Source code for ipfx.bin.generate_fx_input

import os
import allensdk.core.json_utilities as ju
import ipfx.sweep_props as sp
from ipfx.bin.run_sweep_extraction import run_sweep_extraction
from ipfx.bin.generate_qc_input import generate_qc_input
from ipfx.bin.generate_se_input import generate_se_input, parse_args
from ipfx.bin.run_qc import run_qc
import ipfx.lims_queries as lq
import ipfx.logging_utils as lu


FX_INPUT_FEATURES = [
                    "stimulus_code",
                    "stimulus_name",
                    "stimulus_amplitude",
                    "sweep_number",
                    "stimulus_units",
                    "bridge_balance_mohm",
                    "leak_pa",
                    "passed",
                    "pre_vm_mv"
                    ]


def generate_fx_input(se_input,
                      se_output,
                      cell_dir,
                      plot_figures=False):

    fx_input = dict(se_input)

    fx_input['sweep_features'] = sp.extract_sweep_features_subset(FX_INPUT_FEATURES,se_output["sweep_features"])

    fx_input['cell_features'] = se_output['cell_features']

    if plot_figures:
        fx_input['qc_fig_dir'] = os.path.join(cell_dir, "qc_figs")

    fx_input['output_nwb_file'] = os.path.join(cell_dir, "output.nwb")

    return fx_input



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("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)

if __name__=="__main__": main()