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Source code for tvb.interfaces.web.controllers.spatial.base_spatio_temporal_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
#
# (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,
# 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 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:: Bogdan Neacsa <bogdan.neacsa@codemart.ro>
.. moduleauthor:: Ionel Ortelecan <ionel.ortelecan@codemart.ro>
"""

import json

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

PARAM_SURFACE = "surface"


@traced
[docs]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='/spatial/stimulus/region/step_1_submit/1/1', title='Region Stimulus', subsection='regionstim', description='Create a new Stimulus on Region level'), dict(link='/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 @expose_page @settings
[docs] 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)
@staticmethod
[docs] 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()) }
@staticmethod
[docs] def get_series_json(data, label): """ For each data point entry, build the FLOT specific JSON. """ return json.dumps([{'data': data, 'label': label}])
@staticmethod
[docs] 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] = '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, ''
@using_template('spatial/spatial_fragment')
[docs] def render_spatial_form(self, adapter_form): show_online_help = common.get_logged_user().is_online_help_active() rendering_dict = adapter_form.get_rendering_dict() rendering_dict.update({'showOnlineHelp': show_online_help}) rendering_dict.update({'isCallout': False}) return rendering_dict