subtom_extract_subtomograms
Extract subtomograms on the cluster.
subtom_extract_subtomograms(
'tomogram_dir', tomogram_dir (''),
'tomo_row', tomo_row (7),
'subtomo_fn_prefix', subtom_fn_prefix ('subtomograms/subtomo'),
'subtomo_digits', subtomo_digits (1),
'all_motl_fn_prefix', all_motl_fn_prefix ('combinedmotl/allmotl'),
'stats_fn_prefix', stats_fn_prefix ('subtomograms/stats/tomo'),
'iteration', iteration (1),
'box_size', box_size (-1),
'process_idx', process_idx (1),
'reextract', reextract (0),
'preload_tomogram', preload_tomogram (1),
'use_tom_red', use_tom_red (0),
'use_memmap', use_memmap (0))
Takes the tomograms given in tomogram_dir
and extracts subtomograms
specified in all_motl_fn_prefix
_#.m where # corresponds to iteration
with size box_size
into scratch_dir
with the name formats
subtomo_fn_prefix
_#.em where # corresponds to the entry in field 4 in
all_motl_fn_prefix
_#.em zero-padded to have at least subtomo_digits
digits.
Tomograms are specified by the field tomo_row
in motive list
all_motl_fn_prefix
_#.em, and the tomogram that will be processed is
selected by process_idx
. A CSV-format file with the subtomogram ID-number,
average, min, max, standard deviation and variance for each subtomogram in the
tomogram is also written with the name format stats_fn_prefix
_#.em where #
corresponds to the tomogram from which subtomograms were extracted.
If reextract
evaluates to true as a boolean, than existing subtomograms will
be overwritten. Otherwise the program will do nothing and exit if
stats_fn_prefix
_#.em already exists, or will also skip any subtomogram it
is trying to extract that already exists. This is for in the case that the
processing crashed at some point in execution and then can just be re-run
without any alterations.
If preload_tomogram
evaluates to true as a boolean, then the whole tomogram
will be read into memory before extraction begins, otherwise the particles will
be read from disk or from a memory-mapped tomogram. If use_tom_red
evaluates
to true as a boolean the old particle extraction code will be used, but this is
only for legacy support and is not suggested for use. Finally if use_memmap
evaluates to true as a boolean then in place of reading each particle from disk
a memory-mapped version of the file of will be created to attempt faster access
in extraction.
Example
subtom_extract_subtomograms(...
'tomogram_dir', '../data/tomos/bin8', ...
'tomo_row', 7, ...
'subtomo_fn_prefix', 'subtomograms/subtomo', ...
'all_motl_fn_prefix', 'combinedmotl/allmotl', ...
'stats_fn_prefix', 'subtomograms/stats/tomo', ...
'iteration', 1, ...
'box_size', 36, ...
'process_idx', 1, ...
'reextract', 0, ...
'preload_tomogram', 1, ...
'use_tom_red', 0, ...
'use_memmap', 0)