public static ExtractedIonChromatogram AverageXICFromFrames(DataReader uimfReader, int frameNumberFrom, int frameNumberTo, double centerMz, double massToleranceInPpm, double centerDriftTimeInMs, double driftTimeErrorInMs)
{
ExtractedIonChromatogram result = new ExtractedIonChromatogram();
for ( int i = frameNumberFrom; i <= frameNumberTo; i++)
{
var xic = new ExtractedIonChromatogram(uimfReader, i, centerMz, massToleranceInPpm, centerDriftTimeInMs, driftTimeErrorInMs);
if (i == frameNumberFrom)
{
result = xic;
}
else
{
result += xic;
}
}
return result;
}
/// <summary>
/// Initializes a new instance of the <see cref="ExtractedIonChromatogram"/> class.
/// XIC is a list of intensity points sorted by Mobility Scan number from low to high.
/// </summary>
/// <param name="a">
/// The a.
/// </param>
/// <param name="b">
/// The b.
/// </param>
/// <exception cref="InvalidOperationException">
/// </exception>
private ExtractedIonChromatogram(ExtractedIonChromatogram a, ExtractedIonChromatogram b)
{
if (a.NumberOfMobilityScans != b.NumberOfMobilityScans || !a.CenterMz.Equals(b.CenterMz))
{
throw new InvalidOperationException("Cannot sum XICs with different number of mobilities or different MZ.");
}
this.CenterMz = a.CenterMz;
this.NumberOfMobilityScans = b.NumberOfMobilityScans;
this.IntensityPoints = addSortedIntensityPointList(a.IntensityPoints, b.IntensityPoints, this.NumberOfMobilityScans);
}
/// <summary>
/// The +.
/// </summary>
/// <param name="A">
/// The a.
/// </param>
/// <param name="B">
/// The b.
/// </param>
/// <returns>
/// </returns>
public static ExtractedIonChromatogram operator +(ExtractedIonChromatogram A, ExtractedIonChromatogram B)
{
ExtractedIonChromatogram result = new ExtractedIonChromatogram(A, B);
return result;
}
/// <summary>
/// The find peaks based on xic.
/// </summary>
/// <param name="group">
/// The group.
/// </param>
/// <param name="chromatogram">
/// The chromatogram.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <returns>
/// The <see cref="IList"/>.
/// </returns>
/// <exception cref="NotImplementedException">
/// </exception>
private List<StandardImsPeak> FindPeaksBasedOnXIC(VoltageGroup voltageGroup, ExtractedIonChromatogram chromatogram, IImsTarget target)
{
if (this.Parameters.PeakDetectorSelection == PeakDetectorEnum.WaterShed)
{
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = chromatogram.IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, this.smoother, this.Parameters.FeatureFilterLevel);
// Recapture the 2D peak using the 1D feature blob from multidimensional peak finder.
return featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, this.uimfReader, voltageGroup, target.MassWithAdduct, this.Parameters.MzWindowHalfWidthInPpm)).ToList();
}
else if (this.Parameters.PeakDetectorSelection == PeakDetectorEnum.MASICPeakFinder)
{
// Find peaks using MASIC peak finder
List<IntensityPoint> intensityPoints = chromatogram.IntensityPoints;
IList<clsPeak> masicPeaks = PeakFinding.FindPeakUsingMasic(intensityPoints, this.NumberOfScans);
// Recapture the 2D peak using the 1D feature blob from multidimensional peak finder.
return masicPeaks.Select(peak => new StandardImsPeak(peak)).ToList();
}
else
{
throw new NotImplementedException(string.Format("{0} not supported", this.Parameters.PeakDetectorSelection));
}
}
