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CMakeLists.txt
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cmake_minimum_required(VERSION 3.9.5)
project(Vesselness)
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
if(APPLE)
set(CMAKE_OSX_SYSROOT /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk)
endif()
# CLI11
include_directories( "${PROJECT_SOURCE_DIR}/lib/" )
find_package(ITK 5.2 REQUIRED)
include(${ITK_USE_FILE})
#set(CMAKE_BUILD_TYPE Release)
#Executable Section:
#Antiga ------------------------
add_executable(Antiga src/Filters/antiga.cpp)
target_include_directories(Antiga PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<INSTALL_INTERFACE:include>"
)
target_link_libraries(Antiga ${ITK_LIBRARIES} )
set_target_properties(Antiga PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# Our own Frangi's implementation -----------------------
# In the benchmark, Antiga implementation is used.
add_executable(Frangi src/Filters/frangi.cpp)
target_include_directories(Frangi PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/Frangi>"
"$<INSTALL_INTERFACE:include/Frangi>"
)
target_link_libraries(Frangi ${ITK_LIBRARIES} )
set_target_properties(Frangi PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# Jerman -----------------------
add_executable(Jerman src/Filters/jerman.cpp)
target_include_directories(Jerman PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/Jerman>"
"$<INSTALL_INTERFACE:include/Jerman>"
)
target_link_libraries(Jerman ${ITK_LIBRARIES})
set_target_properties(Jerman PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# Jerman blobness -----------------------
# add_executable(JermanBlobness src/Filters/jermanBlobness.cpp)
# target_include_directories(JermanBlobness PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/JermanBlobness>"
# "$<INSTALL_INTERFACE:include/JermanBlobness>"
# )
# target_link_libraries(JermanBlobness ${ITK_LIBRARIES})
# set_target_properties(JermanBlobness PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# RhuiZhang -----------------------
add_executable(Zhang src/Filters/ruiZhang.cpp)
target_include_directories(Zhang PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/RuiZhang>"
"$<INSTALL_INTERFACE:include/RuiZhang>"
)
target_link_libraries(Zhang ${ITK_LIBRARIES})
set_target_properties(Zhang PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# Meijering --------------------------
add_executable(Meijering src/Filters/meijering.cpp)
target_include_directories(Meijering PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/Meijering>"
"$<INSTALL_INTERFACE:include/Meijering>"
)
target_link_libraries(Meijering ${ITK_LIBRARIES} )
set_target_properties(Meijering PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# utilities --------------------------------
# Sato -----------------------------
add_executable(Sato src/Filters/sato.cpp)
target_include_directories(Sato PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
)
target_link_libraries(Sato ${ITK_LIBRARIES} )
set_target_properties(Sato PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# OOF ------------------------------
add_executable(OOF src/Filters/oof.cxx)
target_include_directories(OOF PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/OOF>"
"$<INSTALL_INTERFACE:include/OOF>"
)
target_link_libraries(OOF ${ITK_LIBRARIES} )
set_target_properties(OOF PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# OOF Geometric mean -----------------
add_executable(OOF_GM src/Filters/oof_GM.cxx)
target_include_directories(OOF_GM PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/OOF>"
"$<INSTALL_INTERFACE:include/OOF>"
)
target_link_libraries(OOF_GM ${ITK_LIBRARIES} )
set_target_properties(OOF_GM PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# RORPO ----------------------------
add_subdirectory(RORPO)
# rescale Filter
add_executable(Rescale src/Filters/rescale.cpp)
target_include_directories(Rescale PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
)
target_link_libraries(Rescale ${ITK_LIBRARIES} )
set_target_properties(Rescale PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# benchmark ------------------------
add_subdirectory(lib/jsoncpp)
find_package(jsoncpp REQUIRED)
get_target_property(JSON_INC_PATH jsoncpp_static INTERFACE_INCLUDE_DIRECTORIES)
include_directories(${JSON_INC_PATH})
#include(lib/jsoncpp.cmake)
#if(BENCHMARK_VESSEL_USE_LOCAL_JSONCPP)
# set(JSONCPP_FOUND ${JSONCPP_FOUND} PARENT_SCOPE)
# set(JSON_INC_PATH ${JSONCPP_INCLUDE_DIRS} PARENT_SCOPE)
# set(JSONCPP_LIBRARIES ${JSONCPP_LIBRARIES} PARENT_SCOPE)
# set(JSONCPP_SOURCES ${JSONCPP_SOURCES} PARENT_SCOPE)
#else()
# find_package(jsoncpp REQUIRED)
# get_target_property(JSON_INC_PATH jsoncpp_lib INTERFACE_INCLUDE_DIRECTORIES)
# include_directories(${JSON_INC_PATH})
#endif()
