private static void Process(GrowablePeak gpeak, BinaryWriter writer, ICollection <double> centerMasses,
ICollection <float> centerMassErrs, ICollection <float> intensities,
ICollection <float> minTimes, ICollection <float> maxTimes,
ICollection <long> filePos, int minPeaks, IRawFile rawFile, double valleyFactor,
bool split, IPeakCollector collector, bool maxIntensity)
{
Peak peak = gpeak.ToPeak();
if (peak.Count >= minPeaks)
{
peak.RemoveDoublePeaks(rawFile, maxIntensity);
if (peak.Count >= minPeaks)
{
peak.Smooth(maxIntensity);
if (collector != null)
{
collector.AddPeak(peak);
}
Peak[] peaks = peak.Decompose(valleyFactor, split, maxIntensity);
foreach (Peak p in peaks)
{
if (p.Count >= minPeaks)
{
centerMasses.Add(p.CenterMass);
centerMassErrs.Add(p.CenterMassError);
intensities.Add(p.Intensity);
minTimes.Add(p.GetMinTime(rawFile));
maxTimes.Add(p.GetMaxTime(rawFile));
filePos.Add(writer.BaseStream.Position);
p.Write(writer);
}
p.Dispose();
}
}
}
}
public static void Detect(string dir, int missingScans, int pointsForCentroid, CentroidPosition centroidPosition,
bool subtractBackground, int backgroundQuantile, double matchPpm, int minPeaks,
double valleyFactor, bool slicePeaks, double intensityThreshold, IRawFile rawFile,
string basePath, bool maxIntensity, IPeakCollector collector, out double[] centerMassArray,
out float[] centerMassErrorArray, out float[] intensityArray, out float[] minTimeArray,
out float[] maxTimeArray, out long[] filePosArray)
{
int npoints = pointsForCentroid;
FileUtil.Rmdir(dir);
Directory.CreateDirectory(dir);
BinaryWriter writer;
string peaksPath = basePath + ".peaks";
try {
writer = FileUtil.GetBinaryWriter(peaksPath);
} catch (Exception) {
throw new Exception("Cannot open file " + peaksPath + ". It may be used by another program.");
}
List <double> centerMasses = new List <double>();
List <float> centerMassErrors = new List <float>();
List <float> intensities = new List <float>();
List <float> minTimes = new List <float>();
List <float> maxTimes = new List <float>();
List <long> filePos = new List <long>();
int oldMinInd = -1;
int oldMaxInd = -1;
List <Ms1CentroidList> cache = new List <Ms1CentroidList>();
int maxMissingScans = (rawFile.NumberOfMS1MassRanges - 1) * (missingScans + 1) + missingScans;
double[][] massRanges = new double[rawFile.MS1Count][];
for (int i = 0; i < rawFile.MS1Count; i++)
{
massRanges[i] = rawFile.GetMS1MassRange(i);
}
double[] intensityNorm = CalcIntensityNormalization(rawFile, pointsForCentroid, centroidPosition, subtractBackground,
backgroundQuantile, maxIntensity);
for (int i = 0; i < rawFile.MS1Count; i++)
{
int minInd = Math.Max(0, i - maxMissingScans - 1);
int maxInd = Math.Min(rawFile.MS1Count - 1, i + maxMissingScans + 1);
if (i == 0)
{
for (int j = 0; j <= maxInd; j++)
{
Spectrum s = rawFile.GetMS1Spectrum(j, subtractBackground, backgroundQuantile);
cache.Add(DetectPeaks(s, intensityThreshold, maxIntensity, npoints, centroidPosition));
s.Dispose();
}
}
else
{
for (int j = oldMinInd; j < minInd; j++)
{
cache[0].Dispose();
cache.RemoveAt(0);
}
for (int j = oldMaxInd + 1; j <= maxInd; j++)
{
Spectrum s = rawFile.GetMS1Spectrum(j, subtractBackground, backgroundQuantile);
