Update vista3d to use MONAI components (Project-MONAI#627)

Fixes # .

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

### Status
**Ready/Work in progress/Hold**

### Please ensure all the checkboxes:
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Codeformat tests passed locally by running `./runtests.sh
--codeformat`.
- [ ] In-line docstrings updated.
- [ ] Update `version` and `changelog` in `metadata.json` if changing an
existing bundle.
- [ ] Please ensure the naming rules in config files meet our
requirements (please refer to: `CONTRIBUTING.md`).
- [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy`
are correct in `metadata.json`.
- [ ] Descriptions should be consistent with the content, such as
`eval_metrics` of the provided weights and TorchScript modules.
- [ ] Files larger than 25MB are excluded and replaced by providing
download links in `large_file.yml`.
- [ ] Avoid using path that contains personal information within config
files (such as use `/home/your_name/` for `"bundle_root"`).

---------

Signed-off-by: Yiheng Wang <vennw@nvidia.com>
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>

ci/verify_bundle.py

@@ -241,6 +241,8 @@ def check_properties(**kwargs):
     """
     app_properties_path = kwargs.get("properties_path", "")
     kwargs.pop("properties_path", None)
+    print(kwargs)
+
     workflow = create_workflow(**kwargs)
     if app_properties_path is not None and os.path.isfile(app_properties_path):
         shutil.copy(app_properties_path, "ci/bundle_properties.py")

models/vista3d/configs/evaluate.json

@@ -88,7 +88,7 @@
                 ]
             },
             {
-                "_target_": "scripts.monai_trans_utils.RelabelD",
+                "_target_": "monai.apps.vista3d.transforms.Relabeld",
                 "keys": "label",
                 "label_mappings": "@label_mappings",
                 "dtype": "$torch.uint8"
@@ -113,7 +113,7 @@
                 "sigmoid": true
             },
             {
-                "_target_": "scripts.monai_trans_utils.VistaPostTransform",
+                "_target_": "monai.apps.vista3d.transforms.VistaPostTransformd",
                 "keys": "pred"
             },
             {

models/vista3d/configs/inference.json

@@ -3,7 +3,8 @@
         "$import glob",
         "$import os",
         "$import scripts",
-        "$import numpy as np"
+        "$import numpy as np",
+        "$import json"
     ],
     "bundle_root": "./",
     "image_key": "image",
@@ -14,6 +15,11 @@
     "separate_folder": true,
     "input_dict": "${'image': '/data/Task09_Spleen/imagesTr/spleen_10.nii.gz', 'label_prompt': [3]}",
     "everything_labels": "$list(set([i+1 for i in range(132)]) - set([2,16,18,20,21,23,24,25,26,27,128,129,130,131,132]))",
+    "metadata_path": "$@bundle_root + '/configs/metadata.json'",
+    "metadata_file": "$open(@metadata_path,'r', encoding='utf8')",
+    "metadata": "$json.load(@metadata_file)",
+    "close_metadata_file": "$metadata_file.close()",
+    "labels_dict": "$@metadata['network_data_format']['outputs']['pred']['channel_def']",
     "subclass": {
         "2": [
             14,
@@ -43,7 +49,7 @@
     "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
     "use_cfp": false,
     "use_point_window": true,
-    "network_def": "$scripts.vista3d.vista_model_registry['vista3d_segresnet_d'](in_channels=@input_channels, image_size=@patch_size)",
+    "network_def": "$monai.networks.nets.vista3d132(in_channels=@input_channels)",
     "network": "$@network_def.to(@device)",
     "preprocessing_transforms": [
         {
@@ -75,10 +81,10 @@
             "source_key": "@image_key"
         },
         {
-            "_target_": "scripts.monai_trans_utils.VistaPreTransform",
+            "_target_": "monai.apps.vista3d.transforms.VistaPreTransformd",
             "keys": "@image_key",
             "subclass": "@subclass",
-            "bundle_root": "@bundle_root"
+            "labels_dict": "@labels_dict"
         },
         {
             "_target_": "ScaleIntensityRanged",
@@ -134,7 +140,7 @@
                 "_disabled_": true
             },
             {
-                "_target_": "scripts.monai_trans_utils.VistaPostTransform",
+                "_target_": "monai.apps.vista3d.transforms.VistaPostTransformd",
                 "keys": "pred"
             },
             {

