TheVirtualBrain:

TheDocumentationwebsite.

Source code for tvb.adapters.visualizers.connectivity

# -*- 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,
# 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:: Lia Domide <lia.domide@codemart.ro>
.. moduleauthor:: Bogdan Neacsa <bogdan.neacsa@codemart.ro>
"""

import json
import math
import numpy
from copy import copy
from tvb.adapters.visualizers.time_series import ABCSpaceDisplayer
from tvb.adapters.visualizers.surface_view import SurfaceURLGenerator
from tvb.basic.neotraits.api import Attr
from tvb.config import CONNECTIVITY_CREATOR_MODULE, CONNECTIVITY_CREATOR_CLASS
from tvb.core.adapters.abcadapter import ABCAdapterForm
from tvb.core.adapters.abcdisplayer import ABCDisplayer
from tvb.core.adapters.exceptions import LaunchException
from tvb.core.entities.filters.chain import FilterChain
from tvb.adapters.datatypes.db.connectivity import ConnectivityIndex
from tvb.core.entities.load import load_entity_by_gid
from tvb.core.neotraits.forms import TraitDataTypeSelectField, FloatField
from tvb.core.neocom import h5
from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr
from tvb.core.services.algorithm_service import AlgorithmService
from tvb.datatypes.connectivity import Connectivity
from tvb.datatypes.graph import ConnectivityMeasure
from tvb.datatypes.surfaces import Surface


[docs]class ConnectivityViewerModel(ViewModel): """ Attributes meaning: connectivity: GID towards the `Connectivity` object which will be displayed surface_data: if provided, it is displayed as a shadow to give an idea of the connectivity position relative to the full brain cortical surface colors: used to establish a colormap for the nodes displayed in 2D Connectivity viewers rays: used to establish the size of the spheres representing each node in 3D Nodes viewer step: a threshold applied to the 2D Connectivity Viewers to differentiate 2 types of nodes the ones with a value greater that this will be displayed as red discs, instead of yellow """ connectivity = DataTypeGidAttr( linked_datatype=Connectivity, label='Connectivity Matrix' ) surface_data = DataTypeGidAttr( linked_datatype=Surface, required=False, label='Brain Surface', doc='The Brain Surface is used to give you an idea of the connectivity ' 'position relative to the full brain cortical surface. This surface' ' will be displayed as a shadow (only used in 3D Edges tab).' ) step = Attr( field_type=float, required=False, label='Color Threshold', doc='All nodes with a value greater or equal (>=) than this threshold will be ' 'displayed as red discs, otherwise (<) they will be yellow. (This applies to ' '2D Connectivity tabs and the threshold will depend on the metric used to set ' 'the Node Color)' ) colors = DataTypeGidAttr( linked_datatype=ConnectivityMeasure, required=False, label='Node Colors', doc='A ConnectivityMeasure DataType that establishes a colormap for the nodes displayed ' 'in the 2D Connectivity tabs.' ) rays = DataTypeGidAttr( linked_datatype=ConnectivityMeasure, required=False, label='Shapes Dimensions', doc='A ConnectivityMeasure datatype used to establish the size of the spheres representing each node. ' '(It only applies to 3D Nodes tab).' )
[docs]class ConnectivityViewerForm(ABCAdapterForm): def __init__(self, prefix='', project_id=None): super(ConnectivityViewerForm, self).__init__(prefix, project_id) # filters_ui = [UIFilter(linked_elem_name="colors", # linked_elem_field=FilterChain.datatype + "._connectivity"), # UIFilter(linked_elem_name="rays", # linked_elem_field=FilterChain.datatype + "._connectivity")] # json_ui_filter = json.dumps([ui_filter.to_dict() for ui_filter in filters_ui]) # KWARG_FILTERS_UI: json_ui_filter self.connectivity = TraitDataTypeSelectField(ConnectivityViewerModel.connectivity, self, name='input_data', conditions=self.get_filters()) surface_conditions = FilterChain(fields=[FilterChain.datatype + '.surface_type'], operations=["=="], values=['Cortical