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Merged
N-Dekker merged 1 commit into from
Apr 10, 2026
Merged

ENH: Use target based includes #1426

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21 changes: 7 additions & 14 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -129,13 +129,12 @@ if(ELASTIX_USE_OPENCL)
endif()

# Include the OpenCL include directories to elastix
include_directories(${OPENCL_INCLUDE_DIRS})
# Note: OPENCL_INCLUDE_DIRS and -DELASTIX_USE_OPENCL are set as PUBLIC
# target properties on elxOpenCL (Common/OpenCL/CMakeLists.txt) and
# propagate transitively to all targets that link elxOpenCL.

# Add some useful macro's
include(elastixOpenCL)

# Add definition for the OpenCL
add_definitions(-DELASTIX_USE_OPENCL)
endif()

#---------------------------------------------------------------------
Expand All @@ -145,8 +144,6 @@ option(ELASTIX_USE_EIGEN "Use Eigen library." OFF)

if(ELASTIX_USE_EIGEN)
find_package(Eigen3 REQUIRED)
include_directories(${EIGEN3_INCLUDE_DIR})
add_definitions(-DELASTIX_USE_EIGEN)
endif()

#---------------------------------------------------------------------
Expand Down Expand Up @@ -235,6 +232,10 @@ endif()

#---------------------------------------------------------------------
# Include directories
# Note: Target-based include directories are set in the individual
# library CMakeLists.txt files using target_include_directories().
# The variables below are kept for ElastixConfig.cmake generation
# to support external projects that use the old-style include_directories().

set(elxCommon_INCLUDE_DIRECTORIES
${elastix_SOURCE_DIR}/Common
Expand Down Expand Up @@ -284,15 +285,7 @@ set(elxINCLUDE_DIRECTORIES
${ELASTIX_USER_COMPONENT_DIRS}
)

include_directories(${elxINCLUDE_DIRECTORIES})

# include the OpenCL directories
# The key-word BEFORE is important here, because the elastix distribution
# contains some files with the same name as in the ITK distribution.
# Some bugs were fixed and features added. When these are contributed back
# to the ITK the BEFORE keyword is not needed anymore.
if(ELASTIX_USE_OPENCL)
include_directories(BEFORE ${elxCommon_OpenCL_INCLUDE_DIRECTORIES})
list(APPEND elxINCLUDE_DIRECTORIES ${elxCommon_OpenCL_INCLUDE_DIRECTORIES})
endif()

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37 changes: 37 additions & 0 deletions Common/CMakeLists.txt
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Expand Up @@ -217,3 +217,40 @@ endif()
target_link_libraries(elxCommon
${ITK_LIBRARIES}
)

target_include_directories(elxCommon PUBLIC
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Common>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Common/CostFunctions>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Common/ImageSamplers>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Common/LineSearchOptimizers>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Common/Transforms>
# Note: elxTransformIO.h (a public header in Common/Transforms) includes
# ExternalTransform/elxAdvancedTransformAdapter.h from Components/Transforms.
# This is a circular dependency but must be PUBLIC since downstream targets
# also include elxTransformIO.h.
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Components/Transforms>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/CostFunctions>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/ImageSamplers>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/LineSearchOptimizers>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/Transforms>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Components/Transforms>
)

# Note: elxCommon sources have circular dependencies on Core and Components
# headers (e.g. elxTransformFactoryRegistration.cxx includes Component transform
# headers which in turn include Core headers, and elxTransformIO.h includes
# ExternalTransform/elxAdvancedTransformAdapter.h from Components/Transforms).
# These cannot be expressed as target_link_libraries without creating cycles,
# so they are added as PRIVATE include directories.
target_include_directories(elxCommon PRIVATE
${elastix_SOURCE_DIR}/Core
${elastix_SOURCE_DIR}/Core/Kernel
${elastix_SOURCE_DIR}/Core/Install
${elastix_SOURCE_DIR}/Core/ComponentBaseClasses
${elastix_SOURCE_DIR}/Core/Configuration
${elastix_SOURCE_DIR}/Core/Main
${elastix_SOURCE_DIR}/Common/ParameterFileParser
${elastix_SOURCE_DIR}/Common/MevisDicomTiff
${elastix_BINARY_DIR}
)
7 changes: 7 additions & 0 deletions Common/GTesting/CMakeLists.txt
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Expand Up @@ -50,4 +50,11 @@ else()
)
endif()

target_include_directories(CommonGTest PRIVATE
${elastix_SOURCE_DIR}/Components/Metrics
${elastix_SOURCE_DIR}/Components/ResampleInterpolators
${elastix_SOURCE_DIR}/Components/Resamplers
${elastix_SOURCE_DIR}/Components/Transforms
)

add_test(NAME CommonGTest_test COMMAND CommonGTest)
3 changes: 3 additions & 0 deletions Common/MevisDicomTiff/CMakeLists.txt
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Expand Up @@ -25,6 +25,9 @@ if(NOT ELASTIX_NO_INSTALL_DEVELOPMENT)
endif()

target_link_libraries(mevisdcmtiff ${ITK_LIBRARIES})
target_include_directories(mevisdcmtiff PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/MevisDicomTiff>)

