Merge branch 'dev' into fix-compose

.github/workflows/cron.yml

@@ -16,7 +16,8 @@ jobs:
           - "PT110+CUDA113"
           - "PT113+CUDA118"
           - "PT210+CUDA121"
-          - "PTLATEST+CUDA124"
+          - "PT240+CUDA126"
+          - "PTLATEST+CUDA126"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
           - environment: PT110+CUDA113
@@ -28,9 +29,12 @@ jobs:
           - environment: PT210+CUDA121
             pytorch: "pytorch==2.1.0 torchvision==0.16.0 --extra-index-url https://download.pytorch.org/whl/cu121"
             base: "nvcr.io/nvidia/pytorch:23.08-py3"  # CUDA 12.1
-          - environment: PTLATEST+CUDA124
+          - environment: PT240+CUDA126
+            pytorch: "pytorch==2.4.0 torchvision==0.19.0 --extra-index-url https://download.pytorch.org/whl/cu121"
+            base: "nvcr.io/nvidia/pytorch:24.08-py3"  # CUDA 12.6
+          - environment: PTLATEST+CUDA126
             pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu121"
-            base: "nvcr.io/nvidia/pytorch:24.08-py3"  # CUDA 12.4
+            base: "nvcr.io/nvidia/pytorch:24.10-py3"  # CUDA 12.6
     container:
       image: ${{ matrix.base }}
       options: "--gpus all"
@@ -71,7 +75,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -80,7 +84,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:23.08", "pytorch:24.08"]
+        container: ["pytorch:23.08", "pytorch:24.08", "pytorch:24.10"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -119,7 +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
@@ -129,7 +133,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:24.08"]
+        container: ["pytorch:24.10"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -224,7 +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
@@ -233,7 +237,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:24.08-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:24.10-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, integration]
     steps:

.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

Dockerfile

@@ -11,7 +11,7 @@
 
 # To build with a different base image
 # please run `docker build` using the `--build-arg PYTORCH_IMAGE=...` flag.
-ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:24.08-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:24.10-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="monai.contact@gmail.com"
@@ -41,6 +41,10 @@ RUN cp /tmp/requirements.txt /tmp/req.bak \
 COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md versioneer.py setup.py setup.cfg runtests.sh MANIFEST.in ./
 COPY tests ./tests
 COPY monai ./monai
+
+# TODO: remove this line and torch.patch for 24.11
+RUN patch -R -d /usr/local/lib/python3.10/dist-packages/torch/onnx/ < ./monai/torch.patch
+
 RUN BUILD_MONAI=1 FORCE_CUDA=1 python setup.py develop \
   && rm -rf build __pycache__
 
@@ -57,4 +61,6 @@ RUN apt-get update \
 # append /opt/tools to runtime path for NGC CLI to be accessible from all file system locations
 ENV PATH=${PATH}:/opt/tools
 ENV POLYGRAPHY_AUTOINSTALL_DEPS=1
+
+
 WORKDIR /opt/monai

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/apps/utils.py

@@ -15,6 +15,7 @@
 import json
 import logging
 import os
+import re
 import shutil
 import sys
 import tarfile
@@ -30,7 +31,9 @@
 from monai.config.type_definitions import PathLike
 from monai.utils import look_up_option, min_version, optional_import
 
+requests, has_requests = optional_import("requests")
 gdown, has_gdown = optional_import("gdown", "4.7.3")
+BeautifulSoup, has_bs4 = optional_import("bs4", name="BeautifulSoup")
 
 if TYPE_CHECKING:
     from tqdm import tqdm
@@ -298,6 +301,29 @@ def extractall(
     )
 
 
+def get_filename_from_url(data_url: str) -> str:
+    """
+    Get the filename from the URL link.
+    """
+    try:
+        response = requests.head(data_url, allow_redirects=True)
+        content_disposition = response.headers.get("Content-Disposition")
+        if content_disposition:
+            filename = re.findall('filename="?([^";]+)"?', content_disposition)
+            if filename:
+                return str(filename[0])
+        if "drive.google.com" in data_url:
+            response = requests.get(data_url)
+            if "text/html" in response.headers.get("Content-Type", ""):
+                soup = BeautifulSoup(response.text, "html.parser")
+                filename_div = soup.find("span", {"class": "uc-name-size"})
+                if filename_div:
+                    return str(filename_div.find("a").text)
+        return _basename(data_url)
+    except Exception as e:
+        raise Exception(f"Error processing URL: {e}") from e
+
+
 def download_and_extract(
     url: str,
     filepath: PathLike = "",
@@ -327,7 +353,18 @@ def download_and_extract(
             be False.
         progress: whether to display progress bar.
     """
+    url_filename_ext = "".join(Path(get_filename_from_url(url)).suffixes)
+    filepath_ext = "".join(Path(_basename(filepath)).suffixes)
+    if filepath not in ["", "."]:
+        if filepath_ext == "":
+            new_filepath = Path(filepath).with_suffix(url_filename_ext)
+            logger.warning(
+                f"filepath={filepath}, which missing file extension. Auto-appending extension to: {new_filepath}"
+            )
+            filepath = new_filepath
+    if filepath_ext and filepath_ext != url_filename_ext:
+        raise ValueError(f"File extension mismatch: expected extension {url_filename_ext}, but get {filepath_ext}")
     with tempfile.TemporaryDirectory() as tmp_dir:
-        filename = filepath or Path(tmp_dir, _basename(url)).resolve()
+        filename = filepath or Path(tmp_dir, get_filename_from_url(url)).resolve()
         download_url(url=url, filepath=filename, hash_val=hash_val, hash_type=hash_type, progress=progress)
         extractall(filepath=filename, output_dir=output_dir, file_type=file_type, has_base=has_base)

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:
         """

monai/bundle/scripts.py

@@ -1589,6 +1589,8 @@ def trt_export(
     """
     Export the model checkpoint to the given filepath as a TensorRT engine-based TorchScript.
     Currently, this API only supports converting models whose inputs are all tensors.
+    Note: NVIDIA Volta support (GPUs with compute capability 7.0) has been removed starting with TensorRT 10.5.
+    Review the TensorRT Support Matrix for which GPUs are supported.
 
     There are two ways to export a model:
     1, Torch-TensorRT way: PyTorch module ---> TorchScript module ---> TensorRT engine-based TorchScript.