subtom_parallel_xmatrix_msa
Calculates chunks of the X-matrix for processing.
subtom_parallel_xmatrix_msa(
'all_motl_fn_prefix', all_motl_fn_prefix ('combinedmotl/allmotl'),
'xmatrix_fn_prefix', xmatrix_fn_prefix ('class/xmatrix_msa'),
'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),
'prealigned', prealigned (0),
'num_xmatrix_batch', num_xmatrix_batch (1),
'process_idx', process_idx (1))
Aligns a subset of particles using the rotations and shifts given by
all_motl_fn_prefix and iteration, band-pass filters the particle as
described by high_pass_fp, high_pass_sigma, low_pass_fp, and
low_pass_sigma, optionally symmetrizes the particle with C-fold symmetry
nfold, and then places these voxels as a 1-D row vector in a data
sub-matrix which is historically known as the X-matrix (See Borland, Van Heel
1990 J. Opt. Soc. Am. A). This X-matrix can then be used to
speed up the calculation of Eigenvolumes and Eigencoefficients used for
classification. The subset of particles compared is specified by the number of
particles in the motive list and the number of requested batches specified by
num_xmatrix_batch, with the specific subset deteremined by process_idx.
The X-matrix chunk will be written out as specified by xmatrix_fn_prefix,
iteration and process_idx. The location of the particles is specified by
ptcl_fn_prefix. If prealigned evaluates to true as a boolean then the
particles are assumed to be prealigned, which should increase speed of
computation of CC-Matrix calculations. Particles in the X-matrix will be masked
by the file given by mask_fn. If the string ‘none’ is used in place of
mask_fn, a default spherical mask is applied. This mask should be a binary
mask and only voxels within the mask are placed into the X-matrix which can
greatly speed up computations.
Example
subtom_parallel_xmatrix_msa(
'all_motl_fn_prefix', 'combinedmotl/allmotl', ...
'xmatrix_fn_prefix', 'class/xmatrix', ...
'ptcl_fn_prefix', 'subtomograms/subtomo_ali', ...
'mask_fn', 'combinedmotl/classification_mask.em', ...
'high_pass_fp', 1, ...
'high_pass_sigma', 2, ...
'low_pass_fp', 15, ...
'low_pass_sigma', 3, ...
'nfold', 1, ...
'iteration', 1, ...
'prealigned', 1, ...
'num_xmatrix_batch', 100, ...
'process_idx', 1)