Merge pull request #60 from the-virtual-brain/WID-223-new

WID-223: Add ConnectivityWidget

notebooks/Connectivity.ipynb

@@ -0,0 +1,138 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Demonstrate Connectivity Widget "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "# from tvbwidgets.ui.connectivity_react.connectivity_widget 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": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "19-09-2023 10:57:09 - DEBUG - tvbwidgets - Package is not fully installed\n",
+      "19-09-2023 10:57:09 - DEBUG - tvbwidgets - Version read from the internal package.json file\n",
+      "19-09-2023 10:57:09 - INFO - tvbwidgets - Version: 1.5.0\n",
+      "2023-09-19 10:57:15,882 - INFO - tvb.storage.h5.encryption.data_encryption_handler - Cannot import syncrypto library.\n",
+      "19-09-2023 10:57:15 - INFO - tvbwidgets.core.pse.parameters - ImportError: Dask dependency is not included, so this functionality won't be available\n",
+      "2023-09-19 10:57:16,010 - WARNING - tvb.basic.readers - File 'hemispheres' not found in ZIP.\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "b3a81813058645ecbe8abedd7dd6d17f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "ConnectivityWidget(children=(VBox(children=(HTML(value='<h1>Connectivity - 76</h1>'), HBox(children=(Checkbox(…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "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, default_active_tab='viewers') # default_active_tab can be any value between 'viewers'|'operations'|'both'\n",
+    "\n",
+    "display(wid)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table>\n",
+       "<thead><h3>Connectivity</h3></thead>\n",
+       "<tbody>\n",
+       "\n",
+       "<tr><th></th><th style=\"text-align:left;width:80%\">value</th></tr>\n",
+       "<tr><td>Number of connections</td><td style=\"text-align:left;\"><pre>1560</pre></td></tr>\n",
+       "<tr><td>Number of regions</td><td style=\"text-align:left;\"><pre>76</pre></td></tr>\n",
+       "<tr><td>Undirected</td><td style=\"text-align:left;\"><pre>False</pre></td></tr>\n",
+       "<tr><td>areas</td><td style=\"text-align:left;\"><pre> [min, median, max] = [0, 2580.89, 10338.2] dtype = float64 shape = (76,)</pre></td></tr>\n",
+       "<tr><td>tract_lengths</td><td style=\"text-align:left;\"><pre> [min, median, max] = [0, 71.6635, 153.486] dtype = float64 shape = (76, 76)</pre></td></tr>\n",
+       "<tr><td>tract_lengths (connections)</td><td style=\"text-align:left;\"><pre> [min, median, max] = [0, 55.8574, 138.454] dtype = float64 shape = (1560,)</pre></td></tr>\n",
+       "<tr><td>tract_lengths-non-zero</td><td style=\"text-align:left;\"><pre> [min, median, max] = [4.93328, 74.0646, 153.486] dtype = float64 shape = (5402,)</pre></td></tr>\n",
+       "<tr><td>weights</td><td style=\"text-align:left;\"><pre> [min, median, max] = [0, 0, 3] dtype = float64 shape = (76, 76)</pre></td></tr>\n",
+       "<tr><td>weights-non-zero</td><td style=\"text-align:left;\"><pre> [min, median, max] = [0.00462632, 2, 3] dtype = float64 shape = (1560,)</pre></td></tr>\n",
+       "</tbody></table>"
+      ],
+      "text/plain": [
+       "<tvb.datatypes.connectivity.Connectivity at 0x2f09c20e410>"
+      ]
+     },
+     "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"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

notebooks/HeadWidget.ipynb

@@ -190,7 +190,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.8.16"
   }
  },
  "nbformat": 4,

package.json

@@ -1,6 +1,6 @@
 {
   "name": "tvb-widgets",
-  "version": "1.5.0",
+  "version": "1.6.0",
   "description": "GUI widgets for EBRAINS showcases",
   "homepage": "https://github.com/the-virtual-brain/tvb-widgets",
   "license": "GPL-3.0-or-later",

requirements.txt

@@ -1,16 +1,18 @@
 colorcet
 ebrains_drive
-ipympl > 0.8.5
-ipywidgets == 7.7.2
-IPython <= 8.12
+ipympl>0.8.5
+ipywidgets==7.7.2
+IPython<=8.12
 joblib
-mne >= 1.0
-numpy <1.24
-plotly == 5.14.0
+mne>=1.0
+numpy<1.24
+plotly==5.14.0
 pythreejs
-pyvista == 0.37.0
-tvb-library >= 2.5
+pyvista==0.37.0
+ipyreact==0.3.0
+tvb-library>=2.5
 tvb-framework
 plotly-resampler
 pyunicore
-toml
+traitlets>=5.7.1
+toml

tvbwidgets/api.py

@@ -5,6 +5,7 @@
 # (c) 2022-2023, TVB Widgets Team
 #
 
+from .ui.connectivity_ipy.connectivity_widget import ConnectivityWidget
 from .ui.phase_plane_widget import PhasePlaneWidget
 from .ui.storage_widget import StorageWidget
 from .ui.head_widget import HeadBrowser, HeadWidget, HeadWidgetConfig

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