#!/usr/bin/env python3
"""
Use ``utils_prepend`` from UNRAVEL to prepend conditions to filenames based on a CSV key.
Note:
- This command renames files in the current directory based on the conditions specified in the CSV file.
- The sample_key.csv should have two columns: 'dir_name' and 'condition'.
- The command will prepend the 'condition' to the filenames matching the 'dir_name' prefix.
- If needed, files and/or folders can be renamed with ``utils_rename``.
For example, if the CSV contains the following rows:
dir_name,condition
sample01,control
sample02,treatment
Files will be renamed as follows:
'sample01_file.csv' --> 'control_sample01_file.csv'
'sample02_file.csv' --> 'treatment_sample02_file.csv'.
Next commands for voxel-wise stats:
- Check images in FSLeyes and run ``vstats`` to perform voxel-wise stats.
Usage for files:
----------------
utils_prepend -sk <path/sample_key.csv> -f [--recursive] [-v]
Usage for directories:
----------------------
utils_prepend -sk <path/sample_key.csv> -d [--recursive] [-v]
"""
import pandas as pd
from glob import glob
from pathlib import Path
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, print_func_name_args_times
[docs]
def parse_args():
parser = RichArgumentParser(formatter_class=SuppressMetavar, add_help=False, docstring=__doc__)
reqs = parser.add_argument_group('Required arguments')
reqs.add_argument('-sk', '--sample_key', help='path/sample_key.csv w/ directory names and conditions', required=True, action=SM)
opts = parser.add_argument_group('Optional arguments')
opts.add_argument('-f', '--file', help='Rename matching files', action='store_true', default=False)
opts.add_argument('-d', '--dirs', help='Rename matching dirs', action='store_true', default=False)
opts.add_argument('-r', '--recursive', help='Recursively rename files/dirs', action='store_true', default=False)
general = parser.add_argument_group('General arguments')
general.add_argument('-v', '--verbose', help='Increase verbosity. Default: False', action='store_true', default=False)
return parser.parse_args()
[docs]
def rename_items(base_path, dir_name, condition, rename_files, rename_dirs, recursive):
search_pattern = f'**/{dir_name}*' if recursive else f'{dir_name}*'
for item in base_path.glob(search_pattern):
if item.is_file() and rename_files:
new_name = item.parent / f'{condition}_{item.name}'
item.rename(new_name)
elif item.is_dir() and rename_dirs:
new_name = item.parent / f'{condition}_{item.name}'
item.rename(new_name)
[docs]
@print_func_name_args_times()
def prepend_conditions(base_path, csv_file, rename_files, rename_dirs, recursive):
mapping_df = pd.read_csv(csv_file)
for index, row in mapping_df.iterrows():
dir_name = row['dir_name']
condition = row['condition']
rename_items(base_path, dir_name, condition, rename_files, rename_dirs, recursive)
[docs]
@log_command
def main():
install()
args = parse_args()
Configuration.verbose = args.verbose
verbose_start_msg()
base_path = Path.cwd()
prepend_conditions(base_path, args.sample_key, args.file, args.dirs, args.recursive)
verbose_end_msg()
if __name__ == '__main__':
main()