class RunSimulate(object):
_log = logging.getLogger('allensdk.model.biophysical.run_simulate')
def __init__(self, input_json, output_json):
self.input_json = input_json
self.output_json = output_json
self.app_config = None
self.manifest = None
def load_manifest(self):
self.app_config = Config().load(self.input_json)
self.manifest = self.app_config.manifest
fix_sections = ['passive', 'axon_morph,', 'conditions', 'fitting']
self.app_config.fix_unary_sections(fix_sections)
def nrnivmodl(self):
RunSimulate._log.debug("nrnivmodl")
subprocess.call(['nrnivmodl', './modfiles'])
def simulate(self):
from allensdk.internal.api.queries.biophysical_module_reader \
import BiophysicalModuleReader
self.load_manifest()
try:
stimulus_path = self.manifest.get_path('stimulus_path')
RunSimulate._log.info("stimulus path: %s" % (stimulus_path))
except:
raise Exception(
'Could not read input stimulus path from input config.')
try:
out_path = self.manifest.get_path('output_path')
RunSimulate._log.info("result NWB file: %s" % (out_path))
except:
raise Exception('Could not read output path from input config.')
try:
morphology_path = self.manifest.get_path('MORPHOLOGY')
RunSimulate._log.info("morphology path: %s" % (morphology_path))
except:
raise Exception(
'Could not read morphology path from input config.')
single_cell.run(self.app_config)
lims_upload_config = BiophysicalModuleReader()
lims_upload_config.read_json(
self.manifest.get_path('neuronal_model_run_data'))
lims_upload_config.update_well_known_file(out_path)
lims_upload_config.set_workflow_state('passed')
lims_upload_config.write_file(self.output_json)
def load_description(manifest_json_path):
'''Read configuration file.
Parameters
----------
manifest_json_path : string
File containing the experiment configuration.
Returns
-------
Config
Object with all information needed to run the experiment.
'''
description = Config().load(manifest_json_path)
# fix nonstandard description sections
fix_sections = ['passive', 'axon_morph,', 'conditions', 'fitting']
description.fix_unary_sections(fix_sections)
return description
def load_description(manifest_json_path):
'''Read configuration file.
Parameters
----------
manifest_json_path : string
File containing the experiment configuration.
Returns
-------
Config
Object with all information needed to run the experiment.
'''
description = Config().load(manifest_json_path)
# fix nonstandard description sections
fix_sections = ['passive', 'axon_morph,', 'conditions', 'fitting']
description.fix_unary_sections(fix_sections)
return description
def run_nrn(manifest, current, t_start, t_stop):
description = Config().load(manifest)
description.update_data({'axon_type': 'truncated'}, 'biophys')
fix_sections = ['passive', 'axon_morph,', 'conditions', 'fitting']
description.fix_unary_sections(fix_sections)
utils = create_utils(description)
hoc = utils.h
manifest = description.manifest
morphology_path = manifest.get_path('MORPHOLOGY').encode(
'ascii', 'ignore').decode("utf-8")
stimulus_path = description.manifest.get_path('stimulus_path')
utils.generate_morphology(morphology_path)
utils.load_cell_parameters()
utils.read_stimulus(stimulus_path, sweep=35) # needed for sampling rates
stim = hoc.IClamp(hoc.soma[0](0.5))
stim.amp = current
stim.delay = t_start
stim.dur = t_stop - t_start
simulation_dt = 1.0e3 / utils.simulation_sampling_rate
hoc.dt = simulation_dt
hoc.tstop = t_start + t_stop
vec = utils.record_values()
hoc.finitialize()
hoc.run()
recorded_data = utils.get_recorded_data(vec)
vs = recorded_data['v']
ts = recorded_data['t']
return ts, vs
