Implement AROMA classifier

.readthedocs.yml

@@ -2,8 +2,10 @@ version: 2
 
 build:
   os: ubuntu-22.04
+  apt_packages:
+    - graphviz
   tools:
-    python: "3.10"
+    python: "3.11"
   jobs:
     post_checkout:
       # Fetch full history, but don't fail if we already have it

Dockerfile

@@ -2,7 +2,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2023 The NiPreps Developers
+# Copyright (c) The NiPreps Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -22,192 +22,230 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
+# Ubuntu 22.04 LTS - Jammy
+ARG BASE_IMAGE=ubuntu:jammy-20240125
+
+#
+# Build wheel
+#
 FROM python:slim AS src
 RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
-COPY . /src/fmripost_aroma
-RUN python -m build /src/fmripost_aroma
+COPY . /src
+RUN python -m build /src
 
-# Use Ubuntu 22.04 LTS
-FROM ubuntu:jammy-20221130
+#
+# Download stages
+#
 
-# Prepare environment
+# Utilities for downloading packages
+FROM ${BASE_IMAGE} as downloader
+# Bump the date to current to refresh curl/certificates/etc
+RUN echo "2023.07.20"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    apt-utils \
-                    autoconf \
-                    build-essential \
+                    binutils \
                     bzip2 \
                     ca-certificates \
                     curl \
+                    unzip && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# AFNI
+FROM downloader as afni
+# Bump the date to current to update AFNI
+RUN echo "2023.07.20"
+RUN mkdir -p /opt/afni-latest \
+    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
+    | tar -xz -C /opt/afni-latest --strip-components 1 \
+    --exclude "linux_openmp_64/*.gz" \
+    --exclude "linux_openmp_64/funstuff" \
+    --exclude "linux_openmp_64/shiny" \
+    --exclude "linux_openmp_64/afnipy" \
+    --exclude "linux_openmp_64/lib/RetroTS" \
+    --exclude "linux_openmp_64/lib_RetroTS" \
+    --exclude "linux_openmp_64/meica.libs" \
+    # Keep only what we use
+    && find /opt/afni-latest -type f -not -name "3dTshift" -delete
+
+# Connectome Workbench 1.5.0
+FROM downloader as workbench
+RUN mkdir /opt/workbench && \
+    curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
+    unzip workbench-linux64-v1.5.0.zip -d /opt && \
+    rm workbench-linux64-v1.5.0.zip && \
+    rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
+    strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
+
+# Convert3d 1.4.0
+FROM downloader as c3d
+RUN mkdir /opt/convert3d && \
+    curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/Experimental/c3d-1.4.0-Linux-gcc64.tar.gz/download \
+    | tar -xz -C /opt/convert3d --strip-components 1
+
+# Micromamba
+FROM downloader as micromamba
+
+# Install a C compiler to build extensions when needed.
+# traits<6.4 wheels are not available for Python 3.11+, but build easily.
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+WORKDIR /
+# Bump the date to current to force update micromamba
+RUN echo "2024.02.06"
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+COPY env.yml /tmp/env.yml
+WORKDIR /tmp
+RUN micromamba create -y -f /tmp/env.yml && \
+    micromamba clean -y -a
+
+# UV_USE_IO_URING for apparent race-condition (https://github.com/nodejs/node/issues/48444)
+# Check if this is still necessary when updating the base image.
+ENV PATH="/opt/conda/envs/fmripost_aroma/bin:$PATH" \
+    UV_USE_IO_URING=0
+RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
+    rm -r ~/.npm
+
+#
+# Main stage
+#
+FROM ${BASE_IMAGE} as fmripost_aroma
+
+# Configure apt
+ENV DEBIAN_FRONTEND="noninteractive" \
+    LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8"
+
+# Some baseline tools; bc is needed for FreeSurfer, so don't drop it
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    bc \
+                    ca-certificates \
+                    curl \
+                    gcc \
                     git \
                     gnupg \
-                    libtool \
+                    libc-dev \
                     lsb-release \
                     netbase \
-                    pkg-config \
-                    unzip \
                     xvfb && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-ENV DEBIAN_FRONTEND="noninteractive" \
-    LANG="en_US.UTF-8" \
-    LC_ALL="en_US.UTF-8"
+# Configure PPAs for libpng12 and libxp6
+RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
+    && GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
+    && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
+    && echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list
 
