Add Intermediate Data Types (#17)

* Add initial Kspace and NoiseCovariance types
* Move Gadgetron types into MRD v2 model
* Source VERSION from file in CMakeLists.txt
* Clean up CMake target exports
* Add intermediate types for image reconstruction
* Document intermediate types
* Update YARDL_VERSION in Github CI
* Pin Python version for Github CI conda build
* Pin Miniforge version in CI conda build
* Fix version string to work in conda build
* Fix version string to work in docker build
* Change CI docker build to use `just`
* Fix Mac OS X conda build
* Make ISMRMRD an optional dependency
* Simplify C++ build in CI workflow
* Improve intermediate type names

.devcontainer/Dockerfile

@@ -90,7 +90,7 @@ RUN . /opt/conda/etc/profile.d/conda.sh \
 
 
 # Install the yardl tool
-ARG YARDL_VERSION=0.6.1
+ARG YARDL_VERSION=0.6.2
 RUN wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
     && tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
     && mv yardl "/opt/conda/envs/${CONDA_ENVIRONMENT_NAME}/bin/" \

.devcontainer/devcontainer.bashrc

@@ -3,7 +3,12 @@
 
 source /opt/conda/etc/profile.d/conda.sh
 conda activate mrd
+
 source <(yardl completion bash)
+source <(just --completions bash)
+
+export MRD_VERSION_STRING=$(cat "${CONTAINER_WORKSPACE_DIR}/VERSION")
+
 
 if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then
     # We don't want subshells to unnecessarily source this again.

.github/workflows/mrd_build.yml

@@ -11,7 +11,7 @@ on:
 env:
   # Increase this to manually reset the conda environment cache
   CONDA_CACHE_NUMBER: 0
-  YARDL_VERSION: 0.6.1
+  YARDL_VERSION: 0.6.2
 
 defaults:
   run:
@@ -22,18 +22,18 @@ jobs:
   build:
     name: Build and Test C++, Python, MATLAB SDKs
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        cppVersion: [17, 20]
     steps:
     - name: Checkout
       uses: actions/checkout@v4
 
     - name: Configure Build Environment
       uses: ./.github/actions/configure-mrd-build-environment
 
-    - name: Build and Test
-      run: just cpp_version=${{ matrix.cppVersion }} matlab=enabled validate-with-no-changes
+    - name: Build and Test with C++17
+      run: just cpp_version=17 matlab=enabled validate-with-no-changes
+
+    - name: Build and Test with C++20
+      run: just cpp_version=20 matlab=enabled validate-with-no-changes
 
     - name: Package MATLAB toolbox
       run: just build-matlab-toolbox
@@ -61,10 +61,10 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v4
+    - name: Set up just command runner
+      uses: extractions/setup-just@dd310ad5a97d8e7b41793f8ef055398d51ad4de6
     - name: Build and test Docker images
-      run: |
-        ./docker/build-images.sh
-        ./docker/test-docker-images.sh
+      run: just build-docker-images && just test-docker-images
 
   publishDocs:
     name: Publish Documentation
@@ -162,5 +162,7 @@ jobs:
 
     - name: Checkout
       uses: actions/checkout@v4
+    - name: Set up just command runner
+      uses: extractions/setup-just@dd310ad5a97d8e7b41793f8ef055398d51ad4de6
     - name: Push Docker images
-      run: ./docker/build-images.sh --tag "${GITHUB_REF_NAME}" --push
+      run: just build-docker-images --tag "${GITHUB_REF_NAME}" --push

VERSION

@@ -1 +1 @@
-2.0.1
+2.1.0

cpp/CMakeLists.txt

@@ -1,7 +1,17 @@
 cmake_minimum_required(VERSION 3.19)
-project(mrd)
 
-set(MRD_VERSION_STRING $ENV{MRD_VERSION_STRING})
+if (DEFINED ENV{MRD_VERSION_STRING})
+  # Get the current version of MRD from the environment if possible
+  set(MRD_VERSION_STRING $ENV{MRD_VERSION_STRING})
+else ()
+  # Otherwise, try to read it from the VERSION file at the top of this repo
+  if (IS_READABLE "${CMAKE_SOURCE_DIR}/../VERSION")
+    file(STRINGS "${CMAKE_SOURCE_DIR}/../VERSION" MRD_VERSION_STRING)
+  endif ()
+endif ()
+
+project(mrd VERSION ${MRD_VERSION_STRING})
+
 message(STATUS "MRD_VERSION_STRING: ${MRD_VERSION_STRING}")
 