# Group in IDE's like Visual Studio
set_property(TARGET mevisdcmtiff PROPERTY FOLDER "libraries")
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21 changes: 21 additions & 0 deletions Common/OpenCL/CMakeLists.txt
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Expand Up @@ -61,6 +61,27 @@ target_link_libraries(elxOpenCL
${OPENCL_LIBRARIES}
)

target_include_directories(elxOpenCL PUBLIC ${OPENCL_INCLUDE_DIRS})
target_compile_definitions(elxOpenCL PUBLIC ELASTIX_USE_OPENCL)

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@N-Dekker N-Dekker Apr 9, 2026

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I'm getting compile errors saying:

elastix\Common\OpenCL\ITKimprovements\itkOpenCLContext.cxx(19,10): error C1083: Cannot open include file: 'itkOpenCLKernels.h': No such file or directory

To fix these, maybe add the following line:

target_include_directories(elxOpenCL PRIVATE ${OPENCL_KERNELS_DEBUG_PATH})

("itkOpenCLKernels.h.in" is configured to ${OPENCL_KERNELS_DEBUG_PATH}/itkOpenCLKernels.h)

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@blowekamp blowekamp Apr 9, 2026 •
edited
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I just tried and FindOpenCL didn't find the headers on my linux or osx systems, and requires further investigations.

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@N-Dekker N-Dekker Apr 9, 2026

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@blowekamp I have a few fixes that should be applied before your PR:

Note that the USE_OpenCLMovingdGenericPyramid typo fix might have a git merge conflict with your proposed change in "Components/MovingImagePyramids/OpenCLMovingGenericPyramid/CMakeLists.txt", but it's really very simple: just remove the letter d from the middle!

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@blowekamp Can you please rebase your PR onto the latest SuperElastix/elastix main branch? (Including the USE_OpenCLMovingdGenericPyramid typo fix.)

# The key-word BEFORE is important here, because the elastix distribution
# contains some files with the same name as in the ITK distribution.
# Some bugs were fixed and features added. When these are contributed back
# to the ITK the BEFORE keyword is not needed anymore.
target_include_directories(elxOpenCL BEFORE PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/Factories>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/ITKimprovements>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/Filters>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/Kernels>
$<BUILD_INTERFACE:${OPENCL_KERNELS_DEBUG_PATH}>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/OpenCL>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/OpenCL/Factories>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/OpenCL/ITKimprovements>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/OpenCL/Filters>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/OpenCL/Kernels>
)

# Group in IDE's like Visual Studio
set_property(TARGET elxOpenCL PROPERTY FOLDER "libraries")

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12 changes: 12 additions & 0 deletions Common/ParameterFileParser/CMakeLists.txt
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Expand Up @@ -18,6 +18,18 @@ if(NOT ELASTIX_NO_INSTALL_DEVELOPMENT)
endif()

target_link_libraries(param ${ITK_LIBRARIES})
target_include_directories(param PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Common/ParameterFileParser>)
# Note: param sources include elxConfiguration.h and elxConversion.h from Core.
# This is a circular dependency (elxCore links param), so we add these as PRIVATE.
target_include_directories(param PRIVATE
${elastix_SOURCE_DIR}/Common
${elastix_SOURCE_DIR}/Core/Configuration
${elastix_SOURCE_DIR}/Core/Install
${elastix_SOURCE_DIR}/Core/Kernel
${elastix_BINARY_DIR}
)

# Group in IDE's like Visual Studio
set_property(TARGET param PROPERTY FOLDER "libraries")
25 changes: 4 additions & 21 deletions Components/CMakeLists.txt
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Expand Up @@ -6,27 +6,9 @@ project(elxComponents)
#---------------------------------------------------------------------
# Set the libraries to be linked.

