mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
GUI.init_params(param_file_path)
if namespace.fov:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
if not os.path.exists(p['seg_dir']):
sys.exit("Exiting: Segmentation directory, {}, not found.".format(p['seg_dir']))
if not os.path.exists(p['chnl_dir']):
sys.exit("Exiting: Channel directory, {}, not found.".format(p['chnl_dir']))
specs = mm3.load_specs()
# make list of FOVs to process (keys of channel_mask file)
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]
# set segmentation image name for segmented images
seg_suffix_finder = re.compile(r'.+(seg_.+)\.tif$')
test_name = glob.glob(os.path.join(p['seg_dir'],'*xy{:0=3}*.tif'.format(fov_id_list[0])))[0]
mat = seg_suffix_finder.match(test_name)
p['seg_img'] = mat.groups()[0] ## be careful here, it is lookgin for segmented images
# get paired phase file names and mask file names for each fov
fov_filename_dict = {}
for fov_id in fov_id_list:
else:
user_spec_peaks = []
# set segmentation image name for saving and loading segmented images
if namespace.command == 'cells':
p['seg_img'] = 'seg_unet'
elif namespace.command == 'foci':
p['seg_img'] = 'foci_seg_unet'
else:
sys.exit(
"ERROR: your final argument to {} must be either 'cells' or 'foci'"
.format(sys.argv[0]))
# load specs file
if namespace.chtc:
specs = mm3.load_specs(fname=namespace.specfile)
mm3.load_time_table(fname=namespace.timefile)
else:
specs = mm3.load_specs()
mm3.load_time_table()
if namespace.command == 'cells':
if namespace.phase_file_name:
track_single_file(namespace.phase_file_name,
namespace.seg_file_name, p, namespace)
if not os.path.exists(p['cell_dir']):
os.makedirs(p['cell_dir'])
# make list of FOVs to process (keys of channel_mask file)
fov_id_list = sorted([fov_id for fov_id in specs.keys()])
