private void ExamineNarrowPeaks(PeakDataContainer peakData, udtSICPeakFinderOptionsType peakFinderOptions)
{
if (peakData.Peaks.Count <= 0)
{
// No peaks were found; create a new peak list using the original peak location index as the peak center
peakData.Peaks = new List <clsPeak>
{
new clsPeak(peakData.OriginalPeakLocationIndex)
};
return;
}
if (!peakFinderOptions.ReturnClosestPeak)
{
return;
}
// Make sure one of the peaks is within 1 of the original peak location
var blnSuccess = false;
foreach (var peak in peakData.Peaks)
{
if (peak.LocationIndex - peakData.OriginalPeakLocationIndex <= 1)
{
blnSuccess = true;
break;
}
}
if (blnSuccess)
{
// One of the peaks includes data point peakData.OriginalPeakLocationIndex
return;
}
// None of the peaks includes peakData.OriginalPeakLocationIndex
var newPeak = new clsPeak(peakData.OriginalPeakLocationIndex)
{
Area = peakData.YData[peakData.OriginalPeakLocationIndex]
};
peakData.Peaks.Add(newPeak);
}
/// <summary>
///
/// </summary>
/// <param name="peakDetector"></param>
/// <param name="scanNumbers"></param>
/// <param name="peakData"></param>
/// <param name="peakFinderOptions"></param>
/// <returns>Detected peaks will be in the peakData object</returns>
private bool FindPeaksWork(
PeakFinder peakDetector,
IList <int> scanNumbers,
PeakDataContainer peakData,
udtSICPeakFinderOptionsType peakFinderOptions)
{
const float sngPeakMaximum = 0;
bool validPeakFound;
// Smooth the Y data, and store in peakData.SmoothedYData
// Note that if using a Butterworth filter, then we increase peakData.PeakWidthPointsMinimum if too small, compared to 1/SamplingFrequency
var peakWidthPointsMinimum = peakData.PeakWidthPointsMinimum;
var dataIsSmoothed = SmoothData(peakData.YData, peakData.DataCount, peakFinderOptions, ref peakWidthPointsMinimum, out var smoothedYData, out var errorMessage);
// peakWidthPointsMinimum may have been auto-updated
peakData.PeakWidthPointsMinimum = peakWidthPointsMinimum;
// Store the smoothed data in the data container
peakData.SetSmoothedData(smoothedYData);
var peakDetectIntensityThresholdPercentageOfMaximum = (int)Math.Round(peakFinderOptions.IntensityThresholdFractionMax * 100);
const int peakWidthInSigma = 2;
const bool useValleysForPeakWidth = true;
const bool movePeakLocationToMaxIntensity = true;
if (peakFinderOptions.FindPeaksOnSmoothedData && dataIsSmoothed)
{
peakData.Peaks = peakDetector.DetectPeaks(
peakData.XData, peakData.SmoothedYData,
peakFinderOptions.IntensityThresholdAbsoluteMinimum,
peakData.PeakWidthPointsMinimum,
peakDetectIntensityThresholdPercentageOfMaximum,
peakWidthInSigma,
useValleysForPeakWidth,
movePeakLocationToMaxIntensity);
}
else
{
// Look for the peaks, using peakData.PeakWidthPointsMinimum as the minimum peak width
peakData.Peaks = peakDetector.DetectPeaks(
peakData.XData, peakData.YData,
peakFinderOptions.IntensityThresholdAbsoluteMinimum,
peakData.PeakWidthPointsMinimum,
peakDetectIntensityThresholdPercentageOfMaximum,
peakWidthInSigma,
useValleysForPeakWidth,
movePeakLocationToMaxIntensity);
}
if (peakData.Peaks == null)
{
// Fatal error occurred while finding peaks
return(false);
}
if (peakData.PeakWidthPointsMinimum == MINIMUM_PEAK_WIDTH)
{
// Testing the minimum peak width; run some checks
ExamineNarrowPeaks(peakData, peakFinderOptions);
}
if (peakData.Peaks.Count <= 0)
{
// No peaks were found
return(false);
}
foreach (var peak in peakData.Peaks)
{
peak.IsValid = false;
// Find the center and boundaries of this peak
// Make sure peak.LocationIndex is between peak.LeftEdge and peak.RightEdge
if (peak.LeftEdge > peak.LocationIndex)
{
Console.WriteLine("peak.LeftEdge is > peak.LocationIndex; this is probably a programming error");
peak.LeftEdge = peak.LocationIndex;
}
if (peak.RightEdge < peak.LocationIndex)
{
Console.WriteLine("peak.RightEdge is < peak.LocationIndex; this is probably a programming error");
peak.RightEdge = peak.LocationIndex;
}
// See if the peak boundaries (left and right edges) need to be narrowed or expanded
// Do this by stepping left or right while the intensity is decreasing. If an increase is found, but the
// next point after the increasing point is less than the current point, then possibly keep stepping; the
// test for whether to keep stepping is that the next point away from the increasing point must be less
// than the current point. If this is the case, replace the increasing point with the average of the
// current point and the point two points away
//
// Use smoothed data for this step
// Determine the smoothing window based on peakData.PeakWidthPointsMinimum