# Linux gave an error, if param was linked. This was only
# when we still used .dll's. I'm not sure if it will still
# give an error, but as long as linux does not complain
# about the missing param, just leave it out.
if(UNIX)
if(NOT APPLE)
set(elxLinkLibs
elxCommon
elxCore
${ITK_LIBRARIES})
endif()
endif()

# Interestingly, visual c++ and MAC-GCC do need param
if(WIN32 OR APPLE)
set(elxLinkLibs
param
elxCommon
elxCore
${ITK_LIBRARIES})
endif()
set(elxLinkLibs
elxCore
${ITK_LIBRARIES})

#--------------------------------------------------------------------
# Prepare elxInstallComponentFunctionDeclarations.h and
Expand Down Expand Up @@ -130,6 +112,7 @@ macro(ADD_ELXCOMPONENT name)
add_library(${name} STATIC ${filelist})
endif()
target_link_libraries(${name} ${elxLinkLibs})
target_include_directories(${name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
if(NOT ELASTIX_NO_INSTALL_DEVELOPMENT)
install(TARGETS ${name}
ARCHIVE DESTINATION ${ELASTIX_ARCHIVE_DIR}
Expand Down
8 changes: 5 additions & 3 deletions Components/FixedImagePyramids/OpenCLFixedGenericPyramid/CMakeLists.txt
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Expand Up @@ -5,10 +5,12 @@ if(ELASTIX_USE_OPENCL)
elxOpenCLFixedGenericPyramid.hxx
elxOpenCLFixedGenericPyramid.cxx)

include_directories(
../FixedGenericPyramid)

if(USE_OpenCLFixedGenericPyramid)
target_include_directories(OpenCLFixedGenericPyramid PRIVATE
${CMAKE_CURRENT_SOURCE_DIR}/../FixedGenericPyramid)
target_include_directories(OpenCLFixedGenericPyramid BEFORE PRIVATE
${elxCommon_OpenCL_INCLUDE_DIRECTORIES}
${OPENCL_KERNELS_DEBUG_PATH})
target_link_libraries(OpenCLFixedGenericPyramid elxOpenCL)
endif()
else()
Expand Down
15 changes: 9 additions & 6 deletions Components/Metrics/KNNGraphAlphaMutualInformation/KNN/ann_1.1/CMakeLists.txt
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Expand Up @@ -15,12 +15,6 @@ configure_file(
${elastix_BINARY_DIR}/ANN/ANN.h
@ONLY)

# Include these directories to look for header files.
include_directories(
${ANN_SOURCE_DIR}/include
${ANN_SOURCE_DIR}/src
)

# Sources of non-templated classes.
set(ANN_SRCS
src/ANN.cpp
Expand All @@ -42,6 +36,15 @@ set(ANN_SRCS
# Create the ANNlib library
add_library(ANNlib SHARED ${ANN_SRCS})

# Include these directories to look for header files.
target_include_directories(ANNlib
PUBLIC
$<BUILD_INTERFACE:${ANN_SOURCE_DIR}/include>
$<BUILD_INTERFACE:${elastix_BINARY_DIR}>
PRIVATE
${ANN_SOURCE_DIR}/src
)

include(GenerateExportHeader)
generate_export_header(ANNlib
EXPORT_FILE_NAME ${elastix_BINARY_DIR}/ANN/ANNExport.h)
Expand Down
9 changes: 6 additions & 3 deletions Components/MovingImagePyramids/OpenCLMovingGenericPyramid/CMakeLists.txt
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Expand Up @@ -5,13 +5,16 @@ if(ELASTIX_USE_OPENCL)
elxOpenCLMovingGenericPyramid.hxx
elxOpenCLMovingGenericPyramid.cxx)

include_directories(../MovingGenericPyramid)

if(USE_OpenCLMovingGenericPyramid)
target_include_directories(OpenCLMovingGenericPyramid PRIVATE
${CMAKE_CURRENT_SOURCE_DIR}/../MovingGenericPyramid)
target_include_directories(OpenCLMovingGenericPyramid BEFORE PRIVATE
${elxCommon_OpenCL_INCLUDE_DIRECTORIES}
${OPENCL_KERNELS_DEBUG_PATH})
target_link_libraries(OpenCLMovingGenericPyramid elxOpenCL)
endif()
else()
# If the user set USE_OpenCLFixedGenericPyramid ON, but ELASTIX_USE_OPENCL was OFF,
# If the user set USE_OpenCLMovingGenericPyramid ON, but ELASTIX_USE_OPENCL was OFF,
# then issue a warning.
if(USE_OpenCLMovingGenericPyramid)
message(WARNING "You selected to compile OpenCLMovingGenericPyramid, "
Expand Down
5 changes: 5 additions & 0 deletions Components/Optimizers/AdaptiveStochasticLBFGS/CMakeLists.txt
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Expand Up @@ -10,3 +10,8 @@ ADD_ELXCOMPONENT( AdaptiveStochasticLBFGS OFF # OFF by default after elastix 5.0
../StandardStochasticGradientDescent/itkStochasticGradientDescentOptimizer.h
../StandardStochasticGradientDescent/itkStochasticGradientDescentOptimizer.cxx
)

