/// <summary>
/// The input UIMF file needs to be a UIMF file created by direct-injection
/// IMS, with different drift tube voltages at different frames.
/// This constructor intelligently group voltages together by observing
/// sharp changes in running voltage standard deviation. The entire mobility
/// and frame range would be accumulated.
/// </summary>
/// <param name="startScan">
/// The start scan.
/// </param>
/// <param name="endScan">
/// The end scan.
/// </param>
/// <param name="startBin">
/// The start bin.
/// </param>
/// <param name="endBin">
/// The end bin.
/// </param>
/// <param name="xCompression">
/// The x compression.
/// </param>
/// <param name="yCompression">
/// The y compression.
/// </param>
/// <param name="fullScan">
/// The full Scan.
/// </param>
/// <param name="exportFormat">
/// The export Format.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
private bool RunVoltageAccumulationWorkflow(int startScan, int endScan, int startBin, int endBin, double xCompression, double yCompression, bool fullScan, FileFormatEnum exportFormat)
{
CrossSectionSearchParameters defaultParams = new CrossSectionSearchParameters(88);
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(this.UimfReader, 100, defaultParams.MzWindowHalfWidthInPpm, defaultParams.DriftTubeLengthInCm);
IEnumerable<VoltageGroup> voltageGroups = accumulatedXiCs.Keys;
bool success = true;
foreach (var voltageGroup in voltageGroups)
{
// convert to MzML or UIMFs
if (exportFormat == FileFormatEnum.UIMF)
{
string outputPath = Path.Combine(this.OutputDir, this.datasetName + "_" + Math.Round(voltageGroup.MeanVoltageInVolts) + "V.uimf");
UimfExporter uimfExporter = new UimfExporter();
success = success && uimfExporter.ExportVoltageGroupAsSingleFrameUimf(outputPath, voltageGroup, this.UimfReader, this.averageNotSum, startScan, endScan, startBin, endBin, xCompression, yCompression, fullScan);
Console.WriteLine("Writing UIMF files to {0}", outputPath);
}
else if (exportFormat == FileFormatEnum.MzML)
{
string outputPath = Path.Combine(this.OutputDir, this.datasetName + "_" + Math.Round(voltageGroup.MeanVoltageInVolts) + "V.mzML");
RetentionMobilitySwappedMzMLExporter mzMLExporter = new RetentionMobilitySwappedMzMLExporter();
success = success && mzMLExporter.ExportMzML(this.inputPath, outputPath, voltageGroup, this.UimfReader, this.averageNotSum);
Console.WriteLine("Writing MzML files to {0}", outputPath);
}
}
return success;
}
/// <summary>
/// The run libray match workflow.
/// </summary>
/// <param name="target">
/// The Target.
/// </param>
/// <returns>
/// The <see cref="LibraryMatchResult"/>.
/// </returns>
private LibraryMatchResult RunLibrayMatchWorkflow(DriftTimeTarget target)
{
Trace.WriteLine(" Target: " + target.CorrespondingChemical);
Trace.WriteLine(" Target Info: " + target.TargetDescriptor);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
ITheorFeatureGenerator featureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = featureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
// Voltage grouping
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(this.uimfReader, target.MassWithAdduct, this.Parameters.InitialSearchMassToleranceInPpm, target.NormalizedDriftTimeInMs, this.Parameters.DriftTimeToleranceInMs, this.Parameters.DriftTubeLengthInCm);
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
// TODO Verify the temperature, pressure and drift tube voltage of the voltage group
// Because we don't record TVP info in the AMT library. we can't verify it yet, so stick with last voltage group.