-# FSL 6.0.5.1
+# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04)
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
-           bc \
-           dc \
-           file \
-           libfontconfig1 \
-           libfreetype6 \
-           libgl1-mesa-dev \
-           libgl1-mesa-dri \
+           ed \
+           gsl-bin \
+           libglib2.0-0 \
            libglu1-mesa-dev \
+           libglw1-mesa \
            libgomp1 \
-           libice6 \
-           libxcursor1 \
-           libxft2 \
-           libxinerama1 \
-           libxrandr2 \
-           libxrender1 \
-           libxt6 \
-           sudo \
-           wget \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && echo "Downloading FSL ..." \
-    && mkdir -p /opt/fsl-6.0.5.1 \
-    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
-    | tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
-    --exclude "fsl/config" \
-    --exclude "fsl/data/atlases" \
-    --exclude "fsl/data/first" \
-    --exclude "fsl/data/mist" \
-    --exclude "fsl/data/possum" \
-    --exclude "fsl/data/standard/bianca" \
-    --exclude "fsl/data/standard/tissuepriors" \
-    --exclude "fsl/doc" \
-    --exclude "fsl/etc/default_flobs.flobs" \
-    --exclude "fsl/etc/fslconf" \
-    --exclude "fsl/etc/js" \
-    --exclude "fsl/etc/luts" \
-    --exclude "fsl/etc/matlab" \
-    --exclude "fsl/extras" \
-    --exclude "fsl/include" \
-    --exclude "fsl/python" \
-    --exclude "fsl/refdoc" \
-    --exclude "fsl/src" \
-    --exclude "fsl/tcl" \
-    --exclude "fsl/bin/FSLeyes" \
-    && find /opt/fsl-6.0.5.1/bin -type f -not \( \
-        -name "melodic" -or \
-        -name "susan" -or \) -delete \
-    && find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
-ENV FSLDIR="/opt/fsl-6.0.5.1" \
-    PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
-    FSLOUTPUTTYPE="NIFTI_GZ" \
-    FSLMULTIFILEQUIT="TRUE" \
-    FSLLOCKDIR="" \
-    FSLMACHINELIST="" \
-    FSLREMOTECALL="" \
-    FSLGECUDAQ="cuda.q" \
-    LD_LIBRARY_PATH="/opt/fsl-6.0.5.1/lib:$LD_LIBRARY_PATH"
+           libjpeg62 \
+           libpng12-0 \
+           libxm4 \
+           libxp6 \
+           netpbm \
+           tcsh \
+           xfonts-base \
+           xvfb \
+    && curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
+    && dpkg -i /tmp/multiarch.deb \
+    && rm /tmp/multiarch.deb \
+    && apt-get install -f \
+    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+    && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
+    && if [ -n "$gsl2_path" ]; then \
+         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
+    fi \
+    && ldconfig
 
-# Configure PPA for libpng12
-RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
-    && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list
-
-# Installing and setting up ICA_AROMA
-WORKDIR /opt/ICA-AROMA
-RUN curl -sSL "https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz" \
-  | tar -xzC /opt/ICA-AROMA --strip-components 1 && \
-  chmod +x /opt/ICA-AROMA/ICA_AROMA.py
-ENV PATH="/opt/ICA-AROMA:$PATH" \
-    AROMA_VERSION="0.4.5"
-
-WORKDIR /opt
-RUN curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
-    unzip workbench-linux64-v1.5.0.zip && \
-    rm workbench-linux64-v1.5.0.zip && \
-    rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
-    strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
-    # ABI tags can interfere when running on Singularity
+# Install files from stages
+COPY --from=afni /opt/afni-latest /opt/afni-latest
+COPY --from=workbench /opt/workbench /opt/workbench
+COPY --from=c3d /opt/convert3d/bin/c3d_affine_tool /usr/bin/c3d_affine_tool
+
+# AFNI config
+ENV PATH="/opt/afni-latest:$PATH" \
+    AFNI_IMSAVE_WARNINGS="NO" \
+    AFNI_PLUGINPATH="/opt/afni-latest"
 
+# Workbench config
 ENV PATH="/opt/workbench/bin_linux64:$PATH" \
     LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
 
