/// <summary>
/// Gets the peak that fits the point at a given index with a Lorentzian fit.
/// </summary>
/// <param name="index">index of the point in the m/z vectors which is the apex of the peak.</param>
/// <param name="mzs">List of raw data of m\zs.</param>
/// <param name="intensities">List of raw data of intensities.</param>
/// <param name="fwhm"></param>
/// <returns>returns the m/z of the peak.</returns>
private double LorentzianFit(List <double> mzs, List <double> intensities, int index, double fwhm)
{
var a = intensities[index];
var vo = mzs[index];
var e = Math.Abs((vo - mzs[index + 1]) / 100);
if (index < 1)
{
return(mzs[index]);
}
if (index == mzs.Count)
{
return(mzs[index]);
}
var lstart = PeakIndex.GetNearest(mzs, vo + fwhm, index) + 1;
var lstop = PeakIndex.GetNearest(mzs, vo - fwhm, index) - 1;
var currentE = LorentzianLS(mzs, intensities, a, fwhm, vo, lstart, lstop);
for (var i = 0; i < 50; i++)
{
var lastE = currentE;
vo = vo + e;
currentE = LorentzianLS(mzs, intensities, a, fwhm, vo, lstart, lstop);
if (currentE > lastE)
{
break;
}
}
vo = vo - e;
currentE = LorentzianLS(mzs, intensities, a, fwhm, vo, lstart, lstop);
for (var i = 0; i < 50; i++)
{
var lastE = currentE;
vo = vo - e;
currentE = LorentzianLS(mzs, intensities, a, fwhm, vo, lstart, lstop);
if (currentE > lastE)
{
break;
}
}
vo = vo + e;
return(vo);
}
/// <summary>
/// Finds the highest peak from the raw data lists withing the specified m/z range.
/// </summary>
/// <param name="startMz">minimum m\z at which to look for the peak</param>
/// <param name="stopMz">maximum m\z at which to look for the peak.</param>
/// <param name="peak"> instance whose mz and intensity are set to the peak that is found.</param>
/// <remarks>The function only sets the mz, intensity of the peak, not the other members (SN, FWHM etc).</remarks>
public void FindPeak(double startMz, double stopMz, out ThrashV1Peak peak)
{
peak = new ThrashV1Peak(-1);
var width = (stopMz - startMz) / 2;
var foundExistingPeak = GetClosestPeak(startMz + width, width, out peak);
if (foundExistingPeak)
{
// peak already exists. Send it back.
}
else
{
// peak doesn't exist. Lets find a starting index to start looking at.
// perhaps there was a peak there.
var foundPeak = GetClosestPeakFromAll(startMz + width, width, out peak);
var numPts = MzList.Count;
if (foundPeak)
{
var index = peak.DataIndex;
while (index > 0 && MzList[index] >= startMz)
{
var intensity = IntensityList[index];
var mz = MzList[index];
if (intensity > peak.Intensity && mz <= stopMz)
{
peak.Mz = mz;
peak.Intensity = intensity;
peak.DataIndex = index;
}
index--;
}
index = peak.DataIndex;
while (index < numPts && MzList[index] <= stopMz)
{
var intensity = IntensityList[index];
if (intensity > peak.Intensity)
{
var mz = MzList[index];
peak.Mz = mz;
peak.Intensity = intensity;
peak.DataIndex = index;
}
index++;
}
if (peak.Intensity <= 0)
{
peak.Mz = 0;
}
}
else
{
var startIndex = PeakIndex.GetNearestBinary(MzList, startMz, 0, numPts - 1);
if (startIndex > numPts - 1)
{
startIndex = numPts - 1;
}
if (startIndex < 0)
{
startIndex = 0;
}
if (MzList[startIndex] > startMz)
{
while (startIndex > 0 && MzList[startIndex] > startMz)
{
startIndex--;
}
}
else
{
while (startIndex < numPts && MzList[startIndex] < startMz)
{
startIndex++;
}
startIndex--;
}
for (var i = startIndex; i < numPts; i++)
{
var mz = MzList[i];
var intensity = IntensityList[i];
if (mz > stopMz)
{
break;
}
if (intensity > peak.Intensity)
{
peak.Mz = mz;
peak.Intensity = intensity;
peak.DataIndex = i;
}
}
}
}
}
/// <summary>
/// Gets the signal to noise for a point.
/// </summary>
/// <param name="mzList">is List of m/z values.</param>
/// <param name="intensityList">is List of intensity values.</param>
/// <param name="peak">is the m/z value at which we want to find the signal to noise ratio.</param>
/// <returns>returns the signal to noise value of the peak.</returns>
public double GetSignalToNoise(List <double> mzList, List <double> intensityList, double peak)
{
var index = PeakIndex.GetNearest(mzList, peak, 0);
return(PeakStatistician.FindSignalToNoise(intensityList[index], intensityList, index));
}
/// <summary>
/// Gets the FWHM for a point.
