# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2023, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program. If not, see <http://www.gnu.org/licenses/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
#
#
"""
A collection of neuronal dynamics models.
Specific models inherit from the abstract class Model.
.. moduleauthor:: Stuart A. Knock <Stuart@tvb.invalid>
.. moduleauthor:: Paula Sanz Leon <Paula@tvb.invalid>
.. moduleauthor:: Gaurav Malhotra <Gaurav@tvb.invalid>
.. moduleauthor:: Marmaduke Woodman <marmaduke.woodman@univ-amu.fr>
"""
# we don't import all models by default here, since they are time consuming
# to setup (e.g. numba gufunc compilation), but provide them as module-level
# properties for compatibility with previous version of TVB. For example
#
# import tvb.simulator.models.Epileptor
#
# works, but only lazily loads the tvb.simulator.models.epileptor module
# and returns the Epileptor class.
from enum import Enum
[docs]
class ModelsEnum(Enum):
BASE_MODEL = "Model"
EPILEPTOR = "Epileptor"
EPILEPTOR_2D = "Epileptor2D"
EPILEPTOR_RS = "EpileptorRestingState"
EPILEPTOR_CODIM_3 = "EpileptorCodim3"
EPILEPTOR_CODIM_3_SLOW = "EpileptorCodim3SlowMod"
HOPFIELD = "Hopfield"
JANSEN_RIT = "JansenRit"
ZETTERBERG_JANSEN = "ZetterbergJansen"
LARTER_BREAKSPEAR = "LarterBreakspear"
LINEAR = "Linear"
GENERIC_2D_OSCILLATOR = "Generic2dOscillator"
KURAMOTO = "Kuramoto"
SUP_HOPF = "SupHopf"
REDUCED_SET_FITZ_HUGH_NAGUMO = "ReducedSetFitzHughNagumo"
REDUCED_SET_HINDMARSH_ROSE = "ReducedSetHindmarshRose"
WILSON_COWAN = "WilsonCowan"
REDUCED_WONG_WANG = "ReducedWongWang"
REDUCED_WONG_WANG_EXC_INH = "ReducedWongWangExcInh"
ZERLAUT_FIRST_ORDER = "ZerlautAdaptationFirstOrder"
ZERLAUT_SECOND_ORDER = "ZerlautAdaptationSecondOrder"
MONTBRIO_PAZO_ROXIN = "MontbrioPazoRoxin"
COOMBES_BYRNE = "CoombesByrne"
COOMBES_BYRNE_2D = "CoombesByrne2D"
GAST_SCHMIDT_KNOSCHE_SD = "GastSchmidtKnosche_SD"
GAST_SCHMIDT_KNOSCHE_SF = "GastSchmidtKnosche_SF"
DUMONT_GUTKIN = "DumontGutkin"
DECO_BALANCED_EXC_INH = "DecoBalancedExcInh"
K_ION_EXCHANGE = "KIonEx"
[docs]
def get_class(self):
return _get_imported_model(self.value)
[docs]
@staticmethod
def get_base_model_subclasses():
return [model.get_class() for model in list(ModelsEnum) if model != ModelsEnum.BASE_MODEL]
def _get_imported_model(model):
import sys
# Imported modules
imported_modules = sys.modules['tvb.simulator.models']
try:
return getattr(imported_modules, model)
except AttributeError:
return None
_module_models = {
'base': [ModelsEnum.BASE_MODEL],
'epileptor': [ModelsEnum.EPILEPTOR, ModelsEnum.EPILEPTOR_2D],
'epileptor_rs': [ModelsEnum.EPILEPTOR_RS],
'epileptorcodim3': [ModelsEnum.EPILEPTOR_CODIM_3, ModelsEnum.EPILEPTOR_CODIM_3_SLOW],
'hopfield': [ModelsEnum.HOPFIELD],
'jansen_rit': [ModelsEnum.JANSEN_RIT, ModelsEnum.ZETTERBERG_JANSEN],
'larter_breakspear': [ModelsEnum.LARTER_BREAKSPEAR],
'linear': [ModelsEnum.LINEAR],
'oscillator': [ModelsEnum.GENERIC_2D_OSCILLATOR, ModelsEnum.KURAMOTO, ModelsEnum.SUP_HOPF],
'stefanescu_jirsa': [ModelsEnum.REDUCED_SET_HINDMARSH_ROSE, ModelsEnum.REDUCED_SET_FITZ_HUGH_NAGUMO],
'wilson_cowan': [ModelsEnum.WILSON_COWAN],
'wong_wang': [ModelsEnum.REDUCED_WONG_WANG],
'wong_wang_exc_inh': [ModelsEnum.REDUCED_WONG_WANG_EXC_INH, ModelsEnum.DECO_BALANCED_EXC_INH],
'zerlaut': [ModelsEnum.ZERLAUT_FIRST_ORDER, ModelsEnum.ZERLAUT_SECOND_ORDER],
'infinite_theta': [ModelsEnum.MONTBRIO_PAZO_ROXIN, ModelsEnum.COOMBES_BYRNE, ModelsEnum.COOMBES_BYRNE_2D, ModelsEnum.GAST_SCHMIDT_KNOSCHE_SF, ModelsEnum.GAST_SCHMIDT_KNOSCHE_SD, ModelsEnum.DUMONT_GUTKIN],
'k_ion_exchange': [ModelsEnum.K_ION_EXCHANGE],
}
def _find_lems_models():
import os, tvb.dsl
dsl_path = os.path.dirname(os.path.abspath(tvb.dsl.__file__))
xml_folder = os.path.join(dsl_path, 'NeuroML', 'XMLmodels')
for xml_filename in os.listdir(xml_folder):
# try to get model name
fullfilename = os.path.join(xml_folder, xml_filename)
print(fullfilename)
with open(fullfilename, 'r') as fd:
for line in fd.readlines():
if '<ComponentType name=' in line:
_, name_, *_ = line.strip().split()
_, name, _ = name_.split("=")[1].split('"')
break
def _delay_import_one(mod, model):
"""Create getter thunk for module and model name.
"""
import importlib
def do_import(_):
module_name = f'tvb.simulator.models.{mod}'
model_module = importlib.import_module(module_name)
return getattr(model_module, model)
return property(do_import)
def _delay_model_imports():
"""Set up this module with all properties for all models.
"""
# create substitute module class & object
class _Module:
pass
module = _Module()
module.__dict__ = globals()
# create properties for each model
for mod, models in _module_models.items():
for model in models:
setattr(_Module, model.value, _delay_import_one(mod, model.value))
# register module object
import sys
module._module = sys.modules[module.__name__]
module._pmodule = module
sys.modules[module.__name__] = module
_delay_model_imports()
