#!/usr/bin/env python3
"""
Use ``utils_agg_files`` from UNRAVEL to aggregate files from sample?? directories to a target directory.
Next commands for voxel-wise stats:
- If analyzing whole brains, consider using ``vstats_whole_to_avg`` to average left and right hemispheres.
- If using side-specific z-scoring, use ``vstats_hemi_to_avg`` to average the images.
- Prepend condition names with ``utils_prepend``.
- Check images in FSLeyes and run ``vstats`` to perform voxel-wise stats.
Next command for regional stats:
- Use ``rstats_summary`` to summarize the results
Usage:
------
utils_agg_files -i 'atlas_space/<asterisk>_cfos_rb4_30um_CCF_space_z_LRavg.nii.gz' [-td target_output_dir] [-d list of paths] [-p sample??] [-v]
Usage to prepend sample folder name to the name of files being copied:
----------------------------------------------------------------------
utils_agg_files -i 'atlas_space/cfos_rb4_30um_CCF_space_z_LRavg.nii.gz' -a [-td target_output_dir] [-d list of paths] [-p sample??] [-v]
"""
import shutil
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('-i', '--input', help='Glob pattern to match files within sample?? directories', required=True, action=SM)
opts = parser.add_argument_group('Optional arguments')
opts.add_argument('-td', '--target_dir', help='path/target_dir name for gathering files. Default: current working dir', default=None, action=SM)
opts.add_argument('-a', '--add_prefix', help='Add "sample??_" prefix to the output files', action='store_true')
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 aggregate_files_from_sample_dirs(sample_path, glob_pattern, target_dir, add_prefix=False, verbose=False):
# Use glob to find files matching the pattern
if len(list(sample_path.glob(glob_pattern))) == 0:
print(f"\n [red1]No files found matching the pattern:[/] [bold]{glob_pattern}[/] in {sample_path}\n")
return
for src_path in sample_path.glob(glob_pattern):
if add_prefix:
target_output = target_dir / f"{sample_path.name}_{src_path.name}"
if verbose:
print(f"Copying {src_path.name} as {target_output.name}")
else:
target_output = target_dir / src_path.name
if verbose:
print(f"Copying {src_path}")
if src_path.exists():
shutil.copy(src_path, target_output)
[docs]
@log_command
def main():
install()
args = parse_args()
Configuration.verbose = args.verbose
verbose_start_msg()
if args.target_dir is None:
target_dir = Path().cwd()
else:
target_dir = Path(args.target_dir)
target_dir.mkdir(exist_ok=True, parents=True)
if args.verbose:
print(f'\nCopying files to: {target_dir}\n')
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:
aggregate_files_from_sample_dirs(sample_path, args.input, target_dir, args.add_prefix, args.verbose)
progress.update(task_id, advance=1)
verbose_end_msg()
if __name__ == '__main__':
main()