Merge branch 'master' into issue758_linuxdeploy

neutronimaging · Jan 13, 2025 · 012491c · 012491c
2 parents 1384718 + 6a97718
commit 012491c
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Showing 22 changed files with 679 additions and 729 deletions.
diff --git a/.github/workflows/Build-multi-OS.yml b/.github/workflows/Build-multi-OS.yml
@@ -38,7 +38,7 @@ jobs:
             cl: 17
             build_type: Release
             build_root: build-imagingsuite
-          - os: ubuntu-latest
+          - os: ubuntu-22.04
             c_compiler: gcc
             cpp_compiler: g++
             gcc: 11
@@ -149,16 +149,38 @@ jobs:
 
     - name: Ammend shared libraries runpaths
       if: ${{ runner.os == 'Linux' }}
-      working-directory: build-imagingsuite/Release/lib
+      working-directory: build-imagingsuite/Release
       shell: bash
-      run: patchelf --set-rpath '$ORIGIN' *.so*
+      run: |
+        patchelf --set-rpath '$ORIGIN' lib/*.so*
+        patchelf --set-rpath '$ORIGIN:$ORIGIN/../../lib' PlugIns/BackProjectors/*.so*
+        patchelf --set-rpath '$ORIGIN:$ORIGIN/../../lib' PlugIns/Preprocessors/*.so*
 
     - name: Test
       id: tests
       working-directory: ${{ matrix.build_root }}
+      shell: bash
       #Execute tests defined by the CMake configuration. Note that --build-config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
       #See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-      run: ctest --build-config ${{ matrix.build_type }}
+      # The seperation of module files into seperate folders breaks the ctest test discovery, copy temprarily to the root folder for testing
+      run: |
+        if [ "${RUNNER_OS}" == "Windows" ]; then
+          cp ./bin/Release/PlugIns/Preprocessors/* ./bin/Release/PlugIns/BackProjectors/* ./bin/Release/
+        elif [ "${RUNNER_OS}" == "Linux" ]; then
+          cp ./PlugIns/Preprocessors/* ./PlugIns/BackProjectors/* ./lib/
+        elif [ "${RUNNER_OS}" == "macOS" ]; then
+          cp ./lib/Preprocessors/* ./lib/BackProjectors/* ./lib/
+        fi
+
+        ctest --build-config ${{ matrix.build_type }}
+        
+        if [ "${RUNNER_OS}" == "Windows" ]; then
+          rm ./bin/Release/*Modules.dll ./bin/Release/*Projectors.dll
+        elif [ "${RUNNER_OS}" == "Linux" ]; then
+          rm lib/*Modules.so lib/*Projectors.so
+        elif [ "${RUNNER_OS}" == "macOS" ]; then
+          rm -r lib/*Modules.dylib lib/*Projectors.dylib lib/sse2neon
+        fi
       continue-on-error: true
 
     - name: Archive test results
@@ -168,22 +190,33 @@ jobs:
         name: ${{runner.os}}-${{runner.arch}}-test-results
         path: ${{ matrix.build_root }}/Testing
 
-    - name: Compress artifact
-      shell: bash
-      working-directory: ${{ matrix.build_root }}
-      run: |
-        if [ "${RUNNER_OS}" == "Windows" ]; then
-          7z a ../MuhRec-${{runner.os}}-${{runner.arch}}.zip "bin/Release/*" -xr!t*.exe -xr!muhreccli.exe -xr!verticalslicer.exe
-        elif [ "${RUNNER_OS}" == "Linux" ]; then
-          zip -r ../../MuhRec-${{runner.os}}-${{runner.arch}}.zip bin/* lib/* -x "bin/t*" -x "bin/verticalslicer" 
-        elif [ "${RUNNER_OS}" == "macOS" -a "${RUNNER_ARCH}" == "X64" ]; then
-          zip -r ../../MuhRec-${{runner.os}}-${{runner.arch}}.zip lib/* *.app/* -x "lib/*.dylib"
-        elif [ "${RUNNER_OS}" == "macOS" -a "${RUNNER_ARCH}" == "ARM64" ]; then
-          zip -r ../../MuhRec-${{runner.os}}-${{runner.arch}}.zip lib/* *.app/* -x "lib/*.dylib" -x "lib/*.h"
-        fi
+    - name: Save build artifact Windows
+      if: ${{ runner.os == 'Windows' }}
+      uses: actions/upload-artifact@master
+      with:
+        name: MuhRec-${{runner.os}}-${{runner.arch}}
+        path: |
+          ${{ matrix.build_root }}/bin/Release/*
+          !${{ matrix.build_root }}/bin/Release/t*.exe
+          !${{ matrix.build_root }}/bin/Release/*.pyd
 
