The Virtual Brain Project

Source code for tvb.adapters.visualizers.surface_view

# -*- 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) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others
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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 numpy
from tvb.basic.filters.chain import UIFilter, FilterChain
from tvb.basic.traits.core import KWARG_FILTERS_UI
from tvb.core.adapters.abcdisplayer import ABCDisplayer
from tvb.core.entities.storage import dao
from tvb.datatypes.graph import ConnectivityMeasure
from tvb.datatypes.surfaces import FaceSurface
from tvb.datatypes.region_mapping import RegionMapping
from tvb.datatypes.surfaces import Surface


[docs]def prepare_shell_surface_urls(project_id, shell_surface=None, preferred_type=FaceSurface): if shell_surface is None: shell_surface = dao.try_load_last_entity_of_type(project_id, preferred_type) if not shell_surface: raise Exception('No Face object found in current project.') face_vertices, face_normals, _, face_triangles = shell_surface.get_urls_for_rendering() return json.dumps([face_vertices, face_normals, face_triangles])
[docs]class SurfaceViewer(ABCDisplayer): """ Static SurfaceData visualizer - for visual inspecting imported surfaces in TVB. Optionally it can display associated RegionMapping entities. """ _ui_name = "Surface Visualizer" _ui_subsection = "surface"
[docs] def get_input_tree(self): # todo: filter connectivity measures: same length as regions and 1-dimensional filters_ui = [UIFilter(linked_elem_name="region_map", linked_elem_field=FilterChain.datatype + "._surface"), # UIFilter(linked_elem_name="connectivity_measure", # linked_elem_field=FilterChain.datatype + "._surface") ] json_ui_filter = json.dumps([ui_filter.to_dict() for ui_filter in filters_ui]) return [{'name': 'surface', 'label': 'Brain surface', 'type': Surface, 'required': True, 'description': '', KWARG_FILTERS_UI: json_ui_filter}, {'name': 'region_map', 'label': 'Region mapping', 'type': RegionMapping, 'required': False, 'description': 'A region map'}, {'name': 'connectivity_measure', 'label': 'Connectivity measure', 'type': ConnectivityMeasure, 'required': False, 'description': 'A connectivity measure', 'conditions': FilterChain(fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[1])}, {'name': 'shell_surface', 'label': 'Shell Surface', 'type': Surface, 'required': False, 'description': "Face surface to be displayed semi-transparently, for orientation only."}]
@staticmethod def _compute_surface_params(surface, region_map): rendering_urls = [] # we want the URLs in json # But these string are going to be verbatim strings in js source code # This means that js will interpret escapes like \" so the json parser gets " # Double escape is needed \\" for url in surface.get_urls_for_rendering(True, region_map): escaped_url = json.dumps(url).replace('\\', '\\\\') rendering_urls.append(escaped_url) url_vertices, url_normals, url_lines, url_triangles, url_region_map = rendering_urls hemisphere_chunk_mask = surface.get_slices_to_hemisphere_mask() return dict(urlVertices=url_vertices, urlTriangles=url_triangles, urlLines=url_lines, urlNormals=url_normals, urlRegionMap=url_region_map, biHemispheric=surface.bi_hemispheric, hemisphereChunkMask=json.dumps(hemisphere_chunk_mask)) def _compute_measure_points_param(self, surface, region_map): if region_map is None: measure_points_no = 0 url_measure_points = '' url_measure_points_labels = '' boundary_url = '' else: measure_points_no = region_map.connectivity.number_of_regions url_measure_points = self.paths2url(region_map.connectivity, 'centres') url_measure_points_labels = self.paths2url(region_map.connectivity, 'region_labels') boundary_url = surface.get_url_for_region_boundaries(region_map) return dict(noOfMeasurePoints=measure_points_no, urlMeasurePoints=url_measure_points, urlMeasurePointsLabels=url_measure_points_labels, boundaryURL=boundary_url) def _compute_measure_param(self, connectivity_measure, measure_points_no): if connectivity_measure is None: # If there is no measure to show then we what to show the region mapping # The client will generate a range signal for this use case. min_measure = 0 max_measure = measure_points_no client_measure_url = '' else: if connectivity_measure.nr_dimensions != 1: raise ValueError("connectivity measure must be 1 dimensional") if connectivity_measure.length_1d != measure_points_no: raise ValueError("connectivity measure has %d values but the connectivity has %d " "regions" % (connectivity_measure.length_1d, measure_points_no)) min_measure = numpy.min(connectivity_measure.array_data) max_measure = numpy.max(connectivity_measure.array_data) # We assume here that the index 0 in the measure corresponds to # the region 0 of the region map. client_measure_url = self.paths2url(connectivity_measure, "array_data") return dict(minMeasure=min_measure, maxMeasure=max_measure, clientMeasureUrl=client_measure_url)
[docs] def launch(self, surface, region_map=None, connectivity_measure=None, shell_surface=None, title="Surface Visualizer"): params = dict(title=title, extended_view=False, isOneToOneMapping=False, hasRegionMap=region_map is not None) params.update(self._compute_surface_params(surface, region_map)) params.update(self._compute_measure_points_param(surface, region_map)) params.update(self._compute_measure_param(connectivity_measure, params['noOfMeasurePoints'])) try: params['shelfObject'] = prepare_shell_surface_urls(self.current_project_id, shell_surface) except Exception: params['shelfObject'] = None return self.build_display_result("surface/surface_view", params, pages={"controlPage": "surface/surface_viewer_controls"})
[docs] def get_required_memory_size(self): return -1
[docs]class RegionMappingViewer(SurfaceViewer): """ This is a viewer for RegionMapping DataTypes. It reuses almost everything from SurfaceViewer, but it make required another input param. """ _ui_name = "Region Mapping Visualizer" _ui_subsection = "surface"
[docs] def get_input_tree(self): base_tree = SurfaceViewer.get_input_tree(self) base_tree[1]['required'] = True base_tree.pop(0) return base_tree
[docs] def launch(self, region_map, connectivity_measure=None, shell_surface=None): return SurfaceViewer.launch(self, region_map.surface, region_map, connectivity_measure, shell_surface, title=RegionMappingViewer._ui_name)
[docs]class ConnectivityMeasureOnSurfaceViewer(SurfaceViewer): """ This displays a connectivity measure on a surface via a RegionMapping It reuses almost everything from SurfaceViewer, but it make required another input param. """ _ui_name = "Connectivity Measure Surface Visualizer" _ui_subsection = "surface"
[docs] def get_input_tree(self): base_tree = SurfaceViewer.get_input_tree(self) base_tree[2]['required'] = True tree = [base_tree[2], base_tree[1], base_tree[3]] return tree
[docs] def launch(self, connectivity_measure, region_map=None, shell_surface=None): if (region_map is None or region_map.connectivity.number_of_regions != connectivity_measure.connectivity.number_of_regions): # We have no regionmap or the onw we have is not compatible with the measure. # first try to find the associated region map region_maps = dao.get_generic_entity(RegionMapping, connectivity_measure.connectivity.gid, '_connectivity') if region_maps: region_map = region_maps[0] # else: todo fallback on any region map with the right number of nodes return SurfaceViewer.launch(self, region_map.surface, region_map, connectivity_measure, shell_surface, title=connectivity_measure.display_name)