Source code for tvb.simulator.models

# -*- 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
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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 <>


# 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()