if (IMSUtil.IsLastVoltageGroup(voltageGroup, this.NumberOfFrames))
{
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, this.uimfReader);
Trace.WriteLine(string.Format(" Temperature/Pressure/Voltage Adjusted Drift time: {0:F4} ms", IMSUtil.DeNormalizeDriftTime(target.NormalizedDriftTimeInMs, voltageGroup)));
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, this.smoother, this.Parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, this.uimfReader, voltageGroup, target.MassWithAdduct, this.Parameters.InitialSearchMassToleranceInPpm)).ToList();
// Score features
IDictionary<StandardImsPeak, PeakScores> scoresTable = new Dictionary<StandardImsPeak, PeakScores>();
Trace.WriteLine(string.Format(" Voltage Group: {0:F4} V, [{1}-{2}]", voltageGroup.MeanVoltageInVolts, voltageGroup.FirstFrameNumber, voltageGroup.LastFrameNumber));
foreach (StandardImsPeak peak in standardPeaks)
{
PeakScores currentStatistics = FeatureScoreUtilities.ScoreFeature(
peak,
globalMaxIntensity,
this.uimfReader,
this.Parameters.InitialSearchMassToleranceInPpm,
this.Parameters.DriftTimeToleranceInMs,
voltageGroup,
this.NumberOfScans,
target,
IsotopicScoreMethod.Angle,
theoreticalIsotopicProfilePeakList);
scoresTable.Add(peak, currentStatistics);
}
// filter out features with Ims scans at 1% left or right.
Predicate<StandardImsPeak> scanPredicate = blob => FeatureFilters.FilterExtremeDriftTime(blob, (int)this.NumberOfScans);
Predicate<StandardImsPeak> shapeThreshold = blob => FeatureFilters.FilterBadPeakShape(blob, scoresTable[blob].PeakShapeScore, this.Parameters.PeakShapeThreshold);
Predicate<StandardImsPeak> isotopeThreshold = blob => FeatureFilters.FilterBadIsotopicProfile(blob, scoresTable[blob].IsotopicScore, this.Parameters.IsotopicThreshold);
Predicate<StandardImsPeak> massDistanceThreshold = blob => FeatureFilters.FilterHighMzDistance(blob, target, this.Parameters.MatchingMassToleranceInPpm);
// Print out candidate features that pass the intensity threshold.
foreach (StandardImsPeak peak in standardPeaks)
{
DriftTimeFeatureDistance distance = new DriftTimeFeatureDistance(target, peak, voltageGroup);
bool badScanRange = scanPredicate(peak);
bool badPeakShape = shapeThreshold(peak);
bool lowIsotopicAffinity = isotopeThreshold(peak);
bool lowMzAffinity = massDistanceThreshold(peak);
PeakScores currentStatistics = scoresTable[peak];
Trace.WriteLine(string.Empty);
Trace.WriteLine(string.Format(" Candidate feature found at drift time {0:F2} ms (scan number {1})",
peak.PeakApex.DriftTimeCenterInMs,
peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(
string.Format(
" M/Z: {0:F2} Dalton", peak.PeakApex.MzCenterInDalton));
Trace.WriteLine(
string.Format(
" Drift time: {0:F2} ms (scan number {1})",
peak.PeakApex.DriftTimeCenterInMs,
peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(
string.Format(" MzInDalton difference: {0:F2} ppm", distance.MassDifferenceInPpm));
Trace.WriteLine(
string.Format(" Drift time difference: {0:F4} ms", distance.DriftTimeDifferenceInMs));
Trace.WriteLine(string.Format(" Intensity Score: {0:F4}", currentStatistics.IntensityScore));
Trace.WriteLine(string.Format(" Peak Shape Score: {0:F4}", currentStatistics.PeakShapeScore));
Trace.WriteLine(string.Format(" Isotopic Score: {0:F4}", currentStatistics.IsotopicScore));
Trace.WriteLine(string.Format(" AveragedPeakIntensities: {0:F4}", peak.SummedIntensities));
string rejectionReason = badScanRange ? " [Bad scan range] " : " ";
rejectionReason += badPeakShape ? "[Bad Peak Shape] " : string.Empty;
rejectionReason += lowMzAffinity ? "[Inaccurate Mass] " : string.Empty;
rejectionReason += lowIsotopicAffinity ? "[Different Isotopic Profile] " : string.Empty;
if (badScanRange || lowIsotopicAffinity || badPeakShape)
{
Trace.WriteLine(rejectionReason);
}
else
{
Trace.WriteLine(" [Pass]");
}
}
standardPeaks.RemoveAll(scanPredicate);
standardPeaks.RemoveAll(massDistanceThreshold);
standardPeaks.RemoveAll(shapeThreshold);
