Merge pull request #271 from AdityaSavara/Update-to-XYXY-Feature

Update to XYXY Feature

Author: AdityaSavara

DefaultUserInput.py

@@ -155,11 +155,11 @@
 #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']['referenceFileStandardTuning'] = [] #optional: provides tuningCorrectionIntensity feature. Will automatically be used for ReferenceFileExistingTuning if that variable is blank and if createMixedTuningPattern=True.
+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 changed. Should be blank by default.
-UserChoices['measuredReferenceYorN']['referenceFileDesiredTuning'] =[] #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']['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'] .
+UserChoices['measuredReferenceYorN']['referenceFileDesiredTuning'] =[] #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".
 
@@ -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', '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', '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']