Merge pull request #72 from FeTS-AI/fixing_docker_build_for_1.0

Fixing docker build for 1.0

.github/workflows/docker-image.yml

@@ -29,9 +29,9 @@ jobs:
     steps:
     - name: Check out the repository
       uses: actions/checkout@v3
-      # with:
+      with:
       #   lfs: false
-      #   submodules: 'recursive'
+        submodules: 'true'
 
     # - name: Check if the repository has changed
     #   run: ls -l
@@ -53,7 +53,7 @@ jobs:
       run: |
         echo "Free space:"
         df -h
-         
+
     # Install the cosign tool except on PR
     # https://github.com/sigstore/cosign-installer
     - name: Install cosign
@@ -117,7 +117,9 @@ jobs:
     # Run the image from the base entrypoint as a test
     - name: Test container with entrypoint
       # Run a tag we generated from the metadata extraction above -- they're all the same image, but echo it regardless just so we know.
-      run: docker run --rm ghcr.io/fets-ai/front-end:latest -h
+      run: |
+        docker run --rm ghcr.io/fets-ai/front-end:latest -h
+        docker run --entrypoint /Front-End/bin/install/appdir/usr/bin/BraTSPipeline ghcr.io/fets-ai/front-end:latest -h 
 
     # Push Docker image with Buildx (but don't push on PR)
     # https://github.com/docker/build-push-action
@@ -148,4 +150,3 @@ jobs:
     #  # This step uses the identity token to provision an ephemeral certificate
     #  # against the sigstore community Fulcio instance.
     #  run: cosign sign ghcr.io/fets-ai/front-end@${{ steps.upload.outputs.digest }}
-

CMakeLists.txt

@@ -13,7 +13,7 @@ SET( ${PROJECT_NAME}_Variant "Full" ) # the particular variant of CaPTk (Full/Ne
 
 SET( PROJECT_VERSION_MAJOR 1 )
 SET( PROJECT_VERSION_MINOR 0 )
-SET( PROJECT_VERSION_PATCH 2 )
+SET( PROJECT_VERSION_PATCH 3 )
 SET( PROJECT_VERSION_TWEAK )
 
 # check for the string "nonRelease" in the PROJECT_VERSION_PATCH variable
@@ -581,15 +581,15 @@ IF( NOT BUILD_DOCUMENTATION_ONLY )
   # copy weights from models
   SET( DOWNLOAD_LINK "ftp://www.nitrc.org/home/groups/captk/downloads/models/torch/pt_3dresunet_ss_brainmagebrats_best.pt" )
   SET( FILE_TO_EXTRACT "${PROJECT_SOURCE_DIR}/OpenFederatedLearning/bin/federations/weights/pt_3dresunet_ss_brainmagebrats_best.pt")
-  IF( NOT EXISTS "${FILE_TO_EXTRACT}" )
-
-    # download exe from url
-    MESSAGE( STATUS "Downloading weights for skull stripping" )
-    FILE(DOWNLOAD "${DOWNLOAD_LINK}" "${FILE_TO_EXTRACT}" TIMEOUT 1000000 STATUS STATUS_CODE SHOW_PROGRESS)
-    IF(NOT STATUS_CODE EQUAL 0)
-      MESSAGE(FATAL_ERROR "Failed to download skull-stripping weights. Status=${STATUS_CODE}")
-    ENDIF()
-  ENDIF()
+#   IF( NOT EXISTS "${FILE_TO_EXTRACT}" )
+
+#     # download exe from url
+#     MESSAGE( STATUS "Downloading weights for skull stripping" )
+#     FILE(DOWNLOAD "${DOWNLOAD_LINK}" "${FILE_TO_EXTRACT}" TIMEOUT 1000000 STATUS STATUS_CODE SHOW_PROGRESS)
+#     IF(NOT STATUS_CODE EQUAL 0)
+#       MESSAGE(FATAL_ERROR "Failed to download skull-stripping weights. Status=${STATUS_CODE}")
+#     ENDIF()
+#   ENDIF()
 
   # copy network information
   ## todo: change to a direct installation so that git doesn't get confused that submodule has changed

Dockerfile

@@ -1,58 +1,74 @@
-FROM pytorch/pytorch:1.11.0-cuda11.3-cudnn8-runtime
+FROM ghcr.io/fets-ai/fetstool_docker_dependencies:0.0.2.gpu
 
