Merge remote-tracking branch 'origin/dev' into geometric

.github/workflows/conda.yml

@@ -26,7 +26,7 @@ jobs:
     steps:
     - if: runner.os == 'windows'
       name: Config pagefile (Windows only)
-      uses: al-cheb/configure-pagefile-action@v1.3
+      uses: al-cheb/configure-pagefile-action@v1.4
       with:
         minimum-size: 8GB
         maximum-size: 16GB

.github/workflows/cron.yml

@@ -19,18 +19,18 @@ jobs:
           - "PTLATEST+CUDA121"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
-          - environment: PT191+CUDA113
-            pytorch: "torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113"
-            base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
           - environment: PT110+CUDA113
             pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
           - environment: PT113+CUDA113
             pytorch: "torch==1.13.1 torchvision==0.14.1 --extra-index-url https://download.pytorch.org/whl/cu113"
             base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
-          - environment: PTLATEST+CUDA121
-            pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu118"
+          - environment: PT113+CUDA122
+            pytorch: "torch==1.13.1 torchvision==0.14.1 --extra-index-url https://download.pytorch.org/whl/cu121"
             base: "nvcr.io/nvidia/pytorch:23.08-py3"  # CUDA 12.2
+          - environment: PTLATEST+CUDA124
+            pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu121"
+            base: "nvcr.io/nvidia/pytorch:24.03-py3"  # CUDA 12.4
     container:
       image: ${{ matrix.base }}
       options: "--gpus all"
@@ -76,7 +76,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:22.10", "pytorch:23.08"]
+        container: ["pytorch:23.08", "pytorch:24.03"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -121,7 +121,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:23.08"]
+        container: ["pytorch:24.03"]
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -221,7 +221,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:23.08-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:24.03-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

@@ -29,10 +29,6 @@ jobs:
           - "PT210+CUDA121DOCKER"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
-          - environment: PT19+CUDA114DOCKER
-            # 21.10: 1.10.0a0+0aef44c
-            pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
-            base: "nvcr.io/nvidia/pytorch:21.10-py3"
           - environment: PT110+CUDA111
             pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu111"
             base: "nvcr.io/nvidia/cuda:11.1.1-devel-ubuntu18.04"
@@ -47,6 +43,10 @@ jobs:
             # 23.08: 2.1.0a0+29c30b1
             pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
             base: "nvcr.io/nvidia/pytorch:23.08-py3"
+          - environment: PT210+CUDA121DOCKER
+            # 24.03: 2.3.0a0+40ec155e58.nv24.3
+            pytorch: "-h"  # we explicitly set pytorch to -h to avoid pip install error
+            base: "nvcr.io/nvidia/pytorch:24.03-py3"
     container:
       image: ${{ matrix.base }}
       options: --gpus all --env NVIDIA_DISABLE_REQUIRE=true  # workaround for unsatisfied condition: cuda>=11.6

.github/workflows/pythonapp.yml

@@ -62,7 +62,7 @@ jobs:
     steps:
     - if: runner.os == 'windows'
       name: Config pagefile (Windows only)
-      uses: al-cheb/configure-pagefile-action@v1.3
+      uses: al-cheb/configure-pagefile-action@v1.4
       with:
         minimum-size: 8GB
         maximum-size: 16GB

.pre-commit-config.yaml

@@ -27,7 +27,7 @@ repos:
       - id: end-of-file-fixer
       - id: mixed-line-ending
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.261
+    rev: v0.3.5
     hooks:
     -   id: ruff
         args:

Dockerfile

@@ -11,13 +11,20 @@
 
 # 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:23.08-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:24.03-py3
 FROM ${PYTORCH_IMAGE}
 
 LABEL maintainer="monai.contact@gmail.com"
 
+# TODO: remark for issue [revise the dockerfile](https://github.com/zarr-developers/numcodecs/issues/431)
+WORKDIR /opt
+RUN git clone --recursive https://github.com/zarr-developers/numcodecs.git && pip wheel numcodecs
+
 WORKDIR /opt/monai
 
+# remove opencv-python before opencv-python-headless installation
+RUN pip uninstall -y opencv && rm /usr/local/lib/python3.10/dist-packages/cv2 -r
+
 # install full deps
 COPY requirements.txt requirements-min.txt requirements-dev.txt /tmp/
 RUN cp /tmp/requirements.txt /tmp/req.bak \

docs/source/losses.rst

@@ -73,6 +73,11 @@ Segmentation Losses
 .. autoclass:: ContrastiveLoss
     :members:
 
+`BarlowTwinsLoss`
+~~~~~~~~~~~~~~~~~
+.. autoclass:: BarlowTwinsLoss
+    :members:
+
 `HausdorffDTLoss`
 ~~~~~~~~~~~~~~~~~
 .. autoclass:: HausdorffDTLoss
@@ -134,6 +139,11 @@ Reconstruction Losses
 .. autoclass:: JukeboxLoss
     :members:
 
+`SURELoss`
+~~~~~~~~~~
+.. autoclass:: SURELoss
+    :members:
+
 
 Loss Wrappers
 -------------

docs/source/networks.rst

@@ -408,6 +408,11 @@ Layers
 .. autoclass:: LLTM
     :members:
 
+`ConjugateGradient`
+~~~~~~~~~~~~~~~~~~~
+.. autoclass:: ConjugateGradient
+    :members:
+
 `Utilities`
 ~~~~~~~~~~~
 .. automodule:: monai.networks.layers.convutils

docs/source/transforms.rst

@@ -309,6 +309,12 @@ Intensity
     :members:
     :special-members: __call__
 
+`ClipIntensityPercentiles`
+""""""""""""""""""""""""""
+.. autoclass:: ClipIntensityPercentiles
+    :members:
+    :special-members: __call__
+
 `RandScaleIntensity`
 """"""""""""""""""""
 .. image:: https://raw.githubusercontent.com/Project-MONAI/DocImages/main/transforms/RandScaleIntensity.png
@@ -661,6 +667,27 @@ Post-processing
     :members:
     :special-members: __call__
 
+Regularization
+^^^^^^^^^^^^^^
+
+`CutMix`
+""""""""
+.. autoclass:: CutMix
+    :members:
+    :special-members: __call__
+
+`CutOut`
+""""""""
+.. autoclass:: CutOut
+    :members:
+    :special-members: __call__
+
+`MixUp`
+"""""""
+.. autoclass:: MixUp
+    :members:
+    :special-members: __call__
+
 Signal
 ^^^^^^^
 
@@ -1384,6 +1411,12 @@ Intensity (Dict)
     :members:
     :special-members: __call__
 
+`ClipIntensityPercentilesd`
+"""""""""""""""""""""""""""
+.. autoclass:: ClipIntensityPercentilesd
+    :members:
+    :special-members: __call__
+
 `RandScaleIntensityd`
 """""""""""""""""""""
 .. image:: https://raw.githubusercontent.com/Project-MONAI/DocImages/main/transforms/RandScaleIntensityd.png
@@ -1707,6 +1740,27 @@ Post-processing (Dict)
   :members:
   :special-members: __call__
 
+Regularization (Dict)
+^^^^^^^^^^^^^^^^^^^^^
+
+`CutMixd`
+"""""""""
+.. autoclass:: CutMixd
+    :members:
+    :special-members: __call__
+
+`CutOutd`
+"""""""""
+.. autoclass:: CutOutd
+    :members:
+    :special-members: __call__
+
+`MixUpd`
+""""""""
+.. autoclass:: MixUpd
+    :members:
+    :special-members: __call__
+
 Signal (Dict)
 ^^^^^^^^^^^^^
 

docs/source/transforms_idx.rst

@@ -74,6 +74,16 @@ Post-processing
    post.array
    post.dictionary
 
+Regularization
+^^^^^^^^^^^^^^
+
+.. autosummary::
+   :toctree: _gen
+   :nosignatures:
+
+   regularization.array
+   regularization.dictionary
+
 Signal
 ^^^^^^
 

monai/__init__.py

@@ -83,6 +83,11 @@
     from .utils.tf32 import detect_default_tf32
 
     detect_default_tf32()
+    import torch
+
+    # workaround related to https://github.com/Project-MONAI/MONAI/issues/7575
+    if hasattr(torch.cuda.device_count, "cache_clear"):
+        torch.cuda.device_count.cache_clear()
 except BaseException:
     from .utils.misc import MONAIEnvVars
 

monai/apps/auto3dseg/hpo_gen.py

@@ -193,7 +193,9 @@ def generate(self, output_folder: str = ".") -> None:
         self.obj_filename = os.path.join(write_path, "algo_object.pkl")
 
         if isinstance(self.algo, BundleAlgo):
-            self.algo.export_to_disk(output_folder, task_prefix + task_id, fill_with_datastats=False)
+            self.algo.export_to_disk(
+                output_folder, task_prefix + task_id, bundle_root=write_path, fill_with_datastats=False
+            )
         else:
             ConfigParser.export_config_file(self.params, write_path)
             logger.info(write_path)