standardPeaks.RemoveAll(isotopeThreshold);
if (standardPeaks.Count == 0)
{
Trace.WriteLine(string.Format(" [No Match]"));
Trace.WriteLine(string.Empty);
return new LibraryMatchResult(null, AnalysisStatus.Negative, null);
}
StandardImsPeak closestPeak = standardPeaks.First();
DriftTimeFeatureDistance shortestDistance = new DriftTimeFeatureDistance(target, standardPeaks.First(), voltageGroup);
foreach (var peak in standardPeaks)
{
DriftTimeFeatureDistance distance = new DriftTimeFeatureDistance(target, peak, voltageGroup);
if (distance.CompareTo(shortestDistance) < 0)
{
closestPeak = peak;
}
}
Trace.WriteLine(string.Format(" [Match]"));
Trace.WriteLine(string.Empty);
return new LibraryMatchResult(closestPeak, AnalysisStatus.Positive, shortestDistance);
}
}
throw new Exception("No voltage groups in the Dataset match temerature, pressure, or drift tube voltage setting from the library. Matching failed.");
}
public void TestScoring()
{
string formula = "C9H13ClN6";
string fileLocation = Cae;
MolecularTarget target = new MolecularTarget(formula, IonizationMethod.Protonated, "CAE");
Console.WriteLine("CompositionWithoutAdduct: " + target.CompositionWithoutAdduct);
Console.WriteLine("Monoisotopic ViperCompatibleMass: " + target.MonoisotopicMass);
CrossSectionSearchParameters parameters = new CrossSectionSearchParameters(driftTubeLength);
var smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
CrossSectionWorkfow workflow = new CrossSectionWorkfow(fileLocation, "output", parameters);
Console.WriteLine("Ionization method: " + target.Adduct);
Console.WriteLine("Targeting centerMz: " + target.MassWithAdduct);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.CompositionWithAdduct != null)
{
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
var theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
// Generate VoltageSeparatedAccumulatedXICs
var uimfReader = new DataReader(fileLocation);
Console.WriteLine("Input file: {0}", fileLocation);
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(uimfReader, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm, driftTubeLength);
Console.WriteLine();
// For each voltage, find 2D XIC features
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
Console.WriteLine("Voltage group: {0} V, Frame {1}-{2}, {3:F2}K, {4:F2}Torr",
voltageGroup.MeanVoltageInVolts,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
voltageGroup.MeanTemperatureInKelvin,
voltageGroup.MeanPressureInTorr);
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, smoother, parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, uimfReader, voltageGroup, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm)).ToList();
// feature scorings and Target selection.
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, uimfReader);
// Check each XIC Peak found
foreach (var featurePeak in standardPeaks)
{
// Evaluate feature scores.
double intensityScore = FeatureScoreUtilities.IntensityScore(featurePeak, globalMaxIntensity);
double isotopicScoreAngle = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Angle,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistance = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistance,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScorePerson = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.PearsonCorrelation,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreBhattacharyya = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Bhattacharyya,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistanceAlternative = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistanceAlternative,
globalMaxIntensity,
workflow.NumberOfScans);
double peakShapeScore = FeatureScoreUtilities.PeakShapeScore(featurePeak, workflow.uimfReader, workflow.Parameters.MzWindowHalfWidthInPpm, workflow.Parameters.DriftTimeToleranceInMs, voltageGroup, globalMaxIntensity, workflow.NumberOfScans);
// Report all features.
