{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Install dependencies for this example\n",
    "# Note: This does not include itkwidgets, itself\n",
    "import sys\n",
    "!{sys.executable} -m pip install --upgrade --pre itk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from urllib.request import urlretrieve\n",
    "import os\n",
    "\n",
    "import itk\n",
    "\n",
    "from itkwidgets import view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Example data from ITKTubeTK: https://github.com/KitwareMedical/ITKTubeTK\n",
    "\n",
    "tubes_file = \"Normal071-VascularNetwork.tre\"\n",
    "if not os.path.exists(tubes_file):\n",
    "    url = 'https://data.kitware.com/api/v1/item/5e1b3727af2e2eed35f5c48a/download'\n",
    "    urlretrieve(url, tubes_file)\n",
    "    \n",
    "mra_file = \"Normal071-MRA.mha\"\n",
    "if not os.path.exists(mra_file):\n",
    "    url = 'https://data.kitware.com/api/v1/item/5e1b3721af2e2eed35f5c482/download'\n",
    "    urlretrieve(url, mra_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "PixelType = itk.F\n",
    "Dimension = 3\n",
    "    \n",
    "# Read tre file\n",
    "tubesReader = itk.SpatialObjectReader[Dimension].New()\n",
    "tubesReader.SetFileName(tubes_file)\n",
    "tubesReader.Update()\n",
    "tubes = tubesReader.GetGroup()\n",
    "\n",
    "# Read mra image\n",
    "mra = itk.imread(mra_file, PixelType)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "49aa7a79c4024490829e6ce67fc11ad0",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Viewer(geometries=[], gradient_opacity=0.22, point_set_colors=array([[0.8392157, 0.       , 0.       ]], dtype…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view(image=mra, point_sets=tubes)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.7.6"
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 "nbformat": 4,
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