def main(limit, manifest_path):
app_config = Config()
description = app_config.load(manifest_path)
if 'LOG_CFG' in os.environ:
log_config = os.environ['LOG_CFG']
else:
log_config = resource_filename('allensdk.model.biophysical',
'logging.conf')
os.environ['LOG_CFG'] = log_config
lc.fileConfig(log_config)
run_passive_fit(description)
def main():
import sys
manifest_path = sys.argv[-1]
limit = float(sys.argv[-2])
os.chdir(os.path.dirname(manifest_path))
app_config = Config()
description = app_config.load(manifest_path)
upfile = description.manifest.get_path('upfile')
up_data = np.loadtxt(upfile)
downfile = description.manifest.get_path('downfile')
down_data = np.loadtxt(downfile)
swc_path = description.manifest.get_path('MORPHOLOGY')
output_file = description.manifest.get_path('fit_2_file')
data = neuron_passive_fit2(up_data, down_data, swc_path, limit)
json_utilities.write(output_file, data)
def choose_bps_command(command='bps_simple', conf_file=None):
log = logging.getLogger('allensdk.model.biophys_sim.bps_command')
log.info("bps command: %s" % (command))
if conf_file:
conf_file = os.path.abspath(conf_file)
if command == 'help':
print Config().argparser.parse_args(['--help'])
elif command == 'nrnivmodl':
sp.call(['nrnivmodl', 'modfiles']) # TODO: alternate location in manifest?
elif command == 'run_simple':
app_config = Config()
description = app_config.load(conf_file)
sys.path.insert(1, description.manifest.get_path('CODE_DIR'))
(module_name, function_name) = description.data['runs'][0]['main'].split('#')
run_module(description, module_name, function_name)
else:
raise Exception("unknown command %s" %(command))
def choose_bps_command(command='bps_simple', conf_file=None):
log = logging.getLogger('allensdk.model.biophys_sim.bps_command')
log.info("bps command: %s" % (command))
if conf_file:
conf_file = os.path.abspath(conf_file)
if command == 'help':
print(Config().argparser.parse_args(['--help']))
elif command == 'nrnivmodl':
sp.call(['nrnivmodl', 'modfiles'])
elif command == 'run_simple':
app_config = Config()
description = app_config.load(conf_file)
sys.path.insert(1, description.manifest.get_path('CODE_DIR'))
(module_name,
function_name) = description.data['runs'][0]['main'].split('#')
run_module(description, module_name, function_name)
else:
raise Exception("unknown command %s" % (command))