models/vista3d/configs/metadata.json

@@ -1,19 +1,20 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20240725.json",
-    "version": "0.4.1",
+    "version": "0.4.2",
     "changelog": {
+        "0.4.2": "use MONAI components for network and utils",
         "0.4.1": "initial OSS version"
     },
-    "monai_version": "1.3.1",
-    "pytorch_version": "2.2.2",
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.4.0",
     "numpy_version": "1.24.4",
-    "matplotlib": "3.8.3",
-    "einops": "0.7.0",
     "required_packages_version": {
-        "scikit-image": "0.22.0",
+        "matplotlib": "3.9.1",
+        "einops": "0.7.0",
+        "scikit-image": "0.23.2",
         "nibabel": "5.2.1",
         "pytorch-ignite": "0.4.11",
-        "cucim": "23.08.00"
+        "cucim-cu12": "24.6.0"
     },
     "supported_apps": {
         "vista3d-nim": ""

models/vista3d/configs/train.json

@@ -43,7 +43,7 @@
         128
     ],
     "patch_size_valid": "$@patch_size",
-    "network_def": "$scripts.vista3d.vista_model_registry['vista3d_segresnet_d'](in_channels=@input_channels, image_size=@patch_size)",
+    "network_def": "$monai.networks.nets.vista3d132(in_channels=@input_channels)",
     "network": "$@network_def.to(@device)",
     "loss": {
         "_target_": "DiceCELoss",

models/vista3d/configs/train_continual.json

@@ -74,7 +74,7 @@
             "warn": false
         },
         {
-            "_target_": "scripts.monai_trans_utils.RelabelD",
+            "_target_": "monai.apps.vista3d.transforms.Relabeld",
             "keys": "label",
             "label_mappings": "@label_mappings",
             "dtype": "$torch.uint8"
@@ -101,7 +101,7 @@
     },
     "validate#preprocessing#transforms": "$@train#deterministic_transforms + [@valid_remap]",
     "valid_remap": {
-        "_target_": "scripts.monai_trans_utils.RelabelD",
+        "_target_": "monai.apps.vista3d.transforms.Relabeld",
         "keys": "label",
         "label_mappings": "${'default': [[c, i] for i, c in enumerate(@val_label_set)]}",
         "dtype": "$torch.uint8"

models/vista3d/large_files.yml

@@ -1,3 +1,3 @@
 large_files:
   - path: "models/model.pt"
-    url: "https://drive.google.com/file/d/1eLIxQwnxGsjggxiVjdcAyNvJ5DYtqmdc/view?usp=sharing"
+    url: "https://drive.google.com/file/d/1Sbe6GjlgH-GIcXolZzUiwgqR4DBYNLQ3/view?usp=drive_link"

models/vista3d/scripts/__init__.py

@@ -12,5 +12,4 @@
 # from .evaluator import EnsembleEvaluator, Evaluator, SupervisedEvaluator
 # from .multi_gpu_supervised_trainer import create_multigpu_supervised_evaluator, create_multigpu_supervised_trainer
 
-from . import vista3d
 from .early_stop_score_function import score_function

models/vista3d/scripts/evaluator.py

@@ -243,8 +243,8 @@ def _iteration(self, engine: SupervisedEvaluator, batchdata: dict[str, torch.Ten
                 label_set = np.arange(output_classes).tolist()
             label_prompt = torch.tensor(label_set).to(engine.state.device).unsqueeze(-1)
             # point prompt is generated withing vista3d,provide empty points
-            points = torch.zeros(label_prompt.shape[0], 1, 3)
-            point_labels = -1 + torch.zeros(label_prompt.shape[0], 1)
+            points = torch.zeros(label_prompt.shape[0], 1, 3).to(inputs.device)
+            point_labels = -1 + torch.zeros(label_prompt.shape[0], 1).to(inputs.device)
             if engine.hyper_kwargs["drop_point_prob"] > 0.99:
                 # automatic only validation
                 points = None

models/vista3d/scripts/inferer.py

@@ -13,12 +13,10 @@
 from typing import List, Union
 
 import torch
-from monai.inferers.inferer import Inferer
+from monai.apps.vista3d.inferer import point_based_window_inferer
+from monai.inferers import Inferer, sliding_window_inference
 from torch import Tensor
 
-from .monai_utils import sliding_window_inference
-from .utils import point_based_window_inferer
-
 
 class Vista3dInferer(Inferer):
     """