Merge remote-tracking branch 'origin/main' into fix-maisi

Author: KumoLiu

active_learning/tool_tracking_al/active_learning.py

@@ -469,10 +469,10 @@ def main():
                     variance = np.sum(np.nanvar(vol_input, axis=0), axis=0)
 
                     score_list.append(np.nanmean(variance))
-                    name_list.append(unl_data["image_meta_dict"]["filename_or_obj"][0])
+                    name_list.append(unl_data["image"].meta["filename_or_obj"][0])
                     print(
                         "Variance for image: {} is: {}".format(
-                            unl_data["image_meta_dict"]["filename_or_obj"][0], np.nanmean(variance)
+                            unl_data["image"].meta["filename_or_obj"][0], np.nanmean(variance)
                         )
                     )
 

active_learning/tool_tracking_al/results_uncertainty_analysis.ipynb

@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "d5b36e92",
    "metadata": {},
    "outputs": [],
@@ -56,37 +56,40 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "id": "57ef4a1b",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "MONAI version: 1.0.1\n",
-      "Numpy version: 1.23.4\n",
-      "Pytorch version: 1.13.0+cu117\n",
+      "MONAI version: 1.4.0rc10\n",
+      "Numpy version: 1.24.4\n",
+      "Pytorch version: 2.5.0a0+872d972e41.nv24.08.01\n",
       "MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False\n",
-      "MONAI rev id: 8271a193229fe4437026185e218d5b06f7c8ce69\n",
-      "MONAI __file__: /home/vishwesh/anaconda3/envs/mtk_py38/lib/python3.8/site-packages/monai/__init__.py\n",
+      "MONAI rev id: cac21f6936a2e8d6e4e57e4e958f8e32aae1585e\n",
+      "MONAI __file__: /usr/local/lib/python3.10/dist-packages/monai/__init__.py\n",
       "\n",
       "Optional dependencies:\n",
-      "Pytorch Ignite version: 0.4.10\n",
-      "Nibabel version: 4.0.2\n",
-      "scikit-image version: 0.19.3\n",
-      "Pillow version: 9.3.0\n",
-      "Tensorboard version: 2.11.0\n",
-      "gdown version: 4.5.3\n",
-      "TorchVision version: 0.14.0+cu117\n",
-      "tqdm version: 4.64.1\n",
-      "lmdb version: 1.3.0\n",
-      "psutil version: 5.9.0\n",
-      "pandas version: 1.5.1\n",
-      "einops version: 0.6.0\n",
-      "transformers version: 4.21.3\n",
-      "mlflow version: 2.0.1\n",
-      "pynrrd version: 0.4.3\n",
+      "Pytorch Ignite version: 0.4.11\n",
+      "ITK version: 5.4.0\n",
+      "Nibabel version: 5.2.1\n",
+      "scikit-image version: 0.23.2\n",
+      "scipy version: 1.13.1\n",
+      "Pillow version: 10.4.0\n",
+      "Tensorboard version: 2.17.0\n",
+      "gdown version: 5.2.0\n",
+      "TorchVision version: 0.20.0a0\n",
+      "tqdm version: 4.66.4\n",
+      "lmdb version: 1.5.1\n",
+      "psutil version: 5.9.8\n",
+      "pandas version: 2.2.2\n",
+      "einops version: 0.7.0\n",
+      "transformers version: 4.40.2\n",
+      "mlflow version: 2.16.0\n",
+      "pynrrd version: 1.0.0\n",
+      "clearml version: 1.16.3\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",
@@ -136,7 +139,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "id": "1d14c99c",
    "metadata": {},
    "outputs": [
@@ -188,7 +191,7 @@
     ").cuda()\n",
     "\n",
     "# Load Model Weights\n",
-    "model.load_state_dict(torch.load(model_ckpt))\n",
+    "model.load_state_dict(torch.load(model_ckpt, weights_only=True))\n",
     "\n",
     "# Please note that the model is being put to 'train' mode explicitly for Monte-Carlo simulations\n",
     "model.train()\n",
@@ -197,16 +200,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "22b9db61",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "/scratch_2/robo_tool_dataset_2023/robo_tool/dv13_00098.png\n",
-      "Variance for image: /scratch_2/robo_tool_dataset_2023/robo_tool/dv13_00098.png is: 0.0021140489261597395\n"
+      "/workspace/Data/robo_tool/dv13_00098.png\n",
+      "Variance for image: /workspace/Data/robo_tool/dv13_00098.png is: 0.005063239950686693\n"
      ]
     },
     {
@@ -286,7 +289,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "cc913015",
    "metadata": {},
    "outputs": [],
@@ -344,9 +347,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mtk_py38",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "mtk_py38"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -358,7 +361,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.15"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

pathology/nuclick/nuclei_classification_training_notebook.ipynb

@@ -92,7 +92,7 @@
     "import torch.distributed\n",
     "from IPython.display import Image as IImage\n",
     "from monai.apps.nuclick.transforms import AddLabelAsGuidanced, SetLabelClassd, SplitLabeld\n",
-    "from monai.config import IgniteInfo, print_config\n",
+    "from monai.config import print_config\n",
     "from monai.data import CacheDataset, DataLoader\n",
     "from monai.engines import SupervisedEvaluator, SupervisedTrainer\n",
     "from monai.handlers import CheckpointSaver, ConfusionMatrix, StatsHandler, ValidationHandler, from_engine\n",
@@ -112,7 +112,7 @@
     "    SelectItemsd,\n",
     "    ToTensord,\n",
     ")\n",
-    "from monai.utils import min_version, optional_import\n",
+    "from monai.utils import min_version, optional_import, IgniteInfo\n",
     "from PIL import Image, ImageDraw\n",
     "from scipy.io import loadmat\n",
     "from sklearn.metrics import classification_report\n",

pathology/nuclick/nuclick_training_notebook.ipynb

@@ -94,7 +94,7 @@
     "import torch.distributed\n",
     "from IPython.display import Image as IImage\n",
     "from monai.apps.nuclick.transforms import AddPointGuidanceSignald, SplitLabeld\n",
-    "from monai.config import IgniteInfo, print_config\n",
+    "from monai.config import print_config\n",
     "from monai.data import CacheDataset, DataLoader\n",
     "from monai.engines import SupervisedEvaluator, SupervisedTrainer\n",
     "from monai.handlers import CheckpointSaver, MeanDice, StatsHandler, ValidationHandler, from_engine\n",
@@ -114,7 +114,7 @@
     "    ScaleIntensityRangeD,\n",
     "    SelectItemsd,\n",
     ")\n",
-    "from monai.utils import min_version, optional_import\n",
+    "from monai.utils import min_version, optional_import, IgniteInfo\n",
     "from PIL import Image\n",
     "from scipy.io import loadmat\n",
     "from tqdm import tqdm\n",