/// <summary>
/// Returns the mass spectrum for a specified LC ScanSet and a IMS ScanSet.
/// </summary>
/// <param name="lcScanSet"></param>
/// <param name="imsScanSet"></param>
/// <param name="minMZ"></param>
/// <param name="maxMZ"></param>
public override XYData GetMassSpectrum(ScanSet lcScanSet, ScanSet imsScanSet, double minMZ, double maxMZ)
{
Check.Require(imsScanSet.GetScanCount() > 0, string.Format(
"Cannot get spectrum. Number of scans in ScanSet ({0}) is 0", nameof(imsScanSet)));
Check.Require(lcScanSet.GetScanCount() > 0, string.Format(
"Cannot get spectrum. Number of frames in FrameSet ({0}) is 0", nameof(lcScanSet)));
var startFrameNumber = lcScanSet.GetLowestScanNumber();
var endFrameNumber = lcScanSet.GetHighestScanNumber();
var startScanNumber = imsScanSet.GetLowestScanNumber();
var endScanNumber = imsScanSet.GetHighestScanNumber();
// TODO: If lowest and highest scan numbers are both 0, should we be summing the mass spectrum?
var frameType = (UIMFData.FrameType)GetMSLevel(lcScanSet.PrimaryScanNumber);
try
{
// Prior to January 2015 the SpectrumCache class in the UIMFReader used Dictionary<int, int> for ListOfIntensityDictionaries
// This caused some datasets, e.g. EXP-Mix5_1um_pos_19Jan15_Columbia_DI, to run out of memory when caching 10 spectra
// The UIMFLibrary now uses List<int, int>, which takes up less memory (at the expense having slower lookups by BinNumber, though this does not affect DeconTools' use of the UIMFLibrary)
mReader.SpectraToCache = 10;
mReader.MaxSpectrumCacheMemoryMB = 750;
mReader.GetSpectrum(
startFrameNumber, endFrameNumber, frameType,
startScanNumber, endScanNumber,
minMZ, maxMZ,
out var xVals, out var yVals);
var xyData = new XYData();
if (xVals == null || xVals.Length == 0)
{
xyData.Xvalues = null;
xyData.Yvalues = null;
return(xyData);
}
xyData.Xvalues = xVals;
xyData.Yvalues = yVals.Select <int, double>(i => i).ToArray();
if (xyData.Xvalues[0] < minMZ || xyData.Xvalues[xyData.Xvalues.Length - 1] > maxMZ)
{
xyData = xyData.TrimData(minMZ, maxMZ);
}
return(xyData);
}
catch (Exception ex)
{
Console.WriteLine("Error in UIMF GetMassSpectrum: " + ex.Message);
throw;
}
}
public override XYData GetMassSpectrum(ScanSet scanSet, double minMZ, double maxMZ)
{
Check.Require(scanSet != null, "Can't get mass spectrum; inputted set of scans is null");
if (scanSet == null)
{
return(new XYData());
}
Check.Require(scanSet.IndexValues.Count > 0, "Can't get mass spectrum; no scan numbers inputted");
// Unused: var totScans = GetNumMSScans();
var xVals = new double[0];
var yVals = new double[0];
//if (scanSet.IndexValues.Count == 1) //this is the case of only wanting one MS spectrum
//{
// this.rawData.GetSpectrum(scanSet.IndexValues[0], ref xVals, ref yVals);
//}
//else
//{
// int upperScan = Math.Min(scanSet.GetHighestScanNumber(), this.GetNumMSScans());
// int lowerScan = Math.Max(scanSet.GetLowestScanNumber(), 1);
// this.rawData.GetSummedSpectra(lowerScan, upperScan, minMZ, maxMZ, ref xVals, ref yVals);
//}
var upperScan = Math.Min(scanSet.GetHighestScanNumber(), GetNumMSScans());
var lowerScan = Math.Max(scanSet.GetLowestScanNumber(), 1);
//TODO: Old DeconTools reference!! remove this
RawData.GetSummedSpectra(lowerScan, upperScan, minMZ, maxMZ, ref xVals, ref yVals);
var xydata = new XYData
{
Xvalues = xVals,
Yvalues = yVals
};
return(xydata);
}
private void UpdateReportedSummedPeakIntensities(IsosResult profile, ScanSet lcScanSet, ScanSet imsScanSet)
