allensdk.model.biophysical.runner module¶
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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.
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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
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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.
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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.
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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.