-# nipreps/miniconda:py39_4.12.0rc0
-COPY --from=nipreps/miniconda@sha256:5aa4d2bb46e7e56fccf6e93ab3ff765add74e79f96ffa00449504b4869790cb9 /opt/conda /opt/conda
-
-RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
-    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
-    echo "conda activate base" >> ~/.bashrc
-
-# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
-ENV PATH="/opt/conda/bin:$PATH" \
-    CPATH="/opt/conda/include:$CPATH" \
-    LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH" \
-    LANG="C.UTF-8" \
-    LC_ALL="C.UTF-8" \
-    PYTHONNOUSERSITE=1
-
-RUN conda install -y -n base \
-    -c anaconda \
-    -c conda-forge \
-    convert3d=1.3.0 \
-    && sync \
-    && conda clean -afy; sync \
-    && rm -rf ~/.conda ~/.cache/pip/*; sync \
-    && ldconfig
-
-# Unless otherwise specified each process should only use one thread - nipype
-# will handle parallelization
-ENV MKL_NUM_THREADS=1 \
-    OMP_NUM_THREADS=1
-
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users fmripost_aroma
 WORKDIR /home/fmripost_aroma
 ENV HOME="/home/fmripost_aroma" \
     LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
 
-RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> $HOME/.bashrc && \
-    echo "conda activate base" >> $HOME/.bashrc
+COPY --from=micromamba /bin/micromamba /bin/micromamba
+COPY --from=micromamba /opt/conda/envs/fmripost_aroma /opt/conda/envs/fmripost_aroma
 
-RUN /opt/conda/bin/python -m pip install --no-cache-dir --upgrade templateflow
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+RUN micromamba shell init -s bash && \
+    echo "micromamba activate fmripost_aroma" >> $HOME/.bashrc
+ENV PATH="/opt/conda/envs/fmripost_aroma/bin:$PATH" \
+    CPATH="/opt/conda/envs/fmripost_aroma/include:$CPATH" \
+    LD_LIBRARY_PATH="/opt/conda/envs/fmripost_aroma/lib:$LD_LIBRARY_PATH"
 
 # Precaching atlases
 COPY scripts/fetch_templates.py fetch_templates.py
-
-RUN /opt/conda/bin/python fetch_templates.py && \
+RUN python fetch_templates.py && \
     rm fetch_templates.py && \
     find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
     find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
 
+# FSL environment
+ENV LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1 \
+    FSLDIR="/opt/conda/envs/fmripost_aroma" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q"
+
+# Unless otherwise specified each process should only use one thread - nipype
+# will handle parallelization
+ENV MKL_NUM_THREADS=1 \
+    OMP_NUM_THREADS=1
+
 # Installing fMRIPost-AROMA
-COPY --from=src /src/fmripost_aroma/dist/*.whl .
-RUN /opt/conda/bin/python -m pip install --no-cache-dir $( ls *.whl )[all]
+COPY --from=src /src/dist/*.whl .
+RUN pip install --no-cache-dir $( ls *.whl )[test]
 
 RUN find $HOME -type d -exec chmod go=u {} + && \
     find $HOME -type f -exec chmod go=u {} + && \
     rm -rf $HOME/.npm $HOME/.conda $HOME/.empty
 
+# For detecting the container
 ENV IS_DOCKER_8395080871=1
 
 RUN ldconfig
 WORKDIR /tmp
-ENTRYPOINT ["/opt/conda/bin/fmripost_aroma"]
+ENTRYPOINT ["/opt/conda/envs/fmripost_aroma/bin/fmripost_aroma"]
 
 ARG BUILD_DATE
 ARG VCS_REF
 ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.name="fMRIPost-AROMA" \
-      org.label-schema.description="fMRIPost-AROMA - robust fMRI preprocessing tool" \
-      org.label-schema.url="http://fmripost_aroma.org" \
+      org.label-schema.description="fMRIPost-AROMA - fMRI post-processing with AROMA" \
+      org.label-schema.url="https://fmripost_aroma.org" \
       org.label-schema.vcs-ref=$VCS_REF \
       org.label-schema.vcs-url="https://github.com/nipreps/fmripost_aroma" \
       org.label-schema.version=$VERSION \