The Virtual Brain Project

Source code for tvb.adapters.visualizers.pearson_edge_bundle

# -*- 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
# (c) 2012-2017, 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 <>.
# 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)

import json
import numpy
from tvb.core.adapters.abcdisplayer import ABCDisplayer
from tvb.datatypes.graph import CorrelationCoefficients

[docs]class PearsonEdgeBundle(ABCDisplayer): """ Viewer for Pearson CorrelationCoefficients. Very similar to the CrossCorrelationVisualizer - this one done with Matplotlib """ _ui_name = "Pearson Edge Bundle" _ui_subsection = "correlation_pearson_edge"
[docs] def get_input_tree(self): """ Inform caller of the data we need as input """ return [{"name": "datatype", "type": CorrelationCoefficients, "label": "Pearson Correlation to be displayed in a hierarchical edge bundle", "required": True}]
[docs] def get_required_memory_size(self, datatype): """Return required memory.""" input_size = datatype.read_data_shape() return * 8.0
[docs] def launch(self, datatype): """Construct data for visualization and launch it.""" matrix_shape = datatype.array_data.shape[0:2] parent_ts = datatype.source parent_ts = self.load_entity_by_gid(parent_ts.gid) labels = parent_ts.get_space_labels() state_list = parent_ts.labels_dimensions.get(parent_ts.labels_ordering[1], []) mode_list = range(parent_ts._length_4d) if not labels: labels = None pars = dict(matrix_labels=json.dumps(labels), matrix_shape=json.dumps(matrix_shape), viewer_title='Pearson Edge Bundle', url_base=ABCDisplayer.paths2url(datatype, "get_correlation_data", flatten="True", parameter=""), state_variable=0, mode=mode_list[0], state_list=state_list, mode_list=mode_list, pearson_min=CorrelationCoefficients.PEARSON_MIN, pearson_max=CorrelationCoefficients.PEARSON_MAX, thresh=0.5 ) return self.build_display_result("pearson_edge_bundle/view", pars)