def main():
start_time = datetime.now()
args = cells_standard_space_cli_parser().parse_args()
args.paths = prep.Paths(args.output_dir)
args.paths.standard_space_output_folder = args.output_dir
args.paths.cells_in_standard_space = join(args.paths.output_dir,
"cells_in_standard_space.xml")
cli_path_update(args.paths, args)
args.paths.make_invert_cell_position_paths()
args = define_pixel_sizes(args)
# TODO: implement a recursive function to remove the need to do this
# (probably using pathlib)
system.ensure_directory_exists(args.paths.output_dir)
system.ensure_directory_exists(args.paths.standard_space_output_folder)
tools.start_logging(
args.paths.output_dir,
args=args,
verbose=args.debug,
filename="cells_to_standard_space",
log_header="CELL TRANSFORMATION TO STANDARD SPACE LOG",
)
logging.info("Starting transformation of cell positions")
transform_cells_to_standard_space(args)
logging.info("Finished. Total time taken: %s", datetime.now() - start_time)
def main():
# TODO: remove converting to strings when cellfinder is python >3.6 only
start_time = datetime.now()
args = cube_extract_cli_parser().parse_args()
args = define_pixel_sizes(args)
args = prep_channel_ids(args)
# TODO: can these be set in argparse?
args.output_dir = Path(args.output_dir)
args.cells_file_path = Path(args.cells_file_path)
args.cube_extract_cli = True
args.paths = prep.Paths(args.output_dir)
system.ensure_directory_exists(args.output_dir)
tools.start_logging(
str(args.output_dir),
args=args,
verbose=args.debug,
filename="batch_cube_extraction",
log_header="CELLFINDER BATCH CUBE EXTRACTION LOG",
)
logging.info("Starting cube extraction")
num_channels = len(args.raw_data_paths)
if args.cells_file_path.is_dir():
indv_cells_paths = natsorted(subdirs(args.cells_file_path))
elif args.cells_file_path.is_file():
tmp_paths = tools.get_text_lines(args.cells_file_path)
indv_cells_paths = natsorted([Path(path) for path in tmp_paths])
if indv_cells_paths[0].is_dir():
logging.info("Assuming cube definition data is output from ROI Sorter")
cells_dir_names = [path.name for path in indv_cells_paths]
if tools.is_any_list_overlap(cells_dir_names,
train_data_gen_dir_names):
# If there is only training data from one sample, make a list of 1
indv_cells_paths = [args.cells_file_path]
for idx, sample_dir in enumerate(indv_cells_paths):
logging.info("Extracting cubes from: {}".format(sample_dir.name))
args.all_planes_paths = []
system.ensure_directory_exists(
args.output_dir.joinpath(sample_dir.name))
for channel in range(num_channels):
args.all_planes_paths.append(
tools.get_text_lines(
args.raw_data_paths[channel],
return_lines=idx,
sort=True,
))
for sub_dir_name in train_data_gen_dir_names:
if sub_dir_name in subdirs(sample_dir, names_only=True):
logging.info("Extracting: {}".format(sub_dir_name))
args.paths.tmp__cubes_output_dir = str(
args.output_dir.joinpath(sample_dir.name,
sub_dir_name))
args.paths.cells_file_path = str(
args.cells_file_path.joinpath(sample_dir.name,
sub_dir_name))
extract_loop(args)
else:
if indv_cells_paths[0].suffix in SUPPORTED_CELL_FILE_FORMATS:
logging.info("Cube definition file is: '{}', proceeding."
"".format(indv_cells_paths[0].suffix))
raise NotImplementedError(
"Cube definition file is: '{}', NOT YET SUPPORTED."
"".format(indv_cells_paths[0].suffix))
else:
raise NotImplementedError(
"File format: '{}' is not yet supported. Please use the "
"output of ROI Sorter, or provide one of: {}".format(
indv_cells_paths[0].suffix, SUPPORTED_CELL_FILE_FORMATS))
logging.info("Finished. Total time taken: %s", datetime.now() - start_time)