Source code for emodelrunner.create_hoc

"""Creates .hoc from cell."""

# 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 os
import shutil

from emodelrunner.load import (
from emodelrunner.create_cells import create_cell_using_config
from emodelrunner.create_hoc_tools import (
from emodelrunner.parsing_utilities import get_parser_args, set_verbosity

[docs] def write_hoc(hoc_dir, hoc_file_name, hoc): """Write hoc file. Args: hoc_dir (str): directory to write the file in hoc_file_name (str): name to give to the file hoc (str): content of the file """ hoc_path = os.path.join(hoc_dir, hoc_file_name) with open(hoc_path, "w", encoding="utf-8") as hoc_file: hoc_file.write(hoc)
[docs] def write_hocs( hoc_paths, cell_hoc, simul_hoc, run_hoc, syn_hoc=None, main_protocol_hoc=None ): """Write hoc files. Args: hoc_paths (HocPaths): contains paths of the hoc files to be created cell_hoc (str): content of the cell hoc file simul_hoc (str): content of the 'create simulation' hoc file run_hoc (str): content of the hoc file meant to run the simulation syn_hoc (str): content of the synapses hoc file main_protocol_hoc (str): content of the main protocol hoc file """ # cell hoc write_hoc(hoc_paths.hoc_dir, hoc_paths.cell_hoc_filename, cell_hoc) # createsimulation.hoc write_hoc(hoc_paths.hoc_dir, hoc_paths.simul_hoc_filename, simul_hoc) # run.hoc write_hoc(hoc_paths.hoc_dir, hoc_paths.run_hoc_filename, run_hoc) # synapses hoc if syn_hoc is not None: write_hoc(hoc_paths.syn_dir, hoc_paths.syn_hoc_filename, syn_hoc) # main protocol hoc if main_protocol_hoc is not None: write_hoc( hoc_paths.hoc_dir, hoc_paths.main_protocol_filename, main_protocol_hoc )
[docs] def get_hoc(config): """Return the hoc scripts as strings. Args: config (configparser.ConfigParser): configuration Raises: KeyError: If no voltage_base feature is found for Rin in feature file Returns: (str, str, str, str): cell_hoc, syn_hoc, simul_hoc, run_hoc the hoc scripts for the cell, the synapses, the simulation and the run_launcher. syn_hoc is None if the synapses were not added """ # pylint: disable=too-many-locals # get directories and filenames from config cell_template_path = config.get("Paths", "cell_template_path") run_hoc_template_path = config.get("Paths", "run_hoc_template_path") createsimulation_template_path = config.get( "Paths", "createsimulation_template_path" ) synapses_template_path = config.get("Paths", "synapses_template_path") main_protocol_template_path = config.get("Paths", "main_protocol_template_path") add_synapses = config.getboolean("Synapses", "add_synapses") syn_temp_name = config.get("Synapses", "hoc_synapse_template_name") hoc_paths = config.hoc_paths_args() apical_point_isec = config.get("Protocol", "apical_point_isec") constants_args = { "emodel": config.get("Cell", "emodel"), "morph_path": config.get("Paths", "morph_path"), "gid": config.getint("Cell", "gid"), "dt": config.getfloat("Sim", "dt"), "celsius": config.getfloat("Cell", "celsius"), "v_init": config.getfloat("Cell", "v_init"), "mtype": config.get("Morphology", "mtype"), } # get the protocols definitions protocols_filename = config.get("Paths", "prot_path") with open(protocols_filename, "r", encoding="utf-8") as protocol_file: protocol_definitions = json.load(protocol_file) if "__comment" in protocol_definitions: del protocol_definitions["__comment"] # handle MainProtocol case if "Main" in protocol_definitions.keys(): main_protocol = True new_prot_defs = {} for prot in protocol_definitions["Main"]["pre_protocols"]: new_prot_defs[prot] = protocol_definitions[prot] for prot in protocol_definitions["Main"]["other_protocols"]: new_prot_defs[prot] = protocol_definitions[prot] else: main_protocol = False new_prot_defs = protocol_definitions # get cell cell = create_cell_using_config(config) release_params = get_release_params(config) # get cell hoc cell_hoc = cell.create_custom_hoc( release_params, template_path=cell_template_path, syn_dir=hoc_paths.syn_dir_for_hoc, syn_hoc_filename=hoc_paths.syn_hoc_filename, syn_temp_name=syn_temp_name, ) simul_hoc = create_simul_hoc( template_path=createsimulation_template_path, add_synapses=add_synapses, hoc_paths=hoc_paths, constants_args=constants_args, protocol_definitions=new_prot_defs, apical_point_isec=apical_point_isec, ) run_hoc = create_run_hoc( template_path=run_hoc_template_path, main_protocol=main_protocol, ) if main_protocol: rin_exp_voltage_base = get_rin_exp_voltage_base( config.get("Paths", "features_path") ) main_protocol_hoc = create_main_protocol_hoc( template_path=main_protocol_template_path, protocol_definitions=protocol_definitions, rin_exp_voltage_base=rin_exp_voltage_base, mtype=constants_args["mtype"], ) else: main_protocol_hoc = None # get synapse hoc if cell.add_synapses: # load synapse config data syn_mech_args = config.syn_mech_args() # get synapse hoc syn_hoc = create_synapse_hoc( syn_mech_args=syn_mech_args, syn_hoc_dir=hoc_paths.syn_dir_for_hoc, template_path=synapses_template_path, gid=cell.gid, dt=constants_args["dt"], synapses_template_name=syn_temp_name, ) else: syn_hoc = None return cell_hoc, syn_hoc, simul_hoc, run_hoc, main_protocol_hoc
[docs] def copy_features_hoc(config): """Copy features hoc file into cell directory.""" features_original_path = config.get("Paths", "features_hoc_template_path") features_new_path = os.path.join( config.get("Paths", "memodel_dir"), config.get("Paths", "features_hoc_file") ) shutil.copy(features_original_path, features_new_path)
if __name__ == "__main__": args = get_parser_args() set_verbosity(args.verbosity) config_ = load_config(config_path=args.config_path) cell_hoc_, syn_hoc_, simul_hoc_, run_hoc_, main_protocol_hoc_ = get_hoc( config=config_ ) hoc_paths_ = config_.hoc_paths_args() if main_protocol_hoc_: copy_features_hoc(config_) write_hocs( hoc_paths_, cell_hoc_, simul_hoc_, run_hoc_, syn_hoc_, main_protocol_hoc_, )