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Source code for tvb.interfaces.web.controllers.burst.noise_configuration_controller

# -*- 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
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# This program is free software: you can redistribute it and/or modify it under the
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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)
#
#

"""
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""
import json

import cherrypy
from tvb.adapters.visualizers.connectivity import ConnectivityViewer
from tvb.core.entities import load
from tvb.core.services.burst_config_serialization import SerializationManager
from tvb.interfaces.web.controllers import common
from tvb.interfaces.web.controllers.autologging import traced
from tvb.interfaces.web.controllers.burst.base_controller import BurstBaseController
from tvb.interfaces.web.controllers.decorators import expose_page, handle_error, check_user
from tvb.interfaces.web.controllers.simulator.simulator_wizzard_urls import SimulatorWizzardURLs
from tvb.interfaces.web.entities.context_simulator import SimulatorContext


@traced
[docs]class NoiseConfigurationController(BurstBaseController): """ Controller class for placing noise parameters in nodes. """ def __init__(self): super(NoiseConfigurationController, self).__init__() self.simulator_context = SimulatorContext() @expose_page
[docs] def index(self): des = SerializationManager(self.simulator_context.simulator) conn_idx = load.load_entity_by_gid(des.conf.connectivity) model = des.conf.model integrator = des.conf.integrator state_vars = model.state_variables noise_values = self.init_noise_config_values(model, integrator, conn_idx) initial_noise = self.group_noise_array_by_state_var(noise_values, state_vars, conn_idx.number_of_regions) current_project = common.get_current_project() params = ConnectivityViewer.get_connectivity_parameters(conn_idx, current_project.name, str(conn_idx.fk_from_operation)) params.update({ 'title': 'Noise configuration', 'mainContent': 'burst/noise', 'isSingleMode': True, 'submit_parameters_url': '/burst/noise/submit', 'stateVars': state_vars, 'stateVarsJson': json.dumps(state_vars), 'noiseInputValues': initial_noise[0], 'initialNoiseValues': json.dumps(initial_noise) }) return self.fill_default_attributes(params, 'regionmodel')
@cherrypy.expose @handle_error(redirect=True) @check_user
[docs] def submit(self, node_values): """ Submit noise dispersions :param node_values: A map from state variable names to noise dispersion arrays. Ex {'V': [1,2...74]} """ des = SerializationManager(self.simulator_context.simulator) des.write_noise_parameters(json.loads(node_values)) self.simulator_context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_NOISE_PARAMS_URL) raise cherrypy.HTTPRedirect("/burst/")
@staticmethod
[docs] def group_noise_array_by_state_var(noise_values, state_vars, number_of_regions): initial_noise = [] for i in range(number_of_regions): node_noise = {} for sv_idx, sv in enumerate(state_vars): node_noise[sv] = noise_values[sv_idx][i] initial_noise.append(node_noise) return initial_noise
@staticmethod
[docs] def init_noise_config_values(model, integrator, connectivity): """ Initialize a state var x number of nodes array with noise values. """ state_variables = model.state_variables nr_nodes = connectivity.number_of_regions nr_state_vars = len(state_variables) try: nsig = integrator.noise.nsig noise_values = nsig.tolist() except AttributeError: # Just fallback to default return [[1 for _ in range(nr_nodes)] for _ in state_variables] if nsig.shape == (1,): # Only one number for noise return [noise_values * nr_nodes for _ in state_variables] elif nsig.shape == (nr_state_vars, 1) or nsig.shape == (nr_state_vars,): # Only one number per state variable return [[noise_values[idx]] * nr_nodes for idx in range(nr_state_vars)] elif nsig.shape == (nr_state_vars, nr_nodes): return noise_values else: raise ValueError("Got unexpected noise shape %s." % (nsig.shape,))