adding deepcsr again to avoid rebase issues

Author: hvgazula

.github/workflows/docker-image.yml

@@ -26,7 +26,7 @@ jobs:
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
         
     - name: Build the Docker image
-      run: docker build -t hvgazula/topofit ./docker
+      run: docker build -t hvgazula/deepcsr ./docker
 
     # Cleanup steps to free up disk space
 
@@ -35,4 +35,4 @@ jobs:
 #     if: github.event.pull_request.merged == true
       run: |
           docker login -u ${{ secrets.DOCKER_USERNAME }} -p ${{ secrets.DOCKER_PASSWORD }}
-          docker push hvgazula/topofit
+          docker push hvgazula/deepcsr

docker/CBSI.tar.gz

@@ -1,11 +1,12 @@
-FROM nvidia/cuda:11.3.1-cudnn8-devel-ubuntu20.04 AS spython-base
+FROM nvidia/cuda:11.3.1-cudnn8-devel-ubuntu20.04 
 ENV LANG=C.UTF-8
 ENV LC_ALL=C.UTF-8
 ENV PATH=/opt/miniconda3/bin:$PATH
 ENV PYTHONDONTWRITEBYTECODE=1
 ENV PYTHONUNBUFFERED=1
 ENV PYTHONIOENCODING=UTF-8
 ENV PIPENV_VENV_IN_PROJECT=1
+ENV JCC_JDK=/usr/lib/jvm/java-8-openjdk-amd64
 RUN USE_CUDA=1
 RUN CUDA_VERSION=11.3.1
 RUN CUDNN_VERSION=8
@@ -15,12 +16,15 @@ RUN TORCH_CUDA_ARCH_LIST="7.0 7.5 8.0 8.6"
 RUN rm -f /etc/apt/apt.conf.d/docker-clean; \
 echo 'Binary::apt::APT::Keep-Downloaded-Packages "true";' \
 > /etc/apt/apt.conf.d/keep-cache
-RUN apt-get update && apt-get install -y --no-install-recommends \
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata && apt-get install -y --no-install-recommends \
 build-essential \
 ca-certificates \
 ccache \
 curl \
 git \
+wget \
+cmake \
+openjdk-8-jdk \
 libaio-dev && \
 apt-get install -y --no-install-recommends llvm-10 lldb-10 llvm-10-dev libllvm10 llvm-10-runtime
 RUN rm -rf /var/lib/apt/lists/*
@@ -32,10 +36,23 @@ chmod +x ~/miniconda.sh && \
 
 WORKDIR /app
 COPY environment.yml .
+COPY CBSI.tar.gz .
+RUN tar -xf CBSI.tar.gz
+RUN mkdir niftyreg-build
+ENV CMAKE_BUILD_TYPE=Release
+WORKDIR /app/niftyreg-build
+RUN cmake ../niftyreg-CBSI
+RUN make
+RUN make install
+WORKDIR /app
 RUN conda env create -f environment.yml
-SHELL ["conda", "run", "-n", "topofit", "/bin/bash", "-c"]
-RUN pip install torch-scatter -f https://data.pyg.org/whl/torch-1.11.0+cu113.html
+SHELL ["conda", "run", "-n", "deepcsr", "/bin/bash", "-c"]
+RUN git clone https://github.com/neuroneural/DeepCSR-fork.git
+WORKDIR /app/DeepCSR-fork/docker/nighres
+RUN git checkout tags/docker1
+RUN ./build.sh
+RUN python3 -m pip install .
 RUN apt-get clean
 RUN pip cache purge
 RUN conda clean -a
-
+ENTRYPOINT ["/bin/bash"]

