private void Extend(CrawdadPeak crawdadPeak)
{
// Look a number of steps dependent on the width of the peak, since interval width
// may vary.
int toleranceLen = Math.Max(MinToleranceLen, (int)Math.Round(crawdadPeak.Fwhm * FractionFwhmLen));
crawdadPeak.ResetBoundaries(ExtendBoundary(crawdadPeak, crawdadPeak.StartIndex, -1, toleranceLen),
ExtendBoundary(crawdadPeak, crawdadPeak.EndIndex, 1, toleranceLen));
}
private void Extend(CrawdadPeak crawdadPeak)
{
// Look a number of steps dependent on the width of the peak, since interval width
// may vary.
int toleranceLen = Math.Max(MinToleranceLen, (int)Math.Round(crawdadPeak.Fwhm * FractionFwhmLen));
crawdadPeak.ResetBoundaries(ExtendBoundary(crawdadPeak, crawdadPeak.StartIndex, -1, toleranceLen),
ExtendBoundary(crawdadPeak, crawdadPeak.EndIndex, 1, toleranceLen));
}
public ChromPeak CalcChromPeak(CrawdadPeak peakMax, ChromPeak.FlagValues flags, out CrawdadPeak peak)
{
// Reintegrate all peaks to the max peak, even the max peak itself, since its boundaries may
// have been extended from the Crawdad originals.
if (peakMax == null)
{
peak = null;
return(ChromPeak.EMPTY);
}
peak = CalcPeak(peakMax.StartIndex, peakMax.EndIndex);
return(new ChromPeak(Finder, peak, flags, Times, Intensities, MassErrors10X));
}
private int ExtendBoundary(CrawdadPeak peakPrimary, int indexBoundary, int increment, int toleranceLen)
{
if (peakPrimary.Fwhm >= MinToleranceSmoothFwhm)
{
indexBoundary = ExtendBoundary(peakPrimary, false, indexBoundary, increment, toleranceLen);
}
// TODO:
// Because smoothed data can have a tendency to reach baseline one
// interval sooner than the raw data, do a final check to choose the
// boundary correctly for the raw data.
//indexBoundary = RetractBoundary(peakPrimary, true, indexBoundary, -increment);
//indexBoundary = ExtendBoundary(peakPrimary, true, indexBoundary, increment, toleranceLen);
return(indexBoundary);
}
public void FindPeaks(double[] retentionTimes, bool requireDocNode)
{
Finder = new CrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (requireDocNode && DocNode == null)
{
RawPeaks = new CrawdadPeak[0];
}
else
{
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities);
}
}
private int ExtendBoundary(CrawdadPeak peakPrimary, bool useRaw, int indexBoundary, int increment, int toleranceLen)
{
var intensities = _intensities;
int lenIntensities = intensities.Count;
var boundaryIntensity = intensities[indexBoundary];
var maxIntensity = boundaryIntensity;
// Look for a descent proportional to the height of the peak. Because, SRM data is
// so low noise, just looking for any descent can lead to boundaries very far away from
// the peak.
float height = peakPrimary.Height;
double minDescent = height * DescentTol;
// Put a limit on how high intensity can go before the search is terminated
double maxHeight = ((height - boundaryIntensity) * AscentTol) + boundaryIntensity;
// Extend the index in the direction of the increment
for (int i = indexBoundary + increment;
i > 0 && i < lenIntensities - 1 && Math.Abs(indexBoundary - i) < toleranceLen;
i += increment)
{
double maxIntensityCurrent = intensities[i];
// If intensity goes above the maximum, stop looking
if (maxIntensityCurrent > maxHeight)
{
break;
}
// If descent greater than tolerance, step until it no longer is
while (maxIntensity - maxIntensityCurrent > minDescent)
{
indexBoundary += increment;
if (indexBoundary == i)
{
maxIntensity = maxIntensityCurrent;
}
else
{
maxIntensityCurrent = intensities[indexBoundary];
}
}
}
return(indexBoundary);
}
public ChromPeak CalcChromPeak(CrawdadPeak peakMax, ChromPeak.FlagValues flags)
{
_chromPeak = Data.CalcChromPeak(peakMax, flags, out _crawPeak);
return(_chromPeak);
}
public ChromDataPeak(ChromData data, CrawdadPeak peak)
{
Data = data;
_crawPeak = peak;
}
private int ExtendBoundary(CrawdadPeak peakPrimary, int indexBoundary, int increment, int toleranceLen)
{
if (peakPrimary.Fwhm >= MinToleranceSmoothFwhm)
{
indexBoundary = ExtendBoundary(peakPrimary, false, indexBoundary, increment, toleranceLen);
}
// TODO:
// Because smoothed data can have a tendency to reach baseline one
// interval sooner than the raw data, do a final check to choose the
// boundary correctly for the raw data.
//indexBoundary = RetractBoundary(peakPrimary, true, indexBoundary, -increment);
//indexBoundary = ExtendBoundary(peakPrimary, true, indexBoundary, increment, toleranceLen);
return indexBoundary;
}
private int ExtendBoundary(CrawdadPeak peakPrimary, bool useRaw, int indexBoundary, int increment, int toleranceLen)
{
var intensities = _intensities;
int lenIntensities = intensities.Count;
var boundaryIntensity = intensities[indexBoundary];
var maxIntensity = boundaryIntensity;
// Look for a descent proportional to the height of the peak. Because, SRM data is
// so low noise, just looking for any descent can lead to boundaries very far away from
// the peak.
float height = peakPrimary.Height;
double minDescent = height * DescentTol;
// Put a limit on how high intensity can go before the search is terminated
double maxHeight = ((height - boundaryIntensity) * AscentTol) + boundaryIntensity;
// Extend the index in the direction of the increment
for (int i = indexBoundary + increment;
i > 0 && i < lenIntensities - 1 && Math.Abs(indexBoundary - i) < toleranceLen;
i += increment)
{
double maxIntensityCurrent = intensities[i];
// If intensity goes above the maximum, stop looking
if (maxIntensityCurrent > maxHeight)
break;
// If descent greater than tolerance, step until it no longer is
while (maxIntensity - maxIntensityCurrent > minDescent)
{
indexBoundary += increment;
if (indexBoundary == i)
maxIntensity = maxIntensityCurrent;
else
maxIntensityCurrent = intensities[indexBoundary];
}
}
return indexBoundary;
}