cache.Add(DetectPeaks(s, intensityThreshold, maxIntensity, npoints, centroidPosition));
s.Dispose();
}
}
Ms1CentroidList p = cache[i - minInd];
int[] valids = new int[p.Count];
int count = 0;
for (int j = 0; j < p.Count; j++)
{
double cm = p.CenterMass(j);
bool match = false;
int ntries = 0;
for (int k = i - 1; k >= minInd; k--)
{
double[] massRange = massRanges[k];
if (cm >= massRange[0] && cm <= massRange[1])
{
Ms1CentroidList q = cache[k - minInd];
int ind = q.GetClosestIndex(cm);
double m = q.CenterMass(ind);
if (ind != -1 && MassMatch(cm, m, matchPpm))
{
match = true;
break;
}
ntries++;
if (ntries > missingScans)
{
break;
}
}
}
if (!match)
{
ntries = 0;
for (int k = i + 1; k <= maxInd; k++)
{
double[] massRange = massRanges[k];
if (cm >= massRange[0] && cm <= massRange[1])
{
Ms1CentroidList q = cache[k - minInd];
int ind = q.GetClosestIndex(cm);
double m = q.CenterMass(ind);
if (ind != -1 && MassMatch(cm, m, matchPpm))
{
match = true;
break;
}
ntries++;
if (ntries > missingScans)
{
break;
}
}
}
}
if (match)
{
valids[count++] = j;
}
}
valids = ArrayUtil.SubArray(valids, count);
Ms1CentroidList reduced = p.Extract(valids);
cache[i - minInd] = reduced;
byte range = rawFile.GetMS1MassRangeIndex(i);
for (int j = 0; j < reduced.Count; j++)
{
double cm = reduced.CenterMass(j);
bool match = false;
int ntries = 0;
for (int k = i - 1; k >= minInd; k--)
{
double[] massRange = massRanges[k];
if (cm >= massRange[0] && cm <= massRange[1])
{
Ms1CentroidList q = cache[k - minInd];
int ind = q.GetClosestIndex(cm);
double m = q.CenterMass(ind);
if (ind != -1 && MassMatch(cm, m, matchPpm))
{
GrowablePeak peak = q.GetPeak(ind);
peak.Add(i, j, reduced, range, intensityNorm[range]);
match = true;
break;
}
ntries++;
if (ntries > missingScans)
{
break;
}
}
}
if (!match)
{
GrowablePeak peak = new GrowablePeak();
peak.Add(i, j, reduced, range, intensityNorm[range]);
}
}
Ms1CentroidList last = cache[0];
int nextMinInd = Math.Max(0, i - maxMissingScans);
for (int j = 0; j < last.Count; j++)
{
GrowablePeak peak = last.GetPeak(j);
if (peak.IsDisposed())
{
continue;
}
if (peak.LastScanIndex < nextMinInd)
{
Process(peak, writer, centerMasses, centerMassErrors, intensities, minTimes, maxTimes, filePos, minPeaks,
rawFile, valleyFactor, slicePeaks, collector, maxIntensity);
peak.Dispose();
}
}
oldMinInd = minInd;
oldMaxInd = maxInd;
if (i % 100 == 0)
{
Thread.Sleep(100);
}
}
for (int i = rawFile.MS1Count - maxMissingScans - 1; i < rawFile.MS1Count; i++)
{
Ms1CentroidList last = cache[i - oldMinInd];
for (int j = 0; j < last.Count; j++)
{
GrowablePeak peak = last.GetPeak(j);
if (peak.IsDisposed())
{
continue;
}
if (peak.LastScanIndex == i)
{
Process(peak, writer, centerMasses, centerMassErrors, intensities, minTimes,
maxTimes, filePos, minPeaks, rawFile, valleyFactor, slicePeaks, collector, maxIntensity);
peak.Dispose();
}
}
}
writer.Close();
centerMassArray = centerMasses.ToArray();
int[] o = ArrayUtil.Order(centerMassArray);
centerMassArray = ArrayUtil.SubArray(centerMassArray, o);
centerMassErrorArray = ArrayUtil.SubArray(centerMassErrors, o);
intensityArray = ArrayUtil.SubArray(intensities, o);
minTimeArray = ArrayUtil.SubArray(minTimes, o);
maxTimeArray = ArrayUtil.SubArray(maxTimes, o);
filePosArray = ArrayUtil.SubArray(filePos, o);
}
