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  {
   "cell_type": "markdown",
   "id": "8c3882b9",
   "metadata": {},
   "source": [
    "# Solutions of exercises\n",
    "\n",
    "Exercises are available in a few notebooks. Below are solutions to the exercises.\n",
    "How to use the notebook:\n",
    "\n",
    "* **DO NOT RUN THE NOTEBOOK**\n",
    "* **Copy the code snippet(s) and run the snippet(s) in the relevant notebook**\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "38dce9f9",
   "metadata": {},
   "source": [
    "## Exercises from notebook idr0062_prediction"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "75db4ae2",
   "metadata": {},
   "source": [
    "### Exercise 1 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "47d19053",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Question 1: Read the geojson file:\n",
    "import json\n",
    "with open(geojson_file) as f:\n",
    "    d = json.load(f)\n",
    "    values = d['features']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e8fa7860",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Question 2: Overlay the shapes from a specific plane on the image\n",
    "z = 5\n",
    "ax = plt.subplot()\n",
    "plt.imshow(data[0, 0, z, :, :], cmap='gray')\n",
    "for v in values:\n",
    "    if v[\"properties\"][\"z\"] == z:\n",
    "        label_geojson = numpy.array(v[\"geometry\"][\"coordinates\"])\n",
    "        p = label_geojson.squeeze()\n",
    "        ax.plot(p[:, 0], p[:, 1], linewidth=v[\"properties\"][\"stroke-width\"], color=\"red\")\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dddaad7f",
   "metadata": {},
   "source": [
    "### Exercise 2 \n",
    "\n",
    "In order to save the StarDist labels to an OMERO.server with write access, you will first need to log in and change the image ID."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "e0d0c98b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "False\n"
     ]
    }
   ],
   "source": [
    "from omero.gateway import BlitzGateway\n",
    "from getpass import getpass\n",
    "# To be replaced by the desired host\n",
    "HOST = 'wss://workshop.openmicroscopy.org/omero-ws'\n",
    "conn = BlitzGateway(input(\"Username: \"),\n",
    "                    getpass(\"OMERO Password: \"),\n",
    "                    host=HOST, secure=True)\n",
    "conn.connect()\n",
    "print(conn.connect())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3f3f0360",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Question 1: Convert the StarDist labels into OMERO polygons\n",
    "import omero\n",
    "from omero.rtypes import rint, rstring\n",
    "\n",
    "image_id = REPLACE_WITH_IMAGE_ID\n",
    "\n",
    "image = omero.model.ImageI(image_id, False)\n",
    "rois = []\n",
    "for i in range(len(img)):\n",
    "    new_labels, details = model_versatile.predict_instances(img[i])\n",
    "    # Convert into Polygon\n",
    "    for obj_id, region in enumerate(details['coord']):\n",
    "        roi = omero.model.RoiI()\n",
    "        roi.setName(rstring(\"Object %s\" % obj_id))\n",
    "        polygon = omero.model.PolygonI()\n",
    "        x = region[1]\n",
    "        y = region[0]\n",
    "        points = \" \".join(\n",
    "            [\"{},{}\".format(x[j], y[j]) for j in range(len(x))])\n",
    "        polygon.setPoints(rstring(points))\n",
    "        polygon.theZ = rint(i)\n",
    "        polygon.theC = rint(0)\n",
    "        roi.addShape(polygon)\n",
    "        # Link the ROI and the image\n",
    "        roi.setImage(image)\n",
    "        rois.append(roi)                    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "43eef9bb",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Question 2: Save the ROI\n",
    "rois = conn.getUpdateService().saveAndReturnArray(rois)"
   ]
  }
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