diff --git a/notebooks/Connectivity.ipynb b/notebooks/Connectivity.ipynb index 3e8379e..08d3348 100644 --- a/notebooks/Connectivity.ipynb +++ b/notebooks/Connectivity.ipynb @@ -27,17 +27,51 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "11-09-2023 10:43:09 - DEBUG - tvbwidgets - Package is not fully installed\n", - "11-09-2023 10:43:09 - DEBUG - tvbwidgets - Version read from the internal package.json file\n", - "11-09-2023 10:43:09 - INFO - tvbwidgets - Version: 1.5.0\n" + "14-09-2023 04:28:58 - DEBUG - tvbwidgets - Package is not fully installed\n", + "14-09-2023 04:28:58 - DEBUG - tvbwidgets - Version read from the internal package.json file\n", + "14-09-2023 04:28:58 - INFO - tvbwidgets - Version: 1.5.0\n", + "2023-09-14 16:29:04,296 - INFO - tvb.storage.h5.encryption.data_encryption_handler - Cannot import syncrypto library.\n", + "14-09-2023 04:29:04 - INFO - tvbwidgets.core.pse.parameters - ImportError: Dask dependency is not included, so this functionality won't be available\n", + "2023-09-14 16:29:04,405 - WARNING - tvb.basic.readers - File 'hemispheres' not found in ZIP.\n", + "connectivity.weights: [[2. 2. 0. ... 0. 0. 0.]\n", + " [3. 2. 0. ... 0. 0. 0.]\n", + " [0. 0. 2. ... 0. 0. 0.]\n", + " ...\n", + " [0. 0. 0. ... 2. 2. 0.]\n", + " [0. 0. 0. ... 3. 2. 0.]\n", + " [0. 0. 0. ... 0. 0. 0.]]\n", + "edge_indices: (array([ 0, 0, 0, ..., 74, 74, 74], dtype=int64), array([ 0, 1, 3, ..., 72, 73, 74], dtype=int64))\n", + "edges: [(0, 0), (0, 1), (0, 3), (0, 6), (0, 10), (0, 11), (0, 18), (0, 20), (0, 21), (0, 24), (0, 30), (0, 33), (0, 34), (1, 0), (1, 1), (1, 7), (1, 13), (1, 14), (1, 15), (1, 16), (1, 17), (1, 21), (1, 22), (1, 23), (1, 24), (1, 25), (1, 30), (1, 33), (1, 34), (2, 2), (2, 24), (2, 30), (2, 31), (2, 32), (2, 34), (2, 40), (3, 0), (3, 2), (3, 3), (3, 4), (3, 6), (3, 7), (3, 8), (3, 9), (3, 10), (3, 11), (3, 12), (3, 14), 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-47.084818 -3.13936 ]\n", + " [ -9.885591 -47.084818 -3.13936 ]\n", + " [ -9.885591 -47.084818 -3.13936 ]\n", + " ...\n", + " [-60.66705 12.165386 -6.554734]\n", + " [-66.770666 19.431384 -4.138797]\n", + " [-66.770666 19.431384 -4.138797]]\n" ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "ee27297579f643a68153bcf018bffb97", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "ConnectivityWidget(children=(VBox(children=(HTML(value='

Connectivity - 76

'), HBox(children=(Checkbox(…" + ] + }, + "metadata": {}, + "output_type": "display_data" } ], "source": [ @@ -57,10 +91,44 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "

Connectivity

\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
value
Number of connections
1560
Number of regions
76
Undirected
False
areas
 [min, median, max] = [0, 2580.89, 10338.2] dtype = float64 shape = (76,)
tract_lengths
 [min, median, max] = [0, 71.6635, 153.486] dtype = float64 shape = (76, 76)
tract_lengths (connections)
 [min, median, max] = [0, 55.8574, 138.454] dtype = float64 shape = (1560,)
tract_lengths-non-zero
 [min, median, max] = [4.93328, 74.0646, 153.486] dtype = float64 shape = (5402,)
weights
 [min, median, max] = [0, 0, 3] dtype = float64 shape = (76, 76)
weights-non-zero
 [min, median, max] = [0.00462632, 2, 3] dtype = float64 shape = (1560,)
" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# replace None in the method below with the gid of the connectivity you wish to export\n", + "# if no gid is provided it will export the connectivity currently viewed\n", + "\n", + "new_connectivity = wid.get_connectivity(gid=None) \n", + "new_connectivity" + ] }, { "cell_type": "code", diff --git a/tvbwidgets/ui/connectivity_ipy/connectivity_widget.py b/tvbwidgets/ui/connectivity_ipy/connectivity_widget.py index b7ee63e..cc31987 100644 --- a/tvbwidgets/ui/connectivity_ipy/connectivity_widget.py +++ b/tvbwidgets/ui/connectivity_ipy/connectivity_widget.py @@ -116,10 +116,8 @@ def __init__(self, **kwargs): def init_view_connectivity(self): self.output.plotter.clear() - points, edges, labels = self.add_actors() + points, edges = self.add_actors() points_toggle, edges_toggle, labels_toggle = self._init_controls() - if not labels_toggle.value: - self.output.hide_actor(labels) def on_change_points(change): if change['new']: @@ -139,15 +137,6 @@ def on_change_edges(change): edges_toggle.observe(on_change_edges, 'value') - def on_change_labels(change): - if change['new']: - self.output.display_actor(labels) - else: - self.output.hide_actor(labels) - self.output.update_plot() - - labels_toggle.observe(on_change_labels, 'value') - window_controls = self.output.get_window_controls() self.children = [ @@ -177,9 +166,6 @@ def add_actors(self): mesh_points = pv.PolyData(points) - labels = CONTEXT.connectivity.region_labels - labels_actor = plotter.add_point_labels(points, labels) - points_color = self.output.CONFIG.points_color points_size = self.output.CONFIG.point_size edge_color = self.output.CONFIG.edge_color @@ -187,11 +173,10 @@ def add_actors(self): points_actor = plotter.add_points(mesh_points, color=points_color, point_size=points_size) edges_coords = self._extract_edges() - edges_actor = plotter.add_lines(edges_coords, color=edge_color, width=1) plotter.camera_position = 'xy' - return points_actor, edges_actor, labels_actor + return points_actor, edges_actor def _extract_edges(self): connectivity = CONTEXT.connectivity diff --git a/tvbwidgets/ui/connectivity_ipy/operations.py b/tvbwidgets/ui/connectivity_ipy/operations.py index 3bce1ed..7bab013 100644 --- a/tvbwidgets/ui/connectivity_ipy/operations.py +++ b/tvbwidgets/ui/connectivity_ipy/operations.py @@ -192,7 +192,7 @@ def _cut_connectivity_edges(self, interest_areas, selected=False): if i not in interest_areas or j not in interest_areas: if not selected: new_weights[i][j] = 0 - elif i in interest_areas or j in interest_areas and selected: + elif selected: new_weights[i][j] = 0 final_conn = Connectivity()