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CMakeLists.txt
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#-----------------------------------------------------------------------------
# Top level CMakeLists.txt file for AtlasWerks
CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
PROJECT(AtlasWerks)
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
endif(COMMAND cmake_policy)
#-----------------------------------------------------------------------------
# enable testing
ENABLE_TESTING()
#-----------------------------------------------------------------------------
# Include the standard Dart testing module
# INCLUDE (${CMAKE_ROOT}/Modules/Dart.cmake)
#-----------------------------------------------------------------------------
# set cmake module path
SET(AtlasWerks_CMAKE_DIR "${AtlasWerks_SOURCE_DIR}/CMake")
SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${AtlasWerks_CMAKE_DIR}")
#-----------------------------------------------------------------------------
# set directory for compiled libraries and executables
SET (LIBRARY_OUTPUT_PATH
${PROJECT_BINARY_DIR}/bin
CACHE PATH
"Single Directory for all libraries.")
SET (EXECUTABLE_OUTPUT_PATH
${PROJECT_BINARY_DIR}/bin
CACHE PATH
"Single Directory for all executables.")
MARK_AS_ADVANCED (
LIBRARY_OUTPUT_PATH
EXECUTABLE_OUTPUT_PATH
)
#-----------------------------------------------------------------------------
# set unix specific variables
IF(UNIX)
ENDIF(UNIX)
CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
#-----------------------------------------------------------------------------
# should shared libraries be built?
MARK_AS_ADVANCED(BUILD_SHARED_LIBS)
OPTION(BUILD_SHARED_LIBS "NOT READY YET, LEAVE OFF -- Build shared libraries?" OFF)
IF(BUILD_SHARED_LIBS)
SET(LIBTYPE SHARED)
ELSE(BUILD_SHARED_LIBS)
SET(LIBTYPE STATIC)
ENDIF(BUILD_SHARED_LIBS)
# compute default library install dir
#-----------------------------------------------------------------------------
# Include debug messages?
IF(CMAKE_BUILD_TYPE STREQUAL "Debug")
# logDEBUG4 = 7
ADD_DEFINITIONS(-DERRLOG_MAX_LEVEL=7)
ELSE(CMAKE_BUILD_TYPE STREQUAL "Debug")
# logINFO = 2
ADD_DEFINITIONS(-DERRLOG_MAX_LEVEL=2)
ENDIF(CMAKE_BUILD_TYPE STREQUAL "Debug")
#-----------------------------------------------------------------------------
# Define LIBRARY_INSTALL_DIR
set (_DEFAULT_LIBRARY_INSTALL_DIR lib)
if (EXISTS "${CMAKE_INSTALL_PREFIX}/lib32/" AND CMAKE_SIZEOF_VOID_P EQUAL 4)
set (_DEFAULT_LIBRARY_INSTALL_DIR lib32)
elif (EXISTS "${CMAKE_INSTALL_PREFIX}/lib64/" AND CMAKE_SIZEOF_VOID_P EQUAL 8)
set (_DEFAULT_LIBRARY_INSTALL_DIR lib64)
endif (EXISTS "${CMAKE_INSTALL_PREFIX}/lib32/" AND CMAKE_SIZEOF_VOID_P EQUAL 4)
# the library install dir
set(LIBRARY_INSTALL_DIR "${_DEFAULT_LIBRARY_INSTALL_DIR}" CACHE PATH "Installation directory for libraries")
# make the library install dir an absolute path (can be important e.g. when using CONFIGURE_FILE to embed
# the library installation directory into a file)
if(NOT IS_ABSOLUTE "${LIBRARY_INSTALL_DIR}")
set(LIBRARY_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${LIBRARY_INSTALL_DIR}")
endif(NOT IS_ABSOLUTE "${LIBRARY_INSTALL_DIR}")
#-----------------------------------------------------------------------------
# Compile ImMap?
#MARK_AS_ADVANCED(atlasWerks_COMPILE_APP_IMMAP)
OPTION(atlasWerks_COMPILE_APP_IMMAP "Compile ImMap" ON)