 LABEL authors="FeTS_Admin <[email protected]>"
 
-RUN apt-get update -y
+RUN apt-get update && apt-get update --fix-missing && apt-get install -y libnss3 libnspr4 libxcursor1 libxcursor-dev libasound2 libdbus-1-dev libglfw3-dev libgles2-mesa-dev ffmpeg libsm6 libxext6 python3.8 python3.8-venv python3.8-dev python3-setuptools
 
-RUN apt-get install wget zip unzip software-properties-common gcc g++ make -y
+# older python
+RUN apt-get update -y && apt install -y --reinstall software-properties-common && add-apt-repository ppa:deadsnakes/ppa && apt update -y && apt install -y python3.7 python3.7-venv python3.7-dev python3-setuptools
 
-RUN apt-get update -y && add-apt-repository ppa:deadsnakes/ppa && apt update -y && apt install python3.7 python3.7-venv python3.7-dev python3-setuptools ffmpeg libsm6 libxext6 -y
+ENV PATH=/workspace/CaPTk/bin/qt/5.12.1/bin:/workspace/CaPTk/bin/qt/5.12.1/libexec:$PATH
+ENV CMAKE_PREFIX_PATH=/workspace/CaPTk/bin/ITK-build:/workspace/CaPTk/bin/DCMTK-build:/workspace/CaPTk/bin/qt/5.12.1/lib/cmake/Qt5:$CMAKE_PREFIX_PATH
+ENV SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
 
-# We will do git pull on the FeTS_Front-End master, because that is the repo using which the base image is made
-# We will not do compiles on the PR because the idea is that the Xenial build will check the build status of
-# the PR in any case.
+RUN pwd && ls -l
 
-ARG VERSION=0.0.9
+WORKDIR /Front-End
 
-# download installer
-RUN wget https://fets.projects.nitrc.org/FeTS_${VERSION}_Installer.bin && chmod +x FeTS_${VERSION}_Installer.bin
+COPY . .
 
-# install FeTS and remove installer
-RUN yes yes | ./FeTS_${VERSION}_Installer.bin --target ./FeTS_${VERSION} -- --cudaVersion 11 && rm -rf ./FeTS_${VERSION}_Installer.bin
+RUN pwd && ls -l && mv ./data/Algorithms_for_fetsTool1.0.zip OpenFederatedLearning/submodules/fets_ai/ && cd OpenFederatedLearning/submodules/fets_ai/ && unzip -qq Algorithms_for_fetsTool1.0.zip && rm -rf Algorithms_for_fetsTool1.0.zip
 
-ENV PATH=/workspace/FeTS_${VERSION}/squashfs-root/usr/bin/:$PATH
-ENV LD_LIBRARY_PATH=/workspace/FeTS_${VERSION}/squashfs-root/usr/lib/:$LD_LIBRARY_PATH
-ENV SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL="True"
+RUN pwd && ls -l && mv ./data/GANDLF_for_fetsTool1.0.zip OpenFederatedLearning/submodules/fets_ai/Algorithms && cd OpenFederatedLearning/submodules/fets_ai/Algorithms && unzip -qq GANDLF_for_fetsTool1.0.zip && rm -rf GANDLF_for_fetsTool1.0.zip
+
+## C++ build
+RUN mkdir bin && cd bin && cmake -DCMAKE_INSTALL_PREFIX="./install/appdir/usr" -DITK_DIR="/workspace/CaPTk/bin/ITK-build" -DDCMTK_DIR="/workspace/CaPTk/bin/DCMTK-build" -DBUILD_TESTING=OFF .. && make -j$(nproc) && make install/strip 
+
+# ## Python package installation -- this is for the new docker image, which is much simpler
+# RUN cd bin/install/appdir/usr/bin/ && python3.8 -m venv ./venv && ./venv/bin/pip install --upgrade pip wheel && ./venv/bin/pip install torch==1.13.1+cpu torchvision==0.14.1+cpu torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cpu && ./venv/bin/pip install -e . && ./venv/bin/pip install setuptools-rust Cython scikit-build scikit-learn openvino-dev==2023.0.1 && ./venv/bin/pip install -e .
 
