public void SetOptions(clsPeakProcessorParameters parameters)
{
_parameters = parameters;
// the minimum intensity is not set till the actual data is available in DiscoverPeaks
_peakProcessor.SetOptions(_parameters.SignalToNoiseThreshold, 0, _parameters.ThresholdedData,
_parameters.PeakFitType);
}
public clsPeakProcessor()
{
_peakProcessor = new PeakProcessor();
_parameters = new clsPeakProcessorParameters();
_peakProcessor.SetOptions(_parameters.SignalToNoiseThreshold, 0, false,
_parameters.PeakFitType);
ProfileType = enmProfileType.PROFILE;
}
//TODO: remove code duplication (see DeconToolsPeakDetector)
public override List <Peak> FindPeaks(XYData xyData, double xMin = 0, double xMax = 0)
{
var peakList = new List <Peak>();
if (xyData == null)
{
return(peakList);
}
if (UseNewPeakDetector)
{
_peakDetectorV2.FindPeaks(xyData, xMin, xMax);
}
else
{
var xVals = xyData.Xvalues.ToList();
var yVals = xyData.Yvalues.ToList();
if (_oldPeakProcessor == null)
{
_oldPeakProcessor = new PeakProcessor();
}
BackgroundIntensity = _oldPeakProcessor.GetBackgroundIntensity(yVals);
_oldPeakProcessor.SetOptions(SigNoise, BackgroundIntensity * PeakBackgroundRatio, false, PeakFitType.Quadratic);
//Find peaks using DeconEngine
var largestXValue = xyData.Xvalues[xyData.Xvalues.Length - 1];
try
{
_oldPeakProcessor.DiscoverPeaks(xVals, yVals, 0, largestXValue);
}
catch (Exception ex)
{
Logger.Instance.AddEntry("ChromPeakDetector failed: " + ex.Message, true);
throw;
}
_oldDeconEnginePeaklist = _oldPeakProcessor.PeakData.PeakTops;
foreach (var peak in _oldDeconEnginePeaklist)
{
var chromPeak = new ChromPeak
{
XValue = peak.Mz, // here, mz is actually the scan / or NET
Height = (float)peak.Intensity,
SignalToNoise = peak.SignalToNoise,
Width = (float)peak.FWHM
};
peakList.Add(chromPeak);
}
}
//resultList.Run.PeakList = new List<IPeak>();
return(peakList);
}
/*[gord] the following is currently unused. The idea was to give weighting to the algorithm so that
* the user could favor certain fitting parameters (i.e. space between isotopomers) over others
* public double FindIsotopicDist(PeakProcessing.PeakData peakData, int cs, PeakProcessing.Peak peak,
* IsotopeFitRecord isoRecord, double deleteIntensityThreshold, double spacingWeight, double spacingVar,
* double signalToNoiseWeight, double signalToNoiseThresh, double ratioWeight, double ratioThreshold,
* double fitWeight, double fitThreshold, bool debug = false)
* {
* if (cs <= 0)
* {
* Environment.Exit(1);
* }
*
* //Get theoretical distribution using Mercury algorithm
* double peakMass = (peak.mdbl_mz - ChargeCarrierMass) * cs;
* double resolution = peak.mdbl_mz / peak.mdbl_FWHM;
* GetIsotopeDistribution(peakMass, cs, resolution, out TheoreticalDistMzs,
* out TheoreticalDistIntensities,
* deleteIntensityThreshold, debug);
*
* double theorMostAbundantPeakMz = IsotopeDistribution.mdbl_max_peak_mz;
* double delta = peak.mdbl_mz - theorMostAbundantPeakMz;
* double spacingScore = 0;
* double signalToNoiseScore = 0;
* double ratioScore = 0;
* double totalScore = 0;
* double maximumScore = spacingWeight + signalToNoiseWeight + ratioWeight + fitWeight;
*
* //this will select peaks to the left until
* for (double dd = 1.003 / cs; dd <= 10.03 / cs; dd += 1.003 / cs)
* {
* double theorLeftPeakMz = 0;
* double theorLeftPeakIntensity = 0;
* PeakProcessing.Peak leftPeak;
* peakData.FindPeak(peak.mdbl_mz - dd - peak.mdbl_FWHM, peak.mdbl_mz - dd + peak.mdbl_FWHM, out leftPeak);
* //PeakProcessing.FindPeak
* IsotopeDistribution.FindPeak(theorMostAbundantPeakMz - dd - 0.2 / cs,
* theorMostAbundantPeakMz - dd + 0.2 / cs, out theorLeftPeakMz, out theorLeftPeakIntensity);
*
* if (leftPeak.mdbl_mz > 0) //if there is an experimental peak...