 SET(CMAKE_CXX_FLAGS_DEBUG "-O0 -g")
@@ -13,10 +23,12 @@ if (NOT CMAKE_BUILD_TYPE)
             "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
             FORCE)
 endif ()
+message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
 
 if(NOT CMAKE_CXX_STANDARD)
     set(CMAKE_CXX_STANDARD 17)
 endif()
+message(STATUS "C++ Standard: ${CMAKE_CXX_STANDARD}")
 
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
@@ -31,14 +43,55 @@ add_executable(mrd_minimal_example minimal_example.cc)
 target_link_libraries(mrd_minimal_example mrd_generated)
 install(TARGETS mrd_minimal_example DESTINATION bin)
 
+
+string(REGEX MATCH "[0-9]+" MRD_SOVERSION ${MRD_VERSION_STRING})
+message(STATUS "MRD_SOVERSION: ${MRD_SOVERSION}")
+
 # MRD Library (libmrd)
 add_library(mrd SHARED $<TARGET_OBJECTS:mrd_generated>)
-target_link_libraries(mrd mrd_generated)
-install(TARGETS mrd DESTINATION lib)
+add_library(mrd::mrd ALIAS mrd)
+
+target_include_directories(mrd PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>")
+
+target_link_libraries(mrd PRIVATE mrd_generated)
+set_target_properties(mrd PROPERTIES
+  VERSION ${MRD_VERSION_STRING}
+  SOVERSION ${MRD_SOVERSION}
+)
+
+# Installation (libmrd)
+include(GNUInstallDirs)
+include(CMakePackageConfigHelpers)
 
-# MRD Library Headers
+install(TARGETS mrd EXPORT mrd-targets
+        COMPONENT Devel
+        INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+)
 install(DIRECTORY mrd
-        DESTINATION include
+        TYPE INCLUDE
         COMPONENT Devel
         FILES_MATCHING PATTERN "*.h"
 )
+
+set(MRD_INSTALL_CMAKEDIR "${CMAKE_INSTALL_LIBDIR}/cmake/mrd" CACHE STRING "Path to MRD CMake files")
+
+install(EXPORT mrd-targets
+  FILE mrd-targets.cmake
+  DESTINATION "${MRD_INSTALL_CMAKEDIR}"
+  NAMESPACE mrd::
+  COMPONENT Devel
+)
+
+write_basic_package_version_file(
+  "${CMAKE_CURRENT_BINARY_DIR}/mrd-config-version.cmake"
+  VERSION ${MRD_VERSION_STRING}
+  COMPATIBILITY SameMajorVersion
+)
+
+install(
+  FILES
+    "${CMAKE_CURRENT_SOURCE_DIR}/cmake/mrd-config.cmake"
+    "${CMAKE_CURRENT_BINARY_DIR}/mrd-config-version.cmake"
+  DESTINATION "${MRD_INSTALL_CMAKEDIR}"
+  COMPONENT Devel
+)

cpp/cmake/mrd-config.cmake

@@ -0,0 +1,15 @@
+include(CMakeFindDependencyMacro)
+
+set(HOWARD_HINNANT_DATE_MINIMUM_VERSION "3.0.0")
+find_dependency(date ${HOWARD_HINNANT_DATE_MINIMUM_VERSION} REQUIRED)
+
+set(HDF5_MINIMUM_VERSION "1.10.5")
+find_dependency(HDF5 ${HDF5_MINIMUM_VERSION} REQUIRED COMPONENTS C CXX)
+
+set(XTENSOR_MINIMUM_VERSION "0.21.10")
+find_dependency(xtensor ${XTENSOR_MINIMUM_VERSION} REQUIRED)
+
+set(NLOHMANN_JSON_MINIMUM_VERSION "3.11.1")
+find_dependency(nlohmann_json ${NLOHMANN_JSON_MINIMUM_VERSION} REQUIRED)
+
+include("${CMAKE_CURRENT_LIST_DIR}/MRDTargets.cmake")

cpp/mrd-tools/CMakeLists.txt

@@ -1,95 +1,54 @@
 include_directories(../)
 
-find_package(ISMRMRD 1.13.4 REQUIRED)
+add_executable(mrd_phantom mrd_phantom.cc shepp_logan_phantom.cc)
+target_link_libraries(mrd_phantom mrd_generated fftw3f)
+
+add_executable(mrd_hdf5_to_stream mrd_hdf5_to_stream.cc)
+target_link_libraries(mrd_hdf5_to_stream mrd_generated)
 
