public void FindPeaks(double[] retentionTimes, TimeIntervals timeIntervals, ExplicitRetentionTimeInfo explicitRT)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (timeIntervals == null)
{
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
}
else
{
var identifiedIndices = TimesToIndices(retentionTimes);
var allPeaks = timeIntervals.Intervals.SelectMany(interval =>
FindIntervalPeaks(interval.Key, interval.Value, identifiedIndices));
RawPeaks = allPeaks.OrderByDescending(peak => Tuple.Create(peak.Identified, peak.Area))
.Take(MAX_PEAKS).ToArray();
}
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities.ToArray());
// Accept only peaks within the user-provided RT window, if any
if (explicitRT != null)
{
var winLow = (float)(explicitRT.RetentionTime - 0.5 * (explicitRT.RetentionTimeWindow ?? 0));
var winHigh = winLow + (float)(explicitRT.RetentionTimeWindow ?? 0);
RawPeaks = RawPeaks.Where(rp =>
{
var t = Times[rp.TimeIndex];
return(winLow <= t && t <= winHigh);
});
}
}
public TimeIntervals InferTimeIntervals(IEnumerable <IList <float> > timesList)
{
TimeIntervals result = null;
var timesSet = new HashSet <object>(new IdentityEqualityComparer <object>());
foreach (var times in timesList)
{
if (!timesSet.Add(times))
{
continue;
}
TimeIntervals timeIntervals = InferTimeIntervalsFromScanTimes(times);
if (result == null)
{
result = timeIntervals;
}
else
{
var newResult = result.Intersect(timeIntervals);
result = newResult;
}
}
return(result);
}
public TimeIntervals Intersect(TimeIntervals other)
{
using (var myIntervals = Intervals.GetEnumerator())
using (var otherIntervals = other.Intervals.GetEnumerator())
{
return(FromIntervalsSorted(Intersect(myIntervals, otherIntervals)));
}
}
public static RawTimeIntensities FromChromatogramGroupData(ChromatogramGroupData chromatogramGroupData)
{
var timeIntensitiesList = new List <TimeIntensities>();
var timeLists = chromatogramGroupData.TimeLists.Select(timeList => ImmutableList.ValueOf(timeList.Times)).ToArray();
var scanIdLists = chromatogramGroupData.ScanIdLists
.Select(scanIdList => ImmutableList.ValueOf(scanIdList.ScanIds)).ToArray();
foreach (var chromatogram in chromatogramGroupData.Chromatograms)
{
IEnumerable <float> massErrors = null;
if (chromatogram.MassErrors100X.Count > 0)
{
massErrors = chromatogram.MassErrors100X.Select(error => error / 100.0f);
}
else if (chromatogram.MassErrorsDeprecated.Count > 0)
{
massErrors = chromatogram.MassErrorsDeprecated;
}
var timeIntensities = new TimeIntensities(timeLists[chromatogram.TimeListIndex - 1],
chromatogram.Intensities,
massErrors,
chromatogram.ScanIdListIndex == 0 ? null : scanIdLists[chromatogram.ScanIdListIndex - 1]);
timeIntensitiesList.Add(timeIntensities);
}
InterpolationParams interpolationParams;
if (chromatogramGroupData.InterpolatedNumPoints == 0)
{
interpolationParams = null;
}
else
{
interpolationParams = new InterpolationParams(chromatogramGroupData.InterpolatedStartTime, chromatogramGroupData.InterpolatedEndTime, chromatogramGroupData.InterpolatedNumPoints, chromatogramGroupData.InterpolatedDelta)
.ChangeInferZeroes(chromatogramGroupData.InferZeroes);
}
var rawTimeIntensities = new RawTimeIntensities(timeIntensitiesList, interpolationParams);
if (chromatogramGroupData.TimeIntervals != null)
{
var startTimes = chromatogramGroupData.TimeIntervals.StartTimes;
var endTimes = chromatogramGroupData.TimeIntervals.EndTimes;
var timeIntervals = TimeIntervals.FromIntervals(Enumerable.Range(0, startTimes.Count)
.Select(i => new KeyValuePair <float, float>(startTimes[i], endTimes[i])));
rawTimeIntensities = rawTimeIntensities.ChangeTimeIntervals(timeIntervals);
}
return(rawTimeIntensities);
}
public RawTimeIntensities ChangeTimeIntervals(TimeIntervals timeIntervals)
{
return(ChangeProp(ImClone(this), im => im.TimeIntervals = timeIntervals));
}
public ChromPeak CalcChromPeak(IFoundPeak peakMax, ChromPeak.FlagValues flags, TimeIntervals timeIntervals)
{
_chromPeak = Data.CalcChromPeak(peakMax, flags, timeIntervals, out _crawPeak);
return(_chromPeak);
}
public ChromPeak CalcChromPeak(IFoundPeak peakMax, ChromPeak.FlagValues flags, TimeIntervals timeIntervals, out IFoundPeak 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);
}
var peakIntegrator = new PeakIntegrator(TimeIntensities, Finder)
{
RawTimeIntensities = RawTimeIntensities,
TimeIntervals = timeIntervals
};
var tuple = peakIntegrator.IntegrateFoundPeak(peakMax, flags);
peak = tuple.Item2;
return(tuple.Item1);
}
public TimeIntervals InferTimeIntervalsFromScanTimes(IList <float> times)
{
float medianDuration = GetMedianScanDuration(times);
return(TimeIntervals.FromScanTimes(times, (float)(medianDuration * ScanTimeTolerance)));
}