public static float[] IntegrateTranslatedPeak(Peak peak, double delta, SpectrumCache spectrumCache,
IRawFile rawFile, bool subtractBackground,
int backgroundSubtractionQuantile)
{
int[] scanIndices = peak.GetScanIndices();
float[] intensities = peak.GetOriginalIntensities();
int q = ArrayUtil.MaxInd(intensities);
float maxInt = intensities[q];
int maxScanIndex = scanIndices[q];
float[] result = new float[scanIndices.Length];
for (int i = 0; i < scanIndices.Length; i++)
{
int scanIndex = scanIndices[i];
if (intensities[i] < maxInt * 0.01)
{
continue;
}
if (scanIndex > maxScanIndex + 20 || scanIndex < maxScanIndex - 20)
{
continue;
}
Spectrum spectrum;
if (!spectrumCache.ContainsScanIndex(scanIndex))
{
spectrum = rawFile.GetMS1Spectrum(scanIndex, subtractBackground, backgroundSubtractionQuantile);
spectrumCache.Add(scanIndex, spectrum);
}
else
{
spectrum = spectrumCache[scanIndex];
}
double minMass = peak.GetMinMass(i) + delta;
double maxMass = peak.GetMaxMass(i) + delta;
int minInd = spectrum.GetCeilIndex(minMass);
int maxInd = spectrum.GetFloorIndex(maxMass);
if (minInd == -1 || maxInd == -1)
{
result[i] = 0;
}
else
{
float[] intensityProfile = new float[maxInd - minInd + 1];
for (int ind = minInd; ind <= maxInd; ind++)
{
intensityProfile[ind - minInd] = spectrum.GetIntensity(ind);
}
result[i] = IntegrateProfile(intensityProfile, T01PeakDetection.maxIntensity);
}
}
return(result);
}
private static double[] CalcIntensityNormalization(IRawFile rawFile, int pointsForCentroid,
CentroidPosition centroidPosition,
bool subtractBackground, int backgroundQuantile, bool maxIntensity)
{
int n = rawFile.NumberOfMS1MassRanges;
if (n == 0)
{
return(new double[] { });
}
if (n == 1)
{
return(new double[] { 1 });
}
int npoints = pointsForCentroid;
double[] logAvs = new double[n];
long[] counts = new long[n];
for (int i = 0; i < rawFile.MS1Count; i++)
{
byte range = rawFile.GetMS1MassRangeIndex(i);
Spectrum s = rawFile.GetMS1Spectrum(i, subtractBackground, backgroundQuantile);
double[] specMasses;
double[] specIntensities;
DetectPeaks(s, maxIntensity, npoints, centroidPosition, out specMasses, out specIntensities);
for (int j = 0; j < specMasses.Length; j++)
{
logAvs[range] += Math.Log(specIntensities[j]);
counts[range]++;
}
}
for (int i = 0; i < n; i++)
{
logAvs[i] /= counts[i];
}
double[] norm = new double[n];
norm[0] = 1;
for (int i = 1; i < n; i++)
{
norm[i] = Math.Exp(logAvs[0] - logAvs[i]);
}
return(norm);
}
public static void Detect(string fileName, int missingScans, int pointsForCentroid, CentroidPosition centroidPosition,
bool subtractBackground, int backgroundQuantile, double matchPpm, int minPeaks,
double valleyFactor, bool slicePeaks, double intensityThreshold, IRawFile rawFile,
bool maxIntensity, IPeakCollector collector, out double[] centerMassArray,
out float[] centerMassErrorArray, out float[] intensityArray, out float[] minTimeArray,
out float[] maxTimeArray, out long[] filePosArray)
{
BinaryWriter writer = null;
if (!string.IsNullOrEmpty(fileName))
{
//string peaksPath = fileName + ".peaks";
try
{
writer = new BinaryWriter(new FileStream(fileName, FileMode.Create, FileAccess.Write));
}
catch (Exception)
{
throw new Exception("Cannot open file " + fileName + ". It may be used by another program.");
}
}
int npoints = pointsForCentroid;
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;//TODO What is the difference between NumberOfMS1MassRanges and MS1Count ???
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;
Console.Write("\r{0}% ", ((100 * i) / rawFile.MS1Count));
}
Console.Write("\r{0}% ", 100);
for (int i = rawFile.MS1Count - maxMissingScans - 1; i < rawFile.MS1Count; i++)//i >= oldMinInd
{
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();
}
}
}
if (writer != null)
{
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);
if (writer != null)
{
filePosArray = ArrayUtil.SubArray(filePos, o);
}
else
{
filePosArray = filePos.ToArray();
}
}
