WID-223: add 3d viewer, show points/edges, resize plot, toggle operat…

…ions

notebooks/Connectivity.ipynb

@@ -34,18 +34,18 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "29-08-2023 02:49:39 - DEBUG - tvbwidgets - Package is not fully installed\n",
-      "29-08-2023 02:49:39 - DEBUG - tvbwidgets - Version read from the internal package.json file\n",
-      "29-08-2023 02:49:39 - INFO - tvbwidgets - Version: 1.5.0\n",
-      "2023-08-29 14:49:45,596 - INFO - tvb.storage.h5.encryption.data_encryption_handler - Cannot import syncrypto library.\n",
-      "29-08-2023 02:49:45 - INFO - tvbwidgets.core.pse.parameters - ImportError: Dask dependency is not included, so this functionality won't be available\n",
-      "2023-08-29 14:49:45,789 - WARNING - tvb.basic.readers - File 'hemispheres' not found in ZIP.\n"
+      "11-09-2023 10:13:24 - DEBUG - tvbwidgets - Package is not fully installed\n",
+      "11-09-2023 10:13:24 - DEBUG - tvbwidgets - Version read from the internal package.json file\n",
+      "11-09-2023 10:13:24 - INFO - tvbwidgets - Version: 1.5.0\n",
+      "2023-09-11 10:13:29,835 - INFO - tvb.storage.h5.encryption.data_encryption_handler - Cannot import syncrypto library.\n",
+      "11-09-2023 10:13:29 - INFO - tvbwidgets.core.pse.parameters - ImportError: Dask dependency is not included, so this functionality won't be available\n",
+      "2023-09-11 10:13:29,943 - WARNING - tvb.basic.readers - File 'hemispheres' not found in ZIP.\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "adc5ca9edfd244aa95d31e693301679e",
+       "model_id": "3303c8f259414948800906cc6eb8ae24",
        "version_major": 2,
        "version_minor": 0
       },
@@ -60,14 +60,25 @@
    "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",
     "\n",
     "conn = Connectivity.from_file() # defaults to connectivy_76.zip\n",
     "conn.configure()\n",
     "\n",
     "wid = ConnectivityWidget(conn)\n",
+    "\n",
     "display(wid)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,

tvbwidgets/ui/connectivity_ipy/config.py

@@ -0,0 +1,19 @@
+# -*- coding: utf-8 -*-
+#
+# "TheVirtualBrain - Widgets" package
+#
+# (c) 2022-2023, TVB Widgets Team
+#
+from dataclasses import dataclass
+from numpy import ndarray
+
+
+@dataclass
+class ConnectivityConfig:
+    name: str = 'Connectivity'
+    style: str = 'Points'
+    points_color: str = 'Green'
+    edge_color: str = 'White'
+    light: bool = True
+    size = [500, 500]  # [width, height]
+    point_size: int = 20

tvbwidgets/ui/connectivity_ipy/connectivity_widget.py

@@ -4,34 +4,22 @@
 #
 # (c) 2022-2023, TVB Widgets Team
 #
-import dataclasses
 
 import ipywidgets
-import pyvista
 import matplotlib
+import numpy
+import pyvista as pv
+import numpy as np
 from numpy import ndarray
-from tvb.basic.neotraits._attr import NArray
 from tvb.basic.neotraits.api import HasTraits
 from tvb.datatypes.connectivity import Connectivity
 from tvbwidgets.ui.base_widget import TVBWidget
-
-pyvista.set_jupyter_backend('pythreejs')
+from tvbwidgets.ui.connectivity_ipy.outputs_3d import PyVistaOutput
+from tvbwidgets.ui.connectivity_ipy.config import ConnectivityConfig
 
 DROPDOWN_KEY = 'dropdown'
 
 
-@dataclasses.dataclass
-class ConnectivityConfig:
-    name: str = 'Connectivity'
-    style: str = 'Surface'
-    color: str = 'White'
-    light: bool = True
-    size: int = 1500
-    cmap: str | None = None
-    scalars: ndarray | NArray = None
-    widget: ipywidgets.Widget = None
-
-
 class CustomOutput(ipywidgets.Output):
     CONFIG = ConnectivityConfig()
 
@@ -105,10 +93,109 @@ def on_change(change):
         self.children = (dropdown, *self.children)
 