 # set up environment and install correct version of pytorch
-RUN cd ./FeTS_${VERSION}/squashfs-root/usr/bin/OpenFederatedLearning && \
+RUN echo "Setting up virtual environment for OpenFederatedLearning with base dependencies" && \
+    cd bin/install/appdir/usr/bin/OpenFederatedLearning && \
     rm -rf ./venv && python3.7 -m venv ./venv && ./venv/bin/pip install Cython && \
     ./venv/bin/pip install --upgrade pip setuptools wheel setuptools-rust && \
-    ./venv/bin/pip install torch==1.7.1+cu110 torchvision==0.8.2+cu110 torchaudio==0.7.2 -f https://download.pytorch.org/whl/torch_stable.html 
-
-RUN cd ./FeTS_${VERSION}/squashfs-root/usr/bin/OpenFederatedLearning && \
+    ./venv/bin/pip install torch==1.7.1+cu110 torchvision==0.8.2+cu110 torchaudio==0.7.2 -f https://download.pytorch.org/whl/torch_stable.html && \
     ./venv/bin/pip install wheel && \
-    ./venv/bin/pip install scikit-build scikit-learn && \
     ./venv/bin/pip install SimpleITK==1.2.4 && \
     ./venv/bin/pip install protobuf==3.17.3 grpcio==1.30.0 && \
-    ./venv/bin/pip install opencv-python==4.2.0.34
-    # ./venv/bin/pip install python-gdcm
-
-RUN cd ./FeTS_${VERSION}/squashfs-root/usr/bin/OpenFederatedLearning && \
-    ./venv/bin/pip install setuptools --upgrade && \
+    ./venv/bin/pip install opencv-python==4.2.0.34 && \
+    ./venv/bin/pip install scikit-build scikit-learn && \
     make install_openfl && \
-    make install_fets && \
-    ./venv/bin/pip install -e ./submodules/fets_ai/Algorithms/GANDLF && \
-    cd ../LabelFusion && \
-    rm -rf venv && python3.7 -m venv ./venv && \
+    make install_openfl_pytorch
+
+RUN echo "Setting up virtual environment for OpenFederatedLearning with second-level dependencies" && \
+    cd bin/install/appdir/usr/bin/OpenFederatedLearning && \
+    ./venv/bin/pip install ../BrainMaGe && \
+    ./venv/bin/pip install ./submodules/fets_ai/Algorithms && \
+    ./venv/bin/pip install -e ./submodules/fets_ai/Algorithms/GANDLF
+
+RUN echo "Installing separate environment for LabelFusion" && \
+    cd bin/install/appdir/usr/bin/LabelFusion && \
+    rm -rf venv && python3.8 -m venv ./venv && \
     ./venv/bin/pip install --upgrade pip setuptools wheel setuptools-rust && \
     ./venv/bin/pip install -e .
 
+RUN echo "Downloading model weights" && \
+    cd bin/install/appdir/usr/data && \
+    wget https://upenn.box.com/shared/static/f7zt19d08c545qt3tcaeg7b37z6qafum.zip -O nnunet.zip && \
+    unzip -qq nnunet.zip && rm -rf nnunet.zip && \
+    wget https://upenn.box.com/shared/static/hhvn8nb9xtz6nxcilmdl8kbx9n1afkdu.zip -O ./fets_consensus_models.zip && \
+    unzip -qq fets_consensus_models.zip && rm -rf fets_consensus_models.zip
+
+### put together a data example that is already aligned and ready to invoke the brain extraction and tumor segmentation
+
 # set up the docker for GUI
+ENV LD_LIBRARY_PATH=/CaPTk/bin/qt/5.12.1/lib:$LD_LIBRARY_PATH
+ENV PATH=/Front-End/bin/install/appdir/usr/bin/:$PATH
 ENV QT_X11_NO_MITSHM=1
 ENV QT_GRAPHICSSYSTEM="native"
 
 RUN echo "Env paths\n" && echo $PATH && echo $LD_LIBRARY_PATH
 
 # define entry point
-ENTRYPOINT ["/workspace/FeTS_0.0.9/squashfs-root/usr/bin/FeTS_CLI_Inference"]
+ENTRYPOINT ["/Front-End/bin/install/appdir/usr/bin/FeTS_CLI_Segment"]