"""Functions to create cells."""
# 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 os
from emodelrunner.cell import CellModelCustom
from emodelrunner.load import (
load_mechanisms,
load_syn_mechs,
load_unoptimized_parameters,
)
from emodelrunner.morphology import create_morphology
from emodelrunner.configuration import PackageType
[docs]
def create_cell(
unopt_params_path,
emodel,
add_synapses,
morph,
gid,
syn_mech_args=None,
use_glu_synapse=False,
fixhp=False,
syn_setup_params=None,
v_init=-80,
celsius=34,
):
"""Create a cell.
Args:
unopt_params_path (str): path to the unoptimized parameters json file
emodel (str): name to give to the cell model
add_synapses (bool): whether to add synapses to the cell
morph (ephys.morphologies.NrnFileMorphology): morphology object
gid (int): cell model ID
syn_mech_args (SynMechArgs): synapse-related configuration
use_glu_synapse (bool): whether to use GluSynapseCustom class for synapses
fixhp (bool): to uninsert SK_E2 for hyperpolarization in cell model
syn_setup_params (dict): contains extra parameters to setup synapses
when using GluSynapseCustom
v_init (int): initial voltage (mV)
celsius (int): cell temperature (celsius)
Returns:
CellModelCustom: cell model
"""
# pylint: disable=too-many-arguments, too-many-locals
# load mechanisms
mechs = load_mechanisms(unopt_params_path)
# add synapses mechs
if add_synapses:
mechs += [
load_syn_mechs(
syn_mech_args.seed,
syn_mech_args.rng_settings_mode,
os.path.join(syn_mech_args.syn_dir, syn_mech_args.syn_data_file),
os.path.join(syn_mech_args.syn_dir, syn_mech_args.syn_conf_file),
use_glu_synapse=use_glu_synapse,
syn_setup_params=syn_setup_params,
)
]
# load parameters
params = load_unoptimized_parameters(unopt_params_path, v_init, celsius)
# create cell
cell = CellModelCustom(
name=emodel,
morph=morph,
mechs=mechs,
params=params,
gid=gid,
add_synapses=add_synapses,
fixhp=fixhp,
)
return cell
[docs]
def create_cell_using_config(config):
"""Create a cell given configuration.
Args:
config (configparser.ConfigParser): configuration
Raises:
ValueError: raised when package_type is not supported
Returns:
CellModelCustom: cell model
"""
unopt_params_path = config.get("Paths", "unoptimized_params_path")
# get synapse config data
add_synapses = config.getboolean("Synapses", "add_synapses")
syn_mech_args = config.syn_mech_args()
# get morphology config data
if config.package_type in [PackageType.sscx, PackageType.thalamus]:
morph = create_morphology(config.morph_args(), config.package_type)
else:
raise ValueError(f"unsupported package type: {config.package_type}")
return create_cell(
unopt_params_path,
config.get("Cell", "emodel"),
add_synapses,
morph,
config.getint("Cell", "gid"),
syn_mech_args,
v_init=config.getfloat("Cell", "v_init"),
celsius=config.getfloat("Cell", "celsius"),
)
[docs]
def get_postcell(
config,
fixhp=False,
syn_setup_params=None,
):
"""Return the postcell for synapse plasticity run.
Args:
config (configparser.ConfigParser): configuration
fixhp (bool): to uninsert SK_E2 for hyperpolarization in cell model
syn_setup_params (dict): contains extra parameters to setup synapses
when using GluSynapseCustom
Returns:
CellModelCustom: post-synaptic cell model
"""
emodel = config.get("Cell", "emodel")
gid = config.getint("Cell", "gid")
base_seed = config.getint("SynapsePlasticity", "base_seed")
v_init = config.getfloat("Cell", "v_init")
celsius = config.getfloat("Cell", "celsius")
unopt_params_path = config.get("Paths", "unoptimized_params_path")
# rewrite seed and rng setting mode over basic emodelrunner config defaults
syn_mech_args = config.syn_mech_args(
add_synapses=True, seed=base_seed, rng_settings_mode="Compatibility"
)
morph = create_morphology(config.synplas_morph_args(), config.package_type)
add_synapses = True
cell = create_cell(
unopt_params_path,
emodel,
add_synapses,
morph,
gid,
syn_mech_args,
use_glu_synapse=True,
fixhp=fixhp,
syn_setup_params=syn_setup_params,
v_init=v_init,
celsius=celsius,
)
return cell
[docs]
def get_precell(
config,
fixhp=False,
):
"""Return the precell for synapse plasticity pair simulation run.
Args:
config (configparser.ConfigParser): configuration
fixhp (bool): to uninsert SK_E2 for hyperpolarization in cell model
Returns:
CellModelCustom: pre-synaptic cell model
"""
emodel = config.get("Cell", "emodel")
gid = config.getint("Cell", "gid")
v_init = config.getfloat("Cell", "v_init")
celsius = config.getfloat("Cell", "celsius")
unopt_params_path = config.get("Paths", "precell_unoptimized_params_path")
morph = create_morphology(
config.synplas_morph_args(precell=True), config.package_type
)
add_synapses = False
cell = create_cell(
unopt_params_path,
emodel,
add_synapses,
morph,
gid,
fixhp=fixhp,
v_init=v_init,
celsius=celsius,
)
return cell