public SpectrumData(MsDataFileImpl msDataFileImpl, int scanIndex)
{
ScanIndex = scanIndex;
var spectrum = msDataFileImpl.GetSpectrum(scanIndex);
if (spectrum.Centroided)
{
CentroidMzs = spectrum.Mzs;
CentroidIntensities = spectrum.Intensities;
}
else
{
ProfileMzs = spectrum.Mzs;
ProfileIntensities = spectrum.Intensities;
var centroider = new Centroider(ProfileMzs, ProfileIntensities);
double[] centroidMzs, centroidIntensities;
centroider.GetCentroidedData(out centroidMzs, out centroidIntensities);
CentroidMzs = centroidMzs;
CentroidIntensities = centroidIntensities;
}
Time = spectrum.RetentionTime;
MsLevel = spectrum.Level;
}
private void GenerateChromatograms(ChromatogramTask chromatogramTask)
{
int totalAnalyses = chromatogramTask.AnalysisChromatograms.Count;
if (totalAnalyses == 0)
{
return;
}
if (!UpdateProgress(chromatogramTask, 0))
{
return;
}
var msDataFile = chromatogramTask.MsDataFile;
MsDataFileUtil.InitMsDataFile(chromatogramTask.Workspace, msDataFile);
var analyses = new List <AnalysisChromatograms>(chromatogramTask.AnalysisChromatograms);
MsDataFileImpl pwizMsDataFileImpl;
var path = _workspace.GetDataFilePath(msDataFile.Name);
try
{
pwizMsDataFileImpl = new MsDataFileImpl(path);
}
catch (Exception exception)
{
ErrorHandler.LogException("Chromatogram Generator", "Error opening " + path, exception);
_workspace.RejectMsDataFile(msDataFile);
return;
}
using (pwizMsDataFileImpl)
{
var completeAnalyses = new List <AnalysisChromatograms>();
int totalScanCount = pwizMsDataFileImpl.SpectrumCount;
var lastTimeInDataFile =
chromatogramTask.MsDataFile.GetTime(chromatogramTask.MsDataFile.GetSpectrumCount() - 1);
double minTime = lastTimeInDataFile;
double maxTime = msDataFile.GetTime(0);
foreach (var analysis in analyses)
{
minTime = Math.Min(minTime, analysis.FirstTime);
maxTime = Math.Max(maxTime, analysis.LastTime);
}
int firstScan = msDataFile.FindScanIndex(minTime);
for (int iScan = firstScan; analyses.Count > 0 && iScan < totalScanCount; iScan++)
{
double time = msDataFile.GetTime(iScan);
int progress = (int)(100 * (time - minTime) / (maxTime - minTime));
progress = Math.Min(progress, 100);
progress = Math.Max(progress, 0);
if (!UpdateProgress(chromatogramTask, progress))
{
return;
}
List <AnalysisChromatograms> activeAnalyses = new List <AnalysisChromatograms>();
double nextTime = Double.MaxValue;
if (msDataFile.GetMsLevel(iScan, pwizMsDataFileImpl) != 1)
{
continue;
}
foreach (var analysis in analyses)
{
nextTime = Math.Min(nextTime, analysis.FirstTime);
if (analysis.FirstTime <= time)
{
activeAnalyses.Add(analysis);
}
}
if (activeAnalyses.Count == 0)
{
int nextScan = msDataFile.FindScanIndex(nextTime);
iScan = Math.Max(iScan, nextScan - 1);
continue;
}
bool lowMemory = IsLowOnMemory();
// If we have exceeded the number of analyses we should be working on at once,
// throw out any that we haven't started.
for (int iAnalysis = activeAnalyses.Count - 1; iAnalysis >= 0 &&
(activeAnalyses.Count > _maxConcurrentAnalyses || lowMemory); iAnalysis--)
{
var analysis = activeAnalyses[iAnalysis];
if (analysis.Times.Count > 0)
{
continue;
}
activeAnalyses.RemoveAt(iAnalysis);
analyses.Remove(analysis);
}
double[] mzArray, intensityArray;
pwizMsDataFileImpl.GetSpectrum(iScan, out mzArray, out intensityArray);
if (!pwizMsDataFileImpl.IsCentroided(iScan))
{
var centroider = new Centroider(mzArray, intensityArray);
centroider.GetCentroidedData(out mzArray, out intensityArray);
}
foreach (var analysis in activeAnalyses)
{
var points = new List <ChromatogramPoint>();
foreach (var chromatogram in analysis.Chromatograms)
{
points.Add(MsDataFileUtil.GetPoint(chromatogram.MzRange, mzArray, intensityArray));
}
analysis.AddPoints(iScan, time, points);
}
var incompleteAnalyses = new List <AnalysisChromatograms>();
foreach (var analysis in analyses)
{
if (analysis.LastTime <= time)
{
completeAnalyses.Add(analysis);
}
else
{
incompleteAnalyses.Add(analysis);
}
}
SaveChromatograms(chromatogramTask, completeAnalyses, false);
completeAnalyses.Clear();
analyses = incompleteAnalyses;
}
completeAnalyses.AddRange(analyses);
SaveChromatograms(chromatogramTask, completeAnalyses, true);
}
}