReferenceDataIndex].exportReferencePattern("TuningCorrectorMixedPattern.csv") @@ -877,20 +877,20 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there #this function eliminates (neglects) reference intensities that are below a certain threshold. Useful for solving #data that is giving negatives or over emphasizing small mass fragments,by assuming no contribution from the molecule at that mass fragment. -def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceValueThreshold): +def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceMassFragmentFilterThreshold): numMolecules = len(referenceDataArrayWithAbscissa[0]-1) - if numMolecules > len(list(referenceValueThreshold)): - referenceValueThreshold = list(referenceValueThreshold)* numMolecules + if numMolecules > len(list(referenceMassFragmentFilterThreshold)): + referenceMassFragmentFilterThreshold = list(referenceMassFragmentFilterThreshold)* numMolecules referenceDataArray = referenceDataArrayWithAbscissa[:,1:] #all the data except the line of abscissa- mass fragment numbers for columncounter in range(len(referenceDataArray[0,:])):#goes through all columns in all rows in reference (this loop is one molecule at a time) for rowcounter in range(len(referenceDataArray[:,0])):#goes through all rows in references (one mass fragment at a time) - if len(referenceValueThreshold) == 1: #this is for if a single value was provided for referenceValueThreshold - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[0]: + if len(referenceMassFragmentFilterThreshold) == 1: #this is for if a single value was provided for referenceMassFragmentFilterThreshold + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[0]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero # (len(referenceDataArray[:,0])) #this is masses. # (len(referenceDataArray[0,:])) #this is molecules - else: #this is for if values of referenceValueThreshold were provided for each molecule. - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[columncounter]: + else: #this is for if values of referenceMassFragmentFilterThreshold were provided for each molecule. + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[columncounter]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero referenceDataArrayWithAbscissa[:,1:] = referenceDataArray #this puts changed referenceData back with mass fragment numbers return referenceDataArrayWithAbscissa @@ -1623,7 +1623,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. - ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) + ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceMassFragmentFilterThreshold) ReferenceData.ExportCollector('ReferenceThresholdFilter') #As the program is currently written, this function is called to act upon already threshold filtered standardized reference patterns which could cause innaccuracy. @@ -2318,7 +2318,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.scaleRawDataFactor = G.scaleRawDataFactor #Now going to overwrite parallelized variables with their original versions if they were set to length of chosen molecules. - delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceValueThreshold, referenceSignificantFragmentThresholds' + delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceMassFragmentFilterThreshold, referenceSignificantFragmentThresholds' listOfVariablesToUnparallelize = delimitedStringOfVariablesToUnparallelize.split(", ") #Note that we are using ", " as the delimeter, not just "," for variable in listOfVariablesToUnparallelize: G.nextUserInputModule.__dict__[variable]=G.beforeParsedGDict[variable] @@ -3232,7 +3232,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceMassFragmentFilterThreshold, such as referenceMassFragmentFilterThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -3495,7 +3495,7 @@ def InverseMethodDistinguished(monitored_reference_intensities,reciprocal_matchi try: numpy.linalg.det(reciprocal_matching_correction_values) except: - print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceValueThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") + print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceMassFragmentFilterThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") if numpy.linalg.det(reciprocal_matching_correction_values) != 0:#only solves if determinant is not equal to zero #Now we will solve with the inverse way, and also for uncertainties if that module is present. #The uncertainties module works well for matrix inverse, but not for dot product. So we make a custom function. @@ -4703,7 +4703,7 @@ def SLSMethod(molecules,monitored_reference_intensities,reciprocal_matching_corr except: pass except IndexError: - print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceValueThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") + print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceMassFragmentFilterThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") solutions = numpy.array([None]) #This is just creating a numpy array with an element that has a None object, so that the main function can know that SLSMethod failed. if len(uncertainties_dict) > 0: #Note: the indexing in the solutions must match the original indexing, or errors will occur. Now we take the "filled up" solutions and put everything together. uncertainties_dict['concentrations_relative_uncertainties_one_time'] = uncertainties_dict['concentrations_relative_uncertainties_one_time_after_finisher'].transpose()*1.0 @@ -4953,7 +4953,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -5574,7 +5574,7 @@ def PopulateLogFile(): f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) if G.applyReferenceMassFragmentsThresholds == 'yes': f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) - f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) + f6.write('referenceMassFragmentFilterThreshold = %s \n'%(G.referenceMassFragmentFilterThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) @@ -6098,7 +6098,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py index c1015c7be..8e78dcc21 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEBad1.py @@ -394,7 +394,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ReferencePatternDesiredTuningDict = {} [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form] = readReferenceFile(*ReferencePatternDesiredTuning_FileNameAndForm) @@ -402,7 +402,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ''' Step 3a: Truncate to the molecules which match. @@ -697,7 +697,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there if ReferenceDataList[ReferenceDataIndex].ExportAtEachStep == 'yes': print("line 685", ReferenceDataList[ReferenceDataIndex].relativeIonizationEfficiencies) print("line 686", ReferenceDataList[ReferenceDataIndex].sourceOfIonizationData) - print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']) + print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']) ReferenceDataList[ReferenceDataIndex].ExportCollector('StandardizedReferencePattern', use_provided_reference_patterns=False) ReferenceDataList[ReferenceDataIndex].exportReferencePattern("TuningCorrectorMixedPattern.csv") @@ -709,20 +709,20 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there #this function eliminates (neglects) reference intensities that are below a certain threshold. Useful for solving #data that is giving negatives or over emphasizing small mass fragments,by assuming no contribution from the molecule at that mass fragment. -def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceValueThreshold): +def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceMassFragmentFilterThreshold): numMolecules = len(referenceDataArrayWithAbscissa[0]-1) - if numMolecules > len(list(referenceValueThreshold)): - referenceValueThreshold = list(referenceValueThreshold)* numMolecules + if numMolecules > len(list(referenceMassFragmentFilterThreshold)): + referenceMassFragmentFilterThreshold = list(referenceMassFragmentFilterThreshold)* numMolecules referenceDataArray = referenceDataArrayWithAbscissa[:,1:] #all the data except the line of abscissa- mass fragment numbers for columncounter in range(len(referenceDataArray[0,:])):#goes through all columns in all rows in reference (this loop is one molecule at a time) for rowcounter in range(len(referenceDataArray[:,0])):#goes through all rows in references (one mass fragment at a time) - if len(referenceValueThreshold) == 1: #this is for if a single value was provided for referenceValueThreshold - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[0]: + if len(referenceMassFragmentFilterThreshold) == 1: #this is for if a single value was provided for