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))