nifti read

Signed-off-by: Wenqi Li <[email protected]>

Author: wyli

modules/nifti_read_example.ipynb

@@ -47,27 +47,29 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 0.8.1\n",
-      "Numpy version: 1.21.5\n",
-      "Pytorch version: 1.10.2\n",
-      "MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
-      "MONAI rev id: 71ff399a3ea07aef667b23653620a290364095b1\n",
+      "MONAI version: 0.9.1rc2+2.gc0268266.dirty\n",
+      "Numpy version: 1.23.0\n",
+      "Pytorch version: 1.12.0+cu102\n",
+      "MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False\n",
+      "MONAI rev id: c0268266f688c3bacd9c92ef7458f54b6afdf609\n",
+      "MONAI __file__: /home/wenqil/Documents/MONAI/monai/__init__.py\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.8\n",
-      "Nibabel version: 3.2.1\n",
-      "scikit-image version: 0.19.1\n",
-      "Pillow version: 9.0.0\n",
-      "Tensorboard version: 2.8.0\n",
-      "gdown version: 4.2.0\n",
-      "TorchVision version: 0.11.3\n",
-      "tqdm version: 4.62.3\n",
+      "Pytorch Ignite version: 0.4.9\n",
+      "Nibabel version: 4.0.1\n",
+      "scikit-image version: 0.19.3\n",
+      "Pillow version: 9.2.0\n",
+      "Tensorboard version: 2.9.1\n",
+      "gdown version: 4.5.1\n",
+      "TorchVision version: 0.13.0+cu102\n",
+      "tqdm version: 4.64.0\n",
       "lmdb version: 1.3.0\n",
-      "psutil version: 5.9.0\n",
-      "pandas version: 1.1.5\n",
-      "einops version: 0.4.0\n",
-      "transformers version: 4.16.1\n",
-      "mlflow version: 1.23.1\n",
+      "psutil version: 5.9.1\n",
+      "pandas version: 1.4.3\n",
+      "einops version: 0.4.1\n",
+      "transformers version: 4.20.1\n",
+      "mlflow version: 1.27.0\n",
+      "pynrrd version: 0.4.3\n",
       "\n",
       "For details about installing the optional dependencies, please visit:\n",
       "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
@@ -125,11 +127,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/tmp/tmpkzde8m5b\n"
+     ]
+    }
+   ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
@@ -177,7 +187,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "torch.Size([5, 1, 64, 64, 64]) torch.Size([5, 1, 64, 64, 64])\n"
+      "(5, 1, 64, 64, 64) (5, 1, 64, 64, 64)\n"
      ]
     }
    ],
@@ -187,27 +197,23 @@
     "\n",
     "imtrans = Compose(\n",
     "    [\n",
-    "        LoadImage(image_only=True),\n",
+    "        LoadImage(image_only=True, ensure_channel_first=True),\n",
     "        ScaleIntensity(),\n",
-    "        AddChannel(),\n",
     "        RandSpatialCrop((64, 64, 64), random_size=False),\n",
-    "        EnsureType(),\n",
     "    ]\n",
     ")\n",
     "\n",
     "segtrans = Compose(\n",
     "    [\n",
-    "        LoadImage(image_only=True),\n",
-    "        AddChannel(),\n",
+    "        LoadImage(image_only=True, ensure_channel_first=True),\n",
     "        RandSpatialCrop((64, 64, 64), random_size=False),\n",
-    "        EnsureType(),\n",
     "    ]\n",
     ")\n",
     "\n",
     "ds = ArrayDataset(images, imtrans, segs, segtrans)\n",
     "\n",
     "loader = torch.utils.data.DataLoader(\n",
-    "    ds, batch_size=10, num_workers=2, pin_memory=torch.cuda.is_available()\n",
+    "    ds, batch_size=10, num_workers=0, pin_memory=torch.cuda.is_available()\n",
     ")\n",
     "im, seg = first(loader)\n",
     "print(im.shape, seg.shape)"
@@ -283,7 +289,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -297,7 +303,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.8.0"
   }
  },
  "nbformat": 4,