#-----------------------------------------------------------------------------
# should we use SWIG to generate python wrappers?
OPTION(WRAP_PYTHON "Generate python wrapping using SWIG?" OFF)
IF(WRAP_PYTHON)
FIND_PACKAGE(SWIG REQUIRED)
INCLUDE(${SWIG_USE_FILE})
FIND_PACKAGE(PythonLibs)
INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH})
INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
SET(CMAKE_SWIG_FLAGS "")
SET(PYTHON_INSTALL_DIR
"/usr/lib64/python"
CACHE STRING
"Location to install AtlasWerks python module"
)
# Set up package creation and installation
INSTALL(CODE "EXECUTE_PROCESS(COMMAND chmod ug+x ${AtlasWerks_SOURCE_DIR}/InstallPythonModule.sh)")
INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${AtlasWerks_SOURCE_DIR}/InstallPythonModule.sh ${CMAKE_BINARY_DIR})")
INSTALL(DIRECTORY ${CMAKE_BINARY_DIR}/python/AtlasWerks DESTINATION ${PYTHON_INSTALL_DIR})
ENDIF(WRAP_PYTHON)
#-----------------------------------------------------------------------------
# Should we try to use DCMTK?
MARK_AS_ADVANCED(USE_DCMTK)
OPTION(USE_DCMTK "Use DCMTK libraries?" OFF)
IF(USE_DCMTK)
SET(DCMTK_FOUND TRUE CACHE INTERNAL "")
MARK_AS_ADVANCED(DCMTK_LIBS_SEARCH_DIRS)
SET(DCMTK_LIBS_SEARCH_DIRS
"/usr/local/dicom/lib"
"/usr/local/lib"
CACHE STRING
"Locations to search for DCMTK libs"
)
MARK_AS_ADVANCED(DCMTK_INCLUDE_SEARCH_DIRS)
SET(DCMTK_INCLUDE_SEARCH_DIRS
"/usr/local/dicom/include"
CACHE STRING
"Locations to search for DCMTK libs"
)
find_path(atlasWerks_DCMTK_LIBRARY libdcmdata.a PATHS ${DCMTK_LIBS_SEARCH_DIRS} ENV LD_LIBRARY_PATH)
#message(STATUS "atlasWerks_DCMTK_LIBRARY is ${atlasWerks_DCMTK_LIBRARY}")
if(NOT atlasWerks_DCMTK_LIBRARY)
SET(DCMTK_FOUND FALSE CACHE INTERNAL "")
message(SEND_ERROR "DCMTK libraries not found in search path: ${DCMTK_LIBS_SEARCH_DIRS}; Will not use DCMTK")
endif(NOT atlasWerks_DCMTK_LIBRARY)
if(DCMTK_FOUND)
find_path(atlasWerks_DCMTK_INCLUDE
NAMES "dcmtk/dcmdata/dctk.h"
PATHS "${DCMTK_INCLUDE_SEARCH_DIRS}"
)
#message(STATUS "atlasWerks_DCMTK_INCLUDE is ${atlasWerks_DCMTK_INCLUDE}")
if(NOT atlasWerks_DCMTK_INCLUDE)
SET(DCMTK_FOUND FALSE CACHE INTERNAL "")
message(SEND_ERROR "DCMTK include dir not found in: ${DCMTK_INCLUDE_SEARCH_DIRS}; Will not use DCMTK")
endif(NOT atlasWerks_DCMTK_INCLUDE)
endif(DCMTK_FOUND)
ENDIF(USE_DCMTK)
#-----------------------------------------------------------------------------
# Set up CUDA
OPTION(USE_CUDA "Attempt to compile CUDA code" OFF)
IF(USE_CUDA)
SET(CMAKE_MODULE_PATH "${AtlasWerks_CMAKE_DIR}/cuda" ${CMAKE_MODULE_PATH})
FIND_PACKAGE(CUDA)
IF(NOT CUDA_FOUND)
MESSAGE("Can't find CUDA, will not compile apps requiring CUDA")
ENDIF(NOT CUDA_FOUND)
IF(NOT CUDA_SDK_ROOT_DIR)
MESSAGE("Can't find CUDA SDK, will not compile apps requiring CUDA")
ENDIF(NOT CUDA_SDK_ROOT_DIR)
