TheVirtualBrain:

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Source code for tvb.adapters.visualizers.annotations_viewer

# -*- 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) 2012-2020, 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,
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# program.  If not, see <http://www.gnu.org/licenses/>.
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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:: Lia Domide <lia.domide@codemart.ro>
"""

import json
from tvb.adapters.datatypes.h5.surface_h5 import SurfaceH5
from tvb.adapters.visualizers.surface_view import ABCSurfaceDisplayer, SurfaceURLGenerator
from tvb.adapters.datatypes.db.region_mapping import RegionMappingIndex
from tvb.adapters.datatypes.db.annotation import *
from tvb.core.neocom import h5
from tvb.core.adapters.abcadapter import ABCAdapterForm
from tvb.core.adapters.abcdisplayer import URLGenerator
from tvb.core.adapters.exceptions import LaunchException
from tvb.core.entities.storage import dao
from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr
from tvb.core.neotraits.forms import TraitDataTypeSelectField
from tvb.datatypes.connectivity import Connectivity
from tvb.datatypes.region_mapping import RegionMapping


[docs]class ConnectivityAnnotationsViewModel(ViewModel): connectivity_index = DataTypeGidAttr( linked_datatype=Connectivity, required=False, label='Large Scale Connectivity Matrix' ) annotations_index = DataTypeGidAttr( linked_datatype=ConnectivityAnnotations, label='Ontology Annotations' ) region_mapping_index = DataTypeGidAttr( linked_datatype=RegionMapping, required=False, label='Region mapping', doc='A region map to identify us the Cortical Surface to display, as well as how the mapping ' 'from Connectivity to Cortex is done ' )
[docs]class ConnectivityAnnotationsViewForm(ABCAdapterForm): def __init__(self, prefix='', project_id=None): super(ConnectivityAnnotationsViewForm, self).__init__(prefix, project_id) # Used for filtering self.connectivity_index = TraitDataTypeSelectField(ConnectivityAnnotationsViewModel.connectivity_index, self, 'connectivity_index') self.annotations_index = TraitDataTypeSelectField(ConnectivityAnnotationsViewModel.annotations_index, self, 'annotations_index', conditions=self.get_filters()) self.region_mapping_index = TraitDataTypeSelectField(ConnectivityAnnotationsViewModel.region_mapping_index, self, 'region_mapping_index') @staticmethod
[docs] def get_view_model(): return ConnectivityAnnotationsViewModel
@staticmethod
[docs] def get_required_datatype(): return ConnectivityAnnotationsIndex
@staticmethod
[docs] def get_input_name(): return 'annotations_index'
@staticmethod
[docs] def get_filters(): # filters_ui = [UIFilter(linked_elem_name="annotations", # linked_elem_field=FilterChain.datatype + "._connectivity"), # UIFilter(linked_elem_name="region_map", # linked_elem_field=FilterChain.datatype + "._connectivity"), # UIFilter(linked_elem_name="connectivity_measure", # linked_elem_field=FilterChain.datatype + "._connectivity")] # # json_ui_filter = json.dumps([ui_filter.to_dict() for ui_filter in filters_ui]) return None
[docs]class ConnectivityAnnotationsView(ABCSurfaceDisplayer): """ Given a Connectivity Matrix and a Surface data the viewer will display the matrix 'inside' the surface data. The surface is only displayed as a shadow. """ _ui_name = "Annotations Visualizer" _ui_subsection = "annotations"
[docs] def get_form_class(self): return ConnectivityAnnotationsViewForm
[docs] def get_required_memory_size(self, view_model): # type: (ConnectivityAnnotationsViewModel) -> int return -1
[docs] def launch(self, view_model): # type: (ConnectivityAnnotationsViewModel) -> dict annotations_index = self.load_entity_by_gid(view_model.annotations_index) if view_model.connectivity_index is None: connectivity_index = self.load_entity_by_gid(annotations_index.fk_connectivity_gid) else: connectivity_index = self.load_entity_by_gid(view_model.connectivity_index) if view_model.region_mapping_index is None: region_map = dao.get_generic_entity(RegionMappingIndex, connectivity_index.gid, 'fk_connectivity_gid') if len(region_map) < 1: raise LaunchException( "Can not launch this viewer unless we have at least a RegionMapping for the current Connectivity!") region_mapping_index = region_map[0] else: region_mapping_index = self.load_entity_by_gid(view_model.region_mapping_index) boundary_url = SurfaceURLGenerator.get_url_for_region_boundaries(region_mapping_index.fk_surface_gid, region_mapping_index.gid, self.stored_adapter.id) surface_index = self.load_entity_by_gid(region_mapping_index.fk_surface_gid) surface_h5 = h5.h5_file_for_index(surface_index) assert isinstance(surface_h5, SurfaceH5) url_vertices_pick, url_normals_pick, url_triangles_pick = SurfaceURLGenerator.get_urls_for_pick_rendering( surface_h5) url_vertices, url_normals, _, url_triangles, url_region_map = SurfaceURLGenerator.get_urls_for_rendering( surface_h5, region_mapping_index.gid) params = dict(title="Connectivity Annotations Visualizer", annotationsTreeUrl=URLGenerator.build_url(self.stored_adapter.id, 'tree_json', view_model.annotations_index), urlTriangleToRegion=URLGenerator.build_url(self.stored_adapter.id, "get_triangles_mapping", region_mapping_index.gid), urlActivationPatterns=URLGenerator.paths2url(view_model.annotations_index, "get_activation_patterns"), minValue=0, maxValue=connectivity_index.number_of_regions - 1, urlColors=json.dumps(url_region_map), urlVerticesPick=json.dumps(url_vertices_pick), urlTrianglesPick=json.dumps(url_triangles_pick), urlNormalsPick=json.dumps(url_normals_pick), brainCenter=json.dumps(surface_h5.center()), urlVertices=json.dumps(url_vertices), urlTriangles=json.dumps(url_triangles), urlNormals=json.dumps(url_normals), urlRegionBoundaries=boundary_url) return self.build_display_result("annotations/annotations_view", params, pages={"controlPage": "annotations/annotations_controls"})
def _get_activation_pattern_labels(self, annotations): """ :return: map {brco_id: list of TVB regions LABELS in which the same BRCO term is being subclass} """ map_with_ids = annotations.get_activation_patterns() map_with_labels = dict() for ann_id, activated_ids in list(map_with_ids.items()): map_with_labels[ann_id] = [] for string_idx in activated_ids: int_idx = int(string_idx) conn_label = annotations.connectivity.region_labels[int_idx] map_with_labels[ann_id].append(conn_label) return map_with_labels
[docs] def tree_json(self, annotations_gid): """ :return: JSON to be rendered in a Tree of entities """ annotations = self.load_with_references(annotations_gid) annotations_map = dict() regions_map = dict() for i in range(annotations.connectivity.number_of_regions): regions_map[i] = [] for ann in annotations.region_annotations: ann_obj = AnnotationTerm(ann[0], ann[1], ann[2], ann[3], ann[4], ann[5], ann[6], ann[7], ann[8], ann[9], ann[10]) annotations_map[ann_obj.id] = ann_obj if ann_obj.parent_id < 0: # Root directly under a TVB region node regions_map[ann_obj.parent_left].append(ann_obj) regions_map[ann_obj.parent_right].append(ann_obj) elif ann_obj.parent_id in annotations_map: annotations_map[ann_obj.parent_id].add_child(ann_obj) else: self.logger.warning("Order of processing invalid parent %s child %s" % (ann_obj.parent_id, ann_obj.id)) left_nodes, right_nodes = [], [] activation_patterns = self._get_activation_pattern_labels(annotations) for region_idx, annotations_list in list(regions_map.items()): if_right_hemisphere = annotations.connectivity.is_right_hemisphere(region_idx) childred_json = [] for ann_term in annotations_list: childred_json.append(ann_term.to_json(if_right_hemisphere, activation_patterns)) # This node is built for every TVB region child_json = dict(data=dict(icon=ICON_TVB, title=annotations.connectivity.region_labels[region_idx]), attr=dict(id=NODE_ID_TVB_ROOT + str(region_idx), title=str(region_idx) + " - " + annotations.connectivity.region_labels[ region_idx]), state="close", children=childred_json) if if_right_hemisphere: right_nodes.append(child_json) else: left_nodes.append(child_json) # Group everything under a single root left_root = dict(data=dict(title="Left Hemisphere", icon=ICON_FOLDER), state="open", children=left_nodes) right_root = dict(data=dict(title="Right Hemisphere", icon=ICON_FOLDER), state="open", children=right_nodes) root_root = dict(data=dict(title="Connectivity Annotations", icon=ICON_FOLDER), state="open", children=[left_root, right_root]) return root_root
[docs] def get_triangles_mapping(self, region_mapping_gid): """ :return Numpy array of length triangles and for each the region corresponding to one of its vertices. """ region_mapping = self.load_with_references(region_mapping_gid) triangles_no = region_mapping.surface.number_of_triangles result = [] for i in range(triangles_no): result.append(region_mapping.array_data[region_mapping.surface.triangles[i][0]]) return result