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)