referenceMassFragmentFilterThreshold + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[0]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero # (len(referenceDataArray[:,0])) #this is masses. # (len(referenceDataArray[0,:])) #this is molecules - else: #this is for if values of referenceValueThreshold were provided for each molecule. - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[columncounter]: + else: #this is for if values of referenceMassFragmentFilterThreshold were provided for each molecule. + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[columncounter]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero referenceDataArrayWithAbscissa[:,1:] = referenceDataArray #this puts changed referenceData back with mass fragment numbers return referenceDataArrayWithAbscissa @@ -1498,7 +1498,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. - ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) + ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceMassFragmentFilterThreshold) ReferenceData.ExportCollector('ReferenceThresholdFilter') #As the program is currently written, this function is called to act upon already threshold filtered standardized reference patterns which could cause innaccuracy. @@ -2190,7 +2190,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.scaleRawDataFactor = G.scaleRawDataFactor #Now going to overwrite parallelized variables with their original versions if they were set to length of chosen molecules. - delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceValueThreshold, referenceSignificantFragmentThresholds' + delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceMassFragmentFilterThreshold, referenceSignificantFragmentThresholds' listOfVariablesToUnparallelize = delimitedStringOfVariablesToUnparallelize.split(", ") #Note that we are using ", " as the delimeter, not just "," for variable in listOfVariablesToUnparallelize: G.nextUserInputModule.__dict__[variable]=G.beforeParsedGDict[variable] @@ -3095,7 +3095,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceMassFragmentFilterThreshold, such as referenceMassFragmentFilterThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -3358,7 +3358,7 @@ def InverseMethodDistinguished(monitored_reference_intensities,reciprocal_matchi try: numpy.linalg.det(reciprocal_matching_correction_values) except: - print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceValueThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") + print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceMassFragmentFilterThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") if numpy.linalg.det(reciprocal_matching_correction_values) != 0:#only solves if determinant is not equal to zero #Now we will solve with the inverse way, and also for uncertainties if that module is present. #The uncertainties module works well for matrix inverse, but not for dot product. So we make a custom function. @@ -4568,7 +4568,7 @@ def SLSMethod(molecules,monitored_reference_intensities,reciprocal_matching_corr except: pass except IndexError: - print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceValueThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") + print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceMassFragmentFilterThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") solutions = numpy.array([None]) #This is just creating a numpy array with an element that has a None object, so that the main function can know that SLSMethod failed. if len(uncertainties_dict) > 0: #Note: the indexing in the solutions must match the original indexing, or errors will occur. Now we take the "filled up" solutions and put everything together. uncertainties_dict['concentrations_relative_uncertainties_one_time'] = uncertainties_dict['concentrations_relative_uncertainties_one_time_after_finisher'].transpose()*1.0 @@ -4818,7 +4818,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -5439,7 +5439,7 @@ def PopulateLogFile(): f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) if G.applyReferenceMassFragmentsThresholds == 'yes': f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) - f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) + f6.write('referenceMassFragmentFilterThreshold = %s \n'%(G.referenceMassFragmentFilterThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) @@ -5950,7 +5950,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py index a2781e340..cbb976996 100644 --- a/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py +++ b/ExampleTuningCorrectorGasMixture/MSRESOLVEPrevious.py @@ -394,7 +394,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ReferencePatternDesiredTuningDict = {} [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form] = readReferenceFile(*ReferencePatternDesiredTuning_FileNameAndForm) @@ -402,7 +402,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ''' Step 3a: Truncate to the molecules which match. @@ -872,7 +872,7 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there if ReferenceDataList[ReferenceDataIndex].ExportAtEachStep == 'yes': print("line 685", ReferenceDataList[ReferenceDataIndex].relativeIonizationEfficiencies) print("line 686", ReferenceDataList[ReferenceDataIndex].sourceOfIonizationData) - print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']) + print(G.UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']) ReferenceDataList[ReferenceDataIndex].ExportCollector('StandardizedReferencePattern', use_provided_reference_patterns=False) ReferenceDataList[ReferenceDataIndex].exportReferencePattern("TuningCorrectorMixedPattern.csv") @@ -884,20 +884,20 @@ def tuningCorrectorGasMixture(ReferenceDataList, G): #making it clear that there #this function eliminates (neglects) reference intensities that are below a certain threshold. Useful for solving #data that is giving negatives or over emphasizing small mass fragments,by assuming no contribution from the molecule at that mass fragment. -def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceValueThreshold): +def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceMassFragmentFilterThreshold): numMolecules = len(referenceDataArrayWithAbscissa[0]-1) - if numMolecules > len(list(referenceValueThreshold)): - referenceValueThreshold = list(referenceValueThreshold)* numMolecules + if numMolecules > len(list(referenceMassFragmentFilterThreshold)): + referenceMassFragmentFilterThreshold = list(referenceMassFragmentFilterThreshold)* numMolecules referenceDataArray = referenceDataArrayWithAbscissa[:,1:] #all the data except the line of abscissa- mass fragment numbers for columncounter in range(len(referenceDataArray[0,:])):#goes through all columns in all rows in reference (this loop is one molecule at a time) for rowcounter in range(len(referenceDataArray[:,0])):#goes through all rows in references (one mass fragment at a time) - if len(referenceValueThreshold) == 1: #this is for if a single value was provided for referenceValueThreshold - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[0]: + if len(referenceMassFragmentFilterThreshold) == 1: #this is for if a single value was provided for referenceMassFragmentFilterThreshold + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[0]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero # (len(referenceDataArray[:,0])) #this is masses. # (len(referenceDataArray[0,:])) #this is molecules - else: #this is for if values of referenceValueThreshold were provided for each molecule. - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[columncounter]: + else: #this is for if values of referenceMassFragmentFilterThreshold were provided for each molecule. + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[columncounter]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero referenceDataArrayWithAbscissa[:,1:] = referenceDataArray #this puts changed referenceData back with mass fragment numbers return referenceDataArrayWithAbscissa @@ -1629,7 +1629,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. - ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) + ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceMassFragmentFilterThreshold) ReferenceData.ExportCollector('ReferenceThresholdFilter') #As the program is currently written, this function is called to act upon already threshold filtered standardized reference patterns which could cause innaccuracy. @@ -2321,7 +2321,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.scaleRawDataFactor = G.scaleRawDataFactor #Now going to overwrite parallelized variables with their original versions if they were set to length of chosen molecules. - delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceValueThreshold, referenceSignificantFragmentThresholds' + delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceMassFragmentFilterThreshold, referenceSignificantFragmentThresholds' listOfVariablesToUnparallelize = delimitedStringOfVariablesToUnparallelize.split(", ") #Note that we are using ", " as the delimeter, not just "," for variable in listOfVariablesToUnparallelize: G.nextUserInputModule.