{
var minFrame = lcScanSet.GetLowestScanNumber();
var maxFrame = lcScanSet.GetHighestScanNumber();
var minIMSScan = imsScanSet.GetLowestScanNumber();
var maxIMSScan = imsScanSet.GetHighestScanNumber();
var massTolerance = 0.2;
var filteredUnsummedMSFeatures = (from n in _unsummedMSFeatures
where n.ScanSet.PrimaryScanNumber >= minFrame &&
n.ScanSet.PrimaryScanNumber <= maxFrame &&
((UIMFIsosResult)n).IMSScanSet.PrimaryScanNumber >= minIMSScan &&
((UIMFIsosResult)n).IMSScanSet.PrimaryScanNumber <= maxIMSScan &&
n.IsotopicProfile.ChargeState == profile.IsotopicProfile.ChargeState &&
Math.Abs(n.IsotopicProfile.MonoIsotopicMass -
profile.IsotopicProfile.MonoIsotopicMass) < massTolerance
select n).ToList();
var averageMonoMass = profile.IsotopicProfile.MonoIsotopicMass; //initialize and assign original value
var averageMonoMZ = profile.IsotopicProfile.MonoPeakMZ;
var averageMostAbundantPeakMonoMass = profile.IsotopicProfile.MostAbundantIsotopeMass;
//if (filteredUnsummedMSFeatures.Count > 2)
//{
// var higherAbundanceFeatures =
// (from n in filteredUnsummedMSFeatures where n.IntensityAggregate > 100000 select n).
// ToList();
// if (higherAbundanceFeatures.Count>0)
// {
// averageMonoMass = filteredUnsummedMSFeatures.Select(p => p.IsotopicProfile.MonoIsotopicMass).Average();
// averageMonoMZ = filteredUnsummedMSFeatures.Select(p => p.IsotopicProfile.MonoPeakMZ).Average();
// averageMostAbundantPeakMonoMass =
// filteredUnsummedMSFeatures.Select(p => p.IsotopicProfile.MostAbundantIsotopeMass).Average();
// }
//}
//var peaksToSum = (from n in Run.ResultCollection.MSPeakResultList
// where n.Frame_num >= minFrame &&
// n.Frame_num <= maxFrame &&
// n.Scan_num >= minScan &&
// n.Scan_num <= maxScan &&
// n.XValue > minMZ &&
// n.XValue < maxMZ
// select n).ToList();
//double adjustedIntensity = peaksToSum.Sum(p => p.Height);
var unsummedAdjustedMSFeature = (from n in filteredUnsummedMSFeatures
where
n.ScanSet.PrimaryScanNumber == lcScanSet.PrimaryScanNumber &&
((UIMFIsosResult)n).IMSScanSet.PrimaryScanNumber == imsScanSet.PrimaryScanNumber
select n).FirstOrDefault();
profile.IsotopicProfile.OriginalIntensity = unsummedAdjustedMSFeature?.IntensityAggregate ?? 0;
var adjustedIntensity = filteredUnsummedMSFeatures.Sum(p => p.IsotopicProfile.IntensityMostAbundant);
// Uncomment to debug
//if (unsummedAdjustedMSFeature == null)
//{
// Console.WriteLine(profile.IsotopicProfile.MonoPeakMZ.ToString("0.000") + "\t" + profile.IsotopicProfile.ChargeState + "\t" + frameSet.PrimaryFrame + "\t" + scanSet.PrimaryScanNumber + "\t" + profile.IntensityAggregate + "\t" + adjustedIntensity + "\t" + "0");
//}
//else
//{
// Console.WriteLine(profile.IsotopicProfile.MonoPeakMZ.ToString("0.000") + "\t" + profile.IsotopicProfile.ChargeState + "\t" + frameSet.PrimaryFrame + "\t" + scanSet.PrimaryScanNumber + "\t" + profile.IntensityAggregate + "\t" + adjustedIntensity +"\t" + unsummedAdjustedMSFeature.IntensityAggregate);
//}
if (adjustedIntensity > profile.IntensityAggregate)
{
profile.IsotopicProfile.IsSaturated = true;
profile.IntensityAggregate = adjustedIntensity;
profile.IsotopicProfile.IntensityMostAbundant = adjustedIntensity;
if (filteredUnsummedMSFeatures.Count > 0)
{
profile.IsotopicProfile.MonoIsotopicMass = averageMonoMass;
profile.IsotopicProfile.MonoPeakMZ = averageMonoMZ;
profile.IsotopicProfile.MostAbundantIsotopeMass = averageMostAbundantPeakMonoMass;
}
}
}