Source code for emodelrunner.run

"""Create python recordings."""

# Copyright 2020-2022 Blue Brain Project / EPFL

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

#     http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import logging

from bluepyopt import ephys

from emodelrunner.configuration.configparser import PackageType
from emodelrunner.create_cells import create_cell_using_config
from emodelrunner.parsing_utilities import get_parser_args, set_verbosity
from emodelrunner.protocols.create_protocols import ProtocolBuilder
from emodelrunner.load import (
    load_config,
    get_release_params,
)
from emodelrunner.output import write_current
from emodelrunner.output import write_responses

logger = logging.getLogger(__name__)


[docs] def main(config_path): """Main. Args: config_path (str): path to config file The config file should have '.ini' suffix """ # pylint: disable=too-many-locals config = load_config(config_path=config_path) cell = create_cell_using_config(config) release_params = get_release_params(config) cvode_active = config.getboolean("Sim", "cvode_active") # simulator dt = config.getfloat("Sim", "dt") sim = ephys.simulators.NrnSimulator(dt=dt, cvode_active=cvode_active) # create protocols add_synapses = config.getboolean("Synapses", "add_synapses") prot_args = config.prot_args() if config.package_type == PackageType.sscx: protocols = ProtocolBuilder.using_sscx_protocols(add_synapses, prot_args, cell) elif config.package_type == PackageType.thalamus: protocols = ProtocolBuilder.using_thalamus_protocols( add_synapses, prot_args, cell ) else: raise ValueError(f"unsupported package type: {config.package_type}") ephys_protocols = protocols.get_ephys_protocols() # run logger.info("Python Recordings Running...") responses = ephys_protocols.run( cell_model=cell, param_values=release_params, sim=sim, isolate=False ) mtype = config.get("Morphology", "mtype") if config.package_type == PackageType.sscx: currents = protocols.get_stim_currents(responses, dt) elif config.package_type == PackageType.thalamus: currents = protocols.get_thalamus_stim_currents(responses, mtype, dt) # write responses output_dir = config.get("Paths", "output_dir") write_responses(responses, output_dir) write_current(currents, output_dir) logger.info("Python Recordings Done.") logger.info("Responses written to %s", output_dir)
if __name__ == "__main__": args = get_parser_args() set_verbosity(args.verbosity) main(config_path=args.config_path)