__dict__[variable]=G.beforeParsedGDict[variable] @@ -3234,7 +3234,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceMassFragmentFilterThreshold, such as referenceMassFragmentFilterThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -3497,7 +3497,7 @@ def InverseMethodDistinguished(monitored_reference_intensities,reciprocal_matchi try: numpy.linalg.det(reciprocal_matching_correction_values) except: - print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceValueThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") + print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceMassFragmentFilterThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") if numpy.linalg.det(reciprocal_matching_correction_values) != 0:#only solves if determinant is not equal to zero #Now we will solve with the inverse way, and also for uncertainties if that module is present. #The uncertainties module works well for matrix inverse, but not for dot product. So we make a custom function. @@ -4707,7 +4707,7 @@ def SLSMethod(molecules,monitored_reference_intensities,reciprocal_matching_corr except: pass except IndexError: - print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceValueThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") + print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceMassFragmentFilterThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using inverse.") solutions = numpy.array([None]) #This is just creating a numpy array with an element that has a None object, so that the main function can know that SLSMethod failed. if len(uncertainties_dict) > 0: #Note: the indexing in the solutions must match the original indexing, or errors will occur. Now we take the "filled up" solutions and put everything together. uncertainties_dict['concentrations_relative_uncertainties_one_time'] = uncertainties_dict['concentrations_relative_uncertainties_one_time_after_finisher'].transpose()*1.0 @@ -4957,7 +4957,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -5578,7 +5578,7 @@ def PopulateLogFile(): f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) if G.applyReferenceMassFragmentsThresholds == 'yes': f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) - f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) + f6.write('referenceMassFragmentFilterThreshold = %s \n'%(G.referenceMassFragmentFilterThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) @@ -6101,7 +6101,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/ExampleTuningCorrectorGasMixture/UserInput.py b/ExampleTuningCorrectorGasMixture/UserInput.py index 4a4cbdc07..1be1c1004 100644 --- a/ExampleTuningCorrectorGasMixture/UserInput.py +++ b/ExampleTuningCorrectorGasMixture/UserInput.py @@ -185,7 +185,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py index eadde53dd..54a42a19d 100644 --- a/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py +++ b/ExampleTuningCorrectorGasMixture/userInputValidityFunctions.py @@ -142,9 +142,9 @@ def parseUserInput(currentUserInput): #Reference Mass Fragmentation Threshold parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold - currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list + currentUserInput.referenceMassFragmentFilterThreshold = parse.listCast(currentUserInput.referenceMassFragmentFilterThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules - currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) + currentUserInput.referenceMassFragmentFilterThreshold = parse.parallelVectorize(currentUserInput.referenceMassFragmentFilterThreshold,len(chosenMoleculesForParsing)) currentUserInput.referenceSignificantFragmentThresholds = parse.parallelVectorize(currentUserInput.referenceSignificantFragmentThresholds,len(chosenMoleculesForParsing)) @@ -362,7 +362,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceMassFragmentFilterThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on'] diff --git a/MSRESOLVE.py b/MSRESOLVE.py index af76fc14f..74d4742e0 100644 --- a/MSRESOLVE.py +++ b/MSRESOLVE.py @@ -394,7 +394,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternExistingTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternExistingTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternExistingTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternExistingTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternExistingTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ReferencePatternDesiredTuningDict = {} [provided_reference_patterns, electronnumbers, molecules, molecularWeights, SourceOfFragmentationPatterns, sourceOfIonizationData, relativeIonizationEfficiencies, moleculeIonizationType, mass_fragment_numbers_monitored, referenceFileName, form] = readReferenceFile(*ReferencePatternDesiredTuning_FileNameAndForm) @@ -402,7 +402,7 @@ def ABCDetermination(ReferencePatternExistingTuning_FileNameAndForm, ReferencePa ReferencePatternDesiredTuningDict['provided_reference_patterns'] = provided_reference_patterns ReferencePatternDesiredTuningDict['provided_reference_patterns'] = StandardizeReferencePattern(ReferencePatternDesiredTuningDict['provided_reference_patterns'],len(molecules)) #this does have the molecular weight as the first column. if G.applyReferenceMassFragmentsThresholds =='yes': - ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceValueThreshold) + ReferencePatternDesiredTuningDict['provided_reference_patterns'] = ReferenceThresholdFilter(ReferencePatternDesiredTuningDict['provided_reference_patterns'],G.referenceMassFragmentFilterThreshold) ''' Step 3a: Truncate to the molecules which match. @@ -1037,20 +1037,20 @@ def tuningCorrectorGasMixture(ReferenceDataList, G, ExperimentData=None): #makin #this function eliminates (neglects) reference intensities that are below a certain threshold. Useful for solving #data that is giving negatives or over emphasizing small mass fragments,by assuming no contribution from the molecule at that mass fragment. -def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceValueThreshold): +def ReferenceThresholdFilter(referenceDataArrayWithAbscissa,referenceMassFragmentFilterThreshold): numMolecules = len(referenceDataArrayWithAbscissa[0]-1) - if numMolecules > len(list(referenceValueThreshold)): - referenceValueThreshold = list(referenceValueThreshold)* numMolecules + if numMolecules > len(list(referenceMassFragmentFilterThreshold)): + referenceMassFragmentFilterThreshold = list(referenceMassFragmentFilterThreshold)* numMolecules referenceDataArray = referenceDataArrayWithAbscissa[:,1:] #all the data except the line of abscissa- mass fragment numbers for columncounter in range(len(referenceDataArray[0,:])):#goes through all columns in all rows in reference (this loop is one molecule at a time) for rowcounter in range(len(referenceDataArray[:,0])):#goes through all rows in references (one mass fragment at a time) - if len(referenceValueThreshold) == 1: #this is for if a single value was provided for referenceValueThreshold - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[0]: + if len(referenceMassFragmentFilterThreshold) == 1: #this is for if a single value was provided for referenceMassFragmentFilterThreshold + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[0]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero # (len(referenceDataArray[:,0])) #this is masses. # (len(referenceDataArray[0,:])) #this is molecules - else: #this is for if values of referenceValueThreshold were provided for each molecule. - if referenceDataArray[rowcounter,columncounter] < referenceValueThreshold[columncounter]: + else: #this is for if values of referenceMassFragmentFilterThreshold were provided for each molecule. + if referenceDataArray[rowcounter,columncounter] < referenceMassFragmentFilterThreshold[columncounter]: referenceDataArray[rowcounter,columncounter] = 0 #made to be equal to zero referenceDataArrayWithAbscissa[:,1:] = referenceDataArray #this puts changed referenceData back with mass fragment numbers return referenceDataArrayWithAbscissa @@ -1936,7 +1936,7 @@ def ReferenceInputPreProcessing(ReferenceData, verbose=True): if G.applyReferenceMassFragmentsThresholds == 'yes': if G.implicitSLScorrection == True: #This feature requires us to have