Remove dynamic loading and XML configuration and add CLI parameters

.dockerignore

@@ -11,6 +11,7 @@
 !gadgets/
 !justfile
 !libmrd/
+!mri/
 !test/
 !toolboxes/
 !environment.yml

.github/workflows/pingvin-ci.yml

@@ -14,6 +14,7 @@ permissions:
 
 env:
   imageBaseName: ghcr.io/gadgetron/pingvin/ubuntu22.04
+  miniforgeVersion: 24.11.3-0
 
 defaults:
   run:
@@ -105,8 +106,8 @@ jobs:
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-version: latest
-          environment-file: conda/environment.yml
+          miniforge-version: ${{env.miniforgeVersion}}
+          environment-file: conda/build-environment.yml
           activate-environment: pingvin-build
 
       - name: Build conda package
@@ -129,8 +130,8 @@ jobs:
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-version: latest
-          environment-file: conda/environment.yml
+          miniforge-version: ${{env.miniforgeVersion}}
+          environment-file: conda/build-environment.yml
           activate-environment: pingvin-build
 
       - name: Download Conda package

CMakeLists.txt

@@ -273,7 +273,6 @@ if (BUILD_PYTHON_SUPPORT)
 
     message(STATUS "Found NumPy:")
     message(STATUS "NumPy include: ${Python3_NumPy_INCLUDE_DIRS}")
-    message(STATUS "NumPy libraries: ${Python3_NumPy_LIBRARIES}")
     message(STATUS "Python3 libraries: ${Python3_LIBRARIES}")
 
     if (Python3_VERSION_MINOR LESS 7)
@@ -318,6 +317,7 @@ add_subdirectory(cmake)
 add_subdirectory(core)
 add_subdirectory(gadgets)
 add_subdirectory(toolboxes)
+add_subdirectory(mri)
 
 option(BUILD_WITH_GPERFTOOLS_PROFILER "Build with the gperftools profiler." Off)
 if (BUILD_WITH_GPERFTOOLS_PROFILER)

Dockerfile

@@ -23,7 +23,7 @@ RUN groupadd --gid $USER_GID $USERNAME \
     && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \
     && chmod 0440 /etc/sudoers.d/$USERNAME
 
-ARG MINIFORGE_VERSION=24.3.0-0
+ARG MINIFORGE_VERSION=24.11.3-0
 ARG CONDA_GID=900
 
 # Based on https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
@@ -70,13 +70,16 @@ RUN wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_
     && mv yardl "/usr/local/bin/" \
     && rm "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
 
+# Set OMP wait policy for better OpenMP performance on Ubuntu
+ENV OMP_WAIT_POLICY=PASSIVE
+
 FROM pingvin_baseimage AS pingvin_dev_cuda
 ARG USER_UID
 ARG HOME
 USER ${USER_UID}
 RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
 RUN grep -v "#.*\<NOFILTER\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
-RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
+RUN umask 0002 && /opt/conda/bin/mamba env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
 USER root
 
 FROM pingvin_baseimage AS pingvin_dev_nocuda
@@ -85,7 +88,7 @@ ARG HOME
 USER ${USER_UID}
 RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
 RUN grep -v "#.*\<cuda\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
-RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
+RUN umask 0002 && /opt/conda/bin/mamba env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
 USER root
 
 FROM pingvin_dev_cuda AS pingvin_build_cuda
@@ -100,8 +103,7 @@ RUN . /opt/conda/etc/profile.d/conda.sh && umask 0002 && conda activate pingvin
     mkdir build && \
     cd build && \
     cmake ../ -GNinja -DUSE_MKL=ON -DCMAKE_INSTALL_PREFIX=/opt/package && \
-    ninja && \
-    ninja install
+    ninja -j $(nproc) install
 
