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CMakeLists.txt
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cmake_minimum_required(VERSION 3.12.0 FATAL_ERROR)
project(DICOMautomaton LANGUAGES CXX)
#set(DICOMautomaton_VERSION_MAJOR 0)
#set(DICOMautomaton_VERSION_MINOR 0)
#set(DICOMautomaton_VERSION_PATCH 0)
####################################################################################
# User Options
####################################################################################
option(MEMORY_CONSTRAINED_BUILD "Compile slowly, with minimal memory usage." OFF)
option(WITH_IWYU "Compile using clang include-what-you-use." OFF)
option(WITH_ASAN "Compile using ASan, LSan, & UBSan." OFF)
option(WITH_TSAN "Compile using ThreadSanitizer." OFF)
option(WITH_MSAN "Compile using MemorySanitizer." OFF)
option(WITH_EIGEN "Compile assuming Eigen is available." ON)
option(WITH_CGAL "Compile assuming CGAL is available." ON)
option(WITH_NLOPT "Compile assuming nlopt is available." ON)
option(WITH_SFML "Compile assuming SFML is available." ON)
option(WITH_SDL "Compile assuming SDL2 and glew are available." ON)
option(WITH_WT "Compile assuming Wt is available." ON)
option(WITH_GNU_GSL "Compile assuming the GNU GSL is available." ON)
option(WITH_POSTGRES "Compile assuming PostgreSQL libraries are available." ON)
option(WITH_JANSSON "Compile assuming Jansson is available." ON)
option(BUILD_SHARED_LIBS "Build shared-object/dynamicly-loaded binaries." ON)
####################################################################################
# Configuration
####################################################################################
# High-level configuration.
if(NOT BUILD_SHARED_LIBS)
#set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
link_libraries("-static")
set(CMAKE_EXE_LINKER_FLAGS "-static")
endif()
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_EXTENSIONS OFF) # Disable GNU extensions (e.g., std=gnu++14).
set(CMAKE_EXPORT_COMPILE_COMMANDS ON) # For use with clang-tidy et al.
set(THREADS_PREFER_PTHREAD_FLAG ON)
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
set(POSITION_INDEPENDENT_CODE TRUE)
# Set the release type.
if(NOT CMAKE_BUILD_TYPE)
# Default to debug builds.
set(CMAKE_BUILD_TYPE Debug CACHE STRING "default to debug" FORCE)
endif()
####################################################################################
# Dependencies
####################################################################################
# Note: Dependencies are listed in CPACK list below.
find_package(Threads REQUIRED)
if(NOT BUILD_SHARED_LIBS)
set(Boost_USE_STATIC_RUNTIME ON)
set(Boost_USE_STATIC_LIBS ON)
endif()
find_package(Boost REQUIRED COMPONENTS filesystem serialization iostreams thread system)
include_directories(${Boost_INCLUDE_DIRS})
if(WITH_EIGEN)
find_package(PkgConfig REQUIRED)
pkg_check_modules(EIGEN3 REQUIRED eigen3)
include_directories( ${EIGEN3_INCLUDE_DIRS} )
endif()
if(WITH_CGAL)
find_package(CGAL REQUIRED COMPONENTS Core)
include(${CGAL_USE_FILE})
endif()
if(WITH_NLOPT)
find_package(PkgConfig REQUIRED)
pkg_check_modules(NLOPT REQUIRED nlopt)
include_directories( ${NLOPT_INCLUDE_DIRS} )
endif()
if(WITH_SFML)
#find_package(SFML COMPONENTS graphics window system main REQUIRED)
find_package(PkgConfig REQUIRED)
if(NOT BUILD_SHARED_LIBS)
set(SFML_STATIC_LIBRARIES TRUE)
add_definitions(-DSFML_STATIC=1)
endif()
pkg_check_modules(SFML REQUIRED sfml-graphics sfml-window sfml-system)
include_directories( ${SFML_INCLUDE_DIRS} )
endif()
if(WITH_SDL)
set(OpenGL_GL_PREFERENCE GLVND)
find_package(OpenGL REQUIRED COMPONENTS OpenGL) # Will help pick-up opengl32.a with MXE toolchain.
