public static void FitNonlin(double[] x, double[] y, double[] sig, double[] a,
out double chisq, Funcs2 func)
{
MrqminFunc f = delegate(double x1, double[] a1, out double y1, double[] dyda, int na) {
y1 = func(x1, a1);
for (int i = 0; i < na; i++)
{
dyda[i] = Dyda(x1, a1, func, i, 1e-6);
}
};
FitNonlin(x, y, sig, a, out chisq, f);
}
private static double Dyda(double x, double[] a, Funcs2 func, int ind, double epsilon)
{
double[] a1 = new double[a.Length];
double[] a2 = new double[a.Length];
for (int i = 0; i < a.Length; i++)
{
a1[i] = a[i];
a2[i] = a[i];
}
a1[ind] += epsilon / 2.0;
a2[ind] -= epsilon / 2.0;
return((func(x, a1) - func(x, a2)) / epsilon);
}
public static TransformFunc3 Torus(double a) => WrapSphereZ(Funcs2.Circle(), Funcs2.Torus(a));
public static TransformFunc3 Flower(double a, double b, int n) => WrapSphereZ(Funcs2.Flower(n, b), Funcs2.Torus(a));
public static void RecalibrateImpl(SilacType silacType, int nranges, int[] iranges, int[][] chargePairs,
SilacCluster[] silacClusters, ref double[,] mzCalibrationParams,
ref double[,] intensityCalibrationParams, double massErrorNormalization,
IsotopeCluster[] isotopeCluster, IPeakList peakList, float[] intensities)
{
double[] x = new double[chargePairs.Length];
double[] y = new double[chargePairs.Length];
double[] sig = new double[chargePairs.Length];
for (int i = 0; i < chargePairs.Length; i++)
{
x[i] = i;
int ind1 = chargePairs[i][0];
int ind2 = chargePairs[i][1];
SilacCluster sc1 = silacClusters[ind1];
SilacCluster sc2 = silacClusters[ind2];
sig[i] = Math.Sqrt(sc1.GetMassError(massErrorNormalization) * sc1.GetMassError(massErrorNormalization) +
sc2.GetMassError(massErrorNormalization) * sc2.GetMassError(massErrorNormalization));
}
intensityCalibrationParams = new double[nranges, nparamsIntensityFit];
double[,] icp = intensityCalibrationParams;
Funcs2 f = delegate(double x1, double[] aa) {
int ind = (int)Math.Round(x1);
int ind1 = chargePairs[ind][0];
int ind2 = chargePairs[ind][1];
double[,] mzAa = new double[nranges, nparamsMzFit];
int c = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzAa[iranges[j], i] = aa[c++];
}
}
double y1 = GetCalibratedSilacMassStat(silacClusters[ind1], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double y2 = GetCalibratedSilacMassStat(silacClusters[ind2], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double yy = y1 - y2;
return(yy);
};
double chisq;
double[] a = new double[nparamsMzFit * iranges.Length];
int county = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
a[county++] = startValsMzFit[i];
}
}
NumUtil.FitNonlin(x, y, sig, a, out chisq, f);
mzCalibrationParams = new double[nranges, nparamsMzFit];
int s = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzCalibrationParams[iranges[j], i] = a[s++];
}
}
double[,] mcp = mzCalibrationParams;
f = delegate(double x1, double[] aa) {
int ind = (int)Math.Round(x1);
int ind1 = chargePairs[ind][0];
int ind2 = chargePairs[ind][1];
double[,] intensityAa = new double[nranges, nparamsIntensityFit];
int c = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsIntensityFit; i++)
{
intensityAa[iranges[j], i] = aa[c++];
}
}
double y1 = GetCalibratedSilacMassStat(silacClusters[ind1], mcp, intensityAa, silacType, isotopeCluster, peakList,
intensities);
double y2 = GetCalibratedSilacMassStat(silacClusters[ind2], mcp, intensityAa, silacType, isotopeCluster, peakList,
intensities);
double yy = y1 - y2;
return(yy);
};
a = new double[nparamsIntensityFit * iranges.Length];
NumUtil.FitNonlin(x, y, sig, a, out chisq, f);
s = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsIntensityFit; i++)
{
intensityCalibrationParams[iranges[j], i] = a[s++];
}
}
icp = intensityCalibrationParams;
f = delegate(double x1, double[] aa) {
int ind = (int)Math.Round(x1);
int ind1 = chargePairs[ind][0];
int ind2 = chargePairs[ind][1];
double[,] mzAa = new double[nranges, nparamsMzFit];
int c = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzAa[iranges[j], i] = aa[c++];
}
}
double y1 = GetCalibratedSilacMassStat(silacClusters[ind1], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double y2 = GetCalibratedSilacMassStat(silacClusters[ind2], mzAa, icp, silacType, isotopeCluster, peakList,
intensities);
double yy = y1 - y2;
return(yy);
};
a = new double[nparamsMzFit * iranges.Length];
county = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
a[county++] = mzCalibrationParams[iranges[j], i];
}
}
NumUtil.FitNonlin(x, y, sig, a, out chisq, f);
s = 0;
for (int j = 0; j < iranges.Length; j++)
{
for (int i = 0; i < nparamsMzFit; i++)
{
mzCalibrationParams[iranges[j], i] = a[s++];
}
}
}