/// <summary>
/// Get the cosine score for the provided experimental and theoretical peaks
/// </summary>
/// <param name="spec"></param>
/// <param name="isoProfile"></param>
/// <param name="comparer"></param>
/// <returns></returns>
public static double GetCosine(IList <Peak> spec, IList <Peak> isoProfile, IComparer <Peak> comparer)
{
var numPeaksSpec = spec.Count;
var numTheoProfilePeaks = isoProfile.Count;
var index1 = 0;
var index2 = 0;
var theoIntensities = isoProfile.Select(p => p.Intensity).ToArray();
var observedIntensities = new double[numTheoProfilePeaks];
while (index1 < numPeaksSpec && index2 < numTheoProfilePeaks)
{
var comp = comparer.Compare(spec[index1], isoProfile[index2]);
if (comp < 0)
{
++index1;
}
else if (comp > 0)
{
++index2;
}
else
{
if (spec[index1].Intensity > observedIntensities[index2])
{
observedIntensities[index2] = spec[index1].Intensity;
}
++index1;
//++index2;
}
}
return(FitScoreCalculator.GetCosine(theoIntensities, observedIntensities));
}
/// <summary>
/// Try to find the best concentration of the selected isotope
/// by stepping through the concentrations and fitting a theoretical
/// isotopic profile to the provided observed peaks.
/// </summary>
/// <param name="progress">The progress reporter.</param>
public IsotopeConcentrationCorrelationCurve Tune(IProgress <PRISM.ProgressData> progress = null)
{
// Set up progress reporter
var progressData = new PRISM.ProgressData(progress);
ValidateParameters();
// Get default proportions for the selected element.
// Copy it to a new array so we can manipulate it.
var proportions = GetDefaultProportions(Element).ToArray();
// Make sure this is an isotope we know about and that it isn't the monoisotope
if (IsotopeIndex < 1 || IsotopeIndex >= proportions.Length)
{
throw new ArgumentOutOfRangeException(nameof(IsotopeIndex));
}
var defaultProportion = proportions[IsotopeIndex];
// Set the default best point (the first one).
var results = new IsotopeConcentrationCorrelationCurve
{
BestConcentration = new IsotopeConcentrationCorrelationCurve.ConcentrationCorrelationPoint
{
IsotopeConcentration = defaultProportion,
MonoisotopeConcentration = proportions[0],
PearsonCorrelation = 0.0
}
};
// Iterate over concentration values
var numberOfSteps = (int)(MaxConcentration - defaultProportion / StepSize);
for (var i = 0; i <= numberOfSteps; i++)
{
// Update percent complete
progressData.Report(i, numberOfSteps);
// Calculate concentration
var concentrationStep = i * StepSize;
proportions[IsotopeIndex] += concentrationStep; // Increase isotope of interest
proportions[0] -= concentrationStep; // Decrease monoisotope
// Get theoretical isotope profile and align the observed peaks to it
var theoreticalIsotopeProfile = GetTheoreticalIsotopeProfile(proportions);
var alignedObservedPeaks = AlignObservedPeaks(ObservedPeaks, theoreticalIsotopeProfile, Tolerance);
// Break out the intensities of the isotope profiles
var theoIntensities = theoreticalIsotopeProfile.Select(peak => peak.Intensity).ToArray();
var obsIntensities = alignedObservedPeaks.Select(peak => peak.Intensity).ToArray();
// Compute pearson correlation
var pearsonCorrelation = FitScoreCalculator.GetPearsonCorrelation(obsIntensities, theoIntensities);
// Add data point for this concentration to result curve
var dataPoint = new IsotopeConcentrationCorrelationCurve.ConcentrationCorrelationPoint
{
IsotopeConcentration = proportions[IsotopeIndex],
MonoisotopeConcentration = proportions[0],
PearsonCorrelation = pearsonCorrelation
};
results.DataPoints.Add(dataPoint);
// If this concentration has a better fit, update the stored results
if (pearsonCorrelation >= results.BestConcentration.PearsonCorrelation)
{
results.BestConcentration = dataPoint;
}
}
return(results);
}
