Merge pull request #3 from nipreps-containers/mcribs-legacy

ENH: Install legacy MCRIBS

.github/workflows/publish.yml

@@ -13,7 +13,7 @@ on:
   pull_request:
 
 env:
-  IMAGE_NAME: mirtk
+  IMAGE_NAME: mcribs
 
 jobs:
   # Push image to GitHub Packages.

Dockerfile

@@ -1,106 +1,47 @@
-FROM ubuntu:jammy
+# Build docker image for running MCRIBS
 
-RUN apt-get update && apt-get install -y --no-install-recommends \
-                                        build-essential \
-                                        ca-certificates \
-                                        cmake \
-                                        gcc \
-                                        git \
-                                        make \
-                                        python3 \
-                                        wget \
-                                        # vtk
-                                        freeglut3-dev \
-                                        # mirtk
-                                        libarpack2-dev \
-                                        libcgal-dev \
-                                        libeigen3-dev \
-                                        libpng-dev \
-                                        libsuitesparse-dev \
-                                        libtbb-dev && \
-    ln -s /usr/bin/python3 /usr/bin/python && \
-    rm -rf /var/lib/apt/lists/*
-
-# ITK
-WORKDIR /tmp
-RUN git clone --depth 1 --branch v5.3.0 https://github.com/InsightSoftwareConsortium/ITK.git && \
-    mkdir /tmp/itk-build && cd /tmp/itk-build && \
-    cmake \
-        -DBUILD_EXAMPLES=OFF \
-        -DBUILD_TESTING=OFF \
-        -DCMAKE_INSTALL_PREFIX=/opt/itk \
-    /tmp/ITK && \
-    make -j $(nproc) install && \
-    cd /tmp && rm -rf /tmp/ITK /tmp/itk-build
+# Legacy
+FROM ubuntu:18.04
+ARG DEBIAN_FRONTEND=noninteractive
 
-# VTK
-RUN git clone --depth 1 --branch v9.2.2 https://github.com/Kitware/VTK.git
-# Parallelized vtkPolyDataToImageStencil speeds up WM surface step.
-COPY patch/vtkPolyDataToImageStencil.cxx patch/vtkPolyDataToImageStencil.h VTK/Imaging/Stencil/
-RUN mkdir /tmp/vtk-build && cd /tmp/vtk-build && \
-    cmake \
-        -DBUILD_EXAMPLES=OFF \
-        -DBUILD_TESTING=OFF \
-        -DCMAKE_INSTALL_PREFIX=/opt/vtk \
-    /tmp/VTK && \
-    make -j $(nproc) install && \
-    cd /tmp && rm -rf /tmp/VTK /tmp/vtk-build
+# update apt
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        apt-utils \
+        build-essential \
+        ca-certificates \
+        g++ \
+        gcc \
+        cmake \
+        curl \
+        file \
+        git \
+        python3-dev \
+        libboost-dev \
+        libeigen3-dev \
+        libflann-dev \
+        libgl1-mesa-dev \
+        libglu1-mesa-dev \
+        libssl-dev \
+        libtbb-dev \
+        libxt-dev \
+        zlib1g-dev \
+    && ln -s /usr/bin/python3 /usr/bin/python \
+    && rm -rf /var/lib/apt/lists/*
 
+WORKDIR /opt
+# Build MCRIBS + dependencies through their build script
+# Installed dependencies: ITK, VTK, MIRTK
+RUN git clone --branch nib-comp-v1.1 https://github.com/AidanWUSTL/MCRIBS_for_MAKEGI.git /opt/MCRIBS \
+    && cd MCRIBS \
+    && bash build.sh \
+    # clean up and reduce size
+    && rm -rf ITK/ITK/ ITK/ITK-build/ VTK/VTK/ VTK/VTK-build/ MIRTK/MIRTK/ MIRTK/MIRTK-build/
 