/// </summary>
/// <param name="mzList">is List of m/z values.</param>
/// <param name="intensityList">is List of intensity values.</param>
/// <param name="peak">is the m/z value at which we want to find FWHM.</param>
/// <returns>returns the m/z value of the peak.</returns>
public double GetFWHM(List <double> mzList, List <double> intensityList, double peak)
{
var index = PeakIndex.GetNearest(mzList, peak, 0);
return(PeakStatistician.FindFwhm(mzList, intensityList, index));
}
/// <summary>
/// Function discovers peaks in the m/z and intensity vectors supplied within the supplied m/z window.
/// </summary>
/// <param name="mzList">is the pointer to List of m/z values</param>
/// <param name="intensityList">is the pointer to List of intensity values</param>
/// <param name="startMz">minimum m/z of the peak.</param>
/// <param name="stopMz">maximum m/z of the peak.</param>
/// <returns>returns the number of peaks that were found in the vectors.</returns>
/// <remarks>
/// The function uses <see cref="PeakStatistician.FindFwhm" />, and
/// <see cref="PeakStatistician.FindSignalToNoise" />
/// to discover the full width at half maximum and signal to noise values for a peak. The signal to noise of a
/// peak is tested against the threshold value before its accepted as a peak. All peaks are used during the process,
/// but once generated only those which are above <see cref="_peakIntensityThreshold" /> are tested for peptidicity by
/// Deconvolution.HornMassTransform
/// </remarks>
public int DiscoverPeaks(List <double> mzList, List <double> intensityList, double startMz, double stopMz)
{
if (intensityList.Count < 1)
{
return(0);
}
PeakData.Clear();
var numDataPts = intensityList.Count;
var startIndex = PeakIndex.GetNearestBinary(mzList, startMz, 0, numDataPts - 1);
var stopIndex = PeakIndex.GetNearestBinary(mzList, stopMz, startIndex, numDataPts - 1);
if (startIndex <= 0)
{
startIndex = 1;
}
if (stopIndex >= mzList.Count - 2)
{
stopIndex = mzList.Count - 2;
}
for (var index = startIndex; index <= stopIndex; index++)
{
double fwhm = -1;
var currentIntensity = intensityList[index];
var lastIntensity = intensityList[index - 1];
var nextIntensity = intensityList[index + 1];
var currentMz = mzList[index];
if (_arePeaksCentroided)
{
if (currentIntensity >= _peakIntensityThreshold)
{
var mz = mzList[index];
var signalToNoise = currentIntensity / _peakIntensityThreshold;
fwhm = 0.6;
PeakData.AddPeak(new ThrashV1Peak(mz, currentIntensity, signalToNoise, PeakData.GetNumPeaks(), index,
fwhm));
}
}
else
{
//three point peak picking. Check if peak is greater than both the previous and next points
if (currentIntensity >= lastIntensity && currentIntensity >= nextIntensity &&
currentIntensity >= _peakIntensityThreshold)
{
//See if the peak meets the conditions.
//The peak data will be found at _transformData.begin()+i+1.
double signalToNoise;
if (!_isDataThresholded)
{
signalToNoise = PeakStatistician.FindSignalToNoise(currentIntensity, intensityList, index);
}
else
{
signalToNoise = currentIntensity / _backgroundIntensity;
}
// Run Full-Width Half-Max algorithm to try and squeak out a higher SN
if (signalToNoise < _signalToNoiseThreshold)
{
//double mz = mzList[index];
fwhm = PeakStatistician.FindFwhm(mzList, intensityList, index, signalToNoise);
if (fwhm > 0 && fwhm < 0.5)
{
var iLow = PeakIndex.GetNearestBinary(mzList, currentMz - fwhm, 0, index);
var iHigh = PeakIndex.GetNearestBinary(mzList, currentMz + fwhm, index, stopIndex);
var lowIntensity = intensityList[iLow];
var highIntensity = intensityList[iHigh];
var sumIntensity = lowIntensity + highIntensity;
if (sumIntensity > 0)
{
signalToNoise = 2.0 * currentIntensity / sumIntensity;
}
else
{
signalToNoise = 10;
}
}
}
// Found a peak
if (signalToNoise >= _signalToNoiseThreshold)
{
// Find a more accurate m/z location of the peak.
var fittedPeak = _peakFit.Fit(index, mzList, intensityList);
if (fwhm.Equals(-1))
{
fwhm = PeakStatistician.FindFwhm(mzList, intensityList, index, signalToNoise);
}
if (fwhm > 0)
{
PeakData.AddPeak(new ThrashV1Peak(fittedPeak, currentIntensity, signalToNoise,
PeakData.GetNumPeaks(),
index, fwhm));
}
// move beyond peaks have the same intensity.
var incremented = false;
while (index < numDataPts && intensityList[index].Equals(currentIntensity))
{
incremented = true;
index++;
}
if (index > 0 && index < numDataPts &&
incremented)
{
index--;
}
}
}
}
}
PeakData.MzList = mzList;
PeakData.IntensityList = intensityList;
return(PeakData.GetNumPeaks());
}
