private RTandInt Interpolate(double[] starttimes, double[] intensities)
{
List <double> intensityList = new List <double>();
List <double> starttimesList = new List <double>();
//First step is interpolating a spline, then choosing the pointsat which to add values:
CubicSpline interpolation = CubicSpline.InterpolateNatural(starttimes, intensities);
//Now we work out how many to add so we reach at least 100 datapoints and add them:
double stimesinterval = starttimes.Last() - starttimes[0];
int numNeeded = 100 - starttimes.Count();
double intervals = stimesinterval / numNeeded;
intensityList = intensities.OfType <double>().ToList();
starttimesList = starttimes.OfType <double>().ToList();
for (int i = 0; i < numNeeded; i++)
{
double placetobe = starttimes[0] + (intervals * i);
//insert newIntensity into the correct spot in the array
for (int currentintensity = 0; currentintensity < 100; currentintensity++)
{
if (starttimesList[currentintensity] < placetobe)
{
continue;
}
else
{
if (currentintensity > 0)
{
if (starttimesList[currentintensity] == placetobe)
{
placetobe = placetobe + 0.01;
}
double newIntensity = interpolation.Interpolate(placetobe);
intensityList.Insert(currentintensity, newIntensity);
starttimesList.Insert(currentintensity, placetobe);
}
else
{
if (starttimesList[currentintensity] == placetobe)
{
placetobe = placetobe - 0.01;
}
double newIntensity = interpolation.Interpolate(placetobe);
intensityList.Insert(currentintensity, newIntensity);
starttimesList.Insert(currentintensity, placetobe);
}
break;
}
}
}
RTandInt ri = new RTandInt();
ri.intensities = intensityList.Select(item => Convert.ToDouble(item)).ToArray();
ri.starttimes = starttimesList.Select(item => Convert.ToDouble(item)).ToArray();
return(ri);
}
public void GenerateChromatogram(Run run)
{
//Crawdad
foreach (BasePeak basepeak in run.BasePeaks)
{
//for each peak within the spectrum
for (int yyy = 0; yyy < basepeak.BpkRTs.Count(); yyy++)
{
//change these two arrays to be only the spectra surrounding that bpkrt:
intensities = basepeak.Spectrum.Where(x => Math.Abs(x.RetentionTime - basepeak.BpkRTs[yyy]) < run.AnalysisSettings.RtTolerance).Select(x => (double)x.Intensity).ToArray();
starttimes = basepeak.Spectrum.Where(x => Math.Abs(x.RetentionTime - basepeak.BpkRTs[yyy]) < run.AnalysisSettings.RtTolerance).Select(x => (double)x.RetentionTime).ToArray();
if (intensities.Count() > 1)
{
RTandInt inter = new RTandInt();
inter = Interpolate(starttimes, intensities);
starttimes = inter.starttimes;
intensities = inter.intensities;
}
cPF = new CrawdadSharp.CrawdadPeakFinder();
cPF.SetChromatogram(starttimes, intensities);
crawPeaks = cPF.CalcPeaks();
double totalFwhm = 0;
double totalPeakSym = 0;
double totalBaseWidth = 0;
foreach (CrawdadSharp.CrawdadPeak crawPeak in crawPeaks)
{
double peakTime = starttimes[crawPeak.TimeIndex];
double fwhm = crawPeak.Fwhm;
double fvalue = crawPeak.Fvalue;
if (fwhm == 0)
{
continue;
}
else if (fvalue != 0)
{
totalPeakSym += crawPeak.Fwfpct / (2 * crawPeak.Fvalue); //From USP31: General Chapters <621> Chromatography equation for calculating the tailing factor(Available at: http://www.uspbpep.com/usp31/v31261/usp31nf26s1_c621.asp). A high value means that the peak is highly asymmetrical.
}
totalFwhm += fwhm;
if (!float.IsNaN(crawPeak.FwBaseline))
{
totalBaseWidth += crawPeak.FwBaseline;
}
else
{
totalBaseWidth += crawPeak.Fwfpct;
}
}
if (crawPeaks.Count() > 0)
{
basepeak.FWHMs.Add(totalFwhm / crawPeaks.Count());
basepeak.Peaksyms.Add(totalPeakSym / crawPeaks.Count());
basepeak.FullWidthBaselines.Add(totalBaseWidth / crawPeaks.Count());
}
else
{
basepeak.FWHMs.Add(0);
basepeak.FullWidthBaselines.Add(0);
basepeak.Peaksyms.Add(0);
}
}
}
}