 
-class Connectivity3DViewer(ipywidgets.HBox):
+class Connectivity3DViewer(ipywidgets.VBox):
+    PYVISTA = 'PyVista'
+
     def __init__(self, connectivity, **kwargs):
-        super(Connectivity3DViewer, self).__init__(*kwargs)
-        self.children = [ipywidgets.HTML(value='Placeholder for 3d viewer')]
+        self.connectivity = connectivity
+
+        self.output = PyVistaOutput()
+
+        super(Connectivity3DViewer, self).__init__([self.output], *kwargs)
+
+        self.init_view_connectivity()
+
+    def init_view_connectivity(self):
+        points, edges, labels = 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']:
+                self.output.display_actor(points)
+            else:
+                self.output.hide_actor(points)
+            self.output.update_plot()
+
+        points_toggle.observe(on_change_points, 'value')
+
+        def on_change_edges(change):
+            if change['new']:
+                self.output.display_actor(edges)
+            else:
+                self.output.hide_actor(edges)
+            self.output.update_plot()
+
+        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 = [
+            ipywidgets.HBox(children=(
+                points_toggle, edges_toggle, labels_toggle)),
+            window_controls,
+            self.output]
+        self.output.display_actor(points)
+        self.output.display_actor(edges)
+        self.output.update_plot()
+
+    def _init_controls(self):
+        points_toggle = ipywidgets.ToggleButton(value=True,
+                                                description='Points'
+                                                )
+        edges_toggle = ipywidgets.ToggleButton(value=True,
+                                               description='Edges',
+                                               )
+
+        labels_toggle = ipywidgets.ToggleButton(value=False,
+                                                description='Labels')
+        return points_toggle, edges_toggle, labels_toggle
+
+    def add_actors(self):
+        plotter = self.output.plotter
+        points = self.connectivity.centres
+
+        mesh_points = pv.PolyData(points)
+
+        labels = self.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
+
+        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
+
+    def _extract_edges(self):
+        connectivity = self.connectivity
+        edge_indices = np.nonzero(connectivity.weights)
+        edges = list(zip(edge_indices[0], edge_indices[1]))
+
+        edges_coords = []
+        points = connectivity.centres
+
+        for (i, j) in edges:
+            edges_coords.append(points[i])
+            edges_coords.append(points[j])
+
+        return numpy.array(edges_coords)
 
 
 class ConnectivityOperations(ipywidgets.VBox, TVBWidget):
@@ -177,10 +264,7 @@ def on_change_operations(c):
                     ipywidgets.VBox(children=(
                         viewers_checkbox,
                         operations_checkbox
-                    )
-                    )
-
-                )
+                    )))
             ),
             sections_container
         ]

tvbwidgets/ui/connectivity_ipy/exceptions.py

@@ -0,0 +1,10 @@
+# -*- coding: utf-8 -*-
+#
+# "TheVirtualBrain - Widgets" package
+#
+# (c) 2022-2023, TVB Widgets Team
+#
+class UnknownOutputException(Exception):
+    """
+    Exception thrown in case of an unknown output type
+    """

tvbwidgets/ui/connectivity_ipy/outputs_3d.py

@@ -0,0 +1,84 @@
+# -*- coding: utf-8 -*-
+#
+# "TheVirtualBrain - Widgets" package
+#
+# (c) 2022-2023, TVB Widgets Team
+#
+import ipywidgets
+
+from tvbwidgets.ui.connectivity_ipy.config import ConnectivityConfig
+from tvbwidgets.ui.connectivity_ipy.exceptions import UnknownOutputException
+from enum import Enum
+import ipywidgets as widgets
+import pyvista
+
+
+class Output3D(Enum):
+    PYVISTA = 'PyVista'
+
+    def __str__(self):
+        return str(self.value)
+
+
+class PyVistaOutput(widgets.Output):
+    CONFIG = ConnectivityConfig()
+    plotter = pyvista.Plotter()
+
+    def toggle_actor(self, actor, visible):
+        if visible:
+            self.display_actor(actor)
+        else:
+            self.hide_actor(actor)
+        self.update_plot()
+
+    def display_actor(self, actor):
+        self.plotter.renderer.add_actor(actor, render=False)
+
+    def hide_actor(self, actor):
+        self.plotter.renderer.remove_actor(actor, render=False)
+
+    def update_plot(self):
+        with 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"""
+    if output_type == Output3D.PYVISTA:
+        return PyVistaOutput()
+    raise UnknownOutputException(f"No applicable output for {output_type}!")