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Add Jpeg2000 to Docker container #747

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merged 3 commits into from
May 15, 2024
Merged

Add Jpeg2000 to Docker container #747

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ecfebe5
add more options to dcm2niix (jpeg2000, jpeg-ls and Cloudfare zlib) a…
jennan Oct 25, 2022
844b88d
Merge branch 'master' into jpeg2000
jennan Sep 22, 2023
35d9135
Merge branch 'master' into jpeg2000
jennan Mar 5, 2024
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7 changes: 4 additions & 3 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ RUN apt-get update -qq \
&& git checkout v1.0.20220720 \
&& mkdir /tmp/dcm2niix/build \
&& cd /tmp/dcm2niix/build \
&& cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
&& cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
&& make -j1 \
&& make install \
&& rm -rf /tmp/dcm2niix
Expand Down Expand Up @@ -68,6 +68,7 @@ RUN apt-get update -qq \
"numpy" \
"nomkl" \
"pandas" \
"gdcm" \
&& bash -c "source activate base \
&& python -m pip install --no-cache-dir --editable \
"/src/heudiconv[all]"" \
Expand Down Expand Up @@ -98,7 +99,7 @@ RUN printf '{ \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n ca-certificates \\\\\\n cmake \\\\\\n g++ \\\\\\n gcc \\\\\\n git \\\\\\n make \\\\\\n pigz \\\\\\n zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n ca-certificates \\\\\\n cmake \\\\\\n g++ \\\\\\n gcc \\\\\\n git \\\\\\n make \\\\\\n pigz \\\\\\n zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
} \
}, \
{ \
Expand Down Expand Up @@ -142,7 +143,7 @@ RUN printf '{ \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py39_4.12.0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py39_4.12.0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"python=3.9\\" \\\\\\n \\"traits>=4.6.0\\" \\\\\\n \\"scipy\\" \\\\\\n \\"numpy\\" \\\\\\n \\"nomkl\\" \\\\\\n \\"pandas\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir --editable \\\\\\n \\"/src/heudiconv[all]\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py39_4.12.0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py39_4.12.0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"python=3.9\\" \\\\\\n \\"traits>=4.6.0\\" \\\\\\n \\"scipy\\" \\\\\\n \\"numpy\\" \\\\\\n \\"nomkl\\" \\\\\\n \\"pandas\\" \\\\\\n \\"gdcm\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir --editable \\\\\\n \\"/src/heudiconv[all]\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
} \
}, \
{ \
Expand Down
26 changes: 20 additions & 6 deletions utils/gen-docker-image.sh
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Expand Up @@ -7,12 +7,26 @@ VER=$(grep -Po '(?<=^__version__ = ).*' $thisd/../heudiconv/info.py | sed 's/"//

image="kaczmarj/neurodocker:0.9.1"

docker run --rm $image generate docker -b neurodebian:bullseye -p apt \
--dcm2niix version=v1.0.20220720 method=source \
--install git gcc pigz liblzma-dev libc-dev git-annex-standalone netbase \
docker run --rm $image generate docker \
--base-image neurodebian:bullseye \
--pkg-manager apt \
--dcm2niix \
version=v1.0.20220720 \
method=source \
cmake_opts="-DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON" \
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Note: I wonder if we would not get some compatibility issues due to hardware optimized Cloudflare zlib, but I guess we wouldn't know unless we try! ;-)

--install \
git \
gcc \
pigz \
liblzma-dev \
libc-dev \
git-annex-standalone \
netbase \
--copy . /src/heudiconv \
--miniconda version="py39_4.12.0" conda_install="python=3.9 traits>=4.6.0 scipy numpy nomkl pandas" \
pip_install="/src/heudiconv[all]" \
pip_opts="--editable" \
--miniconda \
version="py39_4.12.0" \
conda_install="python=3.9 traits>=4.6.0 scipy numpy nomkl pandas gdcm" \
pip_install="/src/heudiconv[all]" \
pip_opts="--editable" \
--entrypoint "heudiconv" \
> $thisd/../Dockerfile