Cross correlation matrix

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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 particle i -> Pi
  2. rotate and shift particles i
  3. create the missing wedge of particle
  4. rotate missing wedge of particles i RiWi
  5. compute Fourier coefficients common to Cij


Input of a ccmatrix

Computation of ccmatrix

Application of a ccmatrix