public override int Charge(List <IPeak> peaks, double lower, double upper)
{
// default to charge 2
int charge = 2;
// patterson
Dictionary <int, double> patterson = new Dictionary <int, double>();
for (int i = 1; i <= maxCharge; i++)
{
double delta = 1.0 / i;
double val = RountineFunc(delta, peaks, lower, upper);
delta = 1.0 / (i - 1.0 / 3);
val = Math.Max(val, RountineFunc(delta, peaks, lower, upper));
delta = 1.0 / (i + 1.0 / 3);
val = Math.Max(val, RountineFunc(delta, peaks, lower, upper));
patterson[i] = val;
}
// Fourier
Dictionary <int, double> fourier = new Dictionary <int, double>();
// take points from user-selected area
var selected = peaks.Where(p => p.GetMZ() >= lower && p.GetMZ() <= upper);
if (selected.ToList().Count < 2)
{
double bestVal = 0;
foreach (int i in patterson.Keys)
{
if (bestVal < patterson[i])
{
bestVal = patterson[i];
charge = i;
}
}
return(charge);
}
List <double> X = selected.Select(p => p.GetMZ()).ToList();
List <double> Y = selected.Select(p => p.GetIntensity()).ToList();
// baseline corrects
double[,] yArray = new double[1, Y.Count];
for (int i = 0; i < Y.Count; i++)
{
yArray[0, i] = Y[i];
}
double[,] z = airPLS.Correction(yArray);
for (int i = 0; i < Y.Count; i++)
{
Y[i] = z[0, i];
}
// linearized space by cubic spline
List <double> x = new List <double>();
for (double i = X.Min(); i <= X.Max(); i += precison)
{
x.Add(i);
}
List <double> y = Interpolation.Spline(x, X, Y);
// pads the data with zeros to the next power of 2
int size = (int)Math.Pow(2.0, Math.Ceiling(Math.Log(x.Count, 2))) - x.Count;
for (int i = 0; i < size; i++)
{
y.Add(0.0);
}
//FFT to charge map
double[] magnitue = FFT.Transform(y.Select(p => new Complex(Math.Max(0, p), 0)).ToArray())
.Select(p => p.Magnitude).ToArray();
for (int i = 1; i <= Math.Min(maxCharge, magnitue.Count() - 1); i++)
{
fourier[i] = magnitue[i];
}
// combine
double best = 0;
foreach (int i in fourier.Keys)
{
if (patterson.ContainsKey(i))
{
double value = fourier[i] * patterson[i];
if (value > best)
{
best = value;
charge = i;
}
}
}
return(charge);
}
public int Charge(List <IPeak> peaks, double lower, double upper)
{
// default to charge 2
int charge = 2;
if (peaks.Count < 2)
{
return(charge);
}
// take points from user-selected area
var selected = peaks.Where(p => p.GetMZ() >= lower && p.GetMZ() <= upper);
List <double> X = selected.Select(p => p.GetMZ()).ToList();
List <double> Y = selected.Select(p => p.GetIntensity()).ToList();
// baseline corrects by airPLS
double[,] yArray = new double[1, Y.Count];
for (int i = 0; i < Y.Count; i++)
{
yArray[0, i] = Y[i];
}
double[,] z = airPLS.Correction(yArray);
for (int i = 0; i < Y.Count; i++)
{
Y[i] = z[0, i];
}
// linearized space by cubic spline
List <double> x = new List <double>();
for (double i = X.Min(); i <= X.Max(); i += precison)
{
x.Add(i);
}
List <double> y = Interpolation.Spline(x, X, Y);
// pads the data with zeros to the next power of 2
int size = (int)Math.Pow(2.0, Math.Ceiling(Math.Log(x.Count, 2))) - x.Count;
for (int i = 0; i < size; i++)
{
y.Add(0.0);
}
//FFT to charge map
double[] magnitue = FFT.Transform(y.Select(p => new Complex(Math.Max(0, p), 0)).ToArray())
.Select(p => p.Magnitude).ToArray();
double best = 0;
for (int i = 1; i <= Math.Min(maxCharge, magnitue.Count() - 1); i++)
{
if (magnitue[i] > best)
{
best = magnitue[i];
charge = i;
}
}
return(charge);
}