Console.WriteLine(" feature found at scan number {0}", featurePeak.PeakApex.DriftTimeCenterInScanNumber);
Console.WriteLine(" IntensityScore: {0}", intensityScore);
Console.WriteLine(" peakShapeScore: {0}", peakShapeScore);
Console.WriteLine(" isotopicScore - Angle: {0}", isotopicScoreAngle);
Console.WriteLine(" isotopicScore - Distance: {0}", isotopicScoreDistance);
Console.WriteLine(" isotopicScore - Distance2:{0}", isotopicScoreDistanceAlternative);
Console.WriteLine(" isotopicScore - Pearson: {0}", isotopicScorePerson);
Console.WriteLine(" isotopicScore - Bhattacharyya: {0}", isotopicScoreBhattacharyya);
Console.WriteLine();
}
Console.WriteLine();
}
workflow.Dispose();
}
/// <summary>
/// The run molecule informed work flow.
/// </summary>
/// <param name="target">
/// The Target.
/// </param>
/// <param name="detailedVerbose">
/// </param>
/// <returns>
/// The <see cref="CrossSectionWorkflowResult"/>.
/// </returns>
public CrossSectionWorkflowResult RunCrossSectionWorkFlow(IImsTarget target, bool detailedVerbose = true)
{
// Reassign trace listener to print to console as well as the target directory.
using (this.ResetTraceListenerToTarget(target, this.DatasetName))
{
try
{
// Get the monoisotopic mass for viper, which is different from anything else.
double viperFriendlyMass = target.MassWithAdduct;
if (target.ChargeState < 0)
{
viperFriendlyMass = viperFriendlyMass + new Composition(0, target.ChargeState, 0, 0, 0).Mass;
}
else
{
viperFriendlyMass = viperFriendlyMass - new Composition(0, Math.Abs(target.ChargeState), 0, 0, 0).Mass;
}
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.HasCompositionInfo)
{
int chargeStateAbs = Math.Abs(target.ChargeState);
// Again this isotopic profile generator auto adds hydrogen for you depending on charge states. So here take it out.
Composition compensatedComposition = target.CompositionWithAdduct - new Composition(0, chargeStateAbs, 0, 0, 0);
string empiricalFormula = compensatedComposition.ToPlainString();
IsotopicProfile theoreticalIsotopicProfile = this.theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, chargeStateAbs);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
Trace.WriteLine(string.Format("Dataset: {0}", this.uimfReader.UimfFilePath));
ReportTargetInfo(target, detailedVerbose);
double targetMz = Math.Abs(target.MassWithAdduct / target.ChargeState);
// Voltage grouping. Note that we only accumulate frames as needed. Accumulate frames globally is too costly.
// Here we accumulate the XICs around target MZ.
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(this.uimfReader, targetMz, this.Parameters.MzWindowHalfWidthInPpm, this.Parameters.DriftTubeLengthInCm);
// Remove voltage groups that don't have sufficient frame accumulations
IEnumerable<VoltageGroup> remainingVGs = accumulatedXiCs.Keys;
IEnumerable<VoltageGroup> toBeRemoved = VoltageGroupFilters.RemoveVoltageGroupsWithInsufficentFrames(remainingVGs, this.Parameters.InsufficientFramesFraction);
foreach (VoltageGroup voltageGroup in toBeRemoved)
{
accumulatedXiCs.Remove(voltageGroup);
}
// Perform feature detection and scoring and the given MzInDalton range on the accumulated XICs to get the base peaks.
if (detailedVerbose)
{
Trace.WriteLine("Feature detection and scoring: ");
}
IList<VoltageGroup> rejectedVoltageGroups = new List<VoltageGroup>();
IList<ObservedPeak> filteredObservations = new List<ObservedPeak>();
IList<ObservedPeak> allObservations = new List<ObservedPeak>();
IDictionary<string, IList<ObservedPeak>> rejectedObservations = new Dictionary<string, IList<ObservedPeak>>();
var numberOfParticipatingVGs = accumulatedXiCs.Keys.Count;
// Iterate through the features and perform filtering on isotopic affinity, intensity, drift time and peak shape.
