EBR-23. Create Dicom Widget and add demo notebook

notebooks/DicomWidget.ipynb

@@ -0,0 +1,159 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "ce105187-a7e9-4689-ae91-f6bda224845d",
+   "metadata": {},
+   "source": [
+    "## TVB Dicom Widget"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b36747f3-dc0a-43b2-8dc0-c38dba5f2f8d",
+   "metadata": {},
+   "source": [
+    "---"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b77e1d2e-1229-4c14-8ffa-8b26bb0aaacf",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "### This notebook is dedicated to showcasing the Dicom widget using the NIFTI Parser from TVB\n",
+    "#### *Note: This widget accepts 2 types of data: `numpy.ndarray` and `tvb.datatypes.structural.StructuralMRI`.*"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bee554c9-bf38-4ad4-8d7a-f8b8e109cb45",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "from tvbwidgets.api import DicomWidget\n",
+    "from tvb.adapters.uploaders.nifti.parser import NIFTIParser\n",
+    "\n",
+    "from bokeh.io import output_notebook\n",
+    "output_notebook() # tell Bokeh to display the widget inside the notebook"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cb911cd0-e624-473c-97c1-24bef090ece4",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "#### Read and parse NIFTI data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21d549a1-aa69-4964-9d6a-074a1ebf12fe",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "parser = NIFTIParser(data_file='path_to_nii_file')\n",
+    "data = parser.parse()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e1a32181-61b4-4178-b315-9ab5dd10e99a",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "#### Display the widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2bd3dce7-657b-440d-9dcc-f8f494dbd92e",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "widget = DicomWidget(data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "e97e9bbb-9d8f-4f74-8fa4-766c5a491939",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.bokehjs_exec.v0+json": "",
+      "text/html": [
+       "<script id=\"adee33fa-41aa-4009-80e6-9f6dff04c1f7\">\n",
+       "  (function() {\n",
+       "    const xhr = new XMLHttpRequest()\n",
+       "    xhr.responseType = 'blob';\n",
+       "    xhr.open('GET', \"http://localhost:53131/autoload.js?bokeh-autoload-element=adee33fa-41aa-4009-80e6-9f6dff04c1f7&bokeh-absolute-url=http://localhost:53131&resources=none\", true);\n",
+       "    xhr.onload = function (event) {\n",
+       "      const script = document.createElement('script');\n",
+       "      const src = URL.createObjectURL(event.target.response);\n",
+       "      script.src = src;\n",
+       "      document.body.appendChild(script);\n",
+       "    };\n",
+       "    xhr.send();\n",
+       "  })();\n",
+       "</script>"
+      ]
+     },
+     "metadata": {
+      "application/vnd.bokehjs_exec.v0+json": {
+       "server_id": "22277419a6d447b993dc7b83cc4c3b30"
+      }
+     },
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "widget.show_widget()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "52b6f692-753f-4d95-91df-9a4e33ad391c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

tvbwidgets/api.py

@@ -7,6 +7,7 @@
 
 from .ui.connectivity_ipy.connectivity_widget import ConnectivityWidget
 from .ui.connectivity_react.connectivity_widget import ConnectivityWidgetReact
+from .ui.dicom_widget import DicomWidget
 from .ui.phase_plane_widget import PhasePlaneWidget
 from .ui.storage_widget import StorageWidget
 from .ui.head_widget import HeadBrowser, HeadWidget, HeadWidgetConfig