/// <summary>
/// Initializes a new instance of the <see cref="ObservedPeak"/> class with peak and its calculated statistics.
/// </summary>
/// <param name="group">
/// The group.
/// </param>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="statistics">
/// The Statistics.
/// </param>
public ObservedPeak(VoltageGroup group, StandardImsPeak peak, PeakScores statistics)
{
this.VoltageGroup = group;
this.Peak = peak;
this.Statistics = statistics;
this.ObservationType = ObservationType.Peak;
this.mobilityPoint = null;
}
/// <summary>
/// The Peak shape score. Evaluating how "good" the peak looks. A good
/// peak shape score indicates that the peak is not a result of noise
/// or instrument errors. Mostly the feature intensity along is sufficient
/// to exclude noise but a good shape score helps evaluating the experiment
/// and thus the reliability of the data analysis result.
/// </summary>
/// <param name="reader">
/// The reader.
/// </param>
/// <param name="massToleranceInPpm">
/// The mass Tolerance In Ppm.
/// </param>
/// <param name="driftTimeToleranceInMs">
/// The drift Time Tolerance In Scans.
/// </param>
/// <param name="imsPeak">
/// The imsPeak.
/// </param>
/// <param name="voltageGroup">
/// The voltage group.
/// </param>
/// <param name="targetMz">
/// The Target MZ.
/// </param>
/// <param name="globalMaxIntensities">
/// The global Max Intensities.
/// </param>
/// <param name="numberOfScans">
/// The number Of Scans.
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
public static double PeakShapeScore(StandardImsPeak imsPeak, DataReader reader, double massToleranceInPpm, double driftTimeToleranceInMs, VoltageGroup voltageGroup, double globalMaxIntensities, int numberOfScans)
{
int scanRep = imsPeak.PeakApex.DriftTimeCenterInScanNumber;
double toleranceInMz = massToleranceInPpm / 1e6 * imsPeak.PeakApex.MzCenterInDalton;
int scanWidth = (int)Math.Ceiling(driftTimeToleranceInMs / 1000 / voltageGroup.AverageTofWidthInSeconds);
int scanWindowSize = scanWidth * 2 + 1;
int scanNumberMin = scanRep - scanWidth;
int scanNumberMax = scanRep + scanWidth;
if ((scanNumberMin < 0) || (scanNumberMax > numberOfScans - 1))
{
return 0;
}
int[][] intensityWindow = reader.GetFramesAndScanIntensitiesForAGivenMz(
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
DataReader.FrameType.MS1,
scanNumberMin,
scanNumberMax,
imsPeak.PeakApex.MzCenterInDalton,
toleranceInMz);
// Average the intensity window across frames
int frames = intensityWindow.GetLength(0);
double[] averagedPeak = new double[scanWindowSize];
double highestPeak = 0;
for (int i = 0; i < scanWindowSize; i++)
{
for (int j = 0; j < frames; j++)
{
averagedPeak[i] += intensityWindow[j][i];
}
averagedPeak[i] /= frames;
highestPeak = (averagedPeak[i] > highestPeak) ? averagedPeak[i] : highestPeak;
}
// For peaks with peak width lower than 3, return a peak score of 0
// TODO get the intensity threshold here from the noise level instead.
if (scanWindowSize >= 3)
{
if (averagedPeak[scanRep - scanNumberMin] < globalMaxIntensities * 0.0001
|| averagedPeak[scanRep - scanNumberMin - 1] < globalMaxIntensities * 0.0001
|| averagedPeak[scanRep - scanNumberMin + 1] < globalMaxIntensities * 0.0001)
{
return 0;
}
}
// Perform a statistical normality test
double normalityScore = NormalityTest.PeakNormalityTest(averagedPeak, NormalityTest.JaqueBeraTest, 100, globalMaxIntensities);
return normalityScore;
}
/// <summary>
/// The score feature using isotopic profile.
/// </summary>
/// <param name="imsPeak">
/// The ims Peak.
/// </param>
/// <param name="reader">
/// The reader.
/// </param>
/// <param name="target">
/// The Target.
/// </param>
/// <param name="isotopicPeakList">
/// The isotopic peak list.
/// </param>
/// <param name="voltageGroup">
/// The voltage Group.
/// </param>
/// <param name="selectedMethod">
/// The selected Method.
