Source code for patato.convenience_scripts.convert_binary_to_hdf5

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

"""``patato-import-ithera``: A script to convert iThera MSOT Data into the PATATO hdf5 format."""

import argparse




def strtobool(x):
    return x == "True"



from ..io.hdf5_converter import convert_ithera_msot_binary_to_hdf5




def main():
    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", nargs=1, type=str, help="iThera Study Folder")
    parser.add_argument("output", nargs=1, help="Output Folder")
    parser.add_argument(
        "-u", "--update", type=strtobool, default=False, help="Update metadata"
    )
    parser.add_argument(
        "-n",
        "--name",
        type=strtobool,
        default=False,
        help="Keep the user defined scan name and do "
        "not use the iThera defined generic name.",
    )
    args = parser.parse_args()

    convert_ithera_msot_binary_to_hdf5(
        args.input[0], args.output[0], args.update, args.name
    )



if __name__ == "__main__":
    main()