# Add definition for preprocessor
IF(CUDA_FOUND AND CUDA_SDK_ROOT_DIR)
SET(CUDA_ENABLED TRUE)
ADD_DEFINITIONS(-DCUDA_ENABLED)
find_path(CUDA_CUT_INCLUDE_DIR
cutil.h
PATHS ${CUDA_SDK_SEARCH_PATH}
PATH_SUFFIXES "common/inc"
DOC "Location of cutil.h"
NO_DEFAULT_PATH
)
# Now search system paths
find_path(CUDA_CUT_INCLUDE_DIR cutil.h DOC "Location of cutil.h")
mark_as_advanced(CUDA_CUT_INCLUDE_DIR)
INCLUDE_DIRECTORIES(${CUDA_CUT_INCLUDE_DIR})
if(CMAKE_SIZEOF_VOID_P EQUAL 8)
set(cuda_cutil_name cutil_x86_64)
else(CMAKE_SIZEOF_VOID_P EQUAL 8)
set(cuda_cutil_name cutil32)
endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
find_library(CUDA_CUT_LIBRARY
NAMES cutil ${cuda_cutil_name}
PATHS ${CUDA_SDK_SEARCH_PATH}
# The new version of the sdk shows up in common/lib, but the old one is in lib
PATH_SUFFIXES "common/lib" "lib"
DOC "Location of cutil library"
NO_DEFAULT_PATH
)
# Now search system paths
find_library(CUDA_CUT_LIBRARY
NAMES cutil ${cuda_cutil_name}
DOC "Location of cutil library")
mark_as_advanced(CUDA_CUT_LIBRARY)
set(CUDA_CUT_LIBRARIES ${CUDA_CUT_LIBRARY})
find_path(CUDA_CUDPP_INCLUDE_DIR
"cudpp/cudpp.h"
PATHS ${CUDA_SDK_SEARCH_PATH}
PATH_SUFFIXES "common/inc"
DOC "Location of cudpp.h"
NO_DEFAULT_PATH
)
# Now search system paths
find_path(CUDA_CUDPP_INCLUDE_DIR "cudpp/cudpp.h" PATH_SUFFIXES "common/inc" DOC "Location of cudpp.h")
mark_as_advanced(CUDA_CUDPP_INCLUDE_DIR)
INCLUDE_DIRECTORIES(${CUDA_CUDPP_INCLUDE_DIR})
find_library(CUDPP_LIB
NAMES cudpp_x86_64 cudpp
PATHS ${CUDA_SDK_SEARCH_PATH}
PATH_SUFFIXES "common/lib/linux"
DOC "Location of cudpp library"
)
IF(NOT CUDPP_LIB)
MESSAGE("Error, CUDPP library not found")
ENDIF(NOT CUDPP_LIB)
SET(CUDA_LIBRARIES
${CUDA_LIBRARIES}
${CUDA_CUT_LIBRARIES}
${CUDA_CUBLAS_LIBRARIES}
${CUDA_CUFFT_LIBRARIES}
${CUDPP_LIB}
)
# Definitions for the cuda version
IF(${CUDA_VERSION} VERSION_EQUAL "4.0")
ADD_DEFINITIONS(-DCUDA_40)
ELSEIF(${CUDA_VERSION} VERSION_EQUAL "3.2")
ADD_DEFINITIONS(-DCUDA_32)
ELSEIF(${CUDA_VERSION} VERSION_EQUAL "3.1")
ADD_DEFINITIONS(-DCUDA_31)
ELSE(${CUDA_VERSION} VERSION_EQUAL "4.0")
MESSAGE(SEND_ERROR
"CUDA version 3.1 or greater required to build AtlasWerks GPU code")
ENDIF(${CUDA_VERSION} VERSION_EQUAL "4.0")
MARK_AS_ADVANCED(CUDA_ARCH_VERSION)
SET(CUDA_ARCH_VERSION
"12"
CACHE STRING
"Cuda architecture version, ie -arch sm_??")
ELSE(CUDA_FOUND AND CUDA_SDK_ROOT_DIR)
SET(CUDA_ENABLED FALSE)
ENDIF(CUDA_FOUND AND CUDA_SDK_ROOT_DIR)
ELSE(USE_CUDA)
# Not using CUDA, make sure this is false
SET(CUDA_ENABLED FALSE)
ENDIF(USE_CUDA)
#-----------------------------------------------------------------------------
# Setup MPI
OPTION(USE_MPI "Attempt to compile MPI code" OFF)
IF(USE_MPI)
find_package(MPI)
IF(MPI_FOUND)
INCLUDE_DIRECTORIES(${MPI_INCLUDE_PATH})
ELSE(MPI_FOUND)
MESSAGE("Could not find MPI directory.")
