EBR-35: comment the connectivity notebook cell that leads to freeze o…

…f jupyter lab, add parameters height and width for Connectivity3DViewer

notebooks/Connectivity.ipynb

@@ -14,33 +14,17 @@
     "tags": []
    },
    "outputs": [],
-   "source": [
-    "from tvbwidgets.api import ConnectivityWidgetReact\n",
-    "from tvb.datatypes.connectivity import Connectivity\n",
-    "\n",
-    "connectivity = Connectivity.from_file() # defaults to connectivy_76.zip\n",
-    "\n",
-    "\n",
-    "wid = ConnectivityWidgetReact(connectivity=connectivity)\n",
-    "wid"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
    "source": [
     "from tvbwidgets.api import ConnectivityWidget\n",
     "from tvb.datatypes.connectivity import Connectivity\n",
     "import pyvista as pv\n",
     "import numpy as np\n",
-    "pv.set_jupyter_backend('pythreejs')\n",
+    "pv.set_jupyter_backend(\"pythreejs\")\n",
     "\n",
     "conn = Connectivity.from_file() # defaults to connectivy_76.zip\n",
     "conn.configure()\n",
     "\n",
-    "wid = ConnectivityWidget(conn, default_active_tab='viewers') # default_active_tab can be any value between 'viewers'|'operations'|'both'\n",
+    "wid = ConnectivityWidget(conn, default_active_tab='viewers', width=500, height=500) # default_active_tab can be any value between 'viewers'|'operations'|'both'\n",
     "\n",
     "display(wid)"
    ]
@@ -63,7 +47,20 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "#  Using the React Connectivity widget may lead to Jupyter Lab freezing or crashing.\n",
+    "#  If you choose to use it, we recommend to run it in Mozilla Firefox web browser.\n",
+    "\n",
+    "\n",
+    "# from tvbwidgets.api import ConnectivityWidgetReact\n",
+    "# from tvb.datatypes.connectivity import Connectivity\n",
+    "\n",
+    "# connectivity = Connectivity.from_file() # defaults to connectivy_76.zip\n",
+    "\n",
+    "\n",
+    "# wid = ConnectivityWidgetReact(connectivity=connectivity)\n",
+    "# wid"
+   ]
   }
  ],
  "metadata": {
@@ -82,7 +79,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.9.18"
   }
  },
  "nbformat": 4,

tvbwidgets/ui/connectivity_ipy/connectivity_widget.py

@@ -109,8 +109,10 @@ def on_ctx_change(value):
 
 class Connectivity3DViewer(ipywidgets.VBox):
 
-    def __init__(self, **kwargs):
+    def __init__(self, width, height, **kwargs):
         self.output = PyVistaOutput()
+        self.output.plotter.window_size = [width, height]
+        self.output.plotter.set_background("darkgrey")
 
         super(Connectivity3DViewer, self).__init__([self.output], *kwargs)
 
@@ -120,7 +122,7 @@ def __init__(self, **kwargs):
     def __init_view_connectivity(self):
         self.output.plotter.clear()
         points, edges = self.__add_actors()
-        points_toggle, edges_toggle, labels_toggle = self.__init_controls()
+        points_toggle, edges_toggle = self.__init_controls()
 
         def on_change_points(change):
             if change['new']:
@@ -140,12 +142,10 @@ def on_change_edges(change):
 
         edges_toggle.observe(on_change_edges, 'value')
 
-        window_controls = self.output.get_window_controls()
 
         self.children = [
             ipywidgets.HBox(children=(
-                points_toggle, edges_toggle, labels_toggle)),
-            window_controls,
+                points_toggle, edges_toggle)),
             self.output]
         self.output.display_actor(points)
         self.output.display_actor(edges)
@@ -159,9 +159,7 @@ def __init_controls(self):
                                                description='Edges',
                                                )
 
-        labels_toggle = ipywidgets.ToggleButton(value=False,
-                                                description='Labels')
-        return points_toggle, edges_toggle, labels_toggle
+        return points_toggle, edges_toggle
 
     def __add_actors(self):
         plotter = self.output.plotter
@@ -197,11 +195,11 @@ def __extract_edges(self):
 
 
 class ConnectivityViewers(ipywidgets.Accordion):
-    def __init__(self, **kwargs):
+    def __init__(self, width, height, **kwargs):
         super().__init__(**kwargs)
         self.children = [
             Connectivity2DViewer(),
-            Connectivity3DViewer()
+            Connectivity3DViewer(width, height)
         ]
         self.set_title(0, '2D Connectivity Matrix viewer')
         self.set_title(1, '3D Connectivity viewer')
@@ -235,7 +233,7 @@ def get_connectivity(self, gid=None):
             return None
         return conn[0]
 
-    def __init__(self, connectivity, default_active_tab='both', **kwargs):
+    def __init__(self, connectivity, default_active_tab='both', width=500, height=500, **kwargs):
 
         style = self.DEFAULT_BORDER
         super().__init__(**kwargs, layout=style)
@@ -246,7 +244,7 @@ def __init__(self, connectivity, default_active_tab='both', **kwargs):
         viewers_visible = default_active_tab in ['both', 'viewers']
         operations_visible = default_active_tab in ['both', 'operations']
 
-        self.viewers_tab = ConnectivityViewers()
+        self.viewers_tab = ConnectivityViewers(width, height)
         self.viewers_tab.layout.display = viewers_visible and 'inline-block' or 'none'
         self.operations_tab = ConnectivityOperations()
         self.operations_tab.layout.display = operations_visible and 'inline-block' or 'none'

tvbwidgets/ui/connectivity_ipy/outputs_3d.py

@@ -4,7 +4,6 @@
 #
 # (c) 2022-2023, TVB Widgets Team
 #
-import ipywidgets
 
 from tvbwidgets.ui.connectivity_ipy.config import ConnectivityConfig
 from tvbwidgets.ui.connectivity_ipy.exceptions import UnknownOutputException
@@ -42,40 +41,6 @@ def update_plot(self):
             self.clear_output(wait=True)
             self.plotter.show()
 
-    def get_window_controls(self):
-        height = ipywidgets.IntSlider(
-            value=self.CONFIG.size[1],
-            min=50,
-            max=1500,
-            step=1,
-            orientation='horizontal',
-            description='Plot height',
-            continuous_update=False,
-        )
-        width = ipywidgets.IntSlider(
-            value=self.CONFIG.size[0],
-            min=50,
-            max=1500,
-            step=1,
-            orientation='horizontal',
-            description='Plot width',
-            continuous_update=False,
-        )
-
-        self.plotter.window_size = [width.value, height.value]
-
-        def on_change_height(value):
-            self.plotter.window_size = [width.value, value['new']]
-            self.update_plot()
-
-        def on_change_width(value):
-            self.plotter.window_size = [value['new'], height.value]
-            self.update_plot()
-
-        height.observe(on_change_height, 'value')
-        width.observe(on_change_width, 'value')
-        return ipywidgets.HBox(children=(width, height))
-
 
 def output_3d_factory(output_type):
     """Factory function for a custom 3d output"""