allensdk.model.biophysical.runner module¶
- allensdk.model.biophysical.runner.load_description(args_dict)[source]¶
Read configurations.
- Parameters:
- args_dictdict
Parsed arguments dictionary with following keys.
- manifest_filestring
.json file with containing the experiment configuration
- axon_typestring
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_pathstring
NWB file name
- nwb_result_pathstring
NWB file name
- allensdk.model.biophysical.runner.run(args, sweeps=None, procs=6)[source]¶
Main function for simulating sweeps in a biophysical experiment.
- Parameters:
- argsdict
Parsed arguments to run the experiment.
- procsint
number of sweeps to simulate simultaneously.
- sweepslist
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:
- descriptionConfig
All information needed to run the experiment.
- sweepslist
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_pathstring
file name of a pre-existing NWB file.
- vnumpy array
voltage
- sweepinteger
which entry to overwrite in the file.