Merge pull request #283 from AdityaSavara/tuningCorrectPatternInterna…

…lVsExternal

Tuning correct pattern internal vs external

DefaultUserInput.py

@@ -155,6 +155,7 @@
 #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 referenceFileStandardTuning and referenceFileExistingTuning must be filled.
 UserChoices['measuredReferenceYorN']['referenceFileStandardTuning'] = [] #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']['referenceFileExistingTuning'] =[] #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'] .
@@ -301,4 +302,4 @@
 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', 'referenceFileStandardTuning', 'createMixedTuningPattern', 'referenceFileExistingTuning','referenceFileDesiredTuning','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']
+__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', 'referenceFileStandardTuning', 'createMixedTuningPattern', 'referenceFileExistingTuning','referenceFileDesiredTuning','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']