Merge branch 'Project-MONAI:dev' into 4980-get-wsi-at-mpp

Author: NikolasSchmitz

.github/workflows/cron.yml

@@ -75,7 +75,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -123,7 +123,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -228,7 +228,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         fail_ci_if_error: false
         files: ./coverage.xml

.github/workflows/pythonapp-gpu.yml

@@ -137,6 +137,6 @@ jobs:
       shell: bash
     - name: Upload coverage
       if: ${{ github.head_ref != 'dev' && github.event.pull_request.merged != true }}
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         files: ./coverage.xml

.github/workflows/setupapp.yml

@@ -72,7 +72,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -119,7 +119,7 @@ jobs:
         BUILD_MONAI=1 ./runtests.sh --build --quick --min
         coverage xml --ignore-errors
     - name: Upload coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         fail_ci_if_error: false
         files: ./coverage.xml

.gitignore

@@ -149,6 +149,9 @@ tests/testing_data/nrrd_example.nrrd
 # clang format tool
 .clang-format-bin/
 
+# ctags
+tags
+
 # VSCode
 .vscode/
 *.zip

docs/source/networks.rst

@@ -630,6 +630,11 @@ Nets
 .. autoclass:: ViTAutoEnc
   :members:
 
+`MaskedAutoEncoderViT`
+~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: MaskedAutoEncoderViT
+  :members:
+
 `FullyConnectedNet`
 ~~~~~~~~~~~~~~~~~~~
 .. autoclass:: FullyConnectedNet

docs/source/transforms.rst

@@ -1180,6 +1180,18 @@ Utility
     :members:
     :special-members: __call__
 
+`TorchIO`
+"""""""""
+.. autoclass:: TorchIO
+    :members:
+    :special-members: __call__
+
+`RandTorchIO`
+"""""""""""""
+.. autoclass:: RandTorchIO
+    :members:
+    :special-members: __call__
+
 `MapLabelValue`
 """""""""""""""
 .. autoclass:: MapLabelValue
@@ -2253,6 +2265,18 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
+`TorchIOd`
+""""""""""
+.. autoclass:: TorchIOd
+    :members:
+    :special-members: __call__
+
+`RandTorchIOd`
+""""""""""""""
+.. autoclass:: RandTorchIOd
+    :members:
+    :special-members: __call__
+
 `MapLabelValued`
 """"""""""""""""
 .. autoclass:: MapLabelValued

environment-dev.yml

@@ -7,6 +7,7 @@ channels:
 dependencies:
   - numpy>=1.24,<2.0
   - pytorch>=1.9
+  - torchio
   - torchvision
   - pytorch-cuda>=11.6
   - pip

monai/bundle/__init__.py

@@ -43,4 +43,4 @@
     MACRO_KEY,
     load_bundle_config,
 )
-from .workflows import BundleWorkflow, ConfigWorkflow
+from .workflows import BundleWorkflow, ConfigWorkflow, PythonicWorkflow

monai/bundle/reference_resolver.py

@@ -192,6 +192,16 @@ def get_resolved_content(self, id: str, **kwargs: Any) -> ConfigExpression | str
         """
         return self._resolve_one_item(id=id, **kwargs)
 
+    def remove_resolved_content(self, id: str) -> Any | None:
+        """
+        Remove the resolved ``ConfigItem`` by id.
+
+        Args:
+            id: id name of the expected item.
+
+        """
+        return self.resolved_content.pop(id) if id in self.resolved_content else None
+
     @classmethod
     def normalize_id(cls, id: str | int) -> str:
         """