unfiltered reference patterns to do an implicit/recursive correction at the end. G.currentReferenceDataUnfiltered = copy.deepcopy(ReferenceData) #Make a copy before any filtering occurs. There is an implied return in global variable. - ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceValueThreshold) + ReferenceData.standardized_reference_patterns = ReferenceThresholdFilter(ReferenceData.standardized_reference_patterns,G.referenceMassFragmentFilterThreshold) ReferenceData.ExportCollector('ReferenceThresholdFilter') #As the program is currently written, this function is called to act upon already threshold filtered standardized reference patterns which could cause innaccuracy. @@ -2641,7 +2641,7 @@ def IterativePrepareNextIterationInputFiles(ExperimentDataFullCopy): G.nextUserInputModule.scaleRawDataFactor = G.scaleRawDataFactor #Now going to overwrite parallelized variables with their original versions if they were set to length of chosen molecules. - delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceValueThreshold, referenceSignificantFragmentThresholds' + delimitedStringOfVariablesToUnparallelize = 'moleculeLikelihoods, sensitivityValues, referenceMassFragmentFilterThreshold, referenceSignificantFragmentThresholds' listOfVariablesToUnparallelize = delimitedStringOfVariablesToUnparallelize.split(", ") #Note that we are using ", " as the delimiter, not just "," for variable in listOfVariablesToUnparallelize: G.nextUserInputModule.__dict__[variable]=G.beforeParsedGDict[variable] @@ -3628,7 +3628,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if len(combinations) == 0:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceMassFragmentFilterThreshold, such as referenceMassFragmentFilterThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,num_molecules]) @@ -3891,7 +3891,7 @@ def InverseMethodDistinguished(monitored_reference_intensities,reciprocal_matchi try: numpy.linalg.det(reciprocal_matching_correction_values) except: - print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceValueThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") + print("There is an error in a matrix operation evaluation: The number of feasible mass fragments to check is probably less than the number of molecules. This can happen if referenceMassFragmentFilterThreshold is too strict, leaving not enough feasible fargments to consider. The program is probably about to crash.") if numpy.linalg.det(reciprocal_matching_correction_values) != 0:#only solves if determinant is not equal to zero #Now we will solve with the inverse way, and also for uncertainties if that module is present. #The uncertainties module works well for matrix inverse, but not for dot product. So we make a custom function. @@ -5137,7 +5137,7 @@ def SLSMethod(molecules,monitored_reference_intensities,reciprocal_matching_corr if len(solvedmolecules) == 0: print("Warning: If you have chosen to use unique fragment SLS and your data has no unique fragments (not unique to any molecule), "\ "then the program may be about to crash. If autosolver has been turned on, the program will first attempt to use SLS common and then inverse." \ - " You may want to try using referenceValueThreshold within the feature Reference Mass Fragmentation Threshold, or to raise referenceValueThreshold if already using it.") + " You may want to try using referenceMassFragmentFilterThreshold within the feature Reference Mass Fragmentation Threshold, or to raise referenceMassFragmentFilterThreshold if already using it.") try: #if the molecule wasn't solved for in the inital analysis, then it will have 0 for its solved molecules counter. if solvedmolecules[molecule_iiii] == 0: @@ -5150,7 +5150,7 @@ def SLSMethod(molecules,monitored_reference_intensities,reciprocal_matching_corr except: pass except IndexError: - print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceValueThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using 'inverse' rather than 'sls'.") + print("Warning: SLS could not solve this problem. If you are already using SLS Common, you can try raising the referenceMassFragmentFilterThreshold within the feature Reference Mass Fragmentation Threshold. Alternatively, you can try using 'inverse' rather than 'sls'.") solutions = numpy.array([None]) #This is just creating a numpy array with an element that has a None object, so that the main function can know that SLSMethod failed. if len(uncertainties_dict) > 0: #Note: the indexing in the solutions must match the original indexing, or errors will occur. Now we take the "filled up" solutions and put everything together. uncertainties_dict['concentrations_relative_uncertainties_one_time'] = uncertainties_dict['concentrations_relative_uncertainties_one_time_after_finisher'].transpose()*1.0 @@ -5400,7 +5400,7 @@ def subtract_simulated_signals_of_specific_molecules(moleculeIndicesToSubtract, -#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. +#This function is intended to add back any concentration / intensity that was removed or distorted by reference fragmentation pattern high pass filtering (which is UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold']). It also adds half of the difference to the uncertainties. As of 5/17/20, only a single recursion iteration is performed. #The corrections are performed from largest to smallest (in percentage), with only one molecule's correction per sls mass. That is, the effect of molecule A's filtering on molecule B's concentration, for example. A molecule can be its largest self correction (A to A). Each molecule is corrected in kind, so serial (stacked) correction is among the possibilities that can occur. #TODO: May 17 2020. Right now, we only take the LARGEST correction for each sls when deciding which sls mass to correct, then we apply that correction. But maybe we should take a single recursion of all molecules affecting? Then apply all molecules to that sls mass before moving to the next one? This would still be a single recursion, but would matter if (for example) a single molecule's sls was able to occur due to filtering out 20 other molecule's contributions at that mass. class referenceThresholdFilterCorrectingSandbox(): @@ -6024,7 +6024,7 @@ def PopulateLogFile(): f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) if G.applyReferenceMassFragmentsThresholds == 'yes': f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) - f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) + f6.write('referenceMassFragmentFilterThreshold = %s \n'%(G.referenceMassFragmentFilterThreshold)) f6.write('referenceSignificantFragmentThresholds = %s \n'%(G.referenceSignificantFragmentThresholds)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) @@ -6641,7 +6641,7 @@ def main(): referenceAfterFiltering = currentReferenceData slsSolvedMasses = G.massesUsedInSolvingMoleculesForThisPoint if 0 in slsSolvedMasses: - print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] to a highernumber." ) + print("The concentrations are currently not completely solvable by SLS at this time so implicitSLScorrection is being skipped and changed to False. One option to consider is increasing UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] to a highernumber." ) G.implicitSLScorrection = False else: #Now need to move the class out of this area. Currently test 2 is taking 0.08 to 0.20 anlaysis time versus 0.014 for test_1. diff --git a/README.txt b/README.txt index f1a9cc8b2..5fe572f5b 100644 --- a/README.txt +++ b/README.txt @@ -17,7 +17,7 @@ Suggested Procedure for Solving Time Series Data of Mass Signals 2) Create an MSRESOLVE run with SLS Unique and see what masse MSRESOLVE chooses, with ExportedSLSUniqueMassesUsedInSolvingMolecules. 3) If unsatisfied, start narrowing things down with chosen masses. 