Surface']) self.surface_data = TraitDataTypeSelectField(ConnectivityViewerModel.surface_data, self, name='surface_data', conditions=surface_conditions) self.step = FloatField(ConnectivityViewerModel.step, self, name='step') colors_conditions = FilterChain(fields=[FilterChain.datatype + '.ndim'], operations=["=="], values=[1]) self.colors = TraitDataTypeSelectField(ConnectivityViewerModel.colors, self, name='colors', conditions=colors_conditions) rays_conditions = FilterChain(fields=[FilterChain.datatype + '.ndim'], operations=["=="], values=[1]) self.rays = TraitDataTypeSelectField(ConnectivityViewerModel.rays, self, name='rays', conditions=rays_conditions) @staticmethod
[docs] def get_view_model(): return ConnectivityViewerModel
@staticmethod
[docs] def get_required_datatype(): return ConnectivityIndex
@staticmethod
[docs] def get_filters(): return None
@staticmethod
[docs] def get_input_name(): return "input_data"
[docs]class ConnectivityViewer(ABCSpaceDisplayer): """ 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 = "Connectivity Visualizer"
[docs] def get_form_class(self): return ConnectivityViewerForm
[docs] def get_required_memory_size(self, view_model): # type: (ConnectivityViewerModel) -> int """ Return the required memory to run this algorithm. """ surface_index = self.load_entity_by_gid(view_model.surface_data) if surface_index is not None: # Nr of triangles * sizeOf(uint16) + (nr of vertices + nr of normals) * sizeOf(float) return surface_index.number_of_vertices * 6 * 4 + surface_index.number_of_vertices * 6 * 8 # If no surface pass, assume enough memory should be available. return -1
def _load_input_data(self, view_model): connectivity = self.load_traited_by_gid(view_model.connectivity) assert isinstance(connectivity, Connectivity) if view_model.colors: colors_dt = self.load_traited_by_gid(view_model.colors) else: colors_dt = None if view_model.rays: rays_dt = self.load_traited_by_gid(view_model.rays) else: rays_dt = None return connectivity, colors_dt, rays_dt
[docs] def launch(self, view_model): # type: (ConnectivityViewerModel) -> dict """ Given the input connectivity data and the surface data, build the HTML response to be displayed. """ connectivity, colors, rays = self._load_input_data(view_model) global_params, global_pages = self._compute_connectivity_global_params(connectivity) if view_model.surface_data is not None: surface_index = load_entity_by_gid(view_model.surface_data.hex) surface_h5 = h5.h5_file_for_index(surface_index) url_vertices, url_normals, _, url_triangles, _ = SurfaceURLGenerator.get_urls_for_rendering(surface_h5) else: url_vertices, url_normals, url_triangles = [], [], [] global_params["urlVertices"] = json.dumps(url_vertices) global_params["urlTriangles"] = json.dumps(url_triangles) global_params["urlNormals"] = json.dumps(url_normals) global_params['isSingleMode'] = False result_params, result_pages = Connectivity2DViewer().compute_parameters(connectivity, colors, rays, view_model.step) result_params.update(global_params) result_pages.update(global_pages) _params, _pages = Connectivity3DViewer().compute_parameters(connectivity, colors, rays) result_params.update(_params) result_pages.update(_pages) return self.build_display_result("connectivity/main_connectivity", result_params, result_pages)
[docs] def generate_preview(self, view_model, figure_size=None): # type: (ConnectivityViewerModel, (int,int)) -> dict """ Generate the preview for the BURST cockpit. see `launch_` """ connectivity, colors, rays = self._load_input_data(view_model) parameters, _ = Connectivity2DViewer().compute_preview_parameters(connectivity, figure_size[0], figure_size[1], colors, rays, view_model.step) return self.build_display_result("connectivity/portlet_preview", parameters)