/// </param>
/// <param name="globalMaxIntensities">
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
/// <exception cref="InvalidOperationException">
/// </exception>
public static double IsotopicProfileScore(StandardImsPeak imsPeak, DataReader reader, IImsTarget target, List<Peak> isotopicPeakList, VoltageGroup voltageGroup, IsotopicScoreMethod selectedMethod, double globalMaxIntensities, double totalScans)
{
// No need to move on if the isotopic profile is not found
// if (observedIsotopicProfile == null || observedIsotopicProfile.MonoIsotopicMass < 1)
// {
// result.AnalysisStatus = AnalysisStatus.IsotopicProfileNotFound;
// continue;
// }
// Find Isotopic Profile
// List<Peak> massSpectrumPeaks;
// IsotopicProfile observedIsotopicProfile = _msFeatureFinder.IterativelyFindMSFeature(massSpectrum, theoreticalIsotopicProfile, out massSpectrumPeaks);
if (target.CompositionWithoutAdduct == null)
{
throw new InvalidOperationException("Cannot score feature using isotopic profile for Ims Target without CompositionWithoutAdduct provided.");
}
// Bad Feature, so get out
if (imsPeak == null)
{
return 0;
}
// Get the scanWindow size
int scanNumberMax = imsPeak.PeakApex.DriftTimeFullWidthHalfMaxHigherBondInScanNumber;
int scanNumberMin = imsPeak.PeakApex.DriftTimeFullWidthHalfMaxLowerBondInScanNumber;
if ((scanNumberMin < 0) || (scanNumberMax > totalScans - 1))
{
return 0;
}
// Get the mass error from the observed feature peak from the Target theoretical peak
double mzOffset = imsPeak.PeakApex.MzCenterInDalton - target.MassWithAdduct;
List<double> observedIsotopicPeakList = new List<double>();
int totalIsotopicIndex = isotopicPeakList.Count;
int[] isotopicIndexMask = new int[totalIsotopicIndex];
// Find an unsaturated peak in the isotopic profile
for (int i = 0; i < totalIsotopicIndex; i++)
{
// Isotopic centerMz
double Mz = isotopicPeakList[i].XValue;
var peakList = reader.GetXic(Mz + mzOffset,
imsPeak.PeakApex.MzWindowToleranceInPpm,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
scanNumberMin,
scanNumberMax,
DataReader.FrameType.MS1,
DataReader.ToleranceType.PPM);
// Sum the intensities
double sumIntensities = 0;
foreach (var point in peakList)
{
sumIntensities += point.Intensity;
if (point.IsSaturated)
{
isotopicIndexMask[i] = 1;
}
}
sumIntensities /= voltageGroup.FrameAccumulationCount;
observedIsotopicPeakList.Add(sumIntensities);
}
// Return 0 if the intensity sum is really small
if (observedIsotopicPeakList.Sum() < globalMaxIntensities * 0.0003)
{
return 0;
}
// If the unsaturated isotopes are below a certain threshold
if (totalIsotopicIndex - isotopicIndexMask.Sum() <= 1)
{
return 0;
}
if (selectedMethod == IsotopicScoreMethod.Angle)
{
return IsotopicProfileScoreAngle(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.EuclideanDistance)
{
return IsotopicProfileScoreEuclidean(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.PearsonCorrelation)
{
return PearsonCorrelation(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.Bhattacharyya)
{
return BhattacharyyaDistance(observedIsotopicPeakList, isotopicPeakList);
}
else if (selectedMethod == IsotopicScoreMethod.EuclideanDistanceAlternative)
{
return EuclideanAlternative(observedIsotopicPeakList, isotopicPeakList);
}
else
{
throw new NotImplementedException();
}
}
/// <summary>
/// The intensity score.
/// </summary>
/// <param name="featurePeak">
/// The feature blob.
/// </param>
/// <param name="globalMaxIntensity">
/// The global Max Intensity.
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
public static double IntensityScore(StandardImsPeak featurePeak, double globalMaxIntensity)
{
// Sort features by relative intensity
double summedIntensities = featurePeak.SummedIntensities;
// Divide intensities by accumulation (If summing instead of averaging is used)
// summedIntensities /= voltageGroup.FrameAccumulationCount;
// normalize the score
return ScoreUtil.MapToZeroOneTrignometry(summedIntensities, false, globalMaxIntensity / 3);
}
/// <summary>
/// The report feature evaluation.
/// </summary>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="scores">
/// The scores.
/// </param>
/// <param name="verbose">
/// The verbose.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <param name="badScanRange">
/// The bad scan range.
/// </param>
/// <param name="lowAbsoluteIntensity">
/// The low intensity.
/// </param>
/// <param name="lowRelativeIntensity"></param>
/// <param name="badPeakShape">
/// The bad peak shape.
/// </param>
/// <param name="lowIsotopicAffinity">
/// The low isotopic affinity.
/// </param>
/// <returns>
/// If the feature pass all the filters <see cref="bool"/>.
/// </returns>
private static string ReportFeatureEvaluation(StandardImsPeak peak, PeakScores scores, bool verbose, IImsTarget target, bool badScanRange, bool lowAbsoluteIntensity, bool lowRelativeIntensity, bool badPeakShape, bool lowIsotopicAffinity)
{
Trace.WriteLine(string.Format(" Candidate feature found at [centerMz = {0:F4}, drift time = {1:F2} ms(#{2})] ", peak.PeakApex.MzCenterInDalton, peak.PeakApex.DriftTimeCenterInMs, peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(string.Format(" IntensityScore: {0:F4}", scores.IntensityScore));
if (!lowAbsoluteIntensity)
{
Trace.WriteLine(string.Format(" peakShapeScore: {0:F4}", scores.PeakShapeScore));
if (target.HasCompositionInfo)
{
Trace.WriteLine(string.Format(" isotopicScore: {0:F4}", scores.IsotopicScore));
}
}
string rejectionReason = badScanRange ? "[Bad scan range] " :
lowAbsoluteIntensity ? "[Low Absolute Intensity] " :
badPeakShape ? "[Bad Peak Shape] " :
lowIsotopicAffinity ? "[Different Isotopic Profile] " :
lowRelativeIntensity ? "[Low Relative Intensity] " : string.Empty;
bool rejected = badScanRange || lowAbsoluteIntensity || lowIsotopicAffinity || badPeakShape || lowRelativeIntensity;
if (verbose)
{
if (rejected)
{
Trace.WriteLine(" " + rejectionReason);
}
else
{
Trace.WriteLine(" [PASS]");
}
Trace.WriteLine(string.Empty);
}
return rejectionReason;
}
/// <summary>
/// Initializes a new instance of the <see cref="LibraryMatchResult"/> class.
/// </summary>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="conlusion">
/// The conlusion.
/// </param>
/// <param name="distance">
/// The distance.
/// </param>
public LibraryMatchResult(StandardImsPeak peak, AnalysisStatus conlusion, DriftTimeFeatureDistance distance)
{
this.AnalysisStatus = conlusion;
this.ImsFeature = peak;
this.distance = distance;
}