4) Also start using some reference file threshold filtering . -a. UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [1.0] #this is what I am suggesting that you use. +a. UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [1.0] #this is what I am suggesting that you use. 5) If the application warrants doing so, include more sophisticated features of MSRESOLVE, such as mass spectrum tuning correction. diff --git a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py index 00c441bda..d4ca49264 100644 --- a/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py +++ b/Todo/SLS Common vs. Unique Bug/DefaultUserInput.py @@ -144,7 +144,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// @@ -240,7 +240,7 @@ 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', - 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', + 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', 'uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniquePrint','SLSUniqueExport','concentrationFinder','molecule','moleculeSignal','massNumber','moleculeConcentration', diff --git a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py index 10158098b..a7b0d7b8b 100644 --- a/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py +++ b/Todo/SLS Common vs. Unique Bug/MSRESOLVE.py @@ -358,11 +358,11 @@ def CorrectionValueCorrector(reference,referenceCorrectionCoefficients,reference #this function eliminates any fragments that are below a certain threshold, for solving #data that is giving negatives or over emphasizing small mass fragments, this will eliminate #those below a certain user-input value -def ReferenceThreshold(reference,referenceValueThreshold): +def ReferenceThreshold(reference,referenceMassFragmentFilterThreshold): referencedata = reference[:,1:] #all the data except the line of abscissa- mass fragment numbers for rowcounter in range(len(referencedata[:,0])):#goes through all rows in references for columncounter in range(len(referencedata[0,:])):#goes through all columns in all rows in reference - if referencedata[rowcounter,columncounter] < referenceValueThreshold:#user input changes + if referencedata[rowcounter,columncounter] < referenceMassFragmentFilterThreshold:#user input changes referencedata[rowcounter,columncounter] = 0 #made to be equal to zero reference[:,1:] = referencedata #this puts changed reference back with mass fragment numbers return reference @@ -929,7 +929,7 @@ def ReferenceInputPreProcessing(ReferenceData): ReferenceData.ExportCollector('CorrectionValueCorrector') if G.applyReferenceMassFragmentsThresholds == 'yes': - ReferenceData.standardized_reference_intensities = ReferenceThreshold(ReferenceData.standardized_reference_intensities,G.referenceValueThreshold) + ReferenceData.standardized_reference_intensities = ReferenceThreshold(ReferenceData.standardized_reference_intensities,G.referenceMassFragmentFilterThreshold) ReferenceData.ExportCollector('ReferenceThreshold') ReferenceData.correction_values = CorrectionValuesObtain(ReferenceData) @@ -1688,7 +1688,7 @@ def CombinationMaker(reciprocal_matching_correction_values,rawsignalsarrayline,m if combinations == []:#This function will not work without enough mass fragments, so the user must know the problem print('****************************************') print('Not enough matching mass fragments input') - print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceValueThreshold, such as referenceValueThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") + print("This means that at some point in the analysis, there were not enough masses in the reference file to apply the inverse method. It could mean you have too many overlapping masses for the molecules you are trying to resolve. You can get around this by using the '#//Reference Mass Fragmentation Threshold//' feature to exclude tiny fragementation peaks. This would be done by setting the value to 'yes' for applyReferenceMassFragmentsThresholds feature with referenceMassFragmentFilterThreshold, such as referenceMassFragmentFilterThreshold = 5.0 . Alternatively, to be more targeted, if you know *which* fragmentation patterns could be overlapping, you could set those minor fragments to 0 in your reference pattern csv file. TODO: Print out the relevant masses here. This requires keeping track of when they are selected prior to combination maker, and possibly passing them as an additional argument.") print('****************************************') combinations_len = len(combinations) correctionarray = numpy.zeros([1,moleculenum]) @@ -3064,7 +3064,7 @@ def PopulateLogFile(): f6.write('rpcTimeRanges = %s \n'%(G.rpcTimeRanges)) if G.applyReferenceMassFragmentsThresholds == 'yes': f6.write('applyReferenceMassFragmentsThresholds = %s \n'%(G.applyReferenceMassFragmentsThresholds)) - f6.write('referenceValueThreshold = %s \n'%(G.referenceValueThreshold)) + f6.write('referenceMassFragmentFilterThreshold = %s \n'%(G.referenceMassFragmentFilterThreshold)) if G.lowerBoundThresholdChooser == 'yes': f6.write('lowerBoundThresholdChooser = %s \n'%(G.lowerBoundThresholdChooser)) f6.write('massesToLowerBoundThresholdFilter = %s \n'%(G.massesToLowerBoundThresholdFilter )) diff --git a/Todo/SLS Common vs. Unique Bug/UserInput.py b/Todo/SLS Common vs. Unique Bug/UserInput.py index 5ae342d86..4d42fdd48 100644 --- a/Todo/SLS Common vs. Unique Bug/UserInput.py +++ b/Todo/SLS Common vs. Unique Bug/UserInput.py @@ -145,7 +145,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'yes' -referenceValueThreshold = [4.9] +referenceMassFragmentFilterThreshold = [4.9] #//Data Threshold Filter// @@ -247,7 +247,7 @@ 'backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound', 'dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesRange','csvFileName','increments','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor', 'tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF', - 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', + 'rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute', 'dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds', 'rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer', 'uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniquePrint','SLSUniqueExport','concentrationFinder','molecule','moleculeSignal','massNumber','moleculeConcentration', diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py index bdfaab5d3..e33656a06 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_iterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py index ba4fb9468..2f0e56ac1 100644 --- a/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/ConcentrationFinder/test_1_initial_input_noniterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ExtractReferencePatternFromData/test_1_input.py b/UnitTests/ExtractReferencePatternFromData/test_1_input.py index a43723602..dcd678150 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_1_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_1_input.py @@ -137,7 +137,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ExtractReferencePatternFromData/test_2_input.py b/UnitTests/ExtractReferencePatternFromData/test_2_input.py index 92cc2c70b..5c42bebb3 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_2_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_2_input.py @@ -137,7 +137,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ExtractReferencePatternFromData/test_3_input.py b/UnitTests/ExtractReferencePatternFromData/test_3_input.py index 145d8688c..53e5a370e 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_3_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_3_input.py @@ -137,7 +137,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ExtractReferencePatternFromData/test_4_input.py b/UnitTests/ExtractReferencePatternFromData/test_4_input.py index 31a6f42c1..dece1333b 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_4_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_4_input.py @@ -126,7 +126,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ExtractReferencePatternFromData/test_5_input.py b/UnitTests/ExtractReferencePatternFromData/test_5_input.py index dee4d62e9..049293ccd 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_5_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_5_input.py @@ -126,7 +126,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ExtractReferencePatternFromData/test_6_input.py b/UnitTests/ExtractReferencePatternFromData/test_6_input.py index aff4fa212..c5d69746e 100644 --- a/UnitTests/ExtractReferencePatternFromData/test_6_input.py +++ b/UnitTests/ExtractReferencePatternFromData/test_6_input.py @@ -126,7 +126,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py index 777dbbead..20b17a64b 100644 --- a/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py +++ b/UnitTests/FinalOptimizer/test_1_Input_Brute_Finisher.py @@ -184,7 +184,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py index 7757156bc..385fe0af2 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_iterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'yes' -referenceValueThreshold = [1.0] +referenceMassFragmentFilterThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] #//Data Threshold Filter// diff --git a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py index 8e2d534e3..799c214d0 100644 --- a/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysis/test_1_initial_input_noniterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'yes' -referenceValueThreshold = [1.0] +referenceMassFragmentFilterThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py index 4b4c3a92f..7aaa7c6df 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_iterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py index 010990f44..0ccced1f8 100644 --- a/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisConcentrationFinder/test_1_initial_input_noniterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py index f23eadc25..dc1a47713 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py index 24136774d..65aeb2123 100644 --- a/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisInterpolatingMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py index 2446a30fc..02fbd2c9c 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_iterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py index f73eacc0e..c24ed1c7f 100644 --- a/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisMultipleReferencePatterns/test_1_initial_input_noniterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py index 508e5eb3e..1dbe9f45d 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_iterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'yes' -referenceValueThreshold = [1.0] +referenceMassFragmentFilterThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py index b1011220b..2314b4b40 100644 --- a/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py +++ b/UnitTests/IterativeAnalysisScaleRawData/test_1_initial_input_noniterative.py @@ -147,7 +147,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'yes' -referenceValueThreshold = [1.0] +referenceMassFragmentFilterThreshold = [1.0] referenceSignificantFragmentThresholds = [0.0] diff --git a/UnitTests/NegativeAnalyzer/test_1_Input.py b/UnitTests/NegativeAnalyzer/test_1_Input.py index 6228c8bff..a31c0cf36 100644 --- a/UnitTests/NegativeAnalyzer/test_1_Input.py +++ b/UnitTests/NegativeAnalyzer/test_1_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py index 85bc8d3e5..b8d5b40d9 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputA.py @@ -134,7 +134,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py index 01a5fcfd5..4e27e1f83 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputB.py @@ -134,7 +134,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py index b79b27710..1cf18fa2d 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py +++ b/UnitTests/ReferencePatternTimeChooser/test_1_inputC.py @@ -134,7 +134,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/ReferencePatternTimeChooser/test_2_input.py b/UnitTests/ReferencePatternTimeChooser/test_2_input.py index 4a1971f0d..e5b00c731 100644 --- a/UnitTests/ReferencePatternTimeChooser/test_2_input.py +++ b/UnitTests/ReferencePatternTimeChooser/test_2_input.py @@ -134,7 +134,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/TuningCorrector/test_1.py b/UnitTests/TuningCorrector/test_1.py index ef21a9ac7..3080d4cc7 100644 --- a/UnitTests/TuningCorrector/test_1.py +++ b/UnitTests/TuningCorrector/test_1.py @@ -42,7 +42,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' -MSRESOLVE.G.referenceValueThreshold = [6.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] #Now to get started with the test itself... diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff index 1ecc06292..20cf09ae9 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_10.turnedOff @@ -41,7 +41,7 @@ MSRESOLVE.G.dataSmootherYorN = 'no' #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [4.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff index ad3b964b8..866a2d6ad 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/1/test_5.turnedOff @@ -41,7 +41,7 @@ MSRESOLVE.G.dataSmootherYorN = 'no' #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' -MSRESOLVE.G.referenceValueThreshold = [0.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] #Now to get started with the test itself... diff --git a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff index 1ecc06292..20cf09ae9 100644 --- a/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_10 Manual SLS/4/test_10.turnedOff @@ -41,7 +41,7 @@ MSRESOLVE.G.dataSmootherYorN = 'no' #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [4.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_10.py b/UnitTests/TuningCorrector/test_10.py index 2b448a719..ecd3dfe02 100644 --- a/UnitTests/TuningCorrector/test_10.py +++ b/UnitTests/TuningCorrector/test_10.py @@ -41,7 +41,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [4.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff index 1ecc06292..20cf09ae9 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_10.turnedOff @@ -41,7 +41,7 @@ MSRESOLVE.G.dataSmootherYorN = 'no' #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [4.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff index 4e4a2a8cc..b7878d471 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/1/test_11.turnedOff @@ -41,7 +41,7 @@ MSRESOLVE.G.dataSmootherYorN = 'no' #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [4.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' MSRESOLVE.G.implicitSLScorrection = True diff --git a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff index 4e4a2a8cc..b7878d471 100644 --- a/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff +++ b/UnitTests/TuningCorrector/test_11 Manual SLS Implicit/4/test_11.turnedOff @@ -41,7 +41,7 @@ MSRESOLVE.G.dataSmootherYorN = 'no' #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [4.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' MSRESOLVE.G.implicitSLScorrection = True diff --git a/UnitTests/TuningCorrector/test_11.py b/UnitTests/TuningCorrector/test_11.py index 1aa39e81c..311ad52bb 100644 --- a/UnitTests/TuningCorrector/test_11.py +++ b/UnitTests/TuningCorrector/test_11.py @@ -41,7 +41,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [4.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [4.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [6.0] MSRESOLVE.G.answer = 'sls' MSRESOLVE.G.implicitSLScorrection = True diff --git a/UnitTests/TuningCorrector/test_2.py b/UnitTests/TuningCorrector/test_2.py index 378a8271b..fdfa8f0e9 100644 --- a/UnitTests/TuningCorrector/test_2.py +++ b/UnitTests/TuningCorrector/test_2.py @@ -42,7 +42,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [6.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] #Now to get started with the test itself... diff --git a/UnitTests/TuningCorrector/test_3.py b/UnitTests/TuningCorrector/test_3.py index de4a88e30..cb6bc7b44 100644 --- a/UnitTests/TuningCorrector/test_3.py +++ b/UnitTests/TuningCorrector/test_3.py @@ -44,7 +44,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' -MSRESOLVE.G.referenceValueThreshold = [6.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] #Now to get started with the test itself... diff --git a/UnitTests/TuningCorrector/test_4.py b/UnitTests/TuningCorrector/test_4.py index dab06ff84..2af5182ed 100644 --- a/UnitTests/TuningCorrector/test_4.py +++ b/UnitTests/TuningCorrector/test_4.py @@ -42,7 +42,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' -MSRESOLVE.G.referenceValueThreshold = [0.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] #Now to get started with the test itself... diff --git a/UnitTests/TuningCorrector/test_5.py b/UnitTests/TuningCorrector/test_5.py index 8b17dcabd..5ebe24ec1 100644 --- a/UnitTests/TuningCorrector/test_5.py +++ b/UnitTests/TuningCorrector/test_5.py @@ -41,7 +41,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' -MSRESOLVE.G.referenceValueThreshold = [0.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] #Now to get started with the test itself... diff --git a/UnitTests/TuningCorrector/test_6.py b/UnitTests/TuningCorrector/test_6.py index 650d5cc3e..c12a69670 100644 --- a/UnitTests/TuningCorrector/test_6.py +++ b/UnitTests/TuningCorrector/test_6.py @@ -42,7 +42,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'no' -MSRESOLVE.G.referenceValueThreshold = [0.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [0.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] #Now to get started with the test itself... diff --git a/UnitTests/TuningCorrector/test_7.py b/UnitTests/TuningCorrector/test_7.py index a988b2fa9..5f414b6e7 100644 --- a/UnitTests/TuningCorrector/test_7.py +++ b/UnitTests/TuningCorrector/test_7.py @@ -44,7 +44,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [6.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] MSRESOLVE.G.specificMassFragments = 'yes' diff --git a/UnitTests/TuningCorrector/test_8.py b/UnitTests/TuningCorrector/test_8.py index 1d52d21e4..6763e421f 100644 --- a/UnitTests/TuningCorrector/test_8.py +++ b/UnitTests/TuningCorrector/test_8.py @@ -43,7 +43,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [6.