subtom_parallel_xmatrix_pca
Calculates chunks of the X-matrix for processing.
subtom_parallel_xmatrix_pca(
'all_motl_fn_prefix', all_motl_fn_prefix ('combinedmotl/allmotl'),
'xmatrix_fn_prefix', xmatrix_fn_prefix ('class/xmatrix_pca'),
'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 applies nfold
C-symmetry, 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_pca(
'all_motl_fn_prefix', 'combinedmotl/allmotl', ...
'xmatrix_fn_prefix', 'class/xmatrix', ...
'ptcl_fn_prefix', 'subtomograms/alisubtomo', ...
'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)