-add_executable(
-  mrd_phantom
-  mrd_phantom.cc
-  shepp_logan_phantom.cc
-)
-
-target_link_libraries(
-  mrd_phantom
-  mrd_generated
-  fftw3f
-)
-
-add_executable(
-  mrd_hdf5_to_stream
-  mrd_hdf5_to_stream.cc
-)
-
-target_link_libraries(
-  mrd_hdf5_to_stream
-  mrd_generated
-)
-
-add_executable(
-  mrd_stream_to_hdf5
-  mrd_stream_to_hdf5.cc
-)
-
-target_link_libraries(
-  mrd_stream_to_hdf5
-  mrd_generated
-)
-
-add_executable(
-  mrd_stream_recon
-  mrd_stream_recon.cc
-)
-
-target_link_libraries(
-  mrd_stream_recon
-  fftw3f
-  mrd_generated
-)
-
-add_executable(
-  ismrmrd_to_mrd
-  ismrmrd_to_mrd.cc
-)
-
-target_link_libraries(
-  ismrmrd_to_mrd
-  mrd_generated
-  ISMRMRD::ISMRMRD
-)
-
-add_executable(
-  mrd_to_ismrmrd
-  mrd_to_ismrmrd.cc
-)
-
-target_link_libraries(
-  mrd_to_ismrmrd
-  mrd_generated
-  ISMRMRD::ISMRMRD
-)
-
-find_package(ImageMagick COMPONENTS Magick++ REQUIRED)
-find_package(fmt REQUIRED)
-include_directories(${ImageMagick_INCLUDE_DIRS})
-
-add_executable(
-  mrd_image_stream_to_png
-  mrd_image_stream_to_png.cc
-)
-
-target_compile_options(mrd_image_stream_to_png PRIVATE "-DMAGICKCORE_QUANTUM_DEPTH=8" "-DMAGICKCORE_HDRI_ENABLE=0")
-target_link_libraries(
-  mrd_image_stream_to_png
-  mrd_generated
-  ${ImageMagick_LIBRARIES}
-  fmt::fmt
-)
+add_executable(mrd_stream_to_hdf5 mrd_stream_to_hdf5.cc)
+target_link_libraries(mrd_stream_to_hdf5 mrd_generated)
+
+add_executable(mrd_stream_recon mrd_stream_recon.cc)
+target_link_libraries(mrd_stream_recon fftw3f mrd_generated)
 
 install(TARGETS
-    ismrmrd_to_mrd
     mrd_hdf5_to_stream
-    mrd_image_stream_to_png
     mrd_phantom
     mrd_stream_recon
     mrd_stream_to_hdf5
-    mrd_to_ismrmrd
     DESTINATION bin)
+
+
+find_package(ISMRMRD 1.13.4 REQUIRED)
+
+if (ISMRMRD_FOUND)
+  message(STATUS "ISMRMRD found: ${ISMRMRD_INCLUDE_DIR}")
+
+  add_executable(ismrmrd_to_mrd ismrmrd_to_mrd.cc converters.cc)
+  target_link_libraries(ismrmrd_to_mrd mrd_generated ISMRMRD::ISMRMRD)
+
+  add_executable(mrd_to_ismrmrd mrd_to_ismrmrd.cc converters.cc)
+  target_link_libraries(mrd_to_ismrmrd mrd_generated ISMRMRD::ISMRMRD)
+
+  install(TARGETS ismrmrd_to_mrd mrd_to_ismrmrd DESTINATION bin)
+else()
+  message(STATUS "ISMRMRD not found. Skipping conversion tools.")
+endif()
+
+
+find_package(ImageMagick COMPONENTS Magick++)
+find_package(fmt)
+
+if (ImageMagick_FOUND AND fmt_FOUND)
+  message(STATUS "ImageMagick and fmt found.")
+  include_directories(${ImageMagick_INCLUDE_DIRS})
+
+  add_executable(mrd_image_stream_to_png mrd_image_stream_to_png.cc)
+  target_compile_options(mrd_image_stream_to_png PRIVATE "-DMAGICKCORE_QUANTUM_DEPTH=8" "-DMAGICKCORE_HDRI_ENABLE=0")
+  target_link_libraries(mrd_image_stream_to_png mrd_generated ${ImageMagick_LIBRARIES} fmt::fmt)
+
+  install(TARGETS mrd_image_stream_to_png DESTINATION bin)
+else()
+  message(STATUS "ImageMagick or fmt not found. Skipping mrd_image_stream_to_png.")
+endif()