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)
{
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 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);
}
/// <summary>
/// Copy the data inside into a new one.
/// </summary>
/// <returns></returns>
public ISpectrum Clone()
{
return(_spectrum.Clone());
}
