adding deepcsr again to avoid rebase issues

.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/Dockerfile

@@ -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/environment.yml

@@ -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/nighres/.github/workflows/build.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/.gitignore

@@ -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/.travis.yml

@@ -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/Dockerfile

@@ -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