MetaTensor Fix for NuClick Tutorial (#822)

* MetaTensor Fix for NuClick Tutorial

Signed-off-by: vnath <[email protected]>

Author: finalelement

nuclick/nuclick_infer.ipynb

@@ -15,15 +15,25 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "!python -c \"import cv2\" || pip install -q opencv-python-headless==4.5.5.64\n",
     "!python -c \"import matplotlib\" || pip install -q matplotlib\n",
     "%matplotlib inline"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/vishwesh/anaconda3/envs/nuclick_tutorial/lib/python3.8/site-packages/requests/__init__.py:109: RequestsDependencyWarning: urllib3 (1.25.11) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!\n",
+      "  warnings.warn(\n"
+     ]
+    }
+   ],
    "source": [
     "from monai.apps.nuclick.transforms import (\n",
     "    FlattenLabeld,\n",
@@ -48,6 +58,7 @@
     "from monai.data import (\n",
     "    Dataset,\n",
     "    DataLoader,\n",
+    "    MetaTensor\n",
     ")\n",
     "from monai.networks.nets import BasicUNet\n",
     "from skimage.measure import regionprops\n",
@@ -74,16 +85,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
     "def split_nuclei_dataset(d, centroid_key=\"centroid\", mask_value_key=\"mask_value\", min_area=5):\n",
     "    dataset_json = []\n",
     "\n",
     "    mask = LoadImage(image_only=True, dtype=np.uint8)(d[\"label\"])\n",
-    "    _, labels, _, _ = cv2.connectedComponentsWithStats(mask, 4, cv2.CV_32S)\n",
-    "\n",
+    "    _, labels, _, _ = cv2.connectedComponentsWithStats(mask.array if isinstance(mask, MetaTensor) else mask, 4, cv2.CV_32S)\n",
     "    stats = regionprops(labels)\n",
     "    for stat in stats:\n",
     "        if stat.area < min_area:\n",