docker/Dockerfile

@@ -1,88 +1,85 @@
-name: topofit
+name: deepcsr
 channels:
-  - pytorch
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
-  - blas=1.0=mkl
-  - brotlipy=0.7.0=py37h27cfd23_1003
-  - bzip2=1.0.8=h7b6447c_0
+  - _openmp_mutex=4.5=1_gnu
   - ca-certificates=2022.4.26=h06a4308_0
-  - certifi=2022.5.18.1=py37h06a4308_0
-  - cffi=1.15.0=py37hd667e15_1
-  - charset-normalizer=2.0.4=pyhd3eb1b0_0
-  - cryptography=37.0.1=py37h9ce1e76_0
-  - cudatoolkit=11.3.1=h2bc3f7f_2
-  - ffmpeg=4.3=hf484d3e_0
-  - freetype=2.11.0=h70c0345_0
-  - giflib=5.2.1=h7b6447c_0
-  - gmp=6.2.1=h2531618_2
-  - gnutls=3.6.15=he1e5248_0
-  - idna=3.3=pyhd3eb1b0_0
-  - intel-openmp=2021.4.0=h06a4308_3561
-  - jpeg=9e=h7f8727e_0
-  - lame=3.100=h7b6447c_0
-  - lcms2=2.12=h3be6417_0
-  - ld_impl_linux-64=2.38=h1181459_1
+  - certifi=2021.10.8=py37h06a4308_2
+  - ld_impl_linux-64=2.38=h1181459_0
   - libffi=3.3=he6710b0_2
-  - libgcc-ng=11.2.0=h1234567_0
-  - libgomp=11.2.0=h1234567_0
-  - libiconv=1.16=h7f8727e_2
-  - libidn2=2.3.2=h7f8727e_0
-  - libpng=1.6.37=hbc83047_0
-  - libstdcxx-ng=11.2.0=h1234567_0
-  - libtasn1=4.16.0=h27cfd23_0
-  - libtiff=4.2.0=h2818925_1
-  - libunistring=0.9.10=h27cfd23_0
-  - libuv=1.40.0=h7b6447c_0
-  - libwebp=1.2.2=h55f646e_0
-  - libwebp-base=1.2.2=h7f8727e_0
-  - lz4-c=1.9.3=h295c915_1
-  - mkl=2021.4.0=h06a4308_640
-  - mkl-service=2.4.0=py37h7f8727e_0
-  - mkl_fft=1.3.1=py37hd3c417c_0
-  - mkl_random=1.2.2=py37h51133e4_0
+  - libgcc-ng=9.3.0=h5101ec6_17
+  - libgomp=9.3.0=h5101ec6_17
+  - libstdcxx-ng=9.3.0=hd4cf53a_17
   - ncurses=6.3=h7f8727e_2
-  - nettle=3.7.3=hbbd107a_1
-  - numpy=1.21.5=py37he7a7128_2
-  - numpy-base=1.21.5=py37hf524024_2
-  - openh264=2.1.1=h4ff587b_0
   - openssl=1.1.1o=h7f8727e_0
-  - pillow=9.0.1=py37h22f2fdc_0
   - pip=21.2.2=py37h06a4308_0
-  - pycparser=2.21=pyhd3eb1b0_0
-  - pyopenssl=22.0.0=pyhd3eb1b0_0
-  - pysocks=1.7.1=py37_1
   - python=3.7.13=h12debd9_0
-  - pytorch=1.11.0=py3.7_cuda11.3_cudnn8.2.0_0
-  - pytorch-mutex=1.0=cuda
   - readline=8.1.2=h7f8727e_1
-  - requests=2.27.1=pyhd3eb1b0_0
   - setuptools=61.2.0=py37h06a4308_0
-  - six=1.16.0=pyhd3eb1b0_1
   - sqlite=3.38.3=hc218d9a_0
   - tk=8.6.11=h1ccaba5_1
-  - torchaudio=0.11.0=py37_cu113
-  - torchvision=0.12.0=py37_cu113
-  - typing_extensions=4.1.1=pyh06a4308_0
-  - urllib3=1.26.9=py37h06a4308_0
   - wheel=0.37.1=pyhd3eb1b0_0
   - xz=5.2.5=h7f8727e_1
   - zlib=1.2.12=h7f8727e_2
-  - zstd=1.5.2=ha4553b6_0
   - pip:
-    - cython==0.29.30
-    - install==1.3.5
+    - absl-py==1.0.0
+    - antlr4-python3-runtime==4.8
+    - cachetools==5.1.0
+    - chart-studio==1.1.0
+    - cycler==0.11.0
+    - cython==0.29.29
+    - dataclasses==0.6
+    - fonttools==4.33.3
+    - future==0.18.2
+    - google-auth==2.6.6
+    - google-auth-oauthlib==0.4.6
+    - grpcio==1.46.1
+    - hydra-core==1.1.2
+    - imageio==2.19.2
+    - importlib-metadata==4.11.3
+    - importlib-resources==5.2.3
+    - jcc==3.12
     - joblib==1.1.0
-    - numpy-stl==2.17.1
+    - kiwisolver==1.4.3
+    - markdown==3.3.7
+    - matplotlib==3.5.2
+    - networkx==2.6.3
+    - oauthlib==3.2.0
+    - omegaconf==2.1.2
     - packaging==21.3
+    - patsy==0.5.2
+    - pillow==9.1.0
+    - plotly==5.9.0
+    - protobuf==3.20.1
+    - psutil==5.9.1
+    - pyasn1==0.4.8
+    - pyasn1-modules==0.2.8
     - pyparsing==3.0.9
     - python-dateutil==2.8.2
-    - python-utils==3.3.3
+    - pywavelets==1.3.0
+    - pyyaml==6.0
+    - requests-oauthlib==1.3.1
+    - retrying==1.3.3
+    - rsa==4.8
+    - rtree==1.0.0
+    - scikit-image==0.19.2
     - scikit-learn==1.0.2
     - scipy==1.7.3
-    - stl==0.0.3
-    - surfa==0.0.8
+    - six==1.16.0
+    - statsmodels==0.13.2
+    - tenacity==8.0.1
+    - tensorboard==2.9.0
+    - tensorboard-data-server==0.6.1
+    - tensorboard-plugin-wit==1.8.1
     - threadpoolctl==3.1.0
-prefix: /data/users2/washbee/anaconda3/envs/topofit
+    - tifffile==2021.11.2
+    - torch==1.7.0
+    - torchaudio==0.7.0
+    - torchvision==0.8.1
+    - trimesh==3.12.0
+    - typing-extensions==4.2.0
+    - webcolors==1.12
+    - werkzeug==2.1.2
+    - zipp==3.8.0
+prefix: /data/users2/washbee/anaconda3/envs/deepcsr

