# -*- 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 to download
# TheVirtualBrain-Scientific Package (for simulators). 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
#
#
"""
.. moduleauthor:: Robert Vincze <robert.vincze@codemart.ro>
"""
import uuid
import cherrypy
from tvb.adapters.datatypes.db.graph import ConnectivityMeasureIndex
from tvb.adapters.forms.equation_forms import get_form_for_equation
from tvb.adapters.forms.equation_plot_forms import EquationPlotForm
from tvb.adapters.forms.transfer_vector_form import KEY_TRANSFER, TransferVectorForm
from tvb.adapters.visualizers.histogram import HistogramViewer
from tvb.core.entities.storage import dao
from tvb.core.neocom import h5
from tvb.interfaces.web.controllers.autologging import traced
from tvb.interfaces.web.controllers.base_controller import BaseController
from tvb.interfaces.web.controllers.decorators import expose_page, handle_error, check_user, expose_fragment, jsonify
from tvb.interfaces.web.controllers.simulator.simulator_wizzard_urls import SimulatorWizzardURLs
from tvb.interfaces.web.controllers.spatial.base_spatio_temporal_controller import SpatioTemporalController
from tvb.interfaces.web.entities.context_transfer_vector import TransferVectorContext, KEY_RESULT
from tvb.interfaces.web.entities.context_simulator import SimulatorContext
from tvb.interfaces.web.controllers import common
[docs]@traced
class TransferVectorController(SpatioTemporalController):
"""
Controller class for Applying a transfer function plus a ConnectivityMeasure DT
and producing a Spatial Vector distribution on Model parameters
"""
base_url = '/burst/transfer/'
title = 'Apply Spatial Vector on Model Parameter(s)'
def __init__(self):
super(TransferVectorController, self).__init__()
self.simulator_context = SimulatorContext()
[docs] def no_connectivity_measure_page(self):
params = ({
'title': self.title,
'mainContent': 'burst/transfer_function_apply_empty',
})
return self.fill_default_attributes(params)
[docs] @expose_page
def index(self):
sim_config = self.simulator_context.simulator
connectivity_measures = dao.get_generic_entity(ConnectivityMeasureIndex, sim_config.connectivity.hex,
"fk_connectivity_gid")
if not connectivity_measures:
return self.no_connectivity_measure_page()
model_params_list = self._prepare_model_params_list(self.simulator_context.simulator.model)
context = TransferVectorContext(TransferVectorForm.default_transfer_function.instance,
model_params_list[0].name,
uuid.UUID(connectivity_measures[-1].gid))
common.add2session(KEY_TRANSFER, context)
params = HistogramViewer().prepare_parameters(context.current_connectivity_measure)
config_form = TransferVectorForm(model_params_list)
config_form.model_param.data = context.current_model_param
config_form.connectivity_measure.data = context.current_connectivity_measure
config_form.transfer_function.data = type(context.current_transfer_function)
config_form.transfer_function.subform_field.form.fill_from_trait(context.current_transfer_function)
config_form = self.algorithm_service.prepare_adapter_form(form_instance=config_form)
eq_plot_form = EquationPlotForm()
params.update({'mainContent': 'burst/transfer_function_apply',
'submit_parameters_url': self.build_path('/burst/transfer/submit_model_parameter'),
'applyTransferFunctionForm': self.render_adapter_form(config_form),
'parametersTransferFunctionPlotForm': self.render_adapter_form(eq_plot_form),
'isSingleMode': False,
'title': self.title,
'baseUrl': self.base_url})
return self.fill_default_attributes(params)
[docs] @expose_fragment('spatial/equation_displayer')
def get_equation_chart(self, **form_data):
"""
Returns the html which contains the plot with the equation selected by the user for a certain model param.