-    - name: Save build artifact
+    - name: Save build artifact Linux
+      if: ${{ runner.os == 'Linux' }}
+      uses: actions/upload-artifact@master
+      with:
+        name: MuhRec-${{runner.os}}-${{runner.arch}}
+        path: |
+          ${{ matrix.build_root }}/bin/*
+          !${{ matrix.build_root }}/bin/t*
+          ${{ matrix.build_root }}/PlugIns/*
+          ${{ matrix.build_root }}/lib/*
+          !${{ matrix.build_root }}/lib/*cpython*
+          ${{ matrix.build_root }}/resources/*
+
+    - name: Save build artifact MacOS
+      if: ${{ runner.os == 'macOS' }}
       uses: actions/upload-artifact@master
       with:
         name: MuhRec-${{runner.os}}-${{runner.arch}}
-        path: "${{ github.workspace }}/MuhRec*.zip"
+        path: |
+          ${{ matrix.build_root }}/*.app/*
diff --git a/.github/workflows/Build-wheels.yml b/.github/workflows/Build-wheels.yml
@@ -32,16 +32,16 @@ jobs:
       # 4. <MacOS 14 with arm64 arch, Release, Clang 15 compiler toolchain
       # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the list.
       matrix: # Qt requires py7zr==0.20.x which requires python 3.7^
-        python-version: ["3.7","3.8","3.9", "3.10", "3.11", "3.12"]
-        os: [windows-2022, ubuntu-latest, macos-13, macos-14]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [windows-2022, ubuntu-22.04, macos-13, macos-14]
         include:
           - os: windows-2022
             c_compiler: cl
             cpp_compiler: cl
             cl: 17
             build_type: Release
             build_root: build-imagingsuite
-          - os: ubuntu-latest
+          - os: ubuntu-22.04
             c_compiler: gcc
             cpp_compiler: g++
             gcc: 11
@@ -165,29 +165,30 @@ jobs:
           ${QTPATH}/bin/macdeployqt imageviewer.app
         fi
 
-    - name: Ammend shared libraries runpaths
-      if: ${{ runner.os == 'Linux' }}
-      working-directory: build-imagingsuite/Release/lib
-      shell: bash
-      run: patchelf --set-rpath '$ORIGIN' *.so*
-
     - name: Copy bindings and shared libraries to package folder
       shell: bash
       working-directory: build-imagingsuite
       run: |
         if [ "${RUNNER_OS}" == "Windows" ]; then
           cd bin/Release
-          cp *.dll ../../../imagingsuite/package/pymuhrec
+          cp *.dll PlugIns/BackProjectors/*.dll PlugIns/Preprocessors/*.dll ../../../imagingsuite/package/pymuhrec
           cp *.pyd ../../../imagingsuite/package/pymuhrec
         elif [ "${RUNNER_OS}" == "Linux" ]; then
-          cd Release/lib
-          cp * ../../../imagingsuite/package/pymuhrec
+          cd Release
+          cp lib/* PlugIns/BackProjectors/*.so PlugIns/Preprocessors/*.so ../../imagingsuite/package/pymuhrec
         elif [ "${RUNNER_OS}" == "macOS" ]; then
           cd Release/lib
-          cp *.dylib ../../../imagingsuite/package/pymuhrec
+          cp *.dylib BackProjectors/*.dylib Preprocessors/*.dylib ../../../imagingsuite/package/pymuhrec
           cp *.so ../../../imagingsuite/package/pymuhrec
         fi
 