message(STATUS "Proceeding with OPENGL_LIBRARIES = ${OPENGL_LIBRARIES}")
message(STATUS "Proceeding with OPENGL_INCLUDE_DIR = ${OPENGL_INCLUDE_DIR}")
include_directories( ${OPENGL_INCLUDE_DIR} )
find_package(PkgConfig REQUIRED)
pkg_check_modules(SDL2 REQUIRED sdl2)
include_directories( ${SDL2_INCLUDE_DIRS} )
if(NOT BUILD_SHARED_LIBS)
add_definitions(-DGLEW_STATIC=1)
endif()
pkg_check_modules(GLEW REQUIRED glew)
include_directories( ${GLEW_INCLUDE_DIRS} )
endif()
if(WITH_GNU_GSL)
find_package(PkgConfig REQUIRED)
pkg_check_modules(GNU_GSL REQUIRED gsl)
include_directories( ${GNU_GSL_INCLUDE_DIRS} )
endif()
if(WITH_POSTGRES)
find_package(PkgConfig REQUIRED)
pkg_check_modules(POSTGRES REQUIRED libpq libpqxx)
include_directories( ${POSTGRES_INCLUDE_DIRS} )
endif()
####################################################################################
# Compiler Flags
####################################################################################
# Override the default CXX flags, which are controlled by the release type.
#
# Note: The '_DEBUG' flags are only applied when the release mode is 'Debug' -- likewise for the other flags.
#
# Note: If you want to fully override the CXX_FLAGS, then do not supply a build type and specify your CXX_FLAGS by
# defining CMAKE_CXX_FLAGS when calling cmake.
set(CMAKE_CXX_FLAGS_DEBUG "-O2 -g")
set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O3 -g")
if(MEMORY_CONSTRAINED_BUILD)
# Do not overwrite user-provided flags, but do provide sane defaults.
if(NOT CMAKE_CXX_FLAGS)
set(CMAKE_CXX_FLAGS "-O0 -DNDEBUG")
endif()
set(CMAKE_CXX_FLAGS_DEBUG "-O0 -DNDEBUG")
set(CMAKE_CXX_FLAGS_MINSIZEREL "-O0 -DNDEBUG")
set(CMAKE_CXX_FLAGS_RELEASE "-O0 -DNDEBUG")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O0 -DNDEBUG")
endif()
# Add other appropriate CXX flags.
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fdiagnostics-color=always")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-var-tracking-assignments")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wextra")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wpedantic")
if("${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
# Add gprof profiling flag.
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer")
endif()
if(MEMORY_CONSTRAINED_BUILD)
# Trigger garbage collection more frequently.
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --param ggc-min-expand=10")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --param ggc-min-heapsize=32768")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fdiagnostics-color=always")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wextra")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wpedantic")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-ignored-optimization-argument")
if(WITH_IWYU)
set(IWYU_INVOCATION iwyu) # Location of the iwyu binary.
list(APPEND IWYU_INVOCATION "-Xiwyu;--no_comments")
set(CMAKE_CXX_INCLUDE_WHAT_YOU_USE ${IWYU_INVOCATION})
endif()
endif()
# Sanitizers.
if(WITH_ASAN OR WITH_TSAN OR WITH_MSAN)
#set(CMAKE_CXX_FLAGS " ")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-common")
# Also enable coverage instrumentation, since sanitizers will typically be used for testing.
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
# Clang only? Need to confirm ... TODO
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize-coverage=trace-pc-guard")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-instr-generate")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fcoverage-mapping")
add_definitions(-U_FORTIFY_SOURCE)
endif()
if(WITH_ASAN)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address") # <-- includes LSan.
