/// <summary>
/// Get a chromatogram with properly sorted time values.
/// </summary>
public void ReleaseChromatogram(byte[] bytesFromDisk, out TimeIntensities timeIntensities)
{
var times = Times.ToArray(bytesFromDisk);
var intensities = Intensities.ToArray(bytesFromDisk);
var massErrors = MassErrors != null
? MassErrors.ToArray(bytesFromDisk)
: null;
var scanIds = Scans != null
? Scans.ToArray(bytesFromDisk)
: null;
// Make sure times and intensities match in length.
if (times.Length != intensities.Length)
{
throw new InvalidDataException(
string.Format(Resources.ChromCollected_ChromCollected_Times__0__and_intensities__1__disagree_in_point_count,
times.Length, intensities.Length));
}
if (massErrors != null && massErrors.Length != intensities.Length)
{
throw new InvalidDataException(
string.Format(Resources.ChromCollector_ReleaseChromatogram_Intensities___0___and_mass_errors___1___disagree_in_point_count_,
intensities.Length, massErrors.Length));
}
timeIntensities = new TimeIntensities(times, intensities, massErrors, scanIds);
// Release memory.
Times = null;
Intensities = null;
MassErrors = null;
Scans = null;
}
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);
});
}
}
/// <summary>
/// Get a chromatogram with properly sorted time values.
/// </summary>
public void ReleaseChromatogram(byte[] bytesFromDisk, out float[] times, out float[] intensities, out float[] massErrors, out int[] scanIds)
{
times = Times.ToArray(bytesFromDisk);
intensities = Intensities.ToArray(bytesFromDisk);
massErrors = MassErrors != null
? MassErrors.ToArray(bytesFromDisk)
: null;
scanIds = Scans != null
? Scans.ToArray(bytesFromDisk)
: null;
// Release memory.
Times = null;
Intensities = null;
MassErrors = null;
Scans = null;
// Make sure times and intensities match in length.
if (times.Length != intensities.Length)
{
throw new InvalidDataException(
string.Format(Resources.ChromCollected_ChromCollected_Times__0__and_intensities__1__disagree_in_point_count,
times.Length, intensities.Length));
}
}
public void FindPeaks(double[] retentionTimes)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities.ToArray());
}
public void FindPeaks(double[] retentionTimes, bool requireDocNode)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (requireDocNode && DocNode == null)
{
RawPeaks = new IFoundPeak[0];
}
else
{
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities.ToArray());
}
}
