def main():
args = parse_arguments()
logging.getLogger().setLevel(args.log_level)
glif_api = None
if (args.neuron_config_file is None or args.sweeps_file is None
or args.ephys_file is None):
assert args.neuronal_model_id is not None, Exception(
"A neuronal model id is required if no neuron config file, sweeps file, or ephys data file is provided."
)
glif_api = GlifApi()
glif_api.get_neuronal_model(args.neuronal_model_id)
if args.neuron_config_file:
neuron_config = json_utilities.read(args.neuron_config_file)
else:
neuron_config = glif_api.get_neuron_config()
if args.sweeps_file:
sweeps = json_utilities.read(args.sweeps_file)
else:
sweeps = glif_api.get_ephys_sweeps()
if args.ephys_file:
ephys_file = args.ephys_file
else:
ephys_file = 'stimulus_%d.nwb' % args.neuronal_model_id
if not os.path.exists(ephys_file):
logging.info("Downloading stimulus to %s." % ephys_file)
glif_api.cache_stimulus_file(ephys_file)
else:
logging.warning("Reusing %s because it already exists." %
ephys_file)
if args.output_ephys_file:
output_ephys_file = args.output_ephys_file
else:
logging.warning(
"Overwriting input file data with simulated data in place.")
output_ephys_file = ephys_file
neuron = GlifNeuron.from_dict(neuron_config)
# filter out test sweeps
sweep_numbers = [
s['sweep_number'] for s in sweeps if s['stimulus_name'] != 'Test'
]
simulate_neuron(neuron, sweep_numbers, ephys_file, output_ephys_file,
args.spike_cut_value)
def main():
args = parse_arguments()
logging.getLogger().setLevel(args.log_level)
glif_api = None
if (args.neuron_config_file is None or
args.sweeps_file is None or
args.ephys_file is None):
assert args.neuronal_model_id is not None, Exception("A neuronal model id is required if no neuron config file, sweeps file, or ephys data file is provided.")
glif_api = GlifApi()
glif_api.get_neuronal_model(args.neuronal_model_id)
if args.neuron_config_file:
neuron_config = json_utilities.read(args.neuron_config_file)
else:
neuron_config = glif_api.get_neuron_config()
if args.sweeps_file:
sweeps = json_utilities.read(args.sweeps_file)
else:
sweeps = glif_api.get_ephys_sweeps()
if args.ephys_file:
ephys_file = args.ephys_file
else:
ephys_file = 'stimulus_%d.nwb' % args.neuronal_model_id
if not os.path.exists(ephys_file):
logging.info("Downloading stimulus to %s." % ephys_file)
glif_api.cache_stimulus_file(ephys_file)
else:
logging.warning("Reusing %s because it already exists." % ephys_file)
if args.output_ephys_file:
output_ephys_file = args.output_ephys_file
else:
logging.warning("Overwriting input file data with simulated data in place.")
output_ephys_file = ephys_file
neuron = GlifNeuron.from_dict(neuron_config)
# filter out test sweeps
sweep_numbers = [ s['sweep_number'] for s in sweeps if s['stimulus_name'] != 'Test' ]
simulate_neuron(neuron, sweep_numbers, ephys_file, output_ephys_file, args.spike_cut_value)
def test_download():
if os.path.exists(OUTPUT_DIR):
shutil.rmtree(OUTPUT_DIR)
os.makedirs(OUTPUT_DIR)
glif_api = GlifApi()
glif_api.get_neuronal_model(NEURONAL_MODEL_ID)
glif_api.cache_stimulus_file(os.path.join(OUTPUT_DIR, '%d.nwb' % NEURONAL_MODEL_ID))
neuron_config = glif_api.get_neuron_config()
json_utilities.write(os.path.join(OUTPUT_DIR, '%d_neuron_config.json' % NEURONAL_MODEL_ID), neuron_config)
ephys_sweeps = glif_api.get_ephys_sweeps()
json_utilities.write(os.path.join(OUTPUT_DIR, 'ephys_sweeps.json'), ephys_sweeps)
from allensdk.api.queries.glif_api import GlifApi
import allensdk.core.json_utilities as json_utilities
neuronal_model_id = 472423251
glif_api = GlifApi()
glif_api.get_neuronal_model(neuronal_model_id)
glif_api.cache_stimulus_file('stimulus.nwb')
neuron_config = glif_api.get_neuron_config()
json_utilities.write('neuron_config.json', neuron_config)
ephys_sweeps = glif_api.get_ephys_sweeps()
json_utilities.write('ephys_sweeps.json', ephys_sweeps)
from allensdk.api.queries.glif_api import GlifApi
import allensdk.core.json_utilities as json_utilities
neuronal_model_id = 472423251
glif_api = GlifApi()
glif_api.get_neuronal_model(neuronal_model_id)
glif_api.cache_stimulus_file('472423251.nwb')
neuron_config = glif_api.get_neuron_config()
json_utilities.write('472423251_neuron_config.json', neuron_config)
ephys_sweeps = glif_api.get_ephys_sweeps()
json_utilities.write('ephys_sweeps.json', ephys_sweeps)