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize-address-use-after-scope")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=pointer-compare")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=pointer-subtract")
# Add UBSan checks too, since ASan, LSan, and UBSan are all compatible.
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=undefined")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-sanitize-recover=undefined")
# Clang only? Need to confirm ... TODO
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=implicit-conversion")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=local-bounds")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=nullability-arg")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=nullability-assign")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=nullability-return")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=unsigned-integer-overflow")
elseif(WITH_TSAN)
message(WARNING "TSan may not support exceptions (depends on the compiler version and platform).")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread")
elseif(WITH_MSAN)
message(WARNING "MSan may not be available on your system.")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=memory")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIE")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pie")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize-memory-track-origins")
endif()
include(CheckCXXSymbolExists)
check_cxx_symbol_exists(__arm__ "cstdio" ARCH_IS_ARM)
check_cxx_symbol_exists(__aarch64__ "cstdio" ARCH_IS_ARM64)
if(ARCH_IS_ARM OR ARCH_IS_ARM64)
message(STATUS "Detected ARM architecture.")
# Enable to fix linking errors for toolchains that do not auto-detect atomic intrinsics (e.g., some ARM systems).
# Note: Binaries built this way should not be distributed.
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
endif()
####################################################################################
# Definitions
####################################################################################
add_definitions(-DUSTREAM_H) # -DUSE_ICU_STRINGS
if(WITH_EIGEN)
message(STATUS "Assuming Eigen is available.")
add_definitions(-DDCMA_USE_EIGEN=1)
else()
message(STATUS "Assuming Eigen is not available.")
add_definitions(-UDCMA_USE_EIGEN)
endif()
if(WITH_CGAL)
message(STATUS "Assuming CGAL is available.")
add_definitions(-DDCMA_USE_CGAL=1)
if("${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
add_definitions(-DCGAL_DISABLE_ROUNDING_MATH_CHECK=1) # May be needed for Valgrind debugging.
message(WARNING "If profiling/debugging on Arch Linux, disable binary stripping in PKGBUILD.")
endif()
if(WITH_EIGEN)
add_definitions(-DCGAL_EIGEN3_ENABLED=1) # Explicitly instruct CGAL to use Eigen.
endif()
else()
message(STATUS "Assuming CGAL is not available.")
add_definitions(-UDCMA_USE_CGAL)
endif()
if(WITH_NLOPT)
message(STATUS "Assuming NLOPT is available.")
add_definitions(-DDCMA_USE_NLOPT=1)
else()
message(STATUS "Assuming NLOPT is not available.")
add_definitions(-UDCMA_USE_NLOPT)
endif()
if(WITH_SFML)
message(STATUS "Assuming SFML is available.")
add_definitions(-DDCMA_USE_SFML=1)
else()
message(STATUS "Assuming SFML is not available.")
add_definitions(-UDCMA_USE_SFML)
endif()
if(WITH_SDL)
message(STATUS "Assuming SDL is available.")
add_definitions(-DDCMA_USE_SDL=1)
add_definitions(-DDCMA_USE_GLEW=1)
else()
message(STATUS "Assuming SDL is not available.")
add_definitions(-UDCMA_USE_SDL)
add_definitions(-UDCMA_USE_GLEW)
endif()
if(WITH_WT)
message(STATUS "Assuming Wt is available.")
add_definitions(-DDCMA_USE_WT=1)
else()
message(STATUS "Assuming Wt is not available.")
add_definitions(-UDCMA_USE_WT)
endif()
if(WITH_POSTGRES)
message(STATUS "Assuming PostgreSQL client libraries are available.")
add_definitions(-DDCMA_USE_POSTGRES=1)
else()
message(STATUS "Assuming PostgreSQL client libraries are not available.")
add_definitions(-UDCMA_USE_POSTGRES)
endif()
if(WITH_JANSSON)
message(STATUS "Assuming Jansson is available.")
add_definitions(-DDCMA_USE_JANSSON=1)
else()
message(STATUS "Assuming Jansson is not available.")
add_definitions(-UDCMA_USE_JANSSON)
endif()
if(WITH_GNU_GSL)
message(STATUS "Assuming the GNU GSL is available.")
