allensdk.model.biophysical.runner module

allensdk.model.biophysical.runner.load_description(manifest_json_path)

Read configuration file.

Parameters:

manifest_json_path : string

File containing the experiment configuration.

Returns:

Config

Object with all information needed to run the experiment.

allensdk.model.biophysical.runner.prepare_nwb_output(nwb_stimulus_path, nwb_result_path)

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(description, sweeps=None, procs=6)

Main function for simulating sweeps in a biophysical experiment.

Parameters:

description : Config

All information needed 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)

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)

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.