//** aligns the two peak's intensity profiles, returns cosine similarity (A dot B) / (|A| * |B|) **
public static float CalcCorrelation(Peak psI, Peak psJ)
{
//** scan indices of each peak **
int[] indI = psI.GetScanIndices();
int[] indJ = psJ.GetScanIndices();
//** min and max scan indexes over both peaks **
int minIndex = Math.Min(indI[0], indJ[0]);
int maxIndex = Math.Max(indI[indI.Length - 1], indJ[indJ.Length - 1]);
//** range of synthesized indices **
int len = maxIndex - minIndex + 1;
//** intensity profile of peakI **
float[] profileI = new float[len + 2];
for (int a = 0; a < indI.Length; a++)
{
profileI[indI[a] - minIndex + 1] = psI.GetSmoothIntensity(a);
}
//** " peakJ **
float[] profileJ = new float[len + 2];
for (int a = 0; a < indJ.Length; a++)
{
profileJ[indJ[a] - minIndex + 1] = psJ.GetSmoothIntensity(a);
}
int c = 0;
int l = profileI.Length;
int[] valids = new int[l];
//** iterate through I's intensity profile, collecting index of valid peak intensities **
//** valid === one peak has an entry, or its the begnning or end **
for (int x = 0; x < l; x++)
{
if (profileI[x] > 0 || profileJ[x] > 0 || x == 0 || x == l - 1)
{
valids[c++] = x;
}
}
//** trim valid array **
valids = ArrayUtil.SubArray(valids, c);
//** return cosine similarity between the two aligned arrays **
return(ArrayUtil.Cosine(ArrayUtil.SubArray(profileI, valids), ArrayUtil.SubArray(profileJ, valids)));
}
