public ISpectrum Process(ISpectrum spectrum)
{
List <IPeak> peaks = spectrum.GetPeaks();
double[] signal = peaks.Select(p => p.GetIntensity()).ToArray();
SortedDictionary <double, List <double> > matrix =
new SortedDictionary <double, List <double> >();
for (double a = 1.0; a <= maxScale; a += steps)
{
double[] processed = Algorithm.CWT.Transform(signal, a);
matrix[a] = processed.ToList();
}
List <RidgeLine> lines = finder.Find(
spectrum.GetPeaks().Select(p => p.GetMZ()).ToList(),
matrix);
HashSet <double> mz = new HashSet <double>(lines.Select(p => p.Pos).ToList());
List <IPeak> processedPeaks = peaks.Where(p => mz.Contains(p.GetMZ())).ToList();
ISpectrum newSpectrum = spectrum.Clone();
newSpectrum.SetPeaks(processedPeaks);
return(newSpectrum);
}
public ISpectrum Process(ISpectrum spectrum)
{
List <IPeak> peaks = peakpick(spectrum.GetPeaks(), maxPeaks);
peaks.Sort();
NormalizePeaks(peaks, factor);
spectrum.SetPeaks(peaks);
return(spectrum);
}
public void Process(ISpectrum spectrum)
{
List <IPeak> peaks = spectrum.GetPeaks()
.OrderByDescending(pk => pk.GetIntensity())
.Take(maxPeaks)
.OrderBy(pk => pk.GetMZ()).ToList();;
spectrum.SetPeaks(peaks);
}
public ISpectrum Process(ISpectrum spectrum)
{
ISpectrum filtered = peakPicking.Process(spectrum);
List <IPeak> peaks = new List <IPeak>();
double minIntensity = filtered.GetPeaks().Min(p => p.GetIntensity());
filtered.SetPeaks(
peaks.Where(p => p.GetIntensity() > ratio * minIntensity).ToList());
return(filtered);
}
public ISpectrum Process(ISpectrum spectrum)
{
if (spectrum.GetPeaks().Count == 0)
{
return(spectrum);
}
// insert pseudo peaks for large gap
List <IPeak> peaks = new List <IPeak>();
double mz = spectrum.GetPeaks().First().GetMZ();
peaks.Add(new GeneralPeak(mz - precision, 0));
foreach (IPeak peak in spectrum.GetPeaks())
{
if (peak.GetMZ() - mz > precision)
{
double middle = (mz + peak.GetMZ()) / 2;
peaks.Add(new GeneralPeak(middle, 0));
}
peaks.Add(peak);
mz = peak.GetMZ();
}
peaks.Add(new GeneralPeak(mz + precision, 0));
List <IPeak> processedPeaks = new List <IPeak>();
int index = 1;
int end = peaks.Count - 1;
int head = index + 1;
while (index < end)
{
if (peaks[index - 1].GetIntensity() < peaks[index].GetIntensity())
{
head = index + 1;
}
while (head < end &&
peaks[head].GetIntensity() == peaks[index].GetIntensity())
{
head++;
}
if (peaks[head].GetIntensity() < peaks[index].GetIntensity())
{
processedPeaks.Add(peaks[index]);
index = head;
}
index++;
}
ISpectrum newSpectrum = spectrum.Clone();
newSpectrum.SetPeaks(processedPeaks);
return(newSpectrum);
}
public void Process(ISpectrum spectrum)
{
List <IPeak> peaks = spectrum.GetPeaks();
//double sumsIntensity = Math.Log10(peaks.Sum(x => x.GetIntensity()));
for (int i = 0; i < peaks.Count; i++)
{
peaks[i].SetIntensity(Math.Log10(peaks[i].GetIntensity()) * scale);
}
spectrum.SetPeaks(peaks);
}
public ISpectrum Process(ISpectrum spectrum)
{
ISpectrum centroid = peakPicking.Process(spectrum);
List <IPeak> peaks = new List <IPeak>();
foreach (IPeak cPeak in centroid.GetPeaks())
{
List <IPeak> neighbors = NeighborPeaks(cPeak, spectrum.GetPeaks());
peaks.Add(Average(cPeak, neighbors));
}
centroid.SetPeaks(peaks);
return(centroid);
}
public ISpectrum Process(ISpectrum spectrum)
{
if (spectrum.GetPeaks().Count == 0)
{
return(spectrum);
}
// insert pseudo peaks for large gap
List <IPeak> peaks = InsertPeaks(spectrum);
List <IPeak> processedPeaks = new List <IPeak>();
int index = 1;
int end = peaks.Count - 1;
int head = index + 1;
while (index < end)
{
if (peaks[index - 1].GetIntensity() < peaks[index].GetIntensity())
{
head = index + 1;
}
while (head < end &&
peaks[head].GetIntensity() == peaks[index].GetIntensity())
{
head++;
}
if (peaks[head].GetIntensity() < peaks[index].GetIntensity())
{
processedPeaks.Add(peaks[index]);
index = head;
}
index++;
}
ISpectrum newSpectrum = spectrum.Clone();
newSpectrum.SetPeaks(processedPeaks);
return(newSpectrum);
}
public void Process(ISpectrum spectrum)
{
List <IPeak> peaks = peakPicker.Picking(spectrum.GetPeaks());
spectrum.SetPeaks(peaks);
}