EBR-23. Create Dicom Widget

notebooks/DicomWidget.ipynb

@@ -0,0 +1,162 @@
+{
+ "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\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": [
+    "import numpy as np\n",
+    "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 input data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5c445018-d57c-45e1-a8fc-8cce82c8ba70",
+   "metadata": {},
+   "source": [
+    "#### Either read and parse the data using the NIFTI Parser from TVB \n",
+    "(Uncomment the 2 lines and replace `path_to_nii_file` with the correct path to your file)"
+   ]
+  },
+  {
+   "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": "07185a9d-f8a4-4ea9-97cc-54fcc523b765",
+   "metadata": {},
+   "source": [
+    "#### Or use an existent numpy.ndarray/ TVB StructuralMRI object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c03cbb47-cbec-454c-8935-61cc00894a21",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "# create demo array just to demonstrate the usage of the API\n",
+    "data = np.random.rand(255,255,255)"
+   ]
+  },
+  {
+   "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": null,
+   "id": "e97e9bbb-9d8f-4f74-8fa4-766c5a491939",
+   "metadata": {},
+   "outputs": [],
+   "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
+}

requirements.txt

@@ -16,3 +16,4 @@ plotly-resampler
 pyunicore==0.15.2
 traitlets>=5.7.1
 toml
+bokeh

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