@staticmethod def _compute_matrix_extrema(m): """Returns the min max and the minimal nonzero value from ``m``""" minv = float('inf') min_nonzero = float('inf') maxv = - float('inf') for data in m: for d in data: minv = min(minv, d) maxv = max(maxv, d) if d != 0: min_nonzero = min(min_nonzero, d) return minv, maxv, min_nonzero def _compute_connectivity_global_params(self, connectivity): """ Returns a dictionary which contains the data needed for drawing a connectivity. :param connectivity: the `Connectivity(HasTraits)` object """ conn_gid = connectivity.gid.hex path_weights = SurfaceURLGenerator.paths2url(conn_gid, 'ordered_weights') path_pos = SurfaceURLGenerator.paths2url(conn_gid, 'ordered_centres') path_tracts = SurfaceURLGenerator.paths2url(conn_gid, 'ordered_tracts') path_labels = SurfaceURLGenerator.paths2url(conn_gid, 'ordered_labels') path_hemisphere_order_indices = SurfaceURLGenerator.paths2url(conn_gid, 'hemisphere_order_indices') algo = AlgorithmService().get_algorithm_by_module_and_class(CONNECTIVITY_CREATOR_MODULE, CONNECTIVITY_CREATOR_CLASS) submit_url = '/{}/{}/{}'.format(SurfaceURLGenerator.FLOW, algo.fk_category, algo.id) global_pages = dict(controlPage="connectivity/top_right_controls") minimum, maximum, minimum_non_zero = self._compute_matrix_extrema(connectivity.ordered_weights) minimum_t, maximum_t, minimum_non_zero_t = self._compute_matrix_extrema(connectivity.ordered_tracts) global_params = dict(urlWeights=path_weights, urlPositions=path_pos, urlTracts=path_tracts, urlLabels=path_labels, originalConnectivity=conn_gid, title="Connectivity Control", submitURL=submit_url, positions=connectivity.ordered_centres, tractsMin=minimum_t, tractsMax=maximum_t, weightsMin=minimum, weightsMax=maximum, tractsNonZeroMin=minimum_non_zero_t, weightsNonZeroMin=minimum_non_zero, pointsLabels=connectivity.ordered_labels, conductionSpeed=1, connectivity_entity=connectivity, base_selection=connectivity.saved_selection_labels, hemisphereOrderUrl=path_hemisphere_order_indices, leftHemisphereCount=(connectivity.hemispheres == 0).sum() ) global_params.update(self.build_params_for_selectable_connectivity(connectivity)) return global_params, global_pages @staticmethod
[docs] def get_connectivity_parameters(input_connectivity, conn_path): """ Returns a dictionary which contains all the needed data for drawing a connectivity. """ viewer = ConnectivityViewer() viewer.storage_path = conn_path conn_dt = h5.load_from_index(input_connectivity) assert isinstance(conn_dt, Connectivity) global_params, global_pages = viewer._compute_connectivity_global_params(conn_dt) global_params.update(global_pages) global_params['selectedConnectivityGid'] = input_connectivity.gid return global_params # # -------------------- Connectivity 3D code starting -------------------
[docs]class Connectivity3DViewer(object): """ Behavior for the HTML/JS 3D representation of the connectivity matrix. """ @staticmethod
[docs] def compute_parameters(input_data, colors=None, rays=None): """ Having as inputs a Connectivity matrix(required) and two arrays that represent the rays and colors of the nodes from the matrix(optional) this method will build the required parameter dictionary that will be sent to the HTML/JS 3D representation of the connectivity matrix. """ if colors is not None: color_list = colors.array_data.tolist() color_list = ABCDisplayer.get_one_dimensional_list(color_list, input_data.number_of_regions, "Invalid input size for Sphere Colors") color_list = numpy.nan_to_num(numpy.array(color_list, dtype=numpy.float64)).tolist() else: color_list = [1.0] * input_data.number_of_regions if rays is not None: rays_list = rays.array_data.tolist() rays_list = ABCDisplayer.get_one_dimensional_list(rays_list, input_data.number_of_regions, "Invalid input size for Sphere Sizes") rays_list = numpy.nan_to_num(numpy.array(rays_list, dtype=numpy.float64)).tolist() else: rays_list = [1.0] * input_data.number_of_regions params = dict(raysArray=json.dumps(rays_list), rayMin=min(rays_list), rayMax=max(rays_list), colorsArray=json.dumps(color_list), colorMin=min(color_list), colorMax=max(color_list)) return params, {} # -------------------- Connectivity 2D code starting ------------------
