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CMakeLists.txt
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CMakeLists.txt
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PROJECT(NiftySeg)
cmake_minimum_required(VERSION 2.8)
cmake_policy(VERSION 2.8)
include(ExternalProject)
#-----------------------------------------------------------------------------
# Preflight Checks - CMake Version, InSource Build Type
#-----------------------------------------------------------------------------
cmake_minimum_required(VERSION 3.0.2)
if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" MATCHES "^3\\.2\\.2$")
mark_as_advanced(FORCE CMAKE_BACKWARDS_COMPATIBILITY)
else("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" MATCHES "^3\\.2\\.2$")
mark_as_advanced(CLEAR CMAKE_BACKWARDS_COMPATIBILITY)
endif("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" MATCHES "^3\\.2\\.2$")
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
message("In-source builds not allowed by niftyseg.")
message("Please make a new directory (i.e. a build directory) and run CMake from there.")
message(FATAL_ERROR "You may need to remove CMakeCache.txt.")
endif(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
#-----------------------------------------------------------------------------
set(NiftySeg_VERSION_MAJOR 0)
set(NiftySeg_VERSION_MINOR 9)
set(NiftySeg_VERSION_PATCH 4)
#-----------------------------------------------------------------------------
# Overall Options
#-----------------------------------------------------------------------------
OPTION(BUILD_ALL "To build the LoAd segmentation tool" ON)
OPTION(BUILD_SHARED_LIBS "Build the libraries as shared." OFF)
OPTION(BUILD_Z "To build the z library tool" ON)
OPTION(INSTALL_PRIORS "Install prior images. Turn this off if you are really short on disk space" ON)
option(USE_THROW_EXEP "To throw exeception rather than exit" OFF)
mark_as_advanced(USE_THROW_EXEP)
#-----------------------------------------------------------------------------
# Set build details - C flags, Build Type, Library_type, OpenMP
#-----------------------------------------------------------------------------
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DFILE_OFFSETBITS=64 -DDIRENT=dirent64 -DREADDIR=readdir64")
SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DFILE_OFFSETBITS=64 -DDIRENT=dirent64 -DREADDIR=readdir64")
IF (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
add_definitions(/W1)
ELSE (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
add_definitions(-Wall)
ENDIF()
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release")
endif(NOT CMAKE_BUILD_TYPE)
string(TOLOWER "${CMAKE_BUILD_TYPE}" cmake_build_type_tolower)
if(NOT cmake_build_type_tolower STREQUAL "debug"
AND NOT cmake_build_type_tolower STREQUAL "release"
AND NOT cmake_build_type_tolower STREQUAL "relwithdebinfo")
message("Unknown build type \"${CMAKE_BUILD_TYPE}\".")
message(FATAL_ERROR "Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).")