* {
* //get spacing score
* spacingScore = spacingWeight * 1;
*
* //get S/N score
* if (leftPeak.mdbl_SN > signalToNoiseThresh)
* {
* signalToNoiseScore = signalToNoiseWeight * 1;
* }
*
* //get Ratio score
* double leftPeakRatio = leftPeak.mdbl_intensity / peak.mdbl_intensity;
* double theorLeftPeakRatio = theorLeftPeakIntensity / 1;
* //TODO: need to check if this most abundant theor peak's intensity is 1
* }
*
* //get Ratio score
* }
* //get S/N score
* //get Fit score
* //calculate maximum score
* //get overall score
* return 0;
* }*/
public PeakData GetTheoreticalIsotopicDistributionPeakList(List <double> xvals, List <double> yvals)
{
var peakList = new PeakData();
var processor = new PeakProcessor();
processor.SetOptions(0.5, 1, false, PeakFitType.Apex);
processor.DiscoverPeaks(xvals, yvals, 0, 10000);
var numpeaks = processor.PeakData.GetNumPeaks();
for (var i = 0; i < numpeaks; i++)
{
ThrashV1Peak peak;
processor.PeakData.GetPeak(i, out peak);
peakList.AddPeak(peak);
}
return(peakList);
}
/// <summary>
/// Finds peaks in XY Data within the specified range of X values. Optionally, to use all XY data points, enter 0 for both min and max values
/// </summary>
/// <param name="xydata"></param>
/// <param name="minX"></param>
/// <param name="maxX"></param>
/// <returns></returns>
public override List <Peak> FindPeaks(XYData xydata, double minX, double maxX)
{
if (xydata == null || xydata.Xvalues == null || xydata.Xvalues.Length == 0)
{
return(null);
}
var xvals = xydata.Xvalues.ToList();
var yvals = xydata.Yvalues.ToList();
//initialize DeconEngine's peakFinding class
peakProcessor = new PeakProcessor();
//initialize options
//this.isDataThresholded = resultList.Run.IsDataThresholded; [commented out: 2010_04_05 by gord]
UpdateDeconEngineParameters();
BackgroundIntensity = peakProcessor.GetBackgroundIntensity(yvals);
peakProcessor.SetOptions(SignalToNoiseThreshold, BackgroundIntensity * PeakToBackgroundRatio, IsDataThresholded, GetDeconPeakFitType(PeakFitType));
//Find peaks using DeconEngine
if (minX == 0 && maxX == 0)
{
minX = xydata.Xvalues.First();
maxX = xydata.Xvalues.Last();
}
try
{
peakProcessor.DiscoverPeaks(xvals, yvals, minX, maxX);
}
catch (Exception ex)
{
Logger.Instance.AddEntry("DeconToolsPeakDetector.FindPeaks exception: " + ex.Message, Logger.Instance.OutputFilename);
throw;
}
DeconEnginePeakList = peakProcessor.PeakData.PeakTops;
return(ConvertDeconEnginePeakList(DeconEnginePeakList));
}
private void UpdateDeconEngineParameters()
{
peakProcessor.SetOptions(SignalToNoiseThreshold, 0, IsDataThresholded, GetDeconPeakFitType(PeakFitType));
}