#!/usr/bin/env python3
"""
Use ``utils_clean_tifs`` from UNRAVEL to clean directories w/ tif series.
Tif directory clean up involves:
- Finding .tif or .ome.tif files in the tif directory
- Moving subdirectories to parent dir
- Moving non-TIF files to parent dir
- Replacing spaces in TIF file names
Note:
- If -d is not provided, the current directory is used to search for sample?? dirs to process.
- If the current dir is a sample?? dir, it will be processed.
- If -d is provided, the specified dirs and/or dirs containing sample?? dirs will be processed.
- If -p is not provided, the default pattern for dirs to process is 'sample??'.
Usage:
------
utils_clean_tifs -t <list of tif dir> --move [-d list of paths] [-p sample??] [-v]
"""
import shutil
from glob import glob
from pathlib import Path
from rich import print
from rich.live import Live
from rich.traceback import install
from unravel.core.help_formatter import RichArgumentParser, SuppressMetavar, SM
from unravel.core.config import Configuration
from unravel.core.utils import log_command, verbose_start_msg, verbose_end_msg, initialize_progress_bar, get_samples
[docs]
def parse_args():
parser = RichArgumentParser(formatter_class=SuppressMetavar, add_help=False, docstring=__doc__)
reqs = parser.add_argument_group('Required arguments')
reqs.add_argument('-t', '--tif_dirs', help='List names of folders with tif series to check (or paths relative to sample??/)', nargs='*', required=True, action=SM)
opts = parser.add_argument_group('Optional arguments')
opts.add_argument('-m', '--move', help='Enable moving of subdirs and non-TIF files to parent dir.', action='store_true', default=False)
general = parser.add_argument_group('General arguments')
general.add_argument('-d', '--dirs', help='Paths to sample?? dirs and/or dirs containing them (space-separated) for batch processing. Default: current dir', nargs='*', default=None, action=SM)
general.add_argument('-p', '--pattern', help='Pattern for directories to process. Default: sample??', default='sample??', action=SM)
general.add_argument('-v', '--verbose', help='Increase verbosity. Default: False', action='store_true', default=False)
return parser.parse_args()
[docs]
def clean_tifs_dir(path_to_tif_dir, move, verbose):
"""Clean up a directory containing TIF files:
- Move subdirs to parent dir
- Move non-TIF files to parent dir.
- Replace spaces in TIF file names with underscores.
Args:
path_to_tif_dir (str): Path to the directory containing the TIF files.
move (bool): Enable moving of subdirs and non-TIF files to parent dir.
verbose (bool): Increase verbosity."""
if verbose:
print(f"\n\nProcessing directory: {path_to_tif_dir}\n")
# Move subdirectories to parent directory
for subdir in path_to_tif_dir.iterdir():
if subdir.is_dir():
if verbose:
print(f"Found subdir: {subdir}")
if move:
new_dir_name = f"{path_to_tif_dir.name}_{subdir.name}".replace(' ', '_')
target_dir = path_to_tif_dir.parent / new_dir_name
if not target_dir.exists():
shutil.move(str(subdir), str(target_dir))
if verbose:
print(f"Moved {subdir} to {target_dir}")
else:
print(f"Skipping {subdir} because {target_dir} already exists/")
# Move non-TIF files and replace spaces in filenames
for file in path_to_tif_dir.iterdir():
if file.is_file() and not file.suffix.lower() in ('.tif', '.ome.tif'):
if verbose:
print(f"Found non-TIF file: {file}")
if move:
new_location = path_to_tif_dir.parent / file.name
if not new_location.exists():
shutil.move(str(file), str(new_location))
print(f"Moved {file} to {new_location}")
else:
print(f"Skipping {file} because {new_location} already exists.")
elif file.suffix.lower() == '.tif':
new_file_name = file.name.replace(' ', '_')
if new_file_name != file.name:
new_file_path = file.with_name(new_file_name)
file.rename(new_file_path)
[docs]
@log_command
def main():
install()
args = parse_args()
Configuration.verbose = args.verbose
verbose_start_msg()
sample_paths = get_samples(args.dirs, args.pattern, args.verbose)
progress, task_id = initialize_progress_bar(len(sample_paths), "[red]Processing samples...")
with Live(progress):
for sample_path in sample_paths:
# Clean TIF directories
tif_dirs = [sample_path / tif_dir for tif_dir in args.tif_dirs]
for tif_dir in tif_dirs:
clean_tifs_dir(Path(tif_dir), args.move, args.verbose)
progress.update(task_id, advance=1)
verbose_end_msg()
if __name__ == '__main__':
main()