X_CANVAS_SMALL = 280 Y_CANVAS_SMALL = 145 X_CANVAS_FULL = 280 Y_CANVAS_FULL = 300
[docs]class Connectivity2DViewer(object): """ Having as inputs a Connectivity matrix(required) and two arrays that represent the colors and shapes of the nodes from the matrix(optional) the viewer will build the required parameter dictionary that will be sent to the HTML/JS 2D representation of the connectivity matrix. """ DEFAULT_COLOR = '#d73027' OTHER_COLOR = '#1a9850' MIN_RAY = 4 MAX_RAY = 40 MIN_WEIGHT_VALUE = 0.0 MAX_WEIGHT_VALUE = 0.6
[docs] def compute_parameters(self, input_data, colors=None, rays=None, step=None): """ Build the required HTML response to be displayed. :raises LaunchException: when number of regions in input_data is less than 3 """ if input_data.number_of_regions <= 3: raise LaunchException('The connectivity matrix you selected has fewer nodes than acceptable for display!') normalized_weights = self._normalize_weights(input_data.ordered_weights) weights = Connectivity2DViewer._get_weights(normalized_weights, input_data.hemispheres) # Compute shapes and colors ad adjacent data norm_rays, min_ray, max_ray = self._normalize_rays(rays, input_data.number_of_regions) colors, step = self._prepare_colors(colors, input_data.number_of_regions, step) if numpy.all((input_data.hemispheres == False)): right_json = "" else: right_json = self._get_json(input_data.ordered_labels[input_data.hemispheres], input_data.ordered_centres[input_data.hemispheres], weights[1], math.pi, 1, 2, numpy.asarray(norm_rays)[input_data.hemispheres], numpy.asarray(colors)[input_data.hemispheres], X_CANVAS_SMALL, Y_CANVAS_SMALL) if numpy.all((input_data.hemispheres == True)): left_json = "" else: left_json = self._get_json(input_data.ordered_labels[~input_data.hemispheres], input_data.ordered_centres[~input_data.hemispheres], weights[0], math.pi, 1, 2, numpy.asarray(norm_rays)[~input_data.hemispheres], numpy.asarray(colors)[~input_data.hemispheres], X_CANVAS_SMALL, Y_CANVAS_SMALL) full_json = self._get_json(input_data.ordered_labels, input_data.ordered_centres, normalized_weights, math.pi, 0, 1, norm_rays, colors, X_CANVAS_FULL, Y_CANVAS_FULL) params = dict(bothHemisphereJson=full_json, rightHemisphereJson=right_json, leftHemisphereJson=left_json, stepValue=step or max_ray, firstColor=self.DEFAULT_COLOR, secondColor=self.OTHER_COLOR, minRay=min_ray, maxRay=max_ray) return params, {}
[docs] def compute_preview_parameters(self, input_data, width, height, colors=None, rays=None, step=None): """ Build the required HTML response to be displayed in the BURST preview iFrame. """ if input_data.number_of_regions <= 3: raise LaunchException('The connectivity matrix you selected has fewer nodes than acceptable for display!') norm_rays, min_ray, max_ray = self._normalize_rays(rays, input_data.number_of_regions) colors, step = self._prepare_colors(colors, input_data.number_of_regions, step) normalizer_size_coeficient = width / 600.0 if height / 700 < normalizer_size_coeficient: normalizer_size_coeficient = (height * 0.8) / 700.0 x_size = X_CANVAS_FULL * normalizer_size_coeficient y_size = Y_CANVAS_FULL * normalizer_size_coeficient full_json = self._get_json(input_data.ordered_labels, input_data.ordered_centres, input_data.ordered_weights, math.pi, 0, 1, norm_rays, colors, x_size, y_size) params = dict(bothHemisphereJson=full_json, stepValue=step or max_ray, firstColor=self.DEFAULT_COLOR, secondColor=self.OTHER_COLOR, minRay=min_ray, maxRay=max_ray) return params, {}