if(USE_AdaptiveStochasticLBFGS AND ELASTIX_USE_EIGEN)
target_include_directories(AdaptiveStochasticLBFGS PRIVATE ${EIGEN3_INCLUDE_DIR})
target_compile_definitions(AdaptiveStochasticLBFGS PRIVATE ELASTIX_USE_EIGEN)
endif()
5 changes: 5 additions & 0 deletions Components/Optimizers/AdaptiveStochasticVarianceReducedGradient/CMakeLists.txt
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Expand Up @@ -8,3 +8,8 @@ ADD_ELXCOMPONENT( AdaptiveStochasticVarianceReducedGradient OFF # OFF by default
itkStandardStochasticVarianceReducedGradientDescentOptimizer.cxx
itkStochasticVarianceReducedGradientDescentOptimizer.cxx
)

if(USE_AdaptiveStochasticVarianceReducedGradient AND ELASTIX_USE_EIGEN)
target_include_directories(AdaptiveStochasticVarianceReducedGradient PRIVATE ${EIGEN3_INCLUDE_DIR})
target_compile_definitions(AdaptiveStochasticVarianceReducedGradient PRIVATE ELASTIX_USE_EIGEN)
endif()
3 changes: 3 additions & 0 deletions Components/Resamplers/OpenCLResampler/CMakeLists.txt
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Expand Up @@ -6,6 +6,9 @@ if(ELASTIX_USE_OPENCL)
elxOpenCLResampler.cxx)

if(USE_OpenCLResampler)
target_include_directories(OpenCLResampler BEFORE PRIVATE
${elxCommon_OpenCL_INCLUDE_DIRECTORIES}
${OPENCL_KERNELS_DEBUG_PATH})
target_link_libraries(OpenCLResampler elxOpenCL)
endif()
else()
Expand Down
17 changes: 17 additions & 0 deletions Core/CMakeLists.txt
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Expand Up @@ -161,6 +161,23 @@ target_link_libraries(elxCore
target_include_directories(elxCore PRIVATE
${ITK_CMAKE_DIR}/../Modules/ThirdParty/DoubleConversion/src/double-conversion)

target_include_directories(elxCore PUBLIC
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Core>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Core/Install>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Core/Kernel>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Core/ComponentBaseClasses>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Core/Configuration>
$<BUILD_INTERFACE:${elastix_SOURCE_DIR}/Core/Main>
$<BUILD_INTERFACE:${elastix_BINARY_DIR}>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Core>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Core/Install>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Core/Kernel>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Core/ComponentBaseClasses>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Core/Configuration>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}/Core/Main>
$<INSTALL_INTERFACE:${ELASTIX_INCLUDE_DIR}>
)

elastix_export_target(elxCommon)
elastix_export_target(param)

Expand Down
7 changes: 6 additions & 1 deletion Testing/CMakeLists.txt
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Expand Up @@ -71,12 +71,13 @@ macro(elx_add_test_core executable_name source_name test_name group)
# Link against other libraries.
target_link_libraries(${executable_name}
param # some test use the CommandLineArgumentParser
elxCommon # provides Common headers (Transforms, CostFunctions, etc.)
${mevisdcmtifflib} # is empty if not selected in CMake
${ITK_LIBRARIES}
)

if(ELASTIX_USE_OPENCL)
include_directories(${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(${executable_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
target_link_libraries(${executable_name} elxOpenCL)
endif()

Expand Down Expand Up @@ -513,6 +514,10 @@ elx_add_test(ThinPlateSplineTransformPerformanceTest "" "Common"
elx_add_test(ThinPlateSplineTransformTest "" "Common"
${TestDataDir}/parameters_TPSTransformTest.txt)
elx_add_test(AdvanceOneStepParallellizationTest "" "Common")
if(ELASTIX_USE_EIGEN)
target_include_directories(itkAdvanceOneStepParallellizationTest PRIVATE ${EIGEN3_INCLUDE_DIR})
target_compile_definitions(itkAdvanceOneStepParallellizationTest PRIVATE ELASTIX_USE_EIGEN)
endif()
elx_add_test(AccumulateDerivativesParallellizationTest "" "Common")
elx_add_test(BSplineTransformPointPerformanceTest "" "Common"
${TestDataDir}/parameters_AdvancedBSplineDeformableTransformTest.txt)
Expand Down
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