//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);
}
/// <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));
}