def track_single_file(phase_file_name, seg_file_name, params, namespace):
mm3.information("Tracking cells in {}.".format(seg_file_name))
# load model to pass to algorithm
mm3.information("Loading model...")
params['tracking']['migrate_model'] = namespace.migrate_modelfile
params['tracking']['child_model'] = namespace.child_modelfile
params['tracking']['appear_model'] = namespace.appear_modelfile
params['tracking']['die_model'] = namespace.die_modelfile
params['tracking']['disappear_model'] = namespace.disappear_modelfile
params['tracking']['born_model'] = namespace.born_modelfile
model_dict = mm3.get_tracking_model_dict()
fov_id, peak_id = extract_fov_and_peak_ids(phase_file_name)
tracks = {}
track_loop(fov_id,
peak_id,
params,
tracks,
model_dict,
phase_file_name=phase_file_name,
seg_file_name=seg_file_name)
track_file_name = "{}_xy{:0=3}_p{:0=4}_tracks.pkl".format(
params['experiment_name'], fov_id, peak_id)
with open(track_file_name, 'wb') as cell_file:
pickle.dump(tracks, cell_file)
sys.exit("Completed tracking cells in stack {}.".format(seg_file_name))
fov_id_list = sorted([fov_id for fov_id in specs.keys()])
# remove fovs if the user specified so
if user_spec_fovs:
fov_id_list[:] = [fov for fov in fov_id_list if fov in user_spec_fovs]
mm3.information("Processing %d FOVs." % len(fov_id_list))
mm3.information("Creating cell lineages.")
mm3.information("Reading track models. This could take a few minutes.")
# read in models as dictionary
# keys are 'migrate_model', 'child_model', 'appear_model', 'die_model', 'disappear_model', etc.
# NOTE on 2019-07-15: For now, some of the models are ignored by the tracking algorithm, as they don't yet perform well
if namespace.command == 'cells':
model_dict = mm3.get_tracking_model_dict()
elif namespace.command == 'foci':
model_dict = mm3.get_focus_tracking_model_dict()
# do lineage creation per fov, per trap
tracks = {}
for i, fov_id in enumerate(fov_id_list):
# tracks[fov_id] = {}
# update will add the output from make_lineages_function, which is a
# dict of Cell entries, into Cells
ana_peak_ids = [
peak_id for peak_id in specs[fov_id].keys()
if specs[fov_id][peak_id] == 1
]
if user_spec_peaks:
ana_peak_ids[:] = [