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, this.uimfReader);
List<StandardImsPeak> standardPeaks = this.FindPeaksBasedOnXIC(voltageGroup, accumulatedXiCs[voltageGroup], target);
// Score features
IDictionary<StandardImsPeak, PeakScores> scoresTable = new Dictionary<StandardImsPeak, PeakScores>();
if (detailedVerbose)
{
Trace.WriteLine(
string.Format(
" Voltage group: {0:F2} V, Frame {1}-{2}, {3:F2}K, {4:F2}Torr",
voltageGroup.MeanVoltageInVolts,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
voltageGroup.MeanTemperatureInKelvin,
voltageGroup.MeanPressureInTorr));
}
foreach (StandardImsPeak peak in standardPeaks)
{
PeakScores currentStatistics = FeatureScoreUtilities.ScoreFeature(
peak,
globalMaxIntensity,
this.uimfReader,
this.Parameters.MzWindowHalfWidthInPpm,
this.Parameters.DriftTimeToleranceInMs,
voltageGroup,
this.NumberOfScans,
target,
IsotopicScoreMethod.Angle,
theoreticalIsotopicProfilePeakList);
scoresTable.Add(peak, currentStatistics);
}
double maxIntensity = standardPeaks.Max(x => x.SummedIntensities);
Predicate<StandardImsPeak> relativeIntensityThreshold = imsPeak => FeatureFilters.FilterOnRelativeIntesity(imsPeak, maxIntensity, this.Parameters.RelativeIntensityPercentageThreshold);
// filter out non Target peaks and noise.
Predicate<StandardImsPeak> absoluteIntensityThreshold = imsPeak => FeatureFilters.FilterOnAbsoluteIntensity(imsPeak, scoresTable[imsPeak].IntensityScore, this.Parameters.AbsoluteIntensityThreshold);
// filter out features with Ims scans at 1% left or right.
Predicate<StandardImsPeak> scanPredicate = imsPeak => FeatureFilters.FilterExtremeDriftTime(imsPeak, this.NumberOfScans);
// filter out features with bad peak shapes.
Predicate<StandardImsPeak> shapeThreshold = imsPeak => FeatureFilters.FilterBadPeakShape(imsPeak, scoresTable[imsPeak].PeakShapeScore, this.Parameters.PeakShapeThreshold);
// filter out features with distant isotopic profile.
Predicate<StandardImsPeak> isotopeThreshold = imsPeak => FeatureFilters.FilterBadIsotopicProfile(imsPeak, scoresTable[imsPeak].IsotopicScore, this.Parameters.IsotopicThreshold);
// Print out candidate features and how they were rejected.
foreach (StandardImsPeak peak in standardPeaks)
{
PeakScores currentStatistics = scoresTable[peak];
string rejectionReason = ReportFeatureEvaluation(
peak,
currentStatistics,
detailedVerbose,
target,
scanPredicate(peak),
absoluteIntensityThreshold(peak),
relativeIntensityThreshold(peak),
shapeThreshold(peak),
isotopeThreshold(peak));
bool pass = string.IsNullOrEmpty(rejectionReason);
ObservedPeak analyzedPeak = new ObservedPeak(voltageGroup, peak, currentStatistics);
if (pass)
{
filteredObservations.Add(analyzedPeak);
}
else
{
if (rejectedObservations.ContainsKey(rejectionReason))
{
rejectedObservations[rejectionReason].Add(analyzedPeak);
}
else
{
rejectedObservations.Add(rejectionReason, new List<ObservedPeak>(){analyzedPeak});
}
}
allObservations.Add(analyzedPeak);
}
standardPeaks.RemoveAll(scanPredicate);
standardPeaks.RemoveAll(absoluteIntensityThreshold);
standardPeaks.RemoveAll(relativeIntensityThreshold);
standardPeaks.RemoveAll(shapeThreshold);
if (target.HasCompositionInfo)
{
standardPeaks.RemoveAll(isotopeThreshold);
}
if (standardPeaks.Count == 0)
{
if (detailedVerbose)
{
Trace.WriteLine(string.Format(" (All features were rejected in voltage group {0:F4} V)", voltageGroup.MeanVoltageInVolts));
Trace.WriteLine(string.Empty);
Trace.WriteLine(string.Empty);
}
rejectedVoltageGroups.Add(voltageGroup);
}
// Rate the feature's VoltageGroupScoring score. VoltageGroupScoring score measures how likely the voltage group contains and detected the Target ion.
