subtom_clean_motl
Cleans a given MOTL file based on distance and or CC scores.
subtom_clean_motl(
'input_motl_fn', input_motl_fn (''),
'output_motl_fn', output_motl_fn (''),
'tomo_row', tomo_row (7),
'do_ccclean', do_ccclean (0),
'cc_fraction', cc_fraction (1),
'cc_cutoff', cc_cutoff (-1),
'do_distance', do_distance (0),
'distance_cutoff', distance_cutoff (Inf),
'do_cluster', do_cluster (0),
'cluster_distance', cluster_distance (0),
'cluster_size', cluster_size (1),
'do_edge', do_edge (0),
'tomogram_dir', tomogram_dir (''),
'box_size', box_size (0),
'write_stats', write_stats (0),
'output_stats_fn', output_stats_fn (''))
Takes the motl given by input_motl_fn, and splits it internally by
tomogram given by the row tomo_row in the MOTL, and then removes particles
by one or multiple methods, if do_ccclean evaluates to true as a boolean
then one of two methods can be applied. Either cc_cutoff is specified and
particles that have a CCC less than cc_cutoff will be discarded.
Alternatively cc_fraction can be specified as a number between 0 and 1 and
that fraction of the data with the highest CCCs will be kept and the rest
discarded. If do_distance evaluates to true as a boolean then particles
that are within distance_cutoff pixels of each other will be determined
and only the particle with the highest CCC, will be kept. If
do_cluster evaluates to true as a boolean,then particles must have at
least cluster_size neighbor particles within cluster_distance to be kept
after cleaning. Finally if do_edge evaluates to true as a boolean then the
program will look for a tomogram in tomogram_dir, and if a particle of
box size box_size would extend outside of the tomogram it will be removed.
Example
subtom_clean_motl(...
'input_motl_fn', 'combinedmotl/allmotl_3.em', ...
'output_motl_fn', 'combinedmotl/allmotl_3_cc0.1_dist4_c2d10.em', ...
'tomo_row', 7, ...
'do_ccclean', 1, ...
'cc_fraction', 1, ...
'cc_cutoff', 0.1, ...
'do_distance', 1, ...
'distance_cutoff', 4, ...
'do_cluster', 1, ...
'cluster_distance', 10, ...
'cluster_size, 2, ...
'do_edge', 1, ...
'tomogram_dir', '../../tomos/bin8', ...
'box_size', 36, ...
'write_stats', 1, ...
'output_stats_fn', 'combinedmotl/allmotl_3_cleaned_stats.csv')