docker/environment.yml

@@ -0,0 +1,24 @@
+name: Build using conda environment
+on: [push, pull_request]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: 'recursive'
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: nighres
+          environment-file: conda-nighres.yml
+          python-version: 3.9
+          auto-activate-base: false
+      - name: Run build process
+        shell: bash -l {0}
+        run: |
+            ./build.sh
+      - name: Run pip install
+        run: |
+            python3 -m pip install .

docker/nighres/.github/workflows/build.yml

@@ -0,0 +1,38 @@
+__pycache__/
+*.pyc
+*~
+*.zip
+*.nt.bz2
+*.tar.gz
+*.tgz
+
+env/
+build/
+cbstools-public/
+imcn-imaging/
+nighresjava/
+develop-eggs/
+dist/
+downloads/
+lib/
+lib64/
+parts/
+sdist/
+var/
+eggs/
+.eggs/
+nighres.egg-info/
+nighres.egg
+.installed.cfg
+
+.so
+.jar
+
+travis.log
+
+doc/_build
+doc/auto_examples
+doc/gen_modules
+doc/modules/generated
+
+nighres_examples

docker/nighres/.gitignore

@@ -0,0 +1,35 @@
+matrix:
+  include:
+  - dist: bionic
+    language: java
+    jdk: openjdk11
+    before_install:
+    - export JCC_JDK=/usr/lib/jvm/java-11-openjdk-amd64
+    - sudo ln -s /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so /usr/lib/libjvm.so
+    - sudo ln -s /usr/lib/jvm/java-11-openjdk-amd64/lib/libjava.so /usr/lib/libjava.so
+    - sudo apt-get update
+    - sudo apt-get install python3.6
+    - sudo apt-get install python3-pip
+    - python3 -m pip install --upgrade --user setuptools
+    - python3 -m pip install --upgrade --user wheel
+    - python3 -m pip install --upgrade --user JCC
+    script: "travis/make_dist.sh"
+    # before_deploy:
+    # - python3 -m pip install --user twine
+    # - python3 -m pip install --user urllib3[secure]
+    # deploy:
+    #   provider: pypi
+    #   #server: https://test.pypi.org/legacy/
+    #   user: "nighres"
+    #   # using plain text password for testpypi, when switching to real pypi use encrypted (below)
+    #   password:
+    #       secure: "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"
+    #   skip_cleanup: true
+    #   on:
+    #     tags: true
+    #     branch: master
+        # condition: $TRAVIS_PYTHON_VERSION = "2.7" once we run travis against
+        # multiple python versions, this ensures that the package will be deployed only once
+
+notifications:
+  email: false

docker/nighres/.travis.yml

@@ -0,0 +1,58 @@
+FROM ubuntu:16.04
+
+RUN apt-get update && \
+    apt-get -y install sudo && \
+    sudo apt-get update -qq && \
+    apt-get install -y python3 \
+                       python3-pip \
+                       python3-dev \
+                       build-essential \
+                       software-properties-common \
+                       openjdk-8-jdk \
+                       git \
+                       wget && \
+    sudo add-apt-repository ppa:openjdk-r/ppa && \
+         apt-get update -qq && \
+         apt-get install -y openjdk-8-jdk
+
+RUN ln -svT "/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)" /docker-java-home
+ENV JAVA_HOME=/docker-java-home \
+    JCC_JDK=/docker-java-home
+
+RUN apt-get install libffi-dev && \
+    python3 -m pip install --upgrade "pip < 21.0" \
+                                     wheel \
+                                     JCC \
+                                     urllib3 && \
+    python3 -m pip install jupyter \
+                           nilearn \
+                           sklearn \
+                           nose \
+                           matplotlib \
+                           scipy \
+                           psutil
+
+RUN useradd --no-user-group --create-home --shell /bin/bash neuro && \
+    mkdir /home/neuro/nighres
+COPY build.sh cbstools-lib-files.sh setup.py MANIFEST.in README.rst LICENSE imcntk-lib-files.sh /home/neuro/nighres/
+COPY nighres /home/neuro/nighres/nighres
+
+RUN cd /home/neuro/nighres && \
+    ./build.sh && \
+    cd /home/neuro/nighres && python3 -m pip install . && \
+    mkdir /home/neuro/notebooks && \
+    chown -R neuro /home/neuro
+
+COPY docker/jupyter_notebook_config.py /etc/jupyter/
+
+EXPOSE 8888
+
+ENV TINI_VERSION v0.6.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
+RUN chmod +x /usr/bin/tini
+ENTRYPOINT ["/usr/bin/tini", "--"]
+
+EXPOSE 8888
+CMD ["jupyter", "notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0"]
+
+USER neuro