voltageGroup.VoltageGroupScore = VoltageGroupScoring.ComputeVoltageGroupStabilityScore(voltageGroup);
}
// Remove voltage groups that were rejected
foreach (VoltageGroup voltageGroup in rejectedVoltageGroups)
{
accumulatedXiCs.Remove(voltageGroup);
}
IEnumerable<ObservedPeak> rejectedPeaks = rejectedObservations.Values.SelectMany(x => x);
// Report analysis as negative
if (accumulatedXiCs.Keys.Count == 0)
{
CrossSectionWorkflowResult informedResult = CrossSectionWorkflowResult.CreateNegativeResult(rejectedPeaks, rejectedVoltageGroups, target, this.DatasetPath, this.OutputPath, this.SampleCollectionDate);
ReportAnslysisResultAndMetrics(informedResult, detailedVerbose);
return informedResult;
}
else
{
// Perform the data association algorithm.
IIonTracker tracker = new CombinatorialIonTracker(3000);
// Because for somereason we are not keeping track of drift tube length in UIMF...so we kind of have to go ask the instrument operator..
double driftTubeLength = this.Parameters.DriftTubeLengthInCm;
AssociationHypothesis optimalAssociationHypothesis = tracker.FindOptimumHypothesis(filteredObservations, driftTubeLength, target, this.Parameters, numberOfParticipatingVGs);
if (optimalAssociationHypothesis == null)
{
CrossSectionWorkflowResult negResult = CrossSectionWorkflowResult.CreateNegativeResult(rejectedPeaks, rejectedVoltageGroups, target, this.DatasetPath, this.OutputPath, this.SampleCollectionDate);
ReportAnslysisResultAndMetrics(negResult, detailedVerbose);
return negResult;
}
if (detailedVerbose)
{
Console.WriteLine("Writes QC plot of fitline to " + this.OutputPath);
Trace.WriteLine(string.Empty);
}
string extension = (this.Parameters.GraphicsExtension.StartsWith(".")) ?
this.Parameters.GraphicsExtension : "." + this.Parameters.GraphicsExtension;
string outputPath = string.Format("{0}target_{1}_in_{2}_QA{3}", this.OutputPath, target.TargetDescriptor, this.DatasetName, extension);
ImsInformedPlotter plotter = new ImsInformedPlotter();
plotter.PlotAssociationHypothesis(optimalAssociationHypothesis, outputPath, this.DatasetName, target, rejectedObservations);
// Printout results
if (detailedVerbose)
{
Trace.WriteLine("Target Data Association");
int count = 0;
foreach (IsomerTrack track in optimalAssociationHypothesis.Tracks)
{
Trace.WriteLine(string.Format(" T{0}: ", count));
foreach (ObservedPeak peak in track.ObservedPeaks)
{
Trace.WriteLine(string.Format(" [td: {0:F4}ms, V: {1:F4}V, T: {2:F4}K, P: {3:F4}Torr]",
peak.Peak.PeakApex.DriftTimeCenterInMs,
peak.VoltageGroup.MeanVoltageInVolts,
peak.VoltageGroup.MeanTemperatureInKelvin,
peak.VoltageGroup.MeanPressureInTorr));
}
count++;
Trace.WriteLine("");
}
Trace.WriteLine("");
}
// Remove outliers with high influence.
// FitLine.RemoveOutliersAboveThreshold(3, minFitPoints);
// Remove outliers until min fit point is reached or good R2 is achieved.
