Source code for emodelrunner.run_pairsim

"""Run pair simulation for synapse plasticity simulation."""

# 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


# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

import json
import logging

import numpy as np
from bluepyopt import ephys
from emodelrunner.create_cells import get_precell, get_postcell
from emodelrunner.parsing_utilities import get_parser_args, set_verbosity
from emodelrunner.protocols.create_protocols import define_pairsim_protocols
from emodelrunner.load import get_release_params
from emodelrunner.load import get_syn_setup_params
from emodelrunner.load import load_config
from emodelrunner.output import write_synplas_output
from emodelrunner.output import write_synplas_precell_output
from emodelrunner.run_synplas import _set_global_params

# Configure logger
logger = logging.getLogger(__name__)

[docs]def run( config_path, cvode_active=True, postsyn_protocol_name="pulse", presyn_protocol_name="presyn_pulse", fixhp=True, ): """Run cell with pulse stimuli and pre-cell spike train. Args: config_path (str): path to config file cvode_active (bool): whether to use variable time step postsyn_protocol_name (str): name of the postsynaptic protocol presyn_protocol_name (str): name of the presynaptic protocol fixhp (bool): to uninsert SK_E2 for hyperpolarization in cell model """ # pylint:disable=too-many-locals config = load_config(config_path=config_path) # load extra_params syn_setup_params = get_syn_setup_params( "synapses/syn_extra_params.json", "synapses/cpre_cpost.json", config.get("Paths", "synplas_fit_params_path"), config.getint("Cell", "gid"), config.getboolean("SynapsePlasticity", "invivo"), ) # load cell postcell = get_postcell( config, fixhp=fixhp, syn_setup_params=syn_setup_params, ) # load cell precell = get_precell( config, fixhp=fixhp, ) sim = ephys.simulators.NrnSimulator(cvode_active=cvode_active) pre_release_params = get_release_params(config, precell=True) post_release_params = get_release_params(config) # set dynamic timestep tolerance sim.neuron.h.cvode.atolscale("v", 0.1) # 0.01 for more precision # load spike_train spike_train_path = config.get("Paths", "spiketrain_path") pre_spike_train = np.unique(np.loadtxt(spike_train_path, skiprows=1)[:, 0]) # get pre-synaptic stimulus parameters presyn_stim_args = config.presyn_stim_args(pre_spike_train) # Set fitted model parameters if syn_setup_params["fit_params"]: _set_global_params(syn_setup_params["fit_params"], sim) # Enable in vivo mode (global) if config.getboolean("SynapsePlasticity", "invivo"): sim.neuron.h.cao_CR_GluSynapse = 1.2 # mM # protocols protocol = define_pairsim_protocols( postcell, presyn_protocol_name, postsyn_protocol_name, cvode_active, json.loads(config.get("SynapsePlasticity", "synrec")), config.getfloat("Protocol", "tstop"), config.getfloat("SynapsePlasticity", "fastforward"), presyn_stim_args, config.get("Paths", "stimuli_path"), ) # run"Python Recordings Running...") responses = precell_model=precell, postcell_model=postcell, pre_param_values=pre_release_params, post_param_values=post_release_params, sim=sim, isolate=False, ) # write responses output_path = config.get("Paths", "pairsim_output_path") precell_output_path = config.get("Paths", "pairsim_precell_output_path") syn_prop_path = config.get("Paths", "syn_prop_path") write_synplas_output(responses[1], pre_spike_train, output_path, syn_prop_path) write_synplas_precell_output( responses[0], presyn_protocol_name, precell_output_path )"Python Recordings Done.")
if __name__ == "__main__": args = get_parser_args() set_verbosity(args.verbosity) run(config_path=args.config_path)