Updated uncertainties unit tests with the raw signal uncertainties bu…

…g fix

UnitTests/BestMassFragmentChooser/bestMassFragCombinations.txt

@@ -1,3 +1,3 @@
 The setting of useExtentOfSLSUniqueSolvable was used. The best combination is the last in this file. 
-Time taken:1.3400261402130127
+Time taken:1.1496350765228271
 [(28.0, 31.0, 44.0, 57.0), (28.0, 31.0, 45.0, 57.0), (28.0, 31.0, 46.0, 57.0), (28.0, 31.0, 50.0, 57.0), (28.0, 31.0, 51.0, 57.0), (28.0, 31.0, 53.0, 57.0), (28.0, 31.0, 54.0, 57.0), (28.0, 31.0, 55.0, 57.0), (28.0, 31.0, 57.0, 71.0), (28.0, 31.0, 57.0, 72.0)]

UnitTests/ConcentrationFinder/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:44:29 2020
+Wed Jul  1 01:31:37 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2_test_2.csv', 'AcetaldehydeNISTRefMixed2_test_2.csv'] 
 form  = ['xyyy', 'xyyy'] 
@@ -20,5 +20,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.34646 seconds 
+Run Time 0.25471 seconds 
 ###################################################################### 

UnitTests/ExtractReferencePatternFromData/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:44:54 2020
+Wed Jul  1 01:31:58 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2.csv'] 
 form  = ['xyyy'] 
@@ -27,5 +27,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 3.69348 seconds 
+Run Time 3.85358 seconds 
 ###################################################################### 

UnitTests/FinalOptimizer/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:01 2020
+Wed Jul  1 01:32:04 2020
 
 referenceFileName = ['ConvertedSpectra.csv'] 
 form  = ['xyyy'] 
@@ -20,5 +20,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 5.30980 seconds 
+Run Time 4.49940 seconds 
 ###################################################################### 

UnitTests/IonizationFactors/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:13 2020
+Wed Jul  1 01:32:13 2020
 
 referenceFileName = ['AcetaldehydeNISTRefDefault.csv'] 
 form  = ['xyyy'] 
@@ -17,5 +17,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.15429 seconds 
+Run Time 0.09840 seconds 
 ###################################################################### 

UnitTests/IterativeAnalysis/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:18 2020
+Wed Jul  1 01:32:17 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2.csv'] 
 form  = ['xyyy'] 
@@ -24,5 +24,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 3.02029 seconds 
+Run Time 1.99509 seconds 
 ###################################################################### 

UnitTests/IterativeAnalysis/_iter_1/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:18 2020
+Wed Jul  1 01:32:17 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2_iter_1.csv'] 
 form  = ['xyyy'] 
@@ -26,5 +26,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.68222 seconds 
+Run Time 0.36831 seconds 
 ###################################################################### 

UnitTests/IterativeAnalysis/_iter_1/UserInput_iter_1.py

@@ -110,8 +110,8 @@
 TotalConcentrationsOutputName = 'TotalConcentrations.csv'
 ExportAtEachStep = 'yes'
 generatePercentages = 'no'
-checkpoint = 4.7398137
-start = 4.739813
+checkpoint = 3.0814512
+start = 3.081451
 timeSinceLastCheckpoint = ''
 iterationNumber = 1
 

UnitTests/IterativeAnalysis/_iter_2/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:19 2020
+Wed Jul  1 01:32:17 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2_iter_2.csv'] 
 form  = ['xyyy'] 
@@ -21,5 +21,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.30652 seconds 
+Run Time 0.26333 seconds 
 ###################################################################### 

UnitTests/IterativeAnalysis/_iter_2/UserInput_iter_2.py

@@ -110,9 +110,9 @@
 TotalConcentrationsOutputName = 'TotalConcentrations.csv'
 ExportAtEachStep = 'yes'
 generatePercentages = 'no'
-checkpoint = 5.4220345
-start = 4.739813
-timeSinceLastCheckpoint = 0.5069764000000001
+checkpoint = 3.4497605
+start = 3.081451
+timeSinceLastCheckpoint = 0.23456110000000008
 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','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','bruteOption','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']

UnitTests/IterativeAnalysis/_iter_3/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:19 2020
+Wed Jul  1 01:32:18 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2_iter_3.csv'] 
 form  = ['xyyy'] 
@@ -21,5 +21,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.45232 seconds 
+Run Time 0.25191 seconds 
 ###################################################################### 

UnitTests/IterativeAnalysis/_iter_3/UserInput_iter_3.py

@@ -110,9 +110,9 @@
 TotalConcentrationsOutputName = 'TotalConcentrations.csv'
 ExportAtEachStep = 'yes'
 generatePercentages = 'no'
-checkpoint = 5.8121172
-start = 5.5055984
-timeSinceLastCheckpoint = 0.2256796000000003
+checkpoint = 3.788583
+start = 3.525252
+timeSinceLastCheckpoint = 0.20203210000000027
 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','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','bruteOption','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']

UnitTests/IterativeAnalysis/_iter_4/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:20 2020
+Wed Jul  1 01:32:18 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2_iter_4.csv'] 
 form  = ['xyyy'] 
@@ -21,5 +21,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.38285 seconds 
+Run Time 0.26583 seconds 
 ###################################################################### 

UnitTests/IterativeAnalysis/_iter_4/UserInput_iter_4.py

@@ -110,9 +110,9 @@
 TotalConcentrationsOutputName = 'TotalConcentrations.csv'
 ExportAtEachStep = 'yes'
 generatePercentages = 'no'
-checkpoint = 6.3624509
-start = 5.9101333
-timeSinceLastCheckpoint = 0.33305130000000016
+checkpoint = 4.1224776
+start = 3.8705699
+timeSinceLastCheckpoint = 0.1948082000000002
 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','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','bruteOption','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']

UnitTests/IterativeAnalysis/_iter_5/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:20 2020
+Wed Jul  1 01:32:18 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2_iter_5.csv'] 
 form  = ['xyyy'] 
@@ -21,5 +21,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.42404 seconds 
+Run Time 0.23362 seconds 
 ###################################################################### 

UnitTests/IterativeAnalysis/_iter_5/UserInput_iter_5.py

@@ -110,9 +110,9 @@
 TotalConcentrationsOutputName = 'TotalConcentrations.csv'
 ExportAtEachStep = 'yes'
 generatePercentages = 'no'
-checkpoint = 6.8962276
-start = 6.5133819
-timeSinceLastCheckpoint = 0.2769219000000005
+checkpoint = 4.4869594
+start = 4.2211254
+timeSinceLastCheckpoint = 0.19609979999999982
 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','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','bruteOption','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']

UnitTests/IterativeAnalysis/_iter_6/LogFile.txt

@@ -1,4 +1,4 @@
-Tue Jun 30 09:45:21 2020
+Wed Jul  1 01:32:19 2020
 
 referenceFileName = ['AcetaldehydeNISTRefMixed2_iter_6.csv'] 
 form  = ['xyyy'] 
@@ -21,5 +21,5 @@ scaleRawDataFactor  = 1.0
 resolvedScaledConcentrationsOutputName  = ScaledConcentrations.csv 
 concentrationsOutputName = ResolvedConcentrations.csv 
 simulatedSignalsOutputName = SimulatedRawSignals.csv 
-Run Time 0.36543 seconds 
+Run Time 0.26024 seconds 
 ######################################################################