CMakeLists.txt

#=========================================================
CMAKE_MINIMUM_REQUIRED(VERSION 3.12.0 FATAL_ERROR)
CMAKE_POLICY(SET CMP0012 NEW) # if() recognizes numbers and boolean constants.
CMAKE_POLICY(SET CMP0025 NEW) # Compiler id for Apple Clang is now AppleClang.
CMAKE_POLICY(SET CMP0057 NEW) # Support new if() IN_LIST operator.
CMAKE_POLICY(SET CMP0072 NEW) # FindOpenGL prefers GLVND by default when available.

#=========================================================
PROJECT(Gate)

SET(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake-modules ${CMAKE_MODULE_PATH})

#=========================================================
# Configure Dart testing support.  This should be done before any
# MESSAGE(FATAL_ERROR ...) commands are invoked.
OPTION(BUILD_TESTING "Build the testing tree." OFF)
INCLUDE(CTest)

IF(BUILD_TESTING)
  ENABLE_TESTING()
  SET(BUILDNAME "${BUILDNAME}" CACHE STRING "Name of build on the dashboard")
  MARK_AS_ADVANCED(BUILDNAME)
ENDIF(BUILD_TESTING)
#=========================================================

#=========================================================
# Help function to debug CMake
MACRO (DD in)
  MESSAGE(${in}=[${${in}}])
ENDMACRO(DD)

#=========================================================
# Do not use RPATH for Mac, it fails to run Gate when install it
IF (APPLE)
  SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
ENDIF()

#=========================================================
# Default build type
IF(NOT CMAKE_BUILD_TYPE)
  SET(CMAKE_BUILD_TYPE Release CACHE STRING
    "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
    FORCE)
ENDIF(NOT CMAKE_BUILD_TYPE)

#=========================================================
# Native compilation
OPTION(GATE_COMPILE_WITH_NATIVE "Build with -march=native (works if build type is Release)" OFF)
IF(UNIX AND GATE_COMPILE_WITH_NATIVE)
  string(FIND ${CMAKE_CXX_FLAGS_RELEASE} -march=native pos_march_cxx)
  string(FIND ${CMAKE_C_FLAGS_RELEASE} -march=native pos_march_c)
  IF(${pos_march_cxx} EQUAL -1)
    SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native")
  ENDIF() 
  IF(${pos_march_c} EQUAL -1)
    SET(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -march=native")
  ENDIF()
ENDIF(UNIX AND GATE_COMPILE_WITH_NATIVE)

#=========================================================
# Option to use visualisation feature of G4
OPTION(GATE_USE_GEANT4_UIVIS "Build example with Geant4 UI and Vis drivers" ON)
IF(GATE_USE_GEANT4_UIVIS)
  FIND_PACKAGE(Geant4 REQUIRED ui_all vis_all)
ELSE()
  FIND_PACKAGE(Geant4 REQUIRED)
ENDIF()
set(CMAKE_CXX_STANDARD ${Geant4_CXX_STANDARD})

#=========================================================
# Refuse to build with MT geant4, allow dev override
IF(Geant4_multithreaded_FOUND)
    MESSAGE(WARNING "GATE should be compiled with a non-multithreaded installation of Geant4")
ENDIF()
#OPTION(GATE_ALLOW_MT_GEANT4 "Allow multithreaded geant4 (for MT Gate development)" OFF)
#IF(Geant4_multithreaded_FOUND)
    #IF(GATE_ALLOW_MT_GEANT4)
        #MESSAGE(WARNING "GATE does not yet work correctly with multithreaded Geant4, proceed with caution...")
    #ELSE()
        #MESSAGE(FATAL_ERROR "GATE should be compiled with a non-multithreaded installation of Geant4")
    #ENDIF()
#ENDIF()

# Check if OpenGL headers are still available
IF(Geant4_qt_FOUND OR Geant4_vis_opengl_x11_FOUND)
  FIND_PACKAGE(OpenGL QUIET)
  INCLUDE_DIRECTORIES(${OPENGL_INCLUDE_DIR})
  SET(GATE_USE_OPENGL ${OPENGL_FOUND})
ENDIF()

#=========================================================
# Build variables for G4 Version

STRING(REGEX REPLACE "(.*)[.](.*)[.](.*)" "\\1" G4VERSION_MAJOR ${Geant4_VERSION})
STRING(REGEX REPLACE "(.*)[.](.*)[.](.*)" "\\2" G4VERSION_MINOR ${Geant4_VERSION})
STRING(REGEX REPLACE "(.*)[.](.*)[.](.*)" "\\3" G4VERSION_PATCH ${Geant4_VERSION})
#MESSAGE(${Geant4_VERSION})
#MESSAGE(${G4VERSION_MAJOR})
#MESSAGE(${G4VERSION_MINOR})
#MESSAGE(${G4VERSION_PATCH})
IF(NOT ${G4VERSION