subtom_parallel_ccmatrix

Calculates pairwise Constrained Cross-Correlation scores of aligned particles.

subtom_parallel_ccmatrix(
    'all_motl_fn_prefix', all_motl_fn_prefix ('combinedmotl/allmotl'),
    'ccmatrix_fn_prefix', ccmatrix_fn_prefix ('class/ccmatrix_pca'),
    'weight_fn_prefix', weight_fn_prefix ('otherinputs/ampspec'),
    'ptcl_fn_prefix', ptcl_fn_prefix ('subtomograms/subtomo'),
    'mask_fn', mask_fn ('none'),
    'high_pass_fp', high_pass_fp (0),
    'high_pass_sigma', high_pass_sigma (0),
    'low_pass_fp', low_pass_fp (0),
    'low_pass_sigma', low_pass_sigma (0),
    'nfold', nfold (1),
    'iteration', iteration (1),
    'tomo_row', tomo_row (7),
    'prealigned', prealigned (0),
    'num_ccmatrix_batch', num_ccmatrix_batch (1),
    'process_idx', process_idx (1))

Aligns a subset of particles using the rotations and shifts in the file given by all_motl_fn_prefix and iteration. If prealigned evaluates to true as boolean, then the particles in ptcl_fn_prefix are assumed to be prealigned, which should increase the speed of the processing. The subset of particles compared is specified by the file given by ccmatrix_fn_prefix, iteration, and process_idx appended with ‘_pairs’, and the output list of cross-correlation coefficients will be written out to the file specified by ccmatrix_fn_prefix, iteration, and process_idx. Fourier weight volumes with name prefix weight_fn_prefix will also be aligned so that the cross-correlation cofficient can be constrained to only overlapping shared regions of Fourier space. tomo_row describes which row of the MOTL file is used to determine the correct tomogram Fourier weight file. The correlation is also constrained by a bandpass filter specified by high_pass_fp, high_pass_sigma, low_pass_fp and low_pass_sigma.

Example

subtom_parallel_ccmatrix(
    'all_motl_fn_prefix', 'combinedmotl/allmotl', ...
    'ccmatrix_fn_prefix', 'class/ccmatrix', ...
    'weight_fn_prefix', 'otherinputs/ampspec', ...
    'ptcl_fn_prefix', 'subtomograms/alisubtomo', ...
    'mask_fn', 'otherinputs/classification_mask.em', ...
    'high_pass_fp', 1, ...
    'high_pass_sigma', 2, ...
    'low_pass_fp', 15, ...
    'low_pass_sigma', 3, ...
    'nfold', 1, ...
    'iteration', 1, ...
    'tomo_row', 7, ...
    'prealigned', 1, ...
    'num_ccmatrix_batch', 100, ...
    'process_idx', 1)

See Also