+    - name: Ammend shared libraries runpaths
+      if: ${{ runner.os == 'Linux' }}
+      working-directory: imagingsuite/package/pymuhrec
+      shell: bash
+      run: |
+        patchelf --set-rpath '$ORIGIN' *.so*
+
     - name: Build wheels
       shell: bash
       working-directory: imagingsuite/package

diff --git a/.gitignore b/.gitignore
@@ -30,7 +30,7 @@ cmake_install.cmake
 *.synctex.gz
 .vscode*
 package/pymuhrec/*.dll
-package/pymuhrec/*.so
+package/pymuhrec/*.so*
 package/pymuhrec/*.dylib
 package/pymuhrec/*.pyd
 package/pymuhrec.egg-info

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -57,16 +57,22 @@ endif()
 
 if (WIN32)
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/Release)
-  set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+  set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/Release)
   set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/Release)
+  set(PREPROCESSOR_MODULES_DIRECTORY ${CMAKE_BINARY_DIR}/bin/Release/PlugIns/Preprocessors)
+  set(PROJECTOR_MODULES_DIRECTORY    ${CMAKE_BINARY_DIR}/bin/Release/PlugIns/BackProjectors)
 elseif (LINUX)
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
   set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
   set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+  set(PREPROCESSOR_MODULES_DIRECTORY ${CMAKE_BINARY_DIR}/PlugIns/Preprocessors)
+  set(PROJECTOR_MODULES_DIRECTORY    ${CMAKE_BINARY_DIR}/PlugIns/BackProjectors)
 elseif (APPLE)
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
   set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
   set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+  set(PREPROCESSOR_MODULES_DIRECTORY ${CMAKE_BINARY_DIR}/lib/Preprocessors)
+  set(PROJECTOR_MODULES_DIRECTORY    ${CMAKE_BINARY_DIR}/lib/BackProjectors)
   include_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
 endif()
 
@@ -234,130 +240,14 @@ add_subdirectory(frameworks/tomography/pyMuhRec)
 add_subdirectory(core/algorithms/pyimgalg)
 add_subdirectory(core/algorithms/pyadvancedfilters)
 