add_definitions(-DDCMA_USE_GNU_GSL=1)
else()
message(STATUS "Assuming the GNU GSL is not available.")
add_definitions(-UDCMA_USE_GNU_GSL)
endif()
# ASIO: target Windows 7 features.
add_definitions(-D_WIN32_WINNT=0x0601)
# Use the directory where CMakeLists.txt is for inclusions.
set(CMAKE_INCLUDE_CURRENT_DIR ON)
set(CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
include(GNUInstallDirs)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
# The following should match the system directory:
set(BASH_COMPLETION_INSTALL_DIR "${CMAKE_INSTALL_DATAROOTDIR}/bash-completion/completions/")
####################################################################################
# Subdirectories
####################################################################################
add_subdirectory(src)
add_subdirectory(config-files)
add_subdirectory(scripts)
####################################################################################
# Packaging
####################################################################################
set(CPACK_GENERATOR "DEB")
#set(CPACK_PACKAGE_NAME "dicomautomaton")
string(TIMESTAMP INVOCATION_TIMESTAMP "%Y%m%d.%H%M%S") # For a time-based version number.
set(CPACK_PACKAGE_VERSION "${INVOCATION_TIMESTAMP}")
set(CPACK_STRIP_FILES TRUE)
set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64") # i386, amd64, armel, armhf, ...
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Various tools for medical physics applications.")
set(CPACK_PACKAGE_CONTACT "hdeanclark@gmail.com")
set(CPACK_PACKAGE_MAINTAINER "Haley Clark <hdeanclark@gmail.com>")
set(CPACK_DEBIAN_PACKAGE_SECTION "Science")
# Ygor build dependencies, e.g., "libc6 (>= 2.3.1-6), libgcc1 (>= 1:3.4.2-12)"
set(BUILD_DEPENDENCY_PACKAGES "")
list(APPEND BUILD_DEPENDENCY_PACKAGES "explicator")
list(APPEND BUILD_DEPENDENCY_PACKAGES "ygorclustering")
list(APPEND BUILD_DEPENDENCY_PACKAGES "ygor")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libz-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libboost-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libboost-filesystem-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libboost-iostreams-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libboost-program-options-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libboost-thread-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libasio-dev")
if(WITH_EIGEN)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libeigen3-dev")
endif()
if(WITH_SFML)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libsfml-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "fonts-freefont-ttf")
list(APPEND BUILD_DEPENDENCY_PACKAGES "fonts-cmu")
endif()
if(WITH_SDL)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libsdl2-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libglew-dev")
endif()
if(WITH_CGAL)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libcgal-dev")
endif()
if(WITH_WT)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libwt-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libwthttp-dev")
endif()
if(WITH_NLOPT)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libnlopt-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libnlopt-cxx-dev")
endif()
if(WITH_GNU_GSL)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libgsl-dev")
endif()
if(WITH_POSTGRES)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libpqxx-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "libpq-dev")
list(APPEND BUILD_DEPENDENCY_PACKAGES "postgresql-client")
endif()
if(WITH_JANSSON)
list(APPEND BUILD_DEPENDENCY_PACKAGES "libjansson-dev")
endif()
list(JOIN BUILD_DEPENDENCY_PACKAGES ", " CPACK_DEBIAN_PACKAGE_DEPENDS)
# Recommended or optional packages, e.g., "liboptional-dev (>= 1.2.3-1), libmaybe-dev (>= 1:1.3.2-10)"
set(RECOMMENDED_PACKAGES "")
list(APPEND RECOMMENDED_PACKAGES "gnuplot")
list(APPEND RECOMMENDED_PACKAGES "zenity")
list(APPEND RECOMMENDED_PACKAGES "libboost-all-dev")
list(APPEND RECOMMENDED_PACKAGES "patchelf")
list(JOIN RECOMMENDED_PACKAGES ", " CPACK_DEBIAN_PACKAGE_RECOMMENDS)
include(CPack)