コード例 #1
0
def main():
    """
    Usage:
    > python generate_qc_input.py --specimen_id SPECIMEN_ID --cell_dir CELL_DIR
    > python generate_qc_input.py --input_nwb_file input_nwb_file --cell_dir CELL_DIR

    """

    args = parse_args()
    se_input = generate_se_input(**args)

    cell_dir = args['cell_dir']
    if not os.path.exists(cell_dir):
        os.makedirs(cell_dir)

    lu.configure_logger(cell_dir)

    ju.write(os.path.join(cell_dir,'se_input.json'), se_input)

    se_output = run_sweep_extraction(se_input["input_nwb_file"],
                                     se_input.get("input_h5_file",None),
                                     se_input.get("stimulus_ontology_file", None))

    ju.write(os.path.join(cell_dir,'se_output.json'),se_output)

    sp.drop_tagged_sweeps(se_output["sweep_features"])

    qc_input = generate_qc_input(se_input, se_output)

    ju.write(os.path.join(cell_dir,'qc_input.json'), qc_input)
コード例 #2
0
def main():
    """
    Usage:
    > python generate_fx_input.py --specimen_id SPECIMEN_ID --cell_dir CELL_DIR
    > python generate_fx_input.py --input_nwb_file INPUT_NWB_FILE --cell_dir CELL_DIR

    """

    kwargs = parse_args()
    se_input = generate_se_input(**kwargs)
    cell_dir = kwargs["cell_dir"]
    lu.configure_logger(cell_dir)

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

    ju.write(os.path.join(cell_dir, 'se_input.json'), se_input)

    se_output = run_sweep_extraction(
        se_input["input_nwb_file"], se_input.get("input_h5_file", None),
        se_input.get("stimulus_ontology_file", None))

    ju.write(os.path.join(cell_dir, 'se_output.json'), se_output)

    sp.drop_tagged_sweeps(se_output["sweep_features"])

    qc_input = generate_qc_input(se_input, se_output)
    ju.write(os.path.join(cell_dir, 'qc_input.json'), qc_input)

    qc_output = run_qc(qc_input.get("stimulus_ontology_file",
                                    None), qc_input["cell_features"],
                       qc_input["sweep_features"], qc_input["qc_criteria"])
    ju.write(os.path.join(cell_dir, 'qc_output.json'), qc_output)

    if kwargs["specimen_id"]:
        manual_sweep_states = lq.get_sweep_states(kwargs["specimen_id"])
    elif kwargs["input_nwb_file"]:
        manual_sweep_states = []

    sp.override_auto_sweep_states(manual_sweep_states,
                                  qc_output["sweep_states"])
    sp.assign_sweep_states(qc_output["sweep_states"],
                           se_output["sweep_features"])

    fx_input = generate_fx_input(se_input,
                                 se_output,
                                 cell_dir,
                                 plot_figures=True)

    ju.write(os.path.join(cell_dir, 'fx_input.json'), fx_input)
コード例 #3
0
def main():
    """
    Usage:
    > python generate_pipeline_input.py --specimen_id SPECIMEN_ID --cell_dir CELL_DIR
    > python generate_pipeline_input.py --input_nwb_file INPUT_NWB_FILE --cell_dir CELL_DIR

    """

    kwargs = parse_args()
    pipe_input = generate_pipeline_input(**kwargs)
    cell_dir = kwargs["cell_dir"]

    input_json = os.path.join(cell_dir, 'pipeline_input.json')

    ju.write(input_json, pipe_input)