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] MSRESOLVE.G.specificMassFragments = 'yes' diff --git a/UnitTests/TuningCorrector/test_9.py b/UnitTests/TuningCorrector/test_9.py index 49a46e2d0..5dca01aa6 100644 --- a/UnitTests/TuningCorrector/test_9.py +++ b/UnitTests/TuningCorrector/test_9.py @@ -44,7 +44,7 @@ #will use applyReferenceMassFragmentsThresholds (single value means it will be applied to all molecules) MSRESOLVE.G.applyReferenceMassFragmentsThresholds= 'yes' -MSRESOLVE.G.referenceValueThreshold = [6.0] +MSRESOLVE.G.referenceMassFragmentFilterThreshold = [6.0] MSRESOLVE.G.referenceSignificantFragmentThresholds = [0.0] MSRESOLVE.G.specificMassFragments = 'no' diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py index 5ed05dbb4..74f1daab3 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture.py @@ -185,7 +185,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py index 41a3ee2d7..64dadaa48 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture2.py @@ -187,7 +187,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py index f6d96eda8..9e60017ad 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture3.py @@ -187,7 +187,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py index 6ee912f6b..75e2d1b44 100644 --- a/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py +++ b/UnitTests/TuningCorrectorGasMixture/UserInputGasMixture4.py @@ -187,7 +187,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py index 071990e6a..718ad7e0b 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYXY.py @@ -188,7 +188,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py index 3192e55ab..cd27d72cc 100644 --- a/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py +++ b/UnitTests/XYXYReferencePattern/test_1_inputXYYY.py @@ -188,7 +188,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #//Data Threshold Filter// @@ -301,4 +301,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py index d30e11375..1155d6f8e 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_1_input.py @@ -145,7 +145,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py index ffc039e2e..340890c48 100644 --- a/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py +++ b/UnitTests/excludeMoleculesIfSignificantFragmentNotObserved/test_2_input.py @@ -145,7 +145,7 @@ #//Reference Mass Fragmentation Threshold// # if you want to exclude tiny fragmentation peaks applyReferenceMassFragmentsThresholds= 'no' -referenceValueThreshold = [6.0] +referenceMassFragmentFilterThreshold = [6.0] #//Data Threshold Filter// diff --git a/UnitTests/implicitSLScorrection/test_1_Input.py b/UnitTests/implicitSLScorrection/test_1_Input.py index 7d388354a..37f10514d 100644 --- a/UnitTests/implicitSLScorrection/test_1_Input.py +++ b/UnitTests/implicitSLScorrection/test_1_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/implicitSLScorrection/test_2_Input.py b/UnitTests/implicitSLScorrection/test_2_Input.py index 149b1d09e..7ee4cca3e 100644 --- a/UnitTests/implicitSLScorrection/test_2_Input.py +++ b/UnitTests/implicitSLScorrection/test_2_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -296,4 +296,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py index c8895f668..f56c274da 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_1_UserInput.py @@ -58,7 +58,7 @@ rpcMoleculesToChangeMF = [[2, 4, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 32, 44]] rpcTimeRanges = [[6745.0, 8000]] applyReferenceMassFragmentsThresholds = 'yes' -referenceValueThreshold = [1.0] +referenceMassFragmentFilterThreshold = [1.0] referenceSignificantFragmentThresholds = [3.0] lowerBoundThresholdChooser = 'no' massesToLowerBoundThresholdFilter = [] @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py index 3e1bb1eb8..6dd9679f7 100644 --- a/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py +++ b/UnitTests/referenceSignificantFragmentThreshold/test_2_UserInput.py @@ -58,7 +58,7 @@ rpcMoleculesToChangeMF = [[2, 4, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 32, 44]] rpcTimeRanges = [[6745.0, 8000]] applyReferenceMassFragmentsThresholds = 'yes' -referenceValueThreshold = [1.0] +referenceMassFragmentFilterThreshold = [1.0] referenceSignificantFragmentThresholds = [1.0, 3.0, 3.0] lowerBoundThresholdChooser = 'no' massesToLowerBoundThresholdFilter = [] @@ -111,4 +111,4 @@ timeSinceLastCheckpoint = '' iterationNumber = None -# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file +# __var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName','oldDataToAnalyzeFileName','nextRefFileName','nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','answer','uniqueOrCommon','slsFinish','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport','concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint','iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsCommon/test_1_Input.py b/UnitTests/slsCommon/test_1_Input.py index 015976792..98dbdfa4d 100644 --- a/UnitTests/slsCommon/test_1_Input.py +++ b/UnitTests/slsCommon/test_1_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -286,4 +286,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py index 51e59a1df..1449e4338 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_1_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -288,4 +288,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py index 1db6a126f..6ac289b16 100644 --- a/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py +++ b/UnitTests/slsUniquePositiveConcentrationsOnly/test_2_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -287,4 +287,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_10_Input.py b/UnitTests/uncertainties/test_10_Input.py index 95dbdf233..2028d9eed 100644 --- a/UnitTests/uncertainties/test_10_Input.py +++ b/UnitTests/uncertainties/test_10_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_11_Input.py b/UnitTests/uncertainties/test_11_Input.py index e26952415..386cf8905 100644 --- a/UnitTests/uncertainties/test_11_Input.py +++ b/UnitTests/uncertainties/test_11_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [0.1] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_12_Input.py b/UnitTests/uncertainties/test_12_Input.py index 10785c7c4..5e0b44a3c 100644 --- a/UnitTests/uncertainties/test_12_Input.py +++ b/UnitTests/uncertainties/test_12_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_13_Input.py b/UnitTests/uncertainties/test_13_Input.py index 746edccb8..19def2983 100644 --- a/UnitTests/uncertainties/test_13_Input.py +++ b/UnitTests/uncertainties/test_13_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [0.1] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_14_Input.py b/UnitTests/uncertainties/test_14_Input.py index e3551c139..1765e1d63 100644 --- a/UnitTests/uncertainties/test_14_Input.py +++ b/UnitTests/uncertainties/test_14_Input.py @@ -186,7 +186,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [0.1] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [2.0] #//Data Threshold Filter// @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_15_Input.py b/UnitTests/uncertainties/test_15_Input.py index 9456cbe42..a811acc1c 100644 --- a/UnitTests/uncertainties/test_15_Input.py +++ b/UnitTests/uncertainties/test_15_Input.py @@ -186,7 +186,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [0.1] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [2.0] #//Data Threshold Filter// @@ -300,4 +300,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_16_Input.py b/UnitTests/uncertainties/test_16_Input.py index 702c0c0a8..f64f11a75 100644 --- a/UnitTests/uncertainties/test_16_Input.py +++ b/UnitTests/uncertainties/test_16_Input.py @@ -185,7 +185,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.1] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [0.1] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [2.0] #//Data Threshold Filter// @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_1_Input.py b/UnitTests/uncertainties/test_1_Input.py index bd198a2a6..bfac06980 100644 --- a/UnitTests/uncertainties/test_1_Input.py +++ b/UnitTests/uncertainties/test_1_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_2_Input.py b/UnitTests/uncertainties/test_2_Input.py index 622dfed2e..365f18707 100644 --- a/UnitTests/uncertainties/test_2_Input.py +++ b/UnitTests/uncertainties/test_2_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -298,4 +298,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_3_Input.py b/UnitTests/uncertainties/test_3_Input.py index 352b05cf7..171b11b1f 100644 --- a/UnitTests/uncertainties/test_3_Input.py +++ b/UnitTests/uncertainties/test_3_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_4_Input.py b/UnitTests/uncertainties/test_4_Input.py index 8f64d986c..c267bc932 100644 --- a/UnitTests/uncertainties/test_4_Input.py +++ b/UnitTests/uncertainties/test_4_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_5_Input.py b/UnitTests/uncertainties/test_5_Input.py index 3c91bc419..e736c404e 100644 --- a/UnitTests/uncertainties/test_5_Input.py +++ b/UnitTests/uncertainties/test_5_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_6_Input.py b/UnitTests/uncertainties/test_6_Input.py index a1e402b70..169401989 100644 --- a/UnitTests/uncertainties/test_6_Input.py +++ b/UnitTests/uncertainties/test_6_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_7_Input.py b/UnitTests/uncertainties/test_7_Input.py index e10d88125..994afcdbc 100644 --- a/UnitTests/uncertainties/test_7_Input.py +++ b/UnitTests/uncertainties/test_7_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_8_Input.py b/UnitTests/uncertainties/test_8_Input.py index 9809dc665..255e6cec3 100644 --- a/UnitTests/uncertainties/test_8_Input.py +++ b/UnitTests/uncertainties/test_8_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [2.0] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [2.0] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UnitTests/uncertainties/test_9_Input.py b/UnitTests/uncertainties/test_9_Input.py index f0ec8b86a..3b29eeeb0 100644 --- a/UnitTests/uncertainties/test_9_Input.py +++ b/UnitTests/uncertainties/test_9_Input.py @@ -183,7 +183,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'yes' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [0.5] +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [0.5] UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [5.0] #//Data Threshold Filter// @@ -297,4 +297,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName','referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection','referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] \ No newline at end of file diff --git a/UserInput.py b/UserInput.py index a3da682d4..517fecf5f 100644 --- a/UserInput.py +++ b/UserInput.py @@ -189,7 +189,7 @@ UserChoices['applyReferenceMassFragmentsThresholds'] = {} #initialize the applyReferenceMassFragmentsThresholds container # if you want to exclude tiny fragmentation peaks UserChoices['applyReferenceMassFragmentsThresholds']['on'] = 'no' -UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. +UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] = [5.0] #typical values are between 1 and 5. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This approximates smaller fragmentation peaks as '0', though implicitSLS will correct for the approximation. UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] = [6.0] #typical values are between 5 and 50. Can be a list (one value for each molecule) or a single value across all molecules. The list case has not been tested with all features. This setting causes MSRESOLVE to favor larger intensity reference peaks (above the number provided) during solving. #//Data Threshold Filter// @@ -303,4 +303,4 @@ SettingsVDictionary = userInputValidityCheck(UserChoices) populateModuleVariablesFromDictionary(thisModuleObject, SettingsVDictionary) ####End of temporary code#### -__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceValueThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] +__var_list__ = ['referencePatternsFileNamesList','referencePatternsFormsList','dataToAnalyzeFileName', 'referencePatternTimeRanges','ionizationDataFileName','iterativeAnalysis','iterationNumber','iterationSuffix','unusedMolecules','oldReferenceFileName', 'oldDataToAnalyzeFileName', 'nextRefFileName', 'nextExpFileName','preProcessing','dataAnalysis','dataSimulation','grapher','stopAtGraphs','timeRangeLimit','timeRangeStart','timeRangeFinish','specificMolecules','chosenMoleculesNames','specificMassFragments','chosenMassFragments','moleculeLikelihoods','sensitivityValues','linearBaselineCorrectionSemiAutomatic','baselineType','massesToBackgroundCorrect','earlyBaselineTimes','lateBaselineTimes','backgroundMassFragment','backgroundSlopes','backgroundIntercepts','interpolateYorN','marginalChangeRestriction','ignorableDeltaYThreshold','dataLowerBound','dataUpperBound','dataRangeSpecifierYorN','signalOrConcentrationRange','csvFile','moleculesToRestrict','csvFileName','bruteIncrements','permutationNum','maxPermutations','scaleRawDataOption','scaleRawDataFactor','tuningCorrection', 'tuningCorrectPatternInternalVsExternal', 'referenceFileStandardTuningAndForm', 'createMixedTuningPattern', 'referenceFileExistingTuningAndForm','referenceFileDesiredTuningAndForm','referenceCorrectionCoefficients','referenceCorrectionCoefficients_cov','extractReferencePatternFromDataOption','rpcMoleculesToChange','rpcMoleculesToChangeMF','rpcTimeRanges','applyReferenceMassFragmentsThresholds','referenceMassFragmentFilterThreshold','referenceSignificantFragmentThresholds','lowerBoundThresholdChooser','massesToLowerBoundThresholdFilter','lowerBoundThresholdPercentage','lowerBoundThresholdAbsolute','dataSmootherYorN','dataSmootherChoice','dataSmootherTimeRadius','dataSmootherPointRadius','dataSmootherHeadersToConfineTo','polynomialOrder','applyRawSignalThresholds','rawSignalThresholdValue','sensitivityThresholdValue','rawSignalThresholdDivider','rawSignalThresholdLimit','rawSignalThresholdLimitPercent','negativeAnalyzerYorN','NegativeAnalyzerTopNContributors','NegativeAnalyzerBaseNumberOfGridIntervals','calculateUncertaintiesInConcentrations' , 'referenceFileUncertainties' ,'collectedFileUncertainties','referenceCorrectionCoefficientsUncertainties', 'referenceCorrectionCoefficientsIonizationUncertainties' ,'answer','uniqueOrCommon','slsWeighting','slsFinish','slsUniquePositiveConcentrationsOnly','objectiveFunctionType','distinguished','fullBrute','SLSUniqueExport', 'implicitSLScorrection', 'implicitSLSRecursion', 'finalOptimization', 'concentrationFinder','moleculesTSC_List','TSC_List_Type','moleculeSignalTSC_List','massNumberTSC_List','moleculeConcentrationTSC_List','unitsTSC','preProcessedDataOutputName','resolvedScaledConcentrationsOutputName','scaledConcentrationsPercentages','concentrationsOutputName','simulatedSignalsOutputName','TotalConcentrationsOutputName','ExportAtEachStep','generatePercentages','checkpoint','start','timeSinceLastCheckpoint', 'iterationNumber'] diff --git a/userInputValidityFunctions.py b/userInputValidityFunctions.py index 34d9d7038..4dc57c79a 100644 --- a/userInputValidityFunctions.py +++ b/userInputValidityFunctions.py @@ -147,9 +147,9 @@ def parseUserInput(currentUserInput): #Reference Mass Fragmentation Threshold parse.strCheck(currentUserInput.applyReferenceMassFragmentsThresholds,'applyReferenceMassFragmentsThresholds') if currentUserInput.applyReferenceMassFragmentsThresholds == 'yes': #If using reference mass fragmentation threshold - currentUserInput.referenceValueThreshold = parse.listCast(currentUserInput.referenceValueThreshold) #reference value threshold is a list + currentUserInput.referenceMassFragmentFilterThreshold = parse.listCast(currentUserInput.referenceMassFragmentFilterThreshold) #reference value threshold is a list #The length of the reference value thresholds needs to be the same length as the number of molecules - currentUserInput.referenceValueThreshold = parse.parallelVectorize(currentUserInput.referenceValueThreshold,len(chosenMoleculesForParsing)) + currentUserInput.referenceMassFragmentFilterThreshold = parse.parallelVectorize(currentUserInput.referenceMassFragmentFilterThreshold,len(chosenMoleculesForParsing)) currentUserInput.referenceSignificantFragmentThresholds = parse.parallelVectorize(currentUserInput.referenceSignificantFragmentThresholds,len(chosenMoleculesForParsing)) #Data Threshold Filter @@ -424,7 +424,7 @@ def userInputValidityCheck(UserChoices): #Right now, currentUserInputModule is t SettingsVDictionary['rpcMoleculesToChangeMF'] = UserChoices['extractReferencePatternFromDataOption']['rpcMoleculesToChangeMF'] SettingsVDictionary['applyReferenceMassFragmentsThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['on'] - SettingsVDictionary['referenceValueThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceValueThreshold'] + SettingsVDictionary['referenceMassFragmentFilterThreshold'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceMassFragmentFilterThreshold'] SettingsVDictionary['referenceSignificantFragmentThresholds'] = UserChoices['applyReferenceMassFragmentsThresholds']['referenceSignificantFragmentThresholds'] SettingsVDictionary['lowerBoundThresholdChooser'] = UserChoices['lowerBoundThresholdChooser']['on']