Source code for patato.convenience_scripts.import_clinical_data

#  Copyright (c) Thomas Else 2023-25.
#  License: MIT

import argparse
import glob
from os import makedirs, system
from os.path import join, split, exists




def init_argparse():
    parser = argparse.ArgumentParser(
        usage="%(prog)s [-hv] input output",
        description="Convert iThera MSOT Data into a hdf5 format. .",
    )
    parser.add_argument(
        "-v", "--version", action="version", version=f"{parser.prog} version 0.1"
    )
    parser.add_argument("input", type=str, help="iThera Studies Folder")
    parser.add_argument("output", help="Empty Output Folder")
    parser.add_argument(
        "-u", "--update", type=bool, default=False, help="Update metadata"
    )
    parser.add_argument(
        "-g", "--dontgetrecons", type=bool, default=False, help="Don't get Recons"
    )
    return parser





def main():
    p = init_argparse()
    args = p.parse_args()

    for folder in glob.glob(join(args.input, "Study_*")):
        study_name = split(folder)[-1]
        print(f"-----{study_name}-----")
        study_output = join(args.output, study_name)
        if not exists(study_output):
            makedirs(study_output)
        system(
            f'patato-import-ithera "{folder}" "{study_output}"'
            + (" -g True" if args.dontgetrecons else "")
        )