# -*- 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:: Bogdan Neacsa <bogdan.neacsa@codemart.ro>
.. moduleauthor:: Ionel Ortelecan <ionel.ortelecan@codemart.ro>
"""
import json
from tvb.adapters.forms.model_forms import get_model_to_form_dict
from tvb.adapters.visualizers.surface_view import SurfaceURLGenerator
from tvb.basic.logger.builder import get_logger
from tvb.core.neocom import h5
from tvb.core.services.operation_service import OperationService
from tvb.interfaces.web.controllers import common
from tvb.interfaces.web.controllers.autologging import traced
from tvb.interfaces.web.controllers.base_controller import BaseController
from tvb.interfaces.web.controllers.common import MissingDataException
from tvb.interfaces.web.controllers.decorators import settings, expose_page, using_template
from tvb.interfaces.web.structure import WebStructure
PARAM_SURFACE = "surface"
[docs]@traced
class SpatioTemporalController(BaseController):
"""
Base class which contains methods related to spatio-temporal actions.
"""
MSG_MISSING_SURFACE = "There is no surface in the current project. Please upload a CORTICAL one to continue!"
def __init__(self):
BaseController.__init__(self)
self.operation_service = OperationService()
self.logger = get_logger(__name__)
editable_entities = [dict(link=self.build_path('/spatial/stimulus/region/step_1_submit/1/1'), title='Region Stimulus',
subsection='regionstim', description='Create a new Stimulus on Region level'),
dict(link=self.build_path('/spatial/stimulus/surface/step_1_submit/1/1'), title='Surface Stimulus',
subsection='surfacestim', description='Create a new Stimulus on Surface level')]
self.submenu_list = editable_entities
[docs] @expose_page
@settings
def index(self, **data):
"""
Displays the main page for the spatio temporal section.
"""
template_specification = {'title': "Spatio temporal", 'data': data, 'mainContent': 'header_menu'}
return self.fill_default_attributes(template_specification)
[docs] @staticmethod
def display_surface(surface_gid, region_mapping_gid=None):
"""
Generates the HTML for displaying the surface with the given ID.
"""
surface_h5 = h5.h5_file_for_gid(surface_gid)
if surface_h5 is None:
raise MissingDataException(SpatioTemporalController.MSG_MISSING_SURFACE + "!!")
common.add2session(PARAM_SURFACE, surface_gid)
url_vertices_pick, url_normals_pick, url_triangles_pick = SurfaceURLGenerator.get_urls_for_pick_rendering(
surface_h5)
url_vertices, url_normals, _, url_triangles, _ = SurfaceURLGenerator.get_urls_for_rendering(surface_h5,
region_mapping_gid)
surface_h5.close()
return {
'urlVerticesPick': json.dumps(url_vertices_pick),
'urlTrianglesPick': json.dumps(url_triangles_pick),
'urlNormalsPick': json.dumps(url_normals_pick),
'urlVertices': json.dumps(url_vertices),
'urlTriangles': json.dumps(url_triangles),
'urlNormals': json.dumps(url_normals),
'brainCenter': json.dumps(surface_h5.center())
}
[docs] @staticmethod
def get_series_json(data, label):
""" For each data point entry, build the FLOT specific JSON. """
return json.dumps([{'data': data, 'label': label}])
[docs] @staticmethod
def get_ui_message(list_of_equation_names):
"""
The message returned by this method should be displayed if
the equation with the given name couldn't be evaluated in all points.
"""
if list_of_equation_names:
return ("Could not evaluate the " + ", ".join(list_of_equation_names) + " equation(s) "
"in all the points. Some of the values were changed.")
else:
return ""
[docs] def fill_default_attributes(self, template_dictionary, subsection='stimulus'):
"""
Overwrite base controller to add required parameters for adapter templates.
"""
template_dictionary[common.KEY_SECTION] = WebStructure.SECTION_STIMULUS
template_dictionary[common.KEY_SUB_SECTION] = subsection
template_dictionary[common.KEY_SUBMENU_LIST] = self.submenu_list
template_dictionary[common.KEY_INCLUDE_RESOURCES] = 'spatial/included_resources'
BaseController.fill_default_attributes(self, template_dictionary)
return template_dictionary
[docs] def get_x_axis_range(self, min_x_str, max_x_str):
"""
Fill range for the X-axis displayed in 2D graph.
"""
try:
min_x = int(min_x_str)
except ValueError:
return 0, 100, "The min value for the x-axis should be an integer value."
try:
max_x = int(max_x_str)
except ValueError:
return 0, 100, "The max value for the x-axis should be an integer value."
if min_x >= max_x:
return 0, 100, "The min value for the x-axis should be smaller then the max value of the x-axis."
return min_x, max_x, ''
def _prepare_model_params_list(self, model):
model_form = get_model_to_form_dict().get(type(model))
model_params = model_form().get_params_configurable_in_phase_plane()
if len(model_params) == 0:
self.logger.warning("The list with configurable parameters for the current model is empty!")
return model_params
