Source code for unravel.allen_institute.abca.merfish.merfish_regions

#!/usr/bin/env python3

"""
Use ``abca_merfish_regions`` or ``mr`` from UNRAVEL to list unique region names from the Allen Brain Cell Atlas MERFISH parcellation annotations.

Note:
    - This is useful for finding region acronyms that are relevant to MERFISH data analysis.
    - For other MERFISH scripts, ``parcellation_`` is prepended to the region-related columns (e.g., ``parcellation_substructure``). 

Usage:
------
    abca_merfish_regions -b path/base_dir [-c column] [-o path/output.csv] [-v]

Usage with piping to grep:
--------------------------
    abca_merfish_regions -b path/base_dir | grep BLA
"""

import pandas as pd
from pathlib import Path
from rich import print
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




def parse_args():
    parser = RichArgumentParser(formatter_class=SuppressMetavar, add_help=False, docstring=__doc__)

    reqs = parser.add_argument_group('Required arguments')
    reqs.add_argument('-b', '--base', help='Path to the root directory of the Allen Brain Cell Atlas data', required=True, action=SM)

    opts = parser.add_argument_group('Optional arguments')
    opts.add_argument('-c', '--column', help='Column: organ, category, division, structure, substructure. Default: substructure', default='substructure', action=SM)
    opts.add_argument('-o', '--output', help='Path to save .csv file. Default: None', default=None, action=SM)

    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()




@log_command
def main():
    install()
    args = parse_args()
    Configuration.verbose = args.verbose
    verbose_start_msg()

    download_base = Path(args.base)

    parcellation_annotation_path = download_base / 'metadata/Allen-CCF-2020/20230630/views/parcellation_to_parcellation_term_membership_acronym.csv'

    parcellation_annotation = pd.read_csv(parcellation_annotation_path, index_col=0)
    
    # Print unique values in the specified column
    unique_values = parcellation_annotation[args.column].unique()
    print(f"Unique values in column '{args.column}':\n{unique_values}\n")

    if args.output:
        output_path = Path(args.output)
        output_path.parent.mkdir(parents=True, exist_ok=True)
        parcellation_annotation[args.column].to_csv(output_path, header=True)
        print(f"Saved unique values to {output_path}")

    verbose_end_msg()


if __name__ == '__main__':
    main()