private MassSpectrumCollection NMerge(IEnumerable <MassSpectrum> spectra)
{
List <double> lowers = new List <double> {
this.seg1Low.Value, this.seg2Low.Value, this.seg3Low.Value
};
List <double> uppers = new List <double> {
this.seg1Upp.Value, this.seg2Upp.Value, this.seg3Upp.Value
};
int nSpecs = spectra.Aggregate(0, (x, y) => x + 1);
int count = 0;
int segs = this.nSegs.Value;
lowers = lowers.GetRange(0, segs);
uppers = uppers.GetRange(0, segs);
// Find if offset needed
double[] overlaps = new double[nSegs.Value];
foreach (int i in Enumerable.Range(0, segs))
{
overlaps[i] = Math.Min(spectra.ElementAt(0).Header.HighPosition, uppers[i]) -
Math.Max(spectra.ElementAt(0).Header.LowPosition, lowers[i]);
}
int offset = overlaps.ToList().IndexOf(overlaps.Max());
MassSpectrumCollection massSpectrumCollection = new MassSpectrumCollection((int)(nSpecs / (double)segs));
int nCentsY = 0;
int nCentsN = 0;
int nCentsYtot = 0;
int nCentsNtot = 0;
int nSpecStart = nSpecs;
base.WriteLogMessage(MessageLevel.Info, "Starting - Number of Specs: {0}", nSpecs);
MassSpectrum buildingSpec = null;
foreach (MassSpectrum spec in spectra)
{
// base.WriteLogMessage(MessageLevel.Info, "Mahieu.NMerge - Header. {0} - {1} - {2} - {3}", spec.Header.ScanRange, spec.Header.MasterScanRange, spec.Header.ScanNumbers, spec.Header.MasterScanNumbers);
// base.WriteLogMessage(MessageLevel.Info, "Mahieu.NMerge - {0} - {1} - {2} - {3}", spec.ScanEvent.IsolationOffset, spec.Header.MasterScanRange, spec.Header.ScanNumbers, spec.Header.MasterScanNumbers);
int currentSeg = (int)(count % segs);
int currentSegBounds = (int)((count + offset) % segs);
if (count > 0 & currentSeg == 0)
{
//buildingSpec.Header.HighPosition = buildingSpec.PeakCentroids.FindClosestPeak(10000).Position;
//buildingSpec.Header.LowPosition = buildingSpec.PeakCentroids.FindClosestPeak(0).Position;
buildingSpec.Header.HighPosition = uppers.Max();
buildingSpec.Header.LowPosition = lowers.Min();
buildingSpec.Header.BasePeakIntensity = buildingSpec.PeakCentroids.FindMostIntensePeak().Intensity;
buildingSpec.Header.BasePeakPosition = buildingSpec.PeakCentroids.FindMostIntensePeak().Position;
buildingSpec.Header.TotalIntensity = buildingSpec.PeakCentroids.Aggregate(0.0, (x, y) => x + y.Intensity);
// fake it. important?
buildingSpec.ScanEvent.IsolationMass = (uppers.Max() + lowers.Min()) / 2;
buildingSpec.ScanEvent.IsolationWidth = (uppers.Max() - lowers.Min());
if (!buildingSpec.IsValid)
{
base.WriteLogMessage(MessageLevel.Info, "Building Spec Invalid");
}
// spec.Precursor.IsolationMass, spec.Precursor.IonInjectTime, spec.Precursor.IsolationWindow = 0; spec.Precursor.MeasuredMonoisotopicPeakCentroids is empty.
// spec.Traits mostly mass accuracy, should be invariant
// spec.ScanEvent Isolation mass and such could be important
// spec.Header - appears to be important.
// Every nSegs specs add the merged spec to the collection and start a new one.
massSpectrumCollection.Add(buildingSpec);
nCentsY = buildingSpec.PeakCentroids.Aggregate(0, (x, y) => x + 1);
nCentsYtot = nCentsYtot + nCentsY;
if (nCentsY < nCentsN)
{
base.WriteLogMessage(MessageLevel.Warn, "Number of centroids kept ({0}) is smaller than number of centroids discarded ({1}). Are scan segments defined appropriately?", nCentsY, nCentsN);
}
if ((double)count % (nSpecs / 4) == 0)
{
base.WriteLogMessage(MessageLevel.Info, "Spot Check - Centroids kept: {0}; Centroids discarded {1}.", nCentsY, nCentsN);
}
nCentsNtot = nCentsNtot + nCentsN;
nCentsY = 0;
nCentsN = 0;
}
if (currentSeg == 0)
{
buildingSpec = new MassSpectrum();
buildingSpec.Header = spec.Header;
buildingSpec.ScanEvent = spec.ScanEvent;
buildingSpec.Precursor = spec.Precursor;
int ncents = buildingSpec.PeakCentroids.Aggregate(0, (x, y) => x + 1);
int nprofs = buildingSpec.ProfilePoints.Aggregate(0, (x, y) => x + 1);
buildingSpec.PeakCentroids = new MassCentroidCollection(ncents * 4);
buildingSpec.ProfilePoints = new SpectrumPointCollection(nprofs * 4);
// buildingSpec = spec;
}
// Merge current scan with buildingSpec
//base.WriteLogMessage(MessageLevel.Info, "Mahieu.NMerge - Current Segment {0}.", currentSeg);
// base.WriteLogMessage(MessageLevel.Info, "Mahieu.NMerge - Precursor Info. {0}", spec.Precursor.MeasuredMonoisotopicPeakCentroids.Max(t => t.Position));
// base.WriteLogMessage(MessageLevel.Info, "Mahieu.NMerge - Precursor Info. {0} - {1} - {2}", spec.ScanEvent.IsolationWidth, spec.ScanEvent.IsolationMass, spec.ScanEvent.IsolationWindow);
foreach (MassCentroid m in spec.PeakCentroids)
{
if ((m.Position >= lowers[currentSegBounds]) && (m.Position < uppers[currentSegBounds]))
{
buildingSpec.PeakCentroids.Add(m);
}
else
{
nCentsN = nCentsN + 1;
// base.WriteLogMessage(MessageLevel.Info, "Mahieu.NMerge - Discarded Centroid.");
}
}
foreach (SpectrumPoint m in spec.ProfilePoints)
{
if ((m.Position >= lowers[currentSegBounds]) && (m.Position < uppers[currentSegBounds]))
{
buildingSpec.ProfilePoints.Add(m);
}
else
{
// counter
}
}
count += 1;
}
int nSpecs2 = massSpectrumCollection.Aggregate(0, (x, y) => x + 1);
SendAndLogMessage("Mahieu NMerge Completed - Specs Remaining: {0}/{1} - Centroids remaining: {3}/{4} - Fraction: {2}", nSpecs2, nSpecStart, (double)nCentsYtot / ((double)nCentsNtot + (double)nCentsYtot), nCentsNtot, nCentsYtot);
if ((double)nCentsYtot / ((double)nCentsNtot + (double)nCentsYtot) < 0.98)
{
SendAndLogWarningMessage("Mahieu NMerge Reported >2% centroids discarded. Are scan segments set appropriately?");
}
return(massSpectrumCollection);
}
/// <summary>
/// REPLACE THIS
///
/// Assumes scan segment order does not vary. Not sure if this is a fair assumption.
/// </returns>
protected override MassSpectrumCollection ProcessSpectra(MassSpectrumCollection spectra)
{
return(NMerge(spectra));
}