// If peakData.PeakWidthPointsMinimum <= 4 then do not filter
if (!dataIsSmoothed)
{
// Need to smooth the data now
peakWidthPointsMinimum = peakData.PeakWidthPointsMinimum;
dataIsSmoothed = SmoothData(
peakData.YData,
peakData.DataCount,
peakFinderOptions,
ref peakWidthPointsMinimum,
out smoothedYData,
out errorMessage);
// peakWidthPointsMinimum may have been auto-updated
peakData.PeakWidthPointsMinimum = peakWidthPointsMinimum;
// Store the smoothed data in the data container
peakData.SetSmoothedData(smoothedYData);
}
// First see if we need to narrow the peak by looking for decreasing intensities moving toward the peak center
// We'll use the unsmoothed data for this
while (peak.LeftEdge < peak.LocationIndex - 1)
{
if (peakData.YData[peak.LeftEdge] > peakData.YData[peak.LeftEdge + 1])
{
// OrElse (usedSmoothedDataForPeakDetection AndAlso peakData.SmoothedYData[peak.LeftEdge) < 0) Then
peak.LeftEdge += 1;
}
else
{
break;
}
}
while (peak.RightEdge > peak.LocationIndex + 1)
{
if (peakData.YData[peak.RightEdge - 1] < peakData.YData[peak.RightEdge])
{
// OrElse (usedSmoothedDataForPeakDetection AndAlso peakData.SmoothedYData[peak.RightEdge) < 0) Then
peak.RightEdge -= 1;
}
else
{
break;
}
}
// Now see if we need to expand the peak by looking for decreasing intensities moving away from the peak center,
// but allowing for small increases
// We'll use the smoothed data for this; if we encounter negative values in the smoothed data, we'll keep going until we reach the low point since huge peaks can cause some odd behavior with the Butterworth filter
// Keep track of the number of times we step over an increased value
ExpandPeakLeftEdge(peakData, peakFinderOptions, peak, sngPeakMaximum, dataIsSmoothed);
ExpandPeakRightEdge(peakData, peakFinderOptions, peak, sngPeakMaximum, dataIsSmoothed);
peak.IsValid = true;
if (!peakFinderOptions.ReturnClosestPeak)
{
continue;
}
// If peakData.OriginalPeakLocationIndex is not between peak.LeftEdge and peak.RightEdge, then check
// if the scan number for peakData.OriginalPeakLocationIndex is within .MaxDistanceScansNoOverlap scans of
// either of the peak edges; if not, then mark the peak as invalid since it does not contain the
// scan for the parent ion
if (peakData.OriginalPeakLocationIndex < peak.LeftEdge)
{
if (
Math.Abs(scanNumbers[peakData.OriginalPeakLocationIndex] -
scanNumbers[peak.LeftEdge]) >
peakFinderOptions.MaxDistanceScansNoOverlap)
{
peak.IsValid = false;
}
}
else if (peakData.OriginalPeakLocationIndex > peak.RightEdge)
{
if (
Math.Abs(scanNumbers[peakData.OriginalPeakLocationIndex] -
scanNumbers[peak.RightEdge]) >
peakFinderOptions.MaxDistanceScansNoOverlap)
{
peak.IsValid = false;
}
}
}
// Find the peak with the largest area that has peakData.PeakIsValid = True
peakData.BestPeak = null;
var bestPeakArea = double.MinValue;
foreach (var peak in peakData.Peaks)
{
if (peak.IsValid)
{
if (peak.Area > bestPeakArea)
{
peakData.BestPeak = peak;
bestPeakArea = peak.Area;
}
}
}
if (peakData.BestPeak != null)
{
validPeakFound = true;
}
else
{
validPeakFound = false;
}
return(validPeakFound);
}
private void ExpandPeakRightEdge(
PeakDataContainer peakData,
udtSICPeakFinderOptionsType peakFinderOptions,
clsPeak peak,
float sngPeakMaximum,
bool dataIsSmoothed)
{
var intStepOverIncreaseCount = 0;
while (peak.RightEdge < peakData.DataCount - 1)
{
if (peakData.SmoothedYData[peak.RightEdge + 1] < peakData.SmoothedYData[peak.RightEdge])
{
// The adjacent point is lower than the current point
peak.RightEdge += 1;
}
else if (Math.Abs(peakData.SmoothedYData[peak.RightEdge + 1] -
peakData.SmoothedYData[peak.RightEdge]) < double.Epsilon)
{
// The adjacent point is equal to the current point
peak.RightEdge += 1;
}
else
{
// The next point to the right is not lower; what about the point after it?
if (peak.RightEdge < peakData.DataCount - 2)
{
if (peakData.SmoothedYData[peak.RightEdge + 2] <=
peakData.SmoothedYData[peak.RightEdge])
{
// Only allow ignoring an upward spike if the delta from this point to the next is <= .MaxAllowedUpwardSpikeFractionMax of sngPeakMaximum
if (peakData.SmoothedYData[peak.RightEdge + 1] -
peakData.SmoothedYData[peak.RightEdge] >
peakFinderOptions.MaxAllowedUpwardSpikeFractionMax * sngPeakMaximum)
{
break;
}
if (dataIsSmoothed)
{
// Only ignore an upward spike twice if the data is smoothed
if (intStepOverIncreaseCount >= 2)
{
break;
}
}
peak.RightEdge += 1;
intStepOverIncreaseCount += 1;
}
else
{
break;
}
}
else
{
break;
}
}
}
}
/// <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);
}