// while (TrackFilter.IsLowR2(FitLine.RSquared) && FitLine.FitPointCollection.Count > minFitPoints)
// {
// FitLine.RemoveOutlierWithHighestCookDistance(minFitPoints);
// }
// Remove the voltage considered outliers
// foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys.Where(p => FitLine.OutlierCollection.Contains(p.FitPoint)).ToList())
// {
// accumulatedXiCs.Remove(voltageGroup);
// }
CrossSectionWorkflowResult informedResult = CrossSectionWorkflowResult.CreateResultFromAssociationHypothesis(
this.Parameters,
optimalAssociationHypothesis,
target,
accumulatedXiCs.Keys,
allObservations,
this.DatasetPath,
this.OutputPath,
this.SampleCollectionDate,
viperFriendlyMass
);
ReportAnslysisResultAndMetrics(informedResult, detailedVerbose);
Trace.Listeners.Clear();
return informedResult;
}
}
catch (Exception e)
{
// Print result
Trace.WriteLine(e.Message);
Trace.WriteLine(e.StackTrace);
Trace.Listeners.Clear();
Trace.Close();
Trace.Listeners.Clear();
// create the error result
return CrossSectionWorkflowResult.CreateErrorResult(target, this.DatasetName, this.DatasetPath, this.OutputPath, this.SampleCollectionDate);
}
}
}
public void TestFormulaPerturbance()
{
List<Tuple<string, string>> formulas = new List<Tuple<string, string>>();
// truth
formulas.Add(new Tuple<string, string>("True formula", "C12H10O4S"));
formulas.Add(new Tuple<string, string>("1 extra H", "C12H11O4S"));
formulas.Add(new Tuple<string, string>("2 extra H", "C12H12O4S"));
formulas.Add(new Tuple<string, string>("3 extra H", "C12H13O4S"));
formulas.Add(new Tuple<string, string>("3 extra H", "C12H14O4S"));
formulas.Add(new Tuple<string, string>("4 extra H", "C12H15O4S"));
formulas.Add(new Tuple<string, string>("5 extra H", "C12H16O4S"));
formulas.Add(new Tuple<string, string>("1 less H", "C12H9O4S"));
formulas.Add(new Tuple<string, string>("2 less H", "C12H8O4S"));
formulas.Add(new Tuple<string, string>("3 less H", "C12H7O4S"));
formulas.Add(new Tuple<string, string>("4 less H", "C12H6O4S"));
Console.WriteLine("[Intensity], [Distance1], [Distance2], [Angle], [Pearson], [Bucha]");
string fileLocation = BPSNegative;
CrossSectionSearchParameters parameters = new CrossSectionSearchParameters(driftTubeLength);
CrossSectionWorkfow workflow = new CrossSectionWorkfow(fileLocation, "output", parameters);
foreach (var form in formulas)
{
bool found = false;
MolecularTarget target = new MolecularTarget(form.Item2, new IonizationAdduct(IonizationMethod.Deprotonated), form.Item1);
Console.Write(form.Item1 + ": ");
var smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.CompositionWithAdduct != null)
{
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
var theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
// Generate VoltageSeparatedAccumulatedXICs
var uimfReader = new DataReader(fileLocation);
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(uimfReader, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm, parameters.DriftTubeLengthInCm);
var voltageGroup = accumulatedXiCs.Keys.First();
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, smoother, parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, uimfReader, voltageGroup, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm)).ToList();
// feature scorings and Target selection.
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, uimfReader);
// Check each XIC Peak found
foreach (var peak in standardPeaks)
{
// Evaluate feature scores.
double intensityScore = FeatureScoreUtilities.IntensityScore(peak, globalMaxIntensity);
double isotopicScoreAngle = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Angle,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistance = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistance,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScorePerson = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.PearsonCorrelation,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreBhattacharyya = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Bhattacharyya,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistanceAlternative = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistanceAlternative,
globalMaxIntensity,
workflow.NumberOfScans);
double peakShapeScore = FeatureScoreUtilities.PeakShapeScore(peak, workflow.uimfReader, workflow.Parameters.MzWindowHalfWidthInPpm, workflow.Parameters.DriftTimeToleranceInMs, voltageGroup, globalMaxIntensity, workflow.NumberOfScans);
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", intensityScore);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreDistance);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreDistanceAlternative);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreAngle);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScorePerson);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreBhattacharyya);
found = true;
}
}
if (!found)
{
Console.Write("No features");
}
Console.WriteLine();
}
// Manually dispose so it doesn't interfere with other tests.
workflow.Dispose();
}
