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Source code for tvb.adapters.simulator.range_parameters

# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
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# (c) 2012-2022, 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,
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# program.  If not, see <http://www.gnu.org/licenses/>.
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#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#
from collections import OrderedDict

from tvb.basic.neotraits.api import NArray, Range
from tvb.core.entities.transient.range_parameter import RangeParameter
from tvb.datatypes.connectivity import Connectivity
from tvb.datatypes.surfaces import Surface
from tvb.simulator.integrators import IntegratorStochastic
from tvb.simulator.simulator import Simulator


[docs]class SimulatorRangeParameters(object): def __init__(self, connectivity_filters=None, surface_filters=None, coupling=None, model=None, integrator_noise=None): self.connectivity_filters = connectivity_filters self.surface_filters = surface_filters self.coupling_parameters = coupling self.model_parameters = model self.integrator_noise_parameters = integrator_noise def _default_range_parameters(self): conduction_speed = RangeParameter(Simulator.conduction_speed.field_name, float, # TODO: Float should support ranges Range(lo=0.01, hi=100.0, step=1.0), isinstance(Simulator.conduction_speed, NArray)) connectivity = RangeParameter(Simulator.connectivity.field_name, Connectivity, self.connectivity_filters) return OrderedDict({Simulator.conduction_speed.field_name: conduction_speed, Simulator.connectivity.field_name: connectivity}) def _ensure_correct_prefix_for_param_name(self, prefix, param): prefix = prefix + '.' if not param.name.startswith(prefix): param_full_name = prefix + param.name param.name = param_full_name def _prepare_dynamic_parameters(self, param_prefix, param_list): dynamic_parameters = {} if param_list is None: return dynamic_parameters for param in param_list: self._ensure_correct_prefix_for_param_name(param_prefix, param) dynamic_parameters.update({param.name: param}) return dynamic_parameters def _prepare_model_parameters(self): return self._prepare_dynamic_parameters(Simulator.model.field_name, self.model_parameters) def _prepare_coupling_parameters(self): return self._prepare_dynamic_parameters(Simulator.coupling.field_name, self.coupling_parameters) def _prepare_integrator_noise_parameters(self): return self._prepare_dynamic_parameters( Simulator.integrator.field_name + '.' + IntegratorStochastic.noise.field_name, self.integrator_noise_parameters)
[docs] def get_all_range_parameters(self): all_range_parameters = self._default_range_parameters() all_range_parameters.update(self._prepare_coupling_parameters()) all_range_parameters.update(self._prepare_model_parameters()) all_range_parameters.update(self._prepare_integrator_noise_parameters()) return all_range_parameters
[docs] def add_connectivity_filter(self, filter): # TODO: add to FilterChain not to list if self.connectivity_filters is None: self.connectivity_filters = [] self.connectivity_filters.append(filter)
[docs] def add_surface_filter(self, filter): if self.surface_filters is None: self.surface_filters = [] self.surface_filters.append(filter)