def test_simulate(): logging.getLogger().setLevel(logging.DEBUG) neuron_config = json_utilities.read(os.path.join(OUTPUT_DIR, '%d_neuron_config.json' % NEURONAL_MODEL_ID)) ephys_sweeps = json_utilities.read(os.path.join(OUTPUT_DIR, 'ephys_sweeps.json')) ephys_file_name = os.path.join(OUTPUT_DIR, '%d.nwb' % NEURONAL_MODEL_ID) neuron = GlifNeuron.from_dict(neuron_config) sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps ] simulate_neuron(neuron, sweep_numbers, ephys_file_name, ephys_file_name, 0.05)
def test_3(): neuron_config = json_utilities.read('neuron_config.json') ephys_sweeps = json_utilities.read('ephys_sweeps.json') ephys_file_name = 'stimulus.nwb' neuron = GlifNeuron.from_dict(neuron_config) # sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps # if s['stimulus_units'] == 'Amps' ] sweep_numbers = [7] simulate_neuron(neuron, sweep_numbers, ephys_file_name, ephys_file_name, 0.05)
def test_3(configured_glif_api, neuron_config_file, ephys_sweeps_file): neuron_config = json_utilities.read(neuron_config_file) ephys_sweeps = json_utilities.read(ephys_sweeps_file) ephys_file_name = 'stimulus.nwb' neuron = GlifNeuron.from_dict(neuron_config) # sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps # if s['stimulus_units'] == 'Amps' ] sweep_numbers = [7] simulate_neuron(neuron, sweep_numbers, ephys_file_name, ephys_file_name, 0.05)
import allensdk.core.json_utilities as json_utilities from allensdk.model.glif.glif_neuron import GlifNeuron from allensdk.model.glif.simulate_neuron import simulate_neuron neuron_config = json_utilities.read('neuron_config.json') ephys_sweeps = json_utilities.read('ephys_sweeps.json') ephys_file_name = 'stimulus.nwb' neuron = GlifNeuron.from_dict(neuron_config) sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps if s['stimulus_units'] == 'Amps' ] simulate_neuron(neuron, sweep_numbers, ephys_file_name, ephys_file_name, 0.05)
#=============================================================================== import allensdk.core.json_utilities as json_utilities from allensdk.model.glif.glif_neuron import GlifNeuron from allensdk.model.glif.simulate_neuron import simulate_neuron neuron_config = json_utilities.read('neuron_config.json')['566302806'] ephys_sweeps = json_utilities.read('ephys_sweeps.json') ephys_file_name = 'stimulus.nwb' neuron = GlifNeuron.from_dict(neuron_config) sweep_numbers = [ s['sweep_number'] for s in ephys_sweeps if s['stimulus_units'] == 'Amps' ] sweep_numbers = sweep_numbers[:1] # for the sake of a speedy example, just run the first one simulate_neuron(neuron, sweep_numbers, ephys_file_name, ephys_file_name, 0.05) #=============================================================================== # example 4 #=============================================================================== import allensdk.core.json_utilities as json_utilities from allensdk.model.glif.glif_neuron import GlifNeuron from allensdk.core.nwb_data_set import NwbDataSet neuron_config = json_utilities.read('neuron_config.json')['566302806'] ephys_sweeps = json_utilities.read('ephys_sweeps.json') ephys_file_name = 'stimulus.nwb' # pull out the stimulus for the current-clamp first sweep ephys_sweep = next( s for s in ephys_sweeps
import allensdk.core.json_utilities as json_utilities from allensdk.model.glif.glif_neuron import GlifNeuron from allensdk.model.glif.simulate_neuron import simulate_neuron neuron_config = json_utilities.read('472423251_neuron_config.json') ephys_sweeps = json_utilities.read('ephys_sweeps.json') ephys_file_name = '472423251.nwb' neuron = GlifNeuron.from_dict(neuron_config) simulate_neuron(neuron, ephys_sweeps, ephys_file_name, ephys_file_name, 0.05)