/// <summary>
/// Construct PeakFitter from initialpeakguess, histogam edges+values,
/// </summary>
/// <param name="guess">Initial peak guess.</param>
/// <param name="edges">edges of the truncated histogram</param>
/// <param name="y">histogram value</param>
/// <param name="sigma">Uncertainty on Y</param>
/// <returns>PeakFitter</returns>
public static PeakFitter FromGuess(InitialPeakGuess guess, double[] edges, double[] y, double[] sigma = null)
{
PeakingPDF pdf = PeakingPDF.OfInitialPeakGuess(guess);
BinChi2 x2 = new BinChi2(pdf.Compute, edges, y, sigma);
string[] paramnames = pdf.ParamNames(); //full paramname with x
string[] pname = new string[paramnames.Length - 1]; //Dock off x
for (int i = 0; i < pname.Length; i++)
{
pname[i] = paramnames[i + 1];
}
Minuit minuit = new Minuit((FCN)(x2.Compute), pname);
minuit.SetInitialValue("mu", guess.mu);
minuit.SetInitialValue("sigma", guess.sigma);
minuit.SetInitialValue("nsig", guess.nsig);
minuit.SetInitialValue("m", guess.m);
minuit.SetInitialValue("c", guess.c);
minuit.SetInitialValue("nbkg", guess.nbkg);
PeakFitter ret = new PeakFitter() { pdf = pdf, minuit = minuit, edges=edges};
return ret;
}
/// <summary>
/// Calculates Metrics based on ChromPeakIqTarget
/// NET Error, Mass Error, Isotopic Fit, & Isotope Correlation
/// </summary>
protected override void ExecuteWorkflow(IqResult result)
{
result.IsExported = false;
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
MSGenerator.IsTICRequested = false;
}
var target = result.Target as ChromPeakIqTarget;
if (target == null)
{
throw new NullReferenceException("The ChromPeakAnalyzerIqWorkflow only works with the ChromPeakIqTarget.");
}
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(target.ChromPeak, Run, WorkflowParameters.SmartChromPeakSelectorNumMSSummed);
//Generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(Run, lcscanset);
massSpectrumXYData = massSpectrumXYData.TrimData(result.Target.MZTheor - 5, result.Target.MZTheor + 15);
//Find isotopic profile
List <Peak> mspeakList;
result.ObservedIsotopicProfile = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
//Default Worst Scores
double iscore = 1;
//Get NET Error
var netError = target.ChromPeak.NETValue - target.ElutionTimeTheor;
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState, mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
if (result.ObservedIsotopicProfile == null)
{
result.IsotopicProfileFound = false;
result.FitScore = 1;
}
else
{
//Get fit score O16 profile
var observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Take(4).ToList(); //first 4 peaks excludes the O18 double label peak (fifth peak)
var theorPeakList = target.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).Take(4).ToList();
result.FitScore = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
// fit score O18 profile
var o18Iso = ((O16O18IqResult)result).ConvertO16ProfileToO18(target.TheorIsotopicProfile, 4);
theorPeakList = o18Iso.Peaklist.Select(p => (Peak)p).ToList();
observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Skip(4).ToList(); //skips the first 4 peaks and thus includes the O18 double label isotopic profile
((O16O18IqResult)result).FitScoreO18Profile = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
//get i_score
iscore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//get ppm error
var massErrorInDaltons = TheorMostIntensePeakMassError(target.TheorIsotopicProfile, result.ObservedIsotopicProfile, target.ChargeState);
var ppmError = (massErrorInDaltons / target.MonoMassTheor) * 1e6;
//Get Isotope Correlation
var scan = lcscanset.PrimaryScanNumber;
var sigma = target.ChromPeak.Width / 2.35;
var chromScanWindowWidth = 4 * sigma;
//Determines where to start and stop chromatogram correlation
var startScan = scan - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scan + (int)Math.Round(chromScanWindowWidth / 2, 0);
result.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, result, startScan, stopScan);
result.LcScanObs = lcscanset.PrimaryScanNumber;
result.ChromPeakSelected = target.ChromPeak;
result.LCScanSetSelected = new ScanSet(lcscanset.PrimaryScanNumber);
result.IsotopicProfileFound = true;
result.InterferenceScore = iscore;
result.IsIsotopicProfileFlagged = hasPeakTotheLeft;
result.NETError = netError;
result.MassErrorBefore = ppmError;
result.IqResultDetail.MassSpectrum = massSpectrumXYData;
result.Abundance = GetAbundance(result);
}
}
