subtom_extract_noise
Extract noise amplitude spectra on the cluster.
subtom_extract_noise(
'tomogram_dir', tomogram_dir (''),
'tomo_row', tomo_row (7),
'ampspec_fn_prefix', ampspec_fn_prefix ('otherinputs/ampspec'),
'binary_fn_prefix', binary_fn_prefix ('otherinputs/binary'),
'all_motl_fn_prefix', all_motl_fn_prefix ('combinedmotl/allmotl'),
'noise_motl_fn_prefix', noise_motl_fn_prefix ('combinedmotl/noisemotl'),
'iteration', iteration (1),
'box_size', box_size (-1),
'just_extract', just_extract (0),
'ptcl_overlap_factor', ptcl_overlap_factor (0),
'noise_overlap_factor', noise_overlap_factor (0),
'num_noise', num_noise (1000),
'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 average amplitude
spectra and binary wedges into files with the name formats ampspec_fn_prefix
_#.em and binary_fn_prefix _ #.em, respectively where # corresponds to the
tomogram from which it was created.
Tomograms are specified by the field tomo_row in motive list
all_motl_fn_prefix _#.em where # corresponds to iteration. and the
tomogram that will be processed is selected by process_idx. Motive lists
with the positions used to generate the amplitude spectrum are written with the
name format noise_motl_fn_prefix _#.em.
num_noise Noise volumes of size box_size are first identified that do not
clash with the subtomogram positions in the input motive list or other already
selected noise volumes. ptcl_overlap_factor and noise_overlap_factor
define how much overlap selected noise volumes can have with subtomograms and
other noise volumes respectively with 1 being complete overlap and 0 being
complete separation.
If noise_motl_fn_prefix _#.em already exists then if just_extract
evaluates to true as a boolean, then noise volume selection is skipped and the
positions in the motive list are extracted and the amplitude spectrum is
generated, whether or not the length of the motive list is less than
num_noise. Otherwise positions will be added to the motive list up to
num_noise.
If reextract evaluates to true as a boolean, than existing amplitude spectra
will be overwritten. Otherwise the program will do nothing and exit if the
volume 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_noise(...
'tomogram_dir', '../data/tomos/bin8', ...
'tomo_row', 7, ...
'ampspec_fn_prefix', 'otherinputs/ampspec', ...
'binary_fn_prefix', 'otherinputs/binary', ...
'all_motl_fn_prefix', 'combinedmotl/allmotl', ...
'noise_motl_prefix', 'combinedmotl/noisemotl', ...
'iteration', 1, ...
'box_size', 36, ...
'just_extract', 0, ...
'ptcl_overlap_factor', 0.0, ...
'noise_overlap_factor, 0.75, ...
'num_noise', 1000,
'process_idx', 1, ...
'reextract', 1, ...
'preload_tomogram', 1, ...
'use_tom_red', 0, ...
'use_memmap', 0)