 FROM pingvin_dev_nocuda AS pingvin_build_nocuda
 ARG USER_UID
@@ -115,16 +117,15 @@ RUN . /opt/conda/etc/profile.d/conda.sh && umask 0002 && conda activate pingvin
     mkdir build && \
     cd build && \
     cmake ../ -GNinja -DUSE_MKL=ON -DCMAKE_INSTALL_PREFIX=/opt/package && \
-    ninja && \
-    ninja install
+    ninja -j $(nproc) install
 
 FROM pingvin_baseimage AS pingvin_rt_cuda
 ARG USER_UID
 ARG HOME
 USER ${USER_UID}
 RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
 RUN grep -v "#.*\<dev\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
-RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
+RUN umask 0002 && /opt/conda/bin/mamba env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
 COPY --from=pingvin_build_cuda --chown=$USER_UID:conda /opt/package /opt/conda/envs/pingvin/
 COPY --from=pingvin_build_cuda --chown=$USER_UID:conda /opt/code/pingvin/docker/entrypoint.sh /opt/
 RUN chmod +x /opt/entrypoint.sh
@@ -138,7 +139,7 @@ ARG HOME
 USER ${USER_UID}
 RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
 RUN grep -v "#.*\<cuda\|dev\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
-RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
+RUN umask 0002 && /opt/conda/bin/mamba env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
 COPY --from=pingvin_build_nocuda --chown=$USER_UID:conda /opt/package /opt/conda/envs/pingvin/
 COPY --from=pingvin_build_nocuda --chown=$USER_UID:conda /opt/code/pingvin/docker/entrypoint.sh /opt/
 RUN chmod +x /opt/entrypoint.sh

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 Gadgetron
+Copyright (c) 2025 Gadgetron
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

apps/CMakeLists.txt

@@ -1 +1 @@
-add_subdirectory(pingvin)
+add_subdirectory(pingvin)

apps/pingvin/CMakeLists.txt

@@ -1,50 +1,22 @@
-find_package(PugiXML REQUIRED)
-
-configure_file(pingvin_config.in pingvin_config.h)
-
-add_executable(pingvin
-        main.cpp
-        initialization.cpp
-        initialization.h
-        system_info.cpp
-
-        Loader.cpp
-        Loader.h
-
-        Config.cpp
-        Config.h
-
-        ErrorHandler.h
-
-        nodes/Processable.h
-        nodes/Processable.cpp
-
-        nodes/Stream.cpp
-        nodes/Stream.h
-        nodes/Parallel.cpp
-        nodes/Parallel.h
-        nodes/ParallelProcess.cpp
-        nodes/ParallelProcess.h
-        nodes/PureStream.cpp
-        nodes/PureStream.h
-        )
+add_executable(pingvin main.cc)
 
 target_link_libraries(pingvin
-        pingvin_core
-        pingvin_toolbox_log
-        pingvin_toolbox_mri_core
+        pingvin_mri
+        pingvin_mricore
+        pingvin_epi
+        pingvin_grappa
+        pingvin_cmr
+        pingvin_examples
         Boost::system
-        Boost::filesystem
         Boost::program_options
-        ${PUGIXML_LIBRARIES}
-        GTBLAS
-        ${CMAKE_DL_LIBS})
+        GTBLAS)
 
 target_include_directories(pingvin
         PRIVATE
         ${CMAKE_CURRENT_SOURCE_DIR}
-        ${CMAKE_CURRENT_BINARY_DIR})
-
+        ${CMAKE_BINARY_DIR}
+        ${CMAKE_SOURCE_DIR}
+        )
 
 if (REQUIRE_SIGNED_CONFIG)
     target_link_libraries(pingvin GTBabylon)
@@ -60,3 +32,6 @@ if (GPERFTOOLS_PROFILER)
 endif ()
 
 install(TARGETS pingvin DESTINATION bin COMPONENT main)
+
+file(GLOB_RECURSE PIPELINE_CONFIG_FILES ${CMAKE_CURRENT_SOURCE_DIR}/pipelines/*/config/*.conf)
+install(FILES ${PIPELINE_CONFIG_FILES} DESTINATION ${PINGVIN_INSTALL_CONFIG_PATH} COMPONENT main)