0_setup.ipynb

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   "source": [
    "# Setup\n",
    "#### [Python and Jupyter Notebook for Medical Image Analysis](https://github.com/sbonaretti/2020_OpenMR_jupyter)\n",
    "#### [OpenMRBenelux](https://openmrbenelux.github.io/) Workshop - January 22, 2020 - Nijmegen (The Netherlands)\n",
    "Content under Creative Commons Attribution license CC-BY-NC-SA 4.0   \n",
    "Code under GNU-GPL v3 License  \n",
    "© 2020 Serena Bonaretti\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Introduction and set up"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In this workshop, you will get to know the Jupyter environment, python, and Simple ITK , a python package for medical image processing and analysis."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To get ready for the workshop, run the following cells to:\n",
    "- Install the python packages we are going to use\n",
    "- Download the images we are going to work with  \n",
    "\n",
    "If you get any issues while running the following cells, open an [issue on the GitHub repository of this workshop](https://github.com/sbonaretti/2020_OpenMR_jupyter/issues)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Install SimpleITK"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Install SimpleITK by clicking in the following cell and then press `shift+return` (if on MacOS) or `shift+enter` (if on Windows or Linux)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! pip install simpleitk # the ! allows you to use this cell as a terminal"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Install watermark"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Install watermark to print out the dependencies: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! pip install watermark"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download images"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In this workshop we will use MR images of the knee. You can download them either: \n",
    "- Directly from [Zenodo](https://zenodo.org/record/3611368#.XiHXRFNKhIY), or\n",
    "- Running the following cells\n",
    "\n",
    "In either case, unzip the files after download."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Install wget: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! pip install wget"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# import the library to download the images from the web\n",
    "import wget "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# file name and zenodo url\n",
    "file_name  = \"data.zip\"\n",
    "zenodo_url = \"https://zenodo.org/record/3611368/files/\" + file_name # 3611368 are the last digits of the specific version of dataset DOI"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# download\n",
    "wget.download(zenodo_url,\".\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Enable Jupyter widgets"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Jupyter widgets are already installed but you need to be enable them. Enabling must be done only once. If you haven't already done that, run the following line:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! jupyter labextension install @jupyter-widgets/jupyterlab-manager"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And then **restart** JupyterLab."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Done!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Great, you are done with the set up! See you at the worshop! "
   ]
  }
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