"""
try:
plot_form = EquationPlotForm()
if form_data:
plot_form.fill_from_post(form_data)
min_x, max_x, ui_message = self.get_x_axis_range(plot_form.min_x.value, plot_form.max_x.value)
ontology_context = common.get_from_session(KEY_TRANSFER)
transfer_function = ontology_context.current_transfer_function
series_data, display_ui_message = transfer_function.get_series_data(min_range=min_x, max_range=max_x)
all_series = self.get_series_json(series_data, "vector")
ui_message = ''
if display_ui_message:
ui_message = self.get_ui_message(["vector"])
return {'allSeries': all_series, 'prefix': 'vector', 'message': ui_message}
except NameError as ex:
self.logger.exception(ex)
return {'allSeries': None, 'errorMsg': "Incorrect parameters for equation passed."}
except SyntaxError as ex:
self.logger.exception(ex)
return {'allSeries': None, 'errorMsg': "Some of the parameters hold invalid characters."}
except Exception as ex:
self.logger.exception(ex)
return {'allSeries': None, 'errorMsg': ex}
[docs] @cherrypy.expose
@handle_error(redirect=False)
def set_model_parameter(self, model_param):
ontology_context = common.get_from_session(KEY_TRANSFER)
ontology_context.current_model_param = model_param
[docs] @cherrypy.expose
@handle_error(redirect=False)
@jsonify
def set_connectivity_measure(self, connectivity_measure):
ontology_context = common.get_from_session(KEY_TRANSFER)
ontology_context.current_connectivity_measure = uuid.UUID(connectivity_measure)
result_dict = HistogramViewer().prepare_parameters(ontology_context.current_connectivity_measure)
return result_dict
[docs] @cherrypy.expose
@handle_error(redirect=False)
def set_transfer_function_param(self, **param):
ontology_context = common.get_from_session(KEY_TRANSFER)
eq_params_form_class = get_form_for_equation(type(ontology_context.current_transfer_function))
eq_params_form = eq_params_form_class()
eq_params_form.fill_from_trait(ontology_context.current_transfer_function)
eq_params_form.fill_from_post(param)
eq_params_form.fill_trait(ontology_context.current_transfer_function)
[docs] @cherrypy.expose
@handle_error(redirect=False)
@jsonify
def apply_transfer_function(self):
context = common.get_from_session(KEY_TRANSFER)
simulator = self.simulator_context.simulator
result = context.apply_transfer_function()
connectivity = h5.load_from_gid(simulator.connectivity)
result_dict = HistogramViewer().gather_params_dict(connectivity.region_labels.tolist(),
result.tolist(), self.title)
result_dict['applied_transfer_functions'] = context.get_applied_transfer_functions()
return result_dict
[docs] @cherrypy.expose
@handle_error(redirect=False)
@jsonify
def clear_histogram(self):
ontology_context = common.get_from_session(KEY_TRANSFER)
result_dict = HistogramViewer().prepare_parameters(ontology_context.current_connectivity_measure)
return result_dict
[docs] @cherrypy.expose
@handle_error(redirect=True)
@check_user
def submit_model_parameter(self, submit_action='cancel_action'):
if submit_action != "cancel_action":
ontology_model = common.get_from_session(KEY_TRANSFER)
for model_param, applied_tf in ontology_model.applied_transfer_functions.items():
setattr(self.simulator_context.simulator.model, model_param, applied_tf[KEY_RESULT])
self.simulator_context.add_last_loaded_form_url_to_session(SimulatorWizzardURLs.SET_INTEGRATOR_URL)
common.remove_from_session(KEY_TRANSFER)
self.redirect("/burst/")
[docs] def fill_default_attributes(self, template_dictionary, subsection='transfer'):
"""
Overwrite base controller to add required parameters for adapter templates.
"""
template_dictionary[common.KEY_SECTION] = 'burst'
template_dictionary[common.KEY_SUBMENU_LIST] = self.burst_submenu
template_dictionary[common.KEY_SUB_SECTION] = subsection
template_dictionary[common.KEY_INCLUDE_RESOURCES] = 'spatial/included_resources'
BaseController.fill_default_attributes(self, template_dictionary)
return template_dictionary