endif()
if(USE_OPENMP)
find_package(OpenMP)
if(NOT OPENMP_FOUND)
set(USE_OPENMP OFF CACHE BOOL "To use openMP for multi-CPU processing" FORCE)
message(WARNING "OpenMP does not appear to be supported by your compiler, forcing USE_OPENMP to OFF")
else(NOT OPENMP_FOUND)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif(NOT OPENMP_FOUND)
endif(USE_OPENMP)
IF(BUILD_SHARED_LIBS)
SET(LIBRARY_TYPE SHARED)
if(WIN32)
add_definitions(-DNIFTYSEG_WINDOWS_EXPORT)
endif(WIN32)
ELSE(BUILD_SHARED_LIBS)
SET(LIBRARY_TYPE STATIC)
ENDIF(BUILD_SHARED_LIBS)
if(NOT ${CMAKE_CXX_COMPILER_ID} MATCHES "Clang")
# OpenMP is disable when the compiler is based on Clang
find_package(OpenMP)
if(OPENMP_FOUND)
option(USE_OPENMP "To use openMP for multi-CPU processing" ON)
endif(OPENMP_FOUND)
endif(NOT ${CMAKE_CXX_COMPILER_ID} MATCHES "Clang")
#-----------------------------------------------------------------------------
# Z library
# Try first to find the z library on the system and built is from the sources if it can not be found
#-----------------------------------------------------------------------------
IF(BUILD_Z)
include_directories(${CMAKE_SOURCE_DIR}/zlib)
message(STATUS "zlib not found - the z library will be built")
subdirs(zlib)
ELSE(BUILD_Z)
find_package(ZLIB)
if(ZLIB_FOUND)
include_directories(${ZLIB_INCLUDE_DIR})
message(STATUS "Found zlib - the z library will not be built")
else(ZLIB_FOUND)
include_directories(${CMAKE_SOURCE_DIR}/zlib)
message(STATUS "zlib not found - the z library will be built")
subdirs(zlib)
endif(ZLIB_FOUND)
ENDIF(BUILD_Z)
SET(ZLIB "z")
#-----------------------------------------------------------------------------
# Include Dirs and Module Paths
#-----------------------------------------------------------------------------
INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/seg-lib)
INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/nifti)
INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/win32)
set(CMAKE_MODULE_PATH
${CMAKE_BINARY_DIR}
${CMAKE_SOURCE_DIR}/CMake
${CMAKE_SOURCE_DIR}/CMake/CMakeExternals
${CMAKE_MODULE_PATH}
)
#-----------------------------------------------------------------------------
# Optional installation of NiftyReg packages
#-----------------------------------------------------------------------------
OPTION(INSTALL_NIFTYREG "Download and Install the NiftyReg package" OFF)
IF(INSTALL_NIFTYREG)
OPTION(USE_SSE "Use SSE in NiftyReg package" OFF)
ExternalProject_Add(NiftyReg
SOURCE_DIR ${PROJECT_BINARY_DIR}/niftyreg/source
PREFIX ${PROJECT_BINARY_DIR}/niftyreg
STAMP_DIR ${PROJECT_BINARY_DIR}/niftyreg/stamps
TMP_DIR ${PROJECT_BINARY_DIR}/niftyreg/tmp
DOWNLOAD_DIR ${PROJECT_BINARY_DIR}/niftyreg
BINARY_DIR ${PROJECT_BINARY_DIR}/niftyreg/build
GIT_REPOSITORY git://git.code.sf.net/p/niftyreg/git
TIMEOUT 100
UPDATE_COMMAND ""
CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX} -DUSE_SSE=${USE_SSE} -DUSE_OPENMP=${USE_OPENMP}
BUILD_COMMAND ${CMAKE_BUILD_TOOL}
INSTALL_COMMAND ${CMAKE_BUILD_TOOL} install
)
ENDIF(INSTALL_NIFTYREG)
#-----------------------------------------------------------------------------
# Search for Eigen. Download and install if not found
#-----------------------------------------------------------------------------
find_package(EIGEN)
if(EIGEN_FOUND)
option(USE_SYSTEM_EIGEN "Use an already installed version of the Eigen library" ON)
else(EIGEN_FOUND)
option(USE_SYSTEM_EIGEN "Use an already installed version of the Eigen library" OFF)
endif(EIGEN_FOUND)
