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; }