public List <XYPair> GetIMSScanProfileFromRawData(DataReader uimfReader, UIMFData.FrameType frameType, double binWidth, double calibrationSlope, double calibrationIntercept)
{
GetMinAndMaxScanLCAndScanIMSAndMSFeatureRep(
out var scanLCMinimum, out var scanLCMaximum,
out var scanIMSMinimum, out var scanIMSMaximum, out var msFeatureRep);
// double currentFWHM = msFeatureRep.Fwhm;
// var currentMonoMZ = msFeatureRep.MassMonoisotopic/msFeatureRep.Charge + 1.0072649;
var mzMostAbundantIsotope = msFeatureRep.MassMostAbundantIsotope / msFeatureRep.Charge + 1.00727649;
////[gord] the following commented-out code sets the m/z range too wide. Can be removed later
//List<double> startMZ = new List<double>();
//List<double> endMZ = new List<double>();
//// Set ranges over which to look for the original data in the UIMF.
//double charge = Convert.ToDouble(this.Charge);
//for (int i = 0; i < 3; i++)
//{
// startMZ.Add(currentMonoMZ + (1.003 * i / charge) - (0.5 * currentFWHM));
// endMZ.Add(currentMonoMZ + (1.003 * i / charge) + (0.5 * currentFWHM));
//}
//double minMZ = startMZ[0];
//double maxMZ = endMZ[endMZ.Count - 1];
//double midPointMZ = (maxMZ + minMZ) / 2;
//double wideToleranceInMZ = midPointMZ - minMZ;
var frameMinimum = ScanLCMap.Mapping[scanLCMinimum];
var frameMaximum = ScanLCMap.Mapping[scanLCMaximum];
int[] scanValues = null;
int[] intensityValues = null;
var sigma = msFeatureRep.Fwhm / 2.35;
var toleranceInMZ = 2 * sigma; // this is a +/- value; so 4* sigma = 95% of a normal distribution
//Before: a wide m/z was used when generating the drift time profile.
//uimfReader.GetDriftTimeProfile(frameIndexMinimum, frameIndexMaximum, frameType, scanIMSMinimum, scanIMSMaximum, midPointMZ, wideToleranceInMZ, ref scanValues, ref intensityValues);
//now: a narrow m/z range is used when generating the drift time profile
uimfReader.GetDriftTimeProfile(frameMinimum, frameMaximum, frameType, scanIMSMinimum, scanIMSMaximum, mzMostAbundantIsotope, toleranceInMZ, ref scanValues, ref intensityValues);
var imsScanProfile = intensityValues.Select((t, i) => new XYPair(scanIMSMinimum + i, t)).ToList();
ConformationDetection.PadXYPairsWithZeros(ref imsScanProfile, 5);
return(imsScanProfile);
}
public List <IntensityPoint> GetXic(int targetBin, UIMFData.FrameType frameType)
{
return(UimfReader.GetXic(targetBin, frameType));
}
// ReSharper disable once UnusedMember.Global
public List <IntensityPoint> GetXic(double targetMz, double tolerance, UIMFData.FrameType frameType, int scanLcMin, int scanLcMax, int scanImsMin, int scanImsMax, DataReader.ToleranceType toleranceType)
{
return(UimfReader.GetXic(targetMz, tolerance, scanLcMin, scanLcMax, scanImsMin, scanImsMax, frameType, toleranceType));
}
public List <IntensityPoint> GetXic(double targetMz, double tolerance, UIMFData.FrameType frameType, DataReader.ToleranceType toleranceType)
{
return(UimfReader.GetXic(targetMz, tolerance, frameType, toleranceType));
}
// ReSharper disable once UnusedMember.Global
public double[,] GetXicAsArray(int targetBin, UIMFData.FrameType frameType)
{
return(UimfReader.GetXicAsArray(targetBin, frameType));
}
public double[,] GetXicAsArray(double targetMz, double tolerance, UIMFData.FrameType frameType, int scanLcMin, int scanLcMax, int scanImsMin, int scanImsMax, DataReader.ToleranceType toleranceType)
{
return(UimfReader.GetXicAsArray(targetMz, tolerance, scanLcMin, scanLcMax, scanImsMin, scanImsMax, frameType, toleranceType));
}
public double[,] GetXicAsArray(double targetMz, double tolerance, UIMFData.FrameType frameType, DataReader.ToleranceType toleranceType)
{
return(UimfReader.GetXicAsArray(targetMz, tolerance, frameType, toleranceType));
}
public IDictionary <double, IEnumerable <FeatureBlobStatistics> > GetFeatureStatistics(IEnumerable <double> targetMzList, double tolerance, UIMFData.FrameType frameType, DataReader.ToleranceType toleranceType)
{
var resultDictionary = new Dictionary <double, IEnumerable <FeatureBlobStatistics> >();
Parallel.ForEach(targetMzList, m_parallelOptions, targetMz =>
{
// Grab a UIMF Util object from the stack
m_uimfUtilStack.TryPop(out var uimfUtil);
// Do Feature Finding
var intensityBlock = uimfUtil.GetXic(targetMz, tolerance, frameType, toleranceType);
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock);
m_smoother.Smooth(ref pointList);
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList);
// Add result to dictionary
resultDictionary.Add(targetMz, featureList.Select(featureBlob => featureBlob.CalculateStatistics()).ToArray());
// Push the UIMF Util object back onto the stack when we are done with it
m_uimfUtilStack.Push(uimfUtil);
});
return(resultDictionary);
}