ENDIF(MPI_FOUND)
ELSE(USE_MPI)
# Not using MPI, make sure this is false
SET(MPI_FOUND FALSE)
ENDIF(USE_MPI)
#-----------------------------------------------------------------------------
# Setup FFTW
# * include directories are added automatically
# * applications must add link libraries ${FFTWF_LIB} or ${FFTWF_THREADS_LIB}
MARK_AS_ADVANCED(USE_FFTWF)
OPTION(USE_FFTWF "Use single precision FFTW if found" ON)
MARK_AS_ADVANCED(USE_FFTWD)
OPTION(USE_FFTWD "Use single precision FFTW if found" ON)
FIND_PACKAGE(FFTW REQUIRED)
include_directories(${FFTW_INCLUDE})
#----------------------------------------------------------------------------
# Set default interpolation method
MARK_AS_ADVANCED(DEFAULT_INTERP_METHOD)
SET(DEFAULT_INTERP_METHOD
"INTERP_LINEAR"
CACHE STRING
"Set the default interpolation method (INTERP_NN,INTERP_LINEAR,INTERP_CUBIC)"
)
ADD_DEFINITIONS(-DDEFAULT_INTERP_METHOD=${DEFAULT_INTERP_METHOD})
#-----------------------------------------------------------------------------
# Setup LAPACK
# * include directories are added automatically
# * applications must add link libraries ${FFTWF_LIB} or ${FFTWF_THREADS_LIB}
MARK_AS_ADVANCED(LAPACK_LIBS)
SET(LAPACK_LIBS
"lapack blas f2c"
CACHE STRING
"The LAPACK libraries (lapack, blas, possibly gfortran)"
)
MARK_AS_ADVANCED(LAPACK_LIBS_SEARCH_DIRS)
SET(LAPACK_LIBS_SEARCH_DIRS
"${LAPACK_DIR}/SRC;${LAPACK_DIR}/BLAS/SRC;${LAPACK_DIR}/F2CLIBS/libf2c"
CACHE STRING
"Locations to search for LAPACK libs"
)
# clear the library var
set(atlasWerks_LAPACK_LIBS
"")
# turn space-separated list into CMAKE style
# semicolon separated list
separate_arguments(LAPACK_LIBS)
# find the path to each specified library
foreach(_library ${LAPACK_LIBS})
#message(STATUS "finding library ${_library}")
find_library(atlasWerks_${_library}_LIBRARY
NAMES ${_library}
PATHS ${LAPACK_LIBS_SEARCH_DIRS}
NO_DEFAULT_PATH
NO_CMAKE_PATH
NO_CMAKE_ENVIRONMENT_PATH
NO_SYSTEM_ENVIRONMENT_PATH
NO_CMAKE_SYSTEM_PATH
)
if(atlasWerks_${_library}_LIBRARY)
#message(STATUS "${_library} found!: ${atlasWerks_${_library}_LIBRARY}")
set(atlasWerks_LAPACK_LIBS
${atlasWerks_LAPACK_LIBS}
${atlasWerks_${_library}_LIBRARY}
CACHE INTERNAL ""
)
else(atlasWerks_${_library}_LIBRARY)
message("${_library} not found!")
endif(atlasWerks_${_library}_LIBRARY)
mark_as_advanced(atlasWerks_${_library}_LIBRARY)
endforeach(_library ${LAPACK_LIBS})
message(STATUS "atlasWerks_LAPACK_LIBS: ${atlasWerks_LAPACK_LIBS}")
#FIND_PACKAGE(LAPACK)
#IF(LAPACK_FOUND)
# # nothing, no include files for lapack
#ELSE(LAPACK_FOUND)
# MESSAGE("Could not find LAPACK directory.")
#ENDIF(LAPACK_FOUND)
#-----------------------------------------------------------------------------
# Setup FLTK if building ImMap
IF(atlasWerks_COMPILE_APP_IMMAP)
FIND_PACKAGE(FLTK)
IF(FLTK_FOUND)
INCLUDE_DIRECTORIES (${FLTK_INCLUDE_DIR})
ELSE(FLTK_FOUND)
MESSAGE("Could not find FLTK directory.")
ENDIF(FLTK_FOUND)
ENDIF(atlasWerks_COMPILE_APP_IMMAP)
#-----------------------------------------------------------------------------
# Setup ITK
# * include directories are added automatically
# * applications must add appropriate libraries to link libraries
#MARK_AS_ADVANCED(USE_ITK)
#OPTION(USE_ITK "Use ITK if found" ON)
FIND_PACKAGE(ITK)
IF(ITK_FOUND)
INCLUDE (${ITK_USE_FILE})
ELSE(ITK_FOUND)
MESSAGE("Could not find ITK directory.")
ENDIF(ITK_FOUND)
#-----------------------------------------------------------------------------
# Setup VTK
# * include directories are added automatically
# * applications must add appropriate libraries to link libraries
#MARK_AS_ADVANCED(USE_VTK)
#OPTION(USE_VTK "Use VTK if found" ON)
FIND_PACKAGE(VTK)
IF(VTK_FOUND)
INCLUDE (${VTK_USE_FILE})
ELSE(VTK_FOUND)
MESSAGE("Could not find VTK directory.")