def _get_json(self, labels, positions, weights, rotate_angle, coord_idx1, coord_idx2, dimensions_list, colors_list, x_canvas, y_canvas): """ Method used for creating a valid JSON for an entire chart. """ max_y = max(positions[:, coord_idx2]) min_y = min(positions[:, coord_idx2]) max_x = max(positions[:, coord_idx1]) min_x = min(positions[:, coord_idx1]) y_scale = 2 * y_canvas / (max_y - min_y) x_scale = 2 * x_canvas / (max_x - min_x) mid_x_value = (max_x + min_x) / 2 mid_y_value = (max_y + min_y) / 2 result_json = [] for i in range(len(positions)): x_coord = (positions[i][coord_idx1] - mid_x_value) * x_scale y_coord = (positions[i][coord_idx2] - mid_y_value) * y_scale adjacencies = Connectivity2DViewer._get_adjacencies_json(weights[i], labels) r = self.point2json(labels[i], x_coord, y_coord, adjacencies, rotate_angle, dimensions_list[i], colors_list[i]) result_json.append(r) return json.dumps(result_json) @staticmethod def _get_weights(weights, hemispheres): """ Method used for calculating the weights for the right and for the left hemispheres. Those matrixes are obtained from a weights matrix which contains data related to both hemispheres. """ l_aux, r_aux = weights[~hemispheres], weights[hemispheres] r_weights = [] l_weights = [] for i in range(len(l_aux)): l_weights.append(l_aux[i][~hemispheres]) for i in range(len(l_aux), len(weights)): r_weights.append(r_aux[i - len(l_aux)][hemispheres]) return l_weights, r_weights
[docs] def point2json(self, node_lbl, x_coord, y_coord, adjacencies, angle, shape_dimension, shape_color): """ Method used for creating a valid JSON for a certain point. """ form = "circle" default_dimension = 6 angle += math.atan2(y_coord, x_coord) radius = math.sqrt(math.pow(x_coord, 2) + math.pow(y_coord, 2)) return { "id": node_lbl, "name": node_lbl, "data": { "$dim": default_dimension, "$type": form, "$color": self.DEFAULT_COLOR, "customShapeDimension": shape_dimension, "customShapeColor": shape_color, "angle": angle, "radius": radius }, "adjacencies": adjacencies }
@staticmethod def _get_adjacencies_json(point_weights, points_labels): """ Method used for obtaining a valid JSON which will contain all the edges of a certain node. """ adjacencies = [] for weight, label in zip(point_weights, points_labels): if weight: adjacencies.append({"nodeTo": label, "data": {"weight": weight}}) return adjacencies def _prepare_colors(self, colors, expected_size, step=None): """ From the input array, all values smaller than step will get a different color """ if colors is None: return [self.DEFAULT_COLOR] * expected_size, None colors = numpy.nan_to_num(numpy.array(colors.array_data, dtype=numpy.float64)).tolist() colors = ABCDisplayer.get_one_dimensional_list(colors, expected_size, "Invalid size for colors array!") result = [] if step is None: step = (max(colors) + min(colors)) / 2 for val in colors: if val < step: result.append(self.OTHER_COLOR) else: result.append(self.DEFAULT_COLOR) return result, step def _normalize_rays(self, rays, expected_size): """ Make sure all rays are in the interval [self.MIN_RAY, self.MAX_RAY] """ if rays is None: value = (self.MAX_RAY + self.MIN_RAY) / 2 return [value] * expected_size, 0.0, 0.0 rays = rays.array_data.tolist() rays = ABCDisplayer.get_one_dimensional_list(rays, expected_size, "Invalid size for rays array.") min_x = min(rays) max_x = max(rays) if min_x >= self.MIN_RAY and max_x <= self.MAX_RAY: # No need to normalize return rays, min_x, max_x result = [] diff = max_x - min_x if min_x == max_x: diff = self.MAX_RAY - self.MIN_RAY for ray in rays: result.append(self.MIN_RAY + self.MAX_RAY * (ray - min_x) / diff) result = numpy.nan_to_num(numpy.array(result, dtype=numpy.float64)).tolist() return result, min(rays), max(rays) def _normalize_weights(self, weights): """ Normalize the weights matrix. The values should be between MIN_WEIGHT_VALUE and MAX_WEIGHT_VALUE """ weights = copy(weights) min_value = numpy.min(weights) max_value = numpy.max(weights) if min_value < self.MIN_WEIGHT_VALUE or max_value > self.MAX_WEIGHT_VALUE: for i, row in enumerate(weights): for j in range(len(row)): if min_value == max_value: weights[i][j] = self.MAX_WEIGHT_VALUE else: weights[i][j] = (self.MIN_WEIGHT_VALUE + ((weights[i][j] - min_value) / (max_value - min_value)) * (self.MAX_WEIGHT_VALUE - self.MIN_WEIGHT_VALUE)) return weights