public static udtSICPeakFinderOptionsType GetDefaultSICPeakFinderOptions()
{
var peakFinderOptions = new udtSICPeakFinderOptionsType
{
IntensityThresholdFractionMax = 0.01f, // 1% of the peak maximum
IntensityThresholdAbsoluteMinimum = 0,
SICBaselineNoiseOptions = NoiseLevelAnalyzer.GetDefaultNoiseThresholdOptions()
};
// Customize a few values
peakFinderOptions.SICBaselineNoiseOptions.BaselineNoiseMode = NoiseLevelAnalyzer.eNoiseThresholdModes.TrimmedMedianByAbundance;
peakFinderOptions.MaxDistanceScansNoOverlap = 0;
peakFinderOptions.MaxAllowedUpwardSpikeFractionMax = 0.2f; // 20%
peakFinderOptions.InitialPeakWidthScansScaler = 1;
peakFinderOptions.InitialPeakWidthScansMaximum = 30;
peakFinderOptions.FindPeaksOnSmoothedData = true;
peakFinderOptions.SmoothDataRegardlessOfMinimumPeakWidth = true;
// If this is true, will ignore UseSavitzkyGolaySmooth
peakFinderOptions.UseButterworthSmooth = true;
peakFinderOptions.ButterworthSamplingFrequency = 0.25f;
peakFinderOptions.ButterworthSamplingFrequencyDoubledForSIMData = true;
peakFinderOptions.UseSavitzkyGolaySmooth = false;
// Moving average filter if 0, Savitzky Golay filter if 2, 4, 6, etc.
peakFinderOptions.SavitzkyGolayFilterOrder = 0;
// Set the default Mass Spectra noise threshold options
peakFinderOptions.MassSpectraNoiseThresholdOptions = NoiseLevelAnalyzer.GetDefaultNoiseThresholdOptions();
// Customize a few values
peakFinderOptions.MassSpectraNoiseThresholdOptions.BaselineNoiseMode = NoiseLevelAnalyzer.eNoiseThresholdModes.TrimmedMedianByAbundance;
peakFinderOptions.MassSpectraNoiseThresholdOptions.TrimmedMeanFractionLowIntensityDataToAverage = 0.5f;
peakFinderOptions.MassSpectraNoiseThresholdOptions.MinimumSignalToNoiseRatio = 2;
peakFinderOptions.SelectedIonMonitoringDataIsPresent = false;
peakFinderOptions.ReturnClosestPeak = true;
return(peakFinderOptions);
}
/// <summary>
///
/// </summary>
/// <param name="peakFinderOptions"></param>
/// <param name="xyData"></param>
/// <param name="originalPeakLocationIndex">
/// Data point index in the x values that should be a part of the peak
/// Used for determining the best peak</param>
/// <param name="smoothedYData">Smoothed Y values</param>
/// <returns></returns>
public List <clsPeak> FindPeaks(
udtSICPeakFinderOptionsType peakFinderOptions,
List <KeyValuePair <int, double> > xyData,
int originalPeakLocationIndex,
out List <double> smoothedYData)
{
if (xyData.Count == 0)
{
smoothedYData = new List <double>();
return(new List <clsPeak>());
}
// Compute the potential peak area for this SIC
var udtSICPotentialAreaStatsForPeak = FindMinimumPotentialPeakArea(xyData, peakFinderOptions);
// Estimate the noise level
var noiseAnalyzer = new NoiseLevelAnalyzer();
const bool ignoreNonPositiveData = false;
var intensityData = new double[xyData.Count];
var scanNumbers = new int[xyData.Count];
for (var index = 0; index < xyData.Count; index++)
{
scanNumbers[index] = xyData[index].Key;
intensityData[index] = xyData[index].Value;
}
noiseAnalyzer.ComputeTrimmedNoiseLevel(intensityData, 0, intensityData.Length - 1,
peakFinderOptions.SICBaselineNoiseOptions, ignoreNonPositiveData,
out var udtBaselineNoiseStats);
// Find maximumPotentialPeakArea and dataPointCountAboveThreshold
var maximumPotentialPeakArea = FindMaximumPotentialPeakArea(intensityData, peakFinderOptions, udtBaselineNoiseStats, out var dataPointCountAboveThreshold);
if (maximumPotentialPeakArea < 1)
{
maximumPotentialPeakArea = 1;
}
var areaBasedSignalToNoise = maximumPotentialPeakArea / udtSICPotentialAreaStatsForPeak.MinimumPotentialPeakArea;
if (areaBasedSignalToNoise < 1)
{
areaBasedSignalToNoise = 1;
}
var peakDetector = new PeakFinder();
var peakData = new PeakDataContainer();
peakData.SetData(xyData);
if (Math.Abs(peakFinderOptions.ButterworthSamplingFrequency) < float.Epsilon)
{
peakFinderOptions.ButterworthSamplingFrequency = 0.25f;
}
peakData.PeakWidthPointsMinimum = (int)Math.Round(peakFinderOptions.InitialPeakWidthScansScaler * Math.Log10(Math.Floor(areaBasedSignalToNoise)) * 10);
// Assure that .InitialPeakWidthScansMaximum is no greater than .InitialPeakWidthScansMaximum
// and no greater than dataPointCountAboveThreshold/2 (rounded up)
peakData.PeakWidthPointsMinimum = Math.Min(peakData.PeakWidthPointsMinimum, peakFinderOptions.InitialPeakWidthScansMaximum);
peakData.PeakWidthPointsMinimum = Math.Min(peakData.PeakWidthPointsMinimum, (int)Math.Ceiling(dataPointCountAboveThreshold / 2.0));
if (peakData.PeakWidthPointsMinimum > peakData.DataCount * 0.8)
{
peakData.PeakWidthPointsMinimum = (int)Math.Floor(peakData.DataCount * 0.8);
}
if (peakData.PeakWidthPointsMinimum < MINIMUM_PEAK_WIDTH)
{
peakData.PeakWidthPointsMinimum = MINIMUM_PEAK_WIDTH;
}
peakData.OriginalPeakLocationIndex = originalPeakLocationIndex;
var peakFoundContainingOriginalPeakLocation = FindPeaksWork(
peakDetector,
scanNumbers,
peakData,
peakFinderOptions);
smoothedYData = peakData.SmoothedYData.ToList();
return(peakData.Peaks);
}