ENDIF(VTK_FOUND)
#-----------------------------------------------------------------------------
# Setup Doxygen
FIND_PACKAGE(Doxygen)
SET(DOXY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/Docs")
SET(DOXY_CONFIG "${DOXY_DIR}/Doxyfile")
IF (DOXYGEN_FOUND)
ADD_CUSTOM_TARGET(doc ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
WORKING_DIRECTORY "${DOXY_DIR}")
ENDIF (DOXYGEN_FOUND)
#-----------------------------------------------------------------------------
# what to compile?
OPTION(AtlasWerks_COMPILE_LIBS "Compile AtlasWerks libraries." ON)
OPTION(AtlasWerks_COMPILE_APPS "Compile AtlasWerks applications." ON)
OPTION(AtlasWerks_COMPILE_TESTING "Compile AtlasWerks testing." ON)
#-----------------------------------------------------------------------------
# add common include directories
INCLUDE_DIRECTORIES(
${AtlasWerks_SOURCE_DIR}/Utilities/DownsampleFilter
${AtlasWerks_SOURCE_DIR}/Utilities/ImMapAttic
${AtlasWerks_SOURCE_DIR}/Utilities/ImMapAttic/ImageIO
${AtlasWerks_SOURCE_DIR}/Utilities/ImMapAttic/ImageIO/Dicom
${AtlasWerks_SOURCE_DIR}/Utilities/ImMapAttic/ImageIO/PlanIM
${AtlasWerks_SOURCE_DIR}/Utilities/Matrix
${AtlasWerks_SOURCE_DIR}/Utilities/planio
${AtlasWerks_SOURCE_DIR}/Utilities/PowerCrust
${AtlasWerks_SOURCE_DIR}/Utilities/tclap
${AtlasWerks_SOURCE_DIR}/Utilities/tinyxml
${AtlasWerks_SOURCE_DIR}/Code/Applications/ImMap
${AtlasWerks_SOURCE_DIR}/Code/Applications/Affine
${AtlasWerks_SOURCE_DIR}/Code/Applications/AffineAtlas
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Algorithms/
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Algorithms/Affine
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Algorithms/Common
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Algorithms/Greedy
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Algorithms/LDMM
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Base
${AtlasWerks_SOURCE_DIR}/Code/Libraries/
${AtlasWerks_SOURCE_DIR}/Code/Libraries/DataTypes
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Numerics
${AtlasWerks_SOURCE_DIR}/Code/Libraries/UtilitiesDataTypes
)
OPTION(COMPILE_EXPERIMENTAL "Compile experimental code?" OFF)
IF(COMPILE_EXPERIMENTAL)
INCLUDE_DIRECTORIES(
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Experimental/Algorithms
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Experimental/Algorithms/MMorph
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Experimental/Metamorphosis
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Experimental/ScanProjection
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Experimental/ScanProjection/ConeBeam
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Experimental/ScanProjection/ImageSlice
${AtlasWerks_SOURCE_DIR}/Code/Libraries/Experimental/ScanProjection/KSpaceLine3D
)
ENDIF(COMPILE_EXPERIMENTAL)
IF(CUDA_ENABLED)
CUDA_INCLUDE_DIRECTORIES(
${CUDA_CUT_INCLUDE_DIRS}
${CUDA_INCLUDE_DIRS}
${AtlasWerks_SOURCE_DIR}/Code/Libraries/CUDACommon/inc
)
INCLUDE_DIRECTORIES(
${CUDA_CUT_INCLUDE_DIRS}
${CUDA_INCLUDE_DIRS}
${AtlasWerks_SOURCE_DIR}/Code/Libraries/CUDACommon/inc
)
ENDIF(CUDA_ENABLED)
#-----------------------------------------------------------------------------
# Build utilities
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Utilities/DownsampleFilter)
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Utilities/Matrix)
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Utilities/planio)
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Utilities/PowerCrust)
# ${AtlasWerks_SOURCE_DIR}/Utilities/tinyxml
IF(atlasWerks_COMPILE_APP_IMMAP)
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Utilities/ImMapAttic)
ENDIF(atlasWerks_COMPILE_APP_IMMAP)
#-----------------------------------------------------------------------------
# go to subdirectories
IF(AtlasWerks_COMPILE_LIBS)
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Code/Libraries)
ENDIF(AtlasWerks_COMPILE_LIBS)
IF(AtlasWerks_COMPILE_APPS)
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Code/Applications)
ENDIF(AtlasWerks_COMPILE_APPS)
IF(AtlasWerks_COMPILE_TESTING)
add_subdirectory(${AtlasWerks_SOURCE_DIR}/Testing)
ENDIF(AtlasWerks_COMPILE_TESTING)