Fix deprecated error in active learning tutorials (#1844)

Fixes #1843 

### Description
A few sentences describing the changes proposed in this pull request.

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [ ] Clean up long text outputs from code cells in the notebook.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>

Author: KumoLiu

active_learning/liver_tumor_al/active_learning.py

@@ -155,7 +155,7 @@ def main():
     # Model Definition
     device = torch.device("cuda:0")
     network = UNet(
-        dimensions=3,
+        spatial_dims=3,
         in_channels=1,
         out_channels=3,
         channels=(16, 32, 64, 128, 256),
@@ -187,7 +187,7 @@ def main():
                 b_max=1.0,
                 clip=True,
             ),
-            CropForegroundd(keys=["image", "label"], source_key="image"),
+            CropForegroundd(keys=["image", "label"], source_key="image", allow_smaller=True),
             SpatialPadd(keys=["image", "label"], spatial_size=(96, 96, 96)),
             RandCropByPosNegLabeld(
                 keys=["image", "label"],
@@ -225,7 +225,7 @@ def main():
                 b_max=1.0,
                 clip=True,
             ),
-            CropForegroundd(keys=["image", "label"], source_key="image"),
+            CropForegroundd(keys=["image", "label"], source_key="image", allow_smaller=True),
             EnsureTyped(keys=["image", "label"]),
         ]
     )
@@ -240,7 +240,7 @@ def main():
                 mode=("bilinear"),
             ),
             ScaleIntensityRanged(keys="image", a_min=-21, a_max=189, b_min=0.0, b_max=1.0, clip=True),
-            CropForegroundd(keys=("image"), source_key="image"),
+            CropForegroundd(keys=("image"), source_key="image", allow_smaller=True),
             EnsureTyped(keys=["image"]),
         ]
     )
@@ -315,7 +315,7 @@ def main():
         unl_loader = DataLoader(unl_ds, batch_size=1)
 
         # Calculation of Epochs based on steps
-        max_epochs = np.int(args.steps / (np.ceil(len(train_d) / args.batch_size)))
+        max_epochs = int(args.steps / (np.ceil(len(train_d) / args.batch_size)))
         print("Epochs Estimated are {} for Active Iter {} with {} Vols".format(max_epochs, active_iter, len(train_d)))
 
         # Model Training begins for one active iteration
@@ -393,7 +393,7 @@ def main():
         prev_best_ckpt = os.path.join(active_model_dir, "model.pt")
 
         device = torch.device("cuda:0")
-        ckpt = torch.load(prev_best_ckpt)
+        ckpt = torch.load(prev_best_ckpt, weights_only=True)
         network.load_state_dict(ckpt)
         network.to(device=device)
 
@@ -487,16 +487,16 @@ def main():
 
                     variance_dims = np.shape(variance)
                     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)
                         )
                     )
 
                     # Plot with matplotlib and save all slices
                     plt.figure(1)
-                    plt.imshow(np.squeeze(variance[:, :, np.int(variance_dims[2] / 2)]))
+                    plt.imshow(np.squeeze(variance[:, :, int(variance_dims[2] / 2)]))
                     plt.colorbar()
                     plt.title("Dropout Uncertainty")
                     fig_path = os.path.join(fig_base_dir, "active_{}_file_{}.png".format(active_iter, counter))

active_learning/liver_tumor_al/results_uncertainty_analysis.ipynb

@@ -281,7 +281,7 @@ def main():
         unl_loader = DataLoader(unl_ds, batch_size=1)
 
         # Calculation of Epochs based on steps
-        max_epochs = np.int(args.steps / (np.ceil(len(train_d) / args.batch_size)))
+        max_epochs = int(args.steps / (np.ceil(len(train_d) / args.batch_size)))
         print("Epochs Estimated are {} for Active Iter {} with {} Vols".format(max_epochs, active_iter, len(train_d)))
 
         # Keep track of Best_metric, it is being used as IoU and not Dice
@@ -379,7 +379,7 @@ def main():
         prev_best_ckpt = os.path.join(active_model_dir, "model.pt")
 
         device = torch.device("cuda:0")
-        ckpt = torch.load(prev_best_ckpt)
+        ckpt = torch.load(prev_best_ckpt, weights_only=True)
         network.load_state_dict(ckpt)
         network.to(device=device)
 

active_learning/tool_tracking_al/active_learning.py

@@ -37,7 +37,10 @@
     "\n",
     "The notebook demonstrates a complete pipeline for training and evaluating a cell segmentation model using the MONAI framework and the Segment Anything Model (SAM) on the Cellpose dataset. Please note we only use a small subset of the cellpose dataset for this tutorial.\n",
     "\n",
-    "For additional information about VISTA-2D please also refer the [MONAI bundle](https://github.com/Project-MONAI/VISTA/tree/main/vista2d) and the [technical blog post](https://developer.nvidia.com/blog/advancing-cell-segmentation-and-morphology-analysis-with-nvidia-ai-foundation-model-vista-2d/)."
+    "For additional information about VISTA-2D please also refer the [MONAI bundle](https://github.com/Project-MONAI/VISTA/tree/main/vista2d) and the [technical blog post](https://developer.nvidia.com/blog/advancing-cell-segmentation-and-morphology-analysis-with-nvidia-ai-foundation-model-vista-2d/).\n",
+    "\n",
+    "For dependency-related issues, you can also check this note:\n",
+    "https://github.com/Project-MONAI/model-zoo/tree/dev/models/vista2d#dependencies."
    ]
   },
   {