Source code for ipfx.bin.generate_se_input

import allensdk.core.json_utilities as ju
import os
import ipfx.lims_queries as lq
import argparse



[docs]def generate_se_input(cell_dir,
                      specimen_id=None,
                      input_nwb_file=None,
                      ):

    se_input = dict()

    if specimen_id:
        input_nwb_file = lq.get_input_nwb_file(specimen_id)

    se_input['input_nwb_file'] = input_nwb_file

    if not os.path.exists(cell_dir):
        os.makedirs(cell_dir)

    return se_input




[docs]def parse_args():

    parser = argparse.ArgumentParser()
    group = parser.add_mutually_exclusive_group(required=True)
    group.add_argument('--specimen_id', type=int)
    group.add_argument('--input_nwb_file', type=str)
    parser.add_argument('--cell_dir', type=str, required=True)
    args = parser.parse_args()

    return vars(args)




[docs]def main():

    """
    Usage:
    > python generate_se_input.py --specimen_id SPECIMEN_ID --cell_dir CELL_DIR
    > python generate_se_input.py --input_nwb_file input_nwb_file --cell_dir CELL_DIR

    """

    kwargs = parse_args()
    se_input = generate_se_input(**kwargs)

    input_json = os.path.join(kwargs["cell_dir"], 'se_input.json')

    ju.write(input_json, se_input)



if __name__=="__main__": main()