image_dataset.ipynb

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

Author: wyli

modules/image_dataset.ipynb

@@ -44,7 +44,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2021-01-14T12:34:04.909819Z",
@@ -59,26 +59,29 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 0.6.0rc1+23.gc6793fd0\n",
-      "Numpy version: 1.20.3\n",
-      "Pytorch version: 1.9.0a0+c3d40fd\n",
-      "MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
-      "MONAI rev id: c6793fd0f316a448778d0047664aaf8c1895fe1c\n",
+      "MONAI version: 0.9.1rc1+6.gcbe16eb3\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: cbe16eb326830ef31479fd34ae1e44d27fc2d64d\n",
+      "MONAI __file__: /home/wenqil/Documents/MONAI/monai/__init__.py\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.5\n",
-      "Nibabel version: 3.2.1\n",
-      "scikit-image version: 0.15.0\n",
-      "Pillow version: 8.2.0\n",
-      "Tensorboard version: 2.5.0\n",
-      "gdown version: 3.13.0\n",
-      "TorchVision version: 0.10.0a0\n",
-      "ITK version: 5.1.2\n",
-      "tqdm version: 4.53.0\n",
-      "lmdb version: 1.2.1\n",
-      "psutil version: 5.8.0\n",
-      "pandas version: 1.1.4\n",
-      "einops version: 0.3.0\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: 5.9.1\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",
@@ -124,7 +127,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -150,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2021-01-14T12:34:07.530773Z",
@@ -173,8 +176,9 @@
    "source": [
     "class TestCompose(Compose):\n",
     "    def __call__(self, data, meta):\n",
-    "        data = self.transforms[0](data, meta)  # ensure channel first\n",
-    "        data, _, meta[\"affine\"] = self.transforms[1](data, meta[\"affine\"])  # spacing\n",
+    "        data = self.transforms[0](data)  # ensure channel first\n",
+    "        data = self.transforms[1](data)  # spacing\n",
+    "        meta = data.meta\n",
     "        if len(self.transforms) == 3:\n",
     "            return self.transforms[2](data), meta  # image contrast\n",
     "        return data, meta\n",
@@ -213,7 +217,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -227,7 +231,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.8.0"
   }
  },
  "nbformat": 4,