allensdk.model.biophysical.runner module

allensdk.model.biophysical.runner.load_description(args_dict)[source]

Read configurations.

Parameters:
args_dict : dict

Parsed arguments dictionary with following keys.

manifest_file : string

.json file with containing the experiment configuration

axon_type : string

Axon handling for the all-active models

Returns:
Config

Object with all information needed to run the experiment.

allensdk.model.biophysical.runner.prepare_nwb_output(nwb_stimulus_path, nwb_result_path)[source]

Copy the stimulus file, zero out the recorded voltages and spike times.

Parameters:
nwb_stimulus_path : string

NWB file name

nwb_result_path : string

NWB file name

allensdk.model.biophysical.runner.run(args, sweeps=None, procs=6)[source]

Main function for simulating sweeps in a biophysical experiment.

Parameters:
args : dict

Parsed arguments to run the experiment.

procs : int

number of sweeps to simulate simultaneously.

sweeps : list

list of experiment sweep numbers to simulate. If None, simulate all sweeps.

allensdk.model.biophysical.runner.run_sync(description, sweeps=None)[source]

Single-process main function for simulating sweeps in a biophysical experiment.

Parameters:
description : Config

All information needed to run the experiment.

sweeps : list

list of experiment sweep numbers to simulate. If None, simulate all sweeps.

allensdk.model.biophysical.runner.save_nwb(output_path, v, sweep, sweeps_by_type)[source]

Save a single voltage output result into an existing sweep in a NWB file. This is intended to overwrite a recorded trace with a simulated voltage.

Parameters:
output_path : string

file name of a pre-existing NWB file.

v : numpy array

voltage

sweep : integer

which entry to overwrite in the file.