add_executable(Benchmark src/Benchmark/benchmark.cpp)
target_include_directories(Benchmark PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/Benchmark>"
"$<INSTALL_INTERFACE:include/Benchmark>"
)
target_link_libraries(Benchmark ${ITK_LIBRARIES} ${JSONCPP_LIBRARIES} jsoncpp_lib)
set_target_properties(Benchmark PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# TEST METRICS -------------------------------------------
add_executable(Test src/Benchmark/test.cpp)
target_include_directories(Test PUBLIC
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/Benchmark>"
"$<INSTALL_INTERFACE:include>"
)
target_link_libraries(Test ${ITK_LIBRARIES} )
set_target_properties(Test PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
# process ircad -------------------
#add_executable(CropImages src/BDDGeneration/crop_ircad_data.cpp)
#target_include_directories(CropImages PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(CropImages ${ITK_LIBRARIES})
#set_target_properties(CropImages PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts" )
# utilities --------------------------------
#add_executable(ChangeLabelDicom src/BDDGeneration/changeLabelDicom.cpp)
#target_include_directories(ChangeLabelDicom PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(ChangeLabelDicom ${ITK_LIBRARIES})
#set_target_properties(ChangeLabelDicom PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin" )
#add_executable(MakeIso src/BDDGeneration/makeIso.cpp)
#target_include_directories(MakeIso PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(MakeIso ${ITK_LIBRARIES})
#set_target_properties(MakeIso PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator/ircad" )
#add_executable(MakeIsoBullit src/BDDGeneration/makeIsoBullit.cpp)
#target_include_directories(MakeIsoBullit PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(MakeIsoBullit ${ITK_LIBRARIES})
#set_target_properties(MakeIsoBullit PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator/bullit" )
#add_executable(MakeVascuSynthGT src/BDDGeneration/makeVascuSynthGT.cpp)
#target_include_directories(MakeVascuSynthGT PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(MakeVascuSynthGT ${ITK_LIBRARIES})
#set_target_properties(MakeVascuSynthGT PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts" )
#add_executable(LabelVessels src/BDDGeneration/labelVessels.cpp)
#target_include_directories(LabelVessels PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(LabelVessels ${ITK_LIBRARIES})
#set_target_properties(LabelVessels PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator" )
#add_executable(LabelVesselsBullit src/BDDGeneration/labelVesselsBullit.cpp)
#target_include_directories(LabelVesselsBullit PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(LabelVesselsBullit ${ITK_LIBRARIES})
#set_target_properties(LabelVesselsBullit PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator/bullit" )
# Bifurcations VascuSynth
#add_executable(MakeVascuSynthBifurcationGT src/BDDGeneration/makeVascuSynthBifurcationGT.cpp)
#target_include_directories(MakeVascuSynthBifurcationGT PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(MakeVascuSynthBifurcationGT ${ITK_LIBRARIES})
#set_target_properties(MakeVascuSynthBifurcationGT PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator/vascuSynth" )
# Bifurcation IRCAD
#add_executable(MakeIrcadBifurcationGT src/BDDGeneration/makeIrcadBifurcation.cpp)
#target_include_directories(MakeIrcadBifurcationGT PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(MakeIrcadBifurcationGT ${ITK_LIBRARIES})
#set_target_properties(MakeIrcadBifurcationGT PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator/ircad" )
# Bifurcation Bullit
#add_executable(MakeBullitBifurcationGT src/BDDGeneration/makeBullitBifurcations.cpp)
#target_include_directories(MakeBullitBifurcationGT PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(MakeBullitBifurcationGT ${ITK_LIBRARIES})
#set_target_properties(MakeBullitBifurcationGT PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator/bullit" )
# Shapes
#add_executable(MakeVascuSynthSizeLabels src/BDDGeneration/makeVascuSizeLabels.cpp)
#target_include_directories(MakeVascuSynthSizeLabels PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(MakeVascuSynthSizeLabels ${ITK_LIBRARIES})
#set_target_properties(MakeVascuSynthSizeLabels PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts/BDDgenerator/vascuSynth" )
# isoFromUnit
#add_executable(isoFromUnit src/BDDGeneration/isoFromUnit.cpp)
#target_include_directories(isoFromUnit PUBLIC
# "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
# "$<INSTALL_INTERFACE:include>"
# )
#target_link_libraries(isoFromUnit ${ITK_LIBRARIES})
#set_target_properties(isoFromUnit PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/scripts" )