if(USE_SYSTEM_EIGEN)
find_package(EIGEN REQUIRED)
else()
set(${PROJECT_NAME}_MD5_SUM_EIGEN 4c46942dc67b48d69fd90f2fd10a4cf6 CACHE STRING "MD5 check sum for EIGEN" FORCE)
set(${PROJECT_NAME}_LOCATION_EIGEN
"http://cmictig.cs.ucl.ac.uk/images/3.3-beta1.tar.gz"
CACHE STRING "Location of Eigen" FORCE)
mark_as_advanced(FORCE ${PROJECT_NAME}_VERSION_EIGEN)
mark_as_advanced(FORCE ${PROJECT_NAME}_MD5_SUM_EIGEN)
mark_as_advanced(FORCE ${PROJECT_NAME}_LOCATION_EIGEN)
ExternalProject_Add(Eigen
URL ${${PROJECT_NAME}_LOCATION_EIGEN}
URL_MD5 ${${PROJECT_NAME}_MD5_SUM_EIGEN}
PREFIX ${PROJECT_BINARY_DIR}/Eigen
DOWNLOAD_DIR ${PROJECT_BINARY_DIR}/Eigen/download
SOURCE_DIR ${PROJECT_BINARY_DIR}/Eigen/install
STAMP_DIR ${PROJECT_BINARY_DIR}/Eigen/stamps
TMP_DIR ${PROJECT_BINARY_DIR}/Eigen/tmpec
BINARY_DIR ${PROJECT_BINARY_DIR}/Eigen/build
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ""
)
set(EIGEN_INCLUDE_DIR ${PROJECT_BINARY_DIR}/Eigen/install/)
install(DIRECTORY ${EIGEN_INCLUDE_DIR}/Eigen DESTINATION include)
endif()
include_directories(${EIGEN_INCLUDE_DIR})
#-----------------------------------------------------------------------------
# Get the GIT HASH if avaiable
#-----------------------------------------------------------------------------
find_package(Git)
if(GIT_FOUND)
execute_process(
COMMAND git rev-parse HEAD
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
OUTPUT_VARIABLE GIT_COMMIT_HASH
RESULT_VARIABLE GIT_FAILED
OUTPUT_STRIP_TRAILING_WHITESPACE
)
if(NOT GIT_FAILED)
add_definitions(-D_GIT_HASH=\"${GIT_COMMIT_HASH}\")
message(STATUS "Found GIT - the hash is added to the source.")
else(NOT GIT_FAILED)
add_definitions(-D_GIT_HASH="${NiftySeg_VERSION_MAJOR}.${NiftySeg_VERSION_MINOR}.${NiftySeg_VERSION_PATCH}")
endif(NOT GIT_FAILED)
else(GIT_FOUND)
add_definitions(-D_GIT_HASH="${NiftySeg_VERSION_MAJOR}.${NiftySeg_VERSION_MINOR}.${NiftySeg_VERSION_PATCH}")
endif(GIT_FOUND)
#-----------------------------------------------------------------------------
# Set Doxigen iof available
#-----------------------------------------------------------------------------
find_package(Doxygen)
if(DOXYGEN_FOUND)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
add_custom_target(doc
${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMENT "Generating API documentation with Doxygen" VERBATIM
)
message(STATUS "Found doxygen")
endif(DOXYGEN_FOUND)
#-----------------------------------------------------------------------------
# Actually install NiftySeg
#-----------------------------------------------------------------------------
if(USE_THROW_EXEP)
add_definitions(-DNS_THROW_EXCEP)
endif(USE_THROW_EXEP)
SUBDIRS(nifti)
SUBDIRS(seg-lib)
SUBDIRS(seg-apps)
IF (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
SUBDIRS(win32)
ENDIF (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
# Install scriqeeqpts
CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/LoAd_brainonly.sh ${CMAKE_BINARY_DIR}/LoAd_brainonly.sh @ONLY )
INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/LoAd_brainonly.sh DESTINATION ${CMAKE_INSTALL_PREFIX}/bin COMPONENT applications)
# Install priors
SET(INSTALL_PRIORS_DIRECTORY ${CMAKE_INSTALL_PREFIX}/priors)
MARK_AS_ADVANCED(INSTALL_PRIORS_DIRECTORY)
IF(INSTALL_PRIORS)
FILE(GLOB PRIOR_FILES priors/*.nii.gz)
INSTALL(PROGRAMS ${PRIOR_FILES} DESTINATION ${INSTALL_PRIORS_DIRECTORY} COMPONENT applications)
ENDIF(INSTALL_PRIORS)
#-----------------------------------------------------------------------------