-# MIRTK (built with FLANN=OFF)
-# library: libflann-dev (1.9.3-2build2)
-# /usr/bin/ld: ../../lib/libMIRTKPointSet.so.0.0.0: undefined reference to `LZ4_resetStreamHC'
-# /usr/bin/ld: ../../lib/libMIRTKPointSet.so.0.0.0: undefined reference to `LZ4_setStreamDecode'
-# /usr/bin/ld: ../../lib/libMIRTKPointSet.so.0.0.0: undefined reference to `LZ4_decompress_safe'
-# /usr/bin/ld: ../../lib/libMIRTKPointSet.so.0.0.0: undefined reference to `LZ4_decompress_safe_continue'
-# /usr/bin/ld: ../../lib/libMIRTKPointSet.so.0.0.0: undefined reference to `LZ4_compress_HC_continue'
-COPY patch/FindTBB.patch patch/Parallel.patch /tmp/patches/
-RUN git clone --depth 1 https://github.com/DevelopmentalImagingMCRI/MCRIBS.git && \
-    cd MCRIBS && mv MIRTK/MIRTK /tmp/MIRTK && \
-    patch /tmp/MIRTK/Modules/Common/src/Parallel.cc /tmp/patches/Parallel.patch && \
-    patch /tmp/MIRTK/CMake/Modules/FindTBB.cmake /tmp/patches/FindTBB.patch && \
-    mkdir /tmp/mirtk-build && cd /tmp/mirtk-build && \
-    ITK_DIR=/opt/itk && VTK_DIR=/opt/vtk && \
-    cmake  \
-        -D CMAKE_INSTALL_PREFIX=/opt/mirtk \
-        -D CMAKE_BUILD_TYPE=Release \
-        -D BUILD_SHARED_LIBS=ON \
-        -D BUILD_APPLICATIONS=ON \
-        -D BUILD_TESTING=OFF \
-        -D BUILD_DOCUMENTATION=OFF \
-        -D BUILD_CHANGELOG=OFF \
-        -D MODULE_Common=ON \
-        -D MODULE_Numerics=ON \
-        -D MODULE_Image=ON \
-        -D MODULE_IO=ON \
-        -D MODULE_PointSet=ON \
-        -D MODULE_Transformation=ON \
-        -D MODULE_Registration=ON \
-        -D MODULE_Deformable=ON \
-        -D MODULE_DrawEM=ON \
-        -D MODULE_Mapping=ON \
-        -D MODULE_Scripting=ON \
-        -D MODULE_Viewer=OFF \
-        -D WITH_ARPACK=ON \
-        -D WITH_FLANN=OFF \
-        -D WITH_MATLAB=OFF \
-        -D WITH_NiftiCLib=ON \
-        -D WITH_PNG=ON \
-        -D WITH_PROFILING=ON \
-        -D WITH_TBB=ON \
-        -D WITH_UMFPACK=ON \
-        -D WITH_ITK=ON \
-        -D WITH_VTK=ON \
-        -D WITH_ZLIB=ON \
-    /tmp/MIRTK && \
-    make -j $(nproc) install && \
-    ldconfig && \
-    cd /tmp && rm -rf /tmp/*
+COPY scripts/fixpy.sh env/setupMCRIBS.sh /opt/
+RUN bash fixpy.sh /opt/MCRIBS/ > fixpy.log
 
-# Avoid hardcoding Python paths
-COPY scripts/fixpy.sh .
-RUN apt-get update && apt-get install -y --no-install-recommends file && \
-    bash fixpy.sh /opt/mirtk
+WORKDIR /usr/lib/x86_64-linux-gnu
+RUN cp libtbb.so.2 libtbbmalloc.so.2 libtbbmalloc_proxy.so.2 /opt/MCRIBS/lib
 
-ENV PATH="/opt/mirtk/bin:$PATH" \
-    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:/opt/vtk/lib:/opt/itk/lib:${LD_LIBRARY_PATH}"
+WORKDIR /work
+ENTRYPOINT ["/opt/setupMCRIBS.sh"]

README.md

@@ -1,21 +1,21 @@
-# MIRTK
-Medical Image Registration ToolKit (MIRTK)
+# MCRIBS
 
+## Description
+This builds a legacy version of the MCRIBS pipeline and its dependencies (ITK, VTK) from source.
+Note: this installation does not include all pieces required to run `MCRIBReconAll`, you will need to have:
+- FreeSurfer
+- FSL
 
-This builds the MCRIBS version of MIRTK (latest commit: https://github.com/DevelopmentalImagingMCRI/MCRIBS/commit/bb57350a88c35487ae1ad2d33975ec83eaa15a45) and its dependencies (ITK, VTK) from source.
-Additionally, a modified version of VTK 9.2.2 is used, following https://github.com/DevelopmentalImagingMCRI/MCRIBS/commit/e0daec6d0798659c54eeea6c2bb2e440ca3de089
-
-
-### Portability
-To use `mirtk` tools in another Dockerfile, you will need to:
-1. COPY /opt/mirtk <dest> and add its `bin/` to `$PATH`
-1. COPY /opt/vtk/lib <shared libraries>
-1. COPY /opt/itk/lib <shared libraries> (Optional)
+## Portability
+To use MCRIBS in another Dockerfile, you will need to:
+1. COPY `/opt/MCRIBS/` and `/opt/setupMCRIBS.sh`
 1. Install the following libraries (jammy):
-    - libarpack2-dev
-    - libcgal-dev
-    - libeigen3-dev
-    - libpng-dev
-    - libsuitesparse-dev
-    - libtbb-dev
-
+    libboost-dev
+    libeigen3-dev
+    libflann-dev
+    libgl1-mesa-dev
+    libglu1-mesa-dev
+    libssl-dev
+    libtbb-dev
+    libxt-dev
+    zlib1g-dev

env/setupMCRIBS.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+export PATH="/opt/MCRIBS/bin:/opt/MCRIBS/MIRTK/MIRTK-install/bin:/opt/MCRIBS/MIRTK/MIRTK-install/lib/tools:${PATH}"
+export LD_LIBRARY_PATH="/opt/MCRIBS/lib:/opt/MCRIBS/ITK/ITK-install/lib:/opt/MCRIBS/VTK/VTK-install/lib:/opt/MCRIBS/MIRTK/MIRTK-install/lib:${LD_LIBRARY_PATH}"
+export MCRIBS_HOME="/opt/MCRIBS" \
+export PYTHONPATH="/opt/MCRIBS/lib/python:$PYTHONPATH"
+
+if [[ -z "$FREESURFER_HOME" ]]; then
+    echo "MCRIBS: missing FreeSurfer installation"
+fi
+
+if [[ -z "$FSLDIR" ]]; then
+    echo "MCRIBS: missing FSL installation"
+fi
+
+# Allow arbitrary commands
+$@