-# if(DYNAMIC_LIB)
-  # install(
-  #   EXPORT ${EXPORT_NAME}
-  #   DESTINATION "lib/cmake/kipl"
-  #   NAMESPACE kipl::
-  # )
-
-  # include(CMakePackageConfigHelpers)
-  # configure_package_config_file(
-  #   ${CMAKE_CURRENT_SOURCE_DIR}/cmake/${PROJECT_NAME}-config.cmake.in
-  #   "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config.cmake"
-  #   INSTALL_DESTINATION lib/cmake/kipl
-  # )
-  # write_basic_package_version_file(
-  #   "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake"
-  #   VERSION "${CMAKE_PROJECT_VERSION}"
-  #   COMPATIBILITY SameMinorVersion # switch to SameMajorVersion after 1.0
-  #                                  # release
-  # )
-  # install(
-  #   FILES "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config.cmake"
-  #         "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake"
-  #   DESTINATION lib/cmake/kipl
-  # )
-  # if (LINUX)
-  #   print('Linux')
-  #   install(FILES 
-  #     ../lib/libkipl.so.1.0.0 
-  #     ../lib/libModuleConfig.so.1.0.0 
-  #     ../lib/libReconFramework.so.1.0.0
-  #     ../lib/libStdBackProjectors.so.1.0.0
-  #     ../lib/libFDKBackProjectors.so.1.0.0
-  #     ../lib/libImagingAlgorithms.so.1.0.0
-  #     ../lib/libReaderConfig.so.1.0.0
-  #     ../lib/libNeXus.so.1.0.0	
-  #     ../lib/libhdf5_cpp.so.11
-  #     ../lib/libNeXusCPP.so.1.0.0
-  #     ../lib/libhdf5_hl.so.10
-  #     ../lib/libhdf5.so.10	
-  #     ../lib/libsz.so.2
-
-  #   DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
-
-  #   execute_process(
-  #     COMMAND for f in `ls *.so.1.0.0`; do ln -s $f `basename $f .so.1.0.0`.so.1; done 
-  #     WORKING_DIRECTORY "${CMAKE_INSTALL_PREFIX}/lib"
-  #   )
-  # endif()
-  # if (APPLE)
-  #   install(FILES 
-  #   # ../ExternalDependencies/macos/${CMAKE_HOST_SYSTEM_PROCESSOR}/lib/libNeXus.1.0.0.dylib
-  #   # ../ExternalDependencies/macos/${CMAKE_HOST_SYSTEM_PROCESSOR}/lib/libNeXusCPP.1.0.0.dylib
-  #   # /opt/homebrew/lib/libhdf5.dylib
-  #   # /opt/homebrew/lib/libhdf5_cpp.dylib 
-
-  #   # external/mac/lib/libNeXus.1.0.0.dylib	
-  #   # external/mac/lib//libhdf5_cpp.11.dylib
-  #   # external/mac/lib//libNeXusCPP.1.0.0.dylib
-  #   # external/mac/lib//libhdf5_hl.10.dylib
-  #   # external/mac/lib//libhdf5.10.dylib	
-  #   # external/mac/lib//libsz.2.dylib
-
-  #   DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
-
-  #   execute_process(
-  #     COMMAND for f in `ls *.1.0.0.*`; do ln -s $f `basename $f .1.0.0.dylib`.1.dylib; done 
-  #     WORKING_DIRECTORY "${CMAKE_INSTALL_PREFIX}/lib"
-  #   )
-  # endif()
-
-
-
-
-# endif(DYNAMIC_LIB)
-# if (WIN32)
-# message("${OpenBLAS_LIBRARIES}")
-# install(FILES 
-#   external/lib64/nexus/NeXus.dll	
-#   external/lib64/nexus/NeXusCPP.dll
-#   external/lib64/hdf5/hdf5_hl.dll
-#   external/lib64/hdf5/hdf5.dll
-#   external/lib64/hdf5/hdf5_cpp.dll
-#   external/lib64/hdf5/zlib.dll
-#   external/lib64/hdf5/szip.dll
-#   external/lib64/libtiff.dll
-#   external/lib64/libjpeg-62.dll
-#   external/lib64/zlib1.dll
-#   external/lib64/libfftw3-3.dll
-#   external/lib64/libfftw3f-3.dll
-
-
-#   # ${OpenBLAS_LIBRARIES}
-#   # external/lib64/libblas.dll
-#   # external/lib64/liblapack.dll
-#   # external/lib64/liblapacke.dll
-#   # external/lib64/libquadmath-0.dll
-#   # external/lib64/libgfortran_64-3.dll
-#   # external/lib64/libwinpthread-1.dll
-#   # external/lib64/libgcc_s_seh-1.dll
-#   # external/lib64/libgcc_s_seh_64-1.dll
-#   # ../ExternalDependencies/windows/bin/libopenblas.dll
-
-#   ../ExternalDependencies/windows/bin/libxml2.dll 
-#   ../ExternalDependencies/windows/bin/cfitsio.dll
-#   ../ExternalDependencies/windows/bin/libopenblas.dll
-
-#   DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
-# endif()
-# message(${CMAKE_CURRENT_SOURCE_DIR})
-
-## define test
-#add_test(
-#  NAME
-#    testBindAverageImage
-#  COMMAND
-#    ${CMAKE_COMMAND} -E env IMAGALG_MODULE_PATH=$<TARGET_FILE_DIR:imagalg>
-#    ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/UnitTests/python/testBindAverageImage.py
-#    ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/UnitTests/python/testBindAverageImage.py
-#)
-#
-#add_test(
-#  NAME
-#    testBindPolynomialCorrection
-#  COMMAND
-#    ${CMAKE_COMMAND} -E env IMAGALG_MODULE_PATH=$<TARGET_FILE_DIR:imagalg>
-#    ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/UnitTests/python/testBindPolynomialCorrection.py
-#)
+set_target_properties(InspectorModules StdPreprocModules
+    PROPERTIES
+    LIBRARY_OUTPUT_DIRECTORY ${PREPROCESSOR_MODULES_DIRECTORY}
+    RUNTIME_OUTPUT_DIRECTORY ${PREPROCESSOR_MODULES_DIRECTORY}
+)
+
+set_target_properties(FDKBackProjectors StdBackProjectors
+    PROPERTIES
+    LIBRARY_OUTPUT_DIRECTORY ${PROJECTOR_MODULES_DIRECTORY}
+    RUNTIME_OUTPUT_DIRECTORY ${PROJECTOR_MODULES_DIRECTORY}
+)