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)