Merge branch 'dev' into fix/8239-cldice-loss-enhancements

Author: aymuos15

.dockerignore

@@ -3,11 +3,15 @@
 __pycache__/
 docs/
 
+.vscode
+.git
+.mypy_cache
+.ruff_cache
+.pytype
 .coverage
 .coverage.*
 .coverage/
 coverage.xml
 .readthedocs.yml
-*.toml
 
 !README.md

.github/workflows/pythonapp.yml

@@ -82,7 +82,7 @@ jobs:
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
     - name: Install the dependencies
       run: |
-        python -m pip install --user --upgrade pip wheel
+        python -m pip install --user --upgrade pip wheel pybind11
         python -m pip install torch==2.5.1 torchvision==0.20.1
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt

.github/workflows/setupapp.yml

@@ -81,7 +81,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v6
       with:
@@ -90,23 +90,12 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v5
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ steps.pip-cache.outputs.datew }}
+        cache: pip
     - name: Install the dependencies
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation -r requirements-dev.txt
     - name: Run quick tests CPU ubuntu
       env:
         NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
@@ -115,8 +104,8 @@ jobs:
       run: |
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        BUILD_MONAI=0 ./runtests.sh --build --quick --unittests
-        BUILD_MONAI=1 ./runtests.sh --build --quick --min
+        BUILD_MONAI=0 ./runtests.sh --build --coverage --quick --unittests
+        BUILD_MONAI=1 ./runtests.sh --build --coverage --quick --min
         coverage xml --ignore-errors
     - name: Upload coverage
       uses: codecov/codecov-action@v5

CONTRIBUTING.md

@@ -380,7 +380,8 @@ All code review comments should be specific, constructive, and actionable.
 
 ### Release a new version
 
-The `dev` branch's `HEAD` always corresponds to MONAI docker image's latest tag: `projectmonai/monai:latest`.
+The `dev` branch's `HEAD` always corresponds to MONAI Docker image's latest tag: `projectmonai/monai:latest`. (No
+release is currently done for the slim MONAI image, this is built locally by users.)
 The `main` branch's `HEAD` always corresponds to the latest MONAI milestone release.
 
 When major features are ready for a milestone, to prepare for a new release:

Dockerfile.slim

@@ -0,0 +1,93 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# This is a slimmed down version of the MONAI Docker image using a smaller base image and multi-stage building. Not all
+# NVIDIA tools will be present but all libraries and compiled code are included. This image isn't provided through
+# Dockerhub so users must build locally: `docker build -t monai_slim -f Dockerfile.slim .`
+# Containers may require more shared memory, eg.: `docker run -ti --rm --gpus all --shm-size=10gb monai_slim /bin/bash`
+
+ARG IMAGE=debian:12-slim
+
+FROM ${IMAGE} AS build
+
+ARG TORCH_CUDA_ARCH_LIST="7.5 8.0 8.6 8.9 9.0+PTX"
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV APT_INSTALL="apt install -y --no-install-recommends"
+
+RUN apt update && apt upgrade -y && \
+    ${APT_INSTALL} ca-certificates python3-pip python-is-python3 git wget libopenslide0 unzip python3-dev && \
+    wget https://developer.download.nvidia.com/compute/cuda/repos/debian12/x86_64/cuda-keyring_1.1-1_all.deb && \
+    dpkg -i cuda-keyring_1.1-1_all.deb && \
+    apt update && \
+    ${APT_INSTALL} cuda-toolkit-12 && \
+    rm -rf /usr/lib/python*/EXTERNALLY-MANAGED /var/lib/apt/lists/* && \
+    python -m pip install --upgrade --no-cache-dir --no-build-isolation pip
+
+# TODO: remark for issue [revise the dockerfile](https://github.com/zarr-developers/numcodecs/issues/431)
+RUN if [[ $(uname -m) =~ "aarch64" ]]; then \
+      CFLAGS="-O3" DISABLE_NUMCODECS_SSE2=true DISABLE_NUMCODECS_AVX2=true python -m pip install numcodecs; \
+    fi
+
+# NGC Client
+WORKDIR /opt/tools
+ARG NGC_CLI_URI="https://ngc.nvidia.com/downloads/ngccli_linux.zip"
+RUN wget -q ${NGC_CLI_URI} && unzip ngccli_linux.zip && chmod u+x ngc-cli/ngc && \
+    find ngc-cli/ -type f -exec md5sum {} + | LC_ALL=C sort | md5sum -c ngc-cli.md5 && \
+    rm -rf ngccli_linux.zip ngc-cli.md5
+
+WORKDIR /opt/monai
+
+# copy relevant parts of repo
+COPY requirements.txt requirements-min.txt requirements-dev.txt versioneer.py setup.py setup.cfg pyproject.toml ./
+COPY LICENSE CHANGELOG.md CODE_OF_CONDUCT.md CONTRIBUTING.md README.md MANIFEST.in runtests.sh ./
+COPY tests ./tests
+COPY monai ./monai
+
+# install full deps
+RUN python -m pip install --no-cache-dir --no-build-isolation -r requirements-dev.txt
+
+# compile ext
+RUN CUDA_HOME=/usr/local/cuda FORCE_CUDA=1 USE_COMPILED=1 BUILD_MONAI=1 python setup.py develop
+
+# recreate the image without the installed CUDA packages then copy the installed MONAI and Python directories
+FROM ${IMAGE} AS build2
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV APT_INSTALL="apt install -y --no-install-recommends"
+
+RUN apt update && apt upgrade -y && \
+    ${APT_INSTALL} ca-certificates python3-pip python-is-python3 git libopenslide0 && \
+    apt clean && \
+    rm -rf /usr/lib/python*/EXTERNALLY-MANAGED /var/lib/apt/lists/* && \
+    python -m pip install --upgrade --no-cache-dir --no-build-isolation pip
+
+COPY --from=build /opt/monai /opt/monai
+COPY --from=build /opt/tools /opt/tools
+ARG PYTHON_VERSION=3.11
+COPY --from=build /usr/local/lib/python${PYTHON_VERSION}/dist-packages /usr/local/lib/python${PYTHON_VERSION}/dist-packages
+COPY --from=build /usr/local/bin /usr/local/bin
+
+RUN rm -rf /opt/monai/build /opt/monai/monai.egg-info && \
+    find /opt /usr/local/lib -type d -name __pycache__ -exec rm -rf {} +
+
+# flatten all layers down to one
+FROM ${IMAGE}
+LABEL maintainer="monai.contact@gmail.com"
+
+COPY --from=build2 / /
+
+WORKDIR /opt/monai
+
+ENV PATH=${PATH}:/opt/tools:/opt/tools/ngc-cli
+ENV POLYGRAPHY_AUTOINSTALL_DEPS=1
+ENV CUDA_HOME=/usr/local/cuda
+ENV BUILD_MONAI=1

MANIFEST.in

@@ -3,3 +3,5 @@ include monai/_version.py
 
 include README.md
 include LICENSE
+
+prune tests

README.md

@@ -61,6 +61,14 @@ Examples and notebook tutorials are located at [Project-MONAI/tutorials](https:/
 
 Technical documentation is available at [docs.monai.io](https://docs.monai.io).
 
+## Docker
+
+The MONAI Docker image is available from [Dockerhub](https://hub.docker.com/r/projectmonai/monai),
+tagged as `latest` for the latest state of `dev` or with a release version. A slimmed down image can also be built
+locally using `Dockerfile.slim`, see that file for instructions.
+
+To get started with the latest MONAI, use `docker run -ti --rm --gpus all projectmonai/monai:latest /bin/bash`.
+
 ## Citation
 
 If you have used MONAI in your research, please cite us! The citation can be exported from: <https://arxiv.org/abs/2211.02701>.

docs/source/losses.rst

@@ -98,6 +98,11 @@ Segmentation Losses
 .. autoclass:: NACLLoss
     :members:
 
+`MCCLoss`
+~~~~~~~~~
+.. autoclass:: MCCLoss
+    :members:
+
 Registration Losses
 -------------------
 

docs/source/metrics.rst

@@ -158,6 +158,13 @@ Metrics
 
 `Fréchet Inception Distance`
 ------------------------------
+`Embedding Collapse`
+------------------------------
+.. autofunction:: compute_embedding_collapse
+
+.. autoclass:: EmbeddingCollapseMetric
+    :members:
+
 .. autofunction:: compute_frechet_distance
 
 .. autoclass:: FIDMetric

monai/apps/auto3dseg/auto_runner.py

@@ -229,7 +229,7 @@ def __init__(
             input = os.path.join(os.path.abspath(work_dir), "input.yaml")
             logger.info(f"Input config is not provided, using the default {input}")
 
-        self.data_src_cfg = dict()
+        self.data_src_cfg = {}
         if isinstance(input, dict):
             self.data_src_cfg = input
         elif isinstance(input, str) and os.path.isfile(input):