The Virtual Brain Project

Source code for tvb.datatypes.noise_framework

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#  TheVirtualBrain-Scientific Package. This package holds all simulators, and 
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#   CITATION:
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#   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)
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"""
Module to handle framework specific methods related to noise sources.


.. moduleauthor:: Marmaduke Woodman <marmaduke.woodman@univ-amu.fr>

"""

import numpy.random

import tvb.basic.traits.parameters_factory as parameters_factory
from tvb.datatypes import equations
from tvb.simulator.noise import Noise

KEY_NOISE = "noise"
PARAMS_NOISE = (KEY_NOISE + '_parameters_')[:-1]
KEY_RANDOM_STREAM = "random_stream"
PARAMS_RANDOM_STREAM = (KEY_RANDOM_STREAM + '_parameters_')[:-1]
KEY_EQUATION = "b"
PARAMS_EQUATION = "b_parameters"


[docs]def build_noise(parent_parameters): """ Build Noise entity from dictionary of parameters. :param parent_parameters: dictionary of parameters for the entity having Noise as attribute. \ The dictionary is after UI form-submit and framework pre-process. :return: Noise entity. """ if KEY_NOISE not in parent_parameters: return None available_noise = parameters_factory.get_traited_subclasses(Noise) if 'Noise' not in available_noise: available_noise['Noise'] = Noise selected_noise = parent_parameters[KEY_NOISE] noise_params = parent_parameters[PARAMS_NOISE] del parent_parameters[KEY_NOISE] del parent_parameters[PARAMS_NOISE] if PARAMS_RANDOM_STREAM in noise_params: stream_params = noise_params[PARAMS_RANDOM_STREAM] random_stream = numpy.random.RandomState(seed=stream_params['init_seed']) del noise_params[PARAMS_RANDOM_STREAM] del noise_params[KEY_RANDOM_STREAM] noise_params[KEY_RANDOM_STREAM] = random_stream if PARAMS_EQUATION in noise_params: available_equations = parameters_factory.get_traited_subclasses(equations.Equation) eq_parameters = noise_params[PARAMS_EQUATION]["parameters"] equation = noise_params[KEY_EQUATION] equation = available_equations[equation](parameters=eq_parameters) del noise_params[PARAMS_EQUATION] del noise_params[KEY_EQUATION] noise_params[KEY_EQUATION] = equation noise_entity = available_noise[str(selected_noise)](**noise_params) parent_parameters[KEY_NOISE] = noise_entity return noise_entity