Cross correlation matrix

The cross correlation matrix (often called ccmatrix in Dynamo jargon) of a set of N particles is an N X N matrix. Each entry (i,j) represents the similarity of particles i and j in the data set.

Definition of similarity

This similarity of particles i and j measured in terms of the normalized cross correlation of the the two aligned particles, filtered to their common fourier components, and restricted to a region in direct space (indicated by a classification mask). The pseudo code will run as:

1. read particles i and j -> p_i, p_j
2. align particles i, and j -> A_ip_i, A_jp_j
3. compute missing wedges for particles i and j -> W_i, W_j
4. rotate missing wedges -> R_iW_i, R_jW_j
5. compute Fourier coefficients common to bCoth rotated missing wedges

C_ij = intersection(R_iW_i, R_jW_j)

1. filter p_i with C_ij
2. compare the filtered particles inside the classification mask.