setup.ipynb

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   "source": [
    "<h1 align=\"center\">SimpleITK Jupyter Notebooks: Biomedical Image Analysis in Python</h1>\n",
    "\n",
    "## Newcomers to Jupyter notebooks:\n",
    "1. We use two types of cells, code and markdown.\n",
    "2. To run a code cell, select it (mouse or arrow key so that it is highlighted) and then press shift+enter which also moves focus to the next cell or ctrl+enter which doesn't.\n",
    "3. Closing the browser window does not close the Jupyter server. To close the server, go to the terminal where you ran it and press ctrl+c twice.\n",
    "\n",
    "For additional details see the [Jupyter Notebook Quick Start Guide](https://jupyter-notebook-beginner-guide.readthedocs.io/en/latest/index.html).\n",
    "\n",
    "\n",
    "## Environment Setup for Course\n",
    "\n",
    "This notebook should be run prior to arriving at the course venue, as it <b>requires network connectivity</b>."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "First, lets check that you have the SimpleITK version which you expect."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import SimpleITK as sitk\n",
    "from downloaddata import fetch_data, fetch_data_all\n",
    "\n",
    "from ipywidgets import interact\n",
    "\n",
    "print(sitk.Version())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we check that the auxiliary program(s) are correctly installed in your environment.\n",
    "\n",
    "We expect that you have an external image viewer installed. The default viewer is <a href=\"https://fiji.sc/#download\">Fiji</a>. If you have another viewer (i.e. ITK-SNAP or 3D Slicer) you will need to set an environment variable to point to it. This is done using an environment variable which can also be set from within a notebook as shown below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "simpleitk_error_allowed": "Exception thrown in SimpleITK ImageViewer_Execute:"
   },
   "outputs": [],
   "source": [
    "# Uncomment the line below to change the default external viewer to your viewer of choice and test that it works.\n",
    "#%env SITK_SHOW_COMMAND path_to_program/ITK-SNAP \n",
    "\n",
    "# Retrieve an image from the network, read it and display using the external viewer\n",
    "image_viewer = sitk.ImageViewer()\n",
    "image_viewer.Execute(sitk.ReadImage(fetch_data(\"SimpleITK.jpg\")))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now we check that the ipywidgets will display correctly. When you run the following cell you should see a slider.\n",
    "\n",
    "If you don't see a slider please shutdown the Jupyter server, at the Anaconda command line prompt press Control-c twice, and then run the following command:\n",
    "\n",
    "```jupyter nbextension enable --py --sys-prefix widgetsnbextension```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "interact(lambda x: x, x=(0,10));"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, we download all of the data used in the notebooks in advance. This step is necessary as we will be running the notebooks without network connectivity.\n",
    "\n",
    "This may take a couple of minutes depending on your network."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "\n",
    "fetch_data_all('data', os.path.join('data','manifest.json'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a href=\"01_spatial_transformations.ipynb\"><h2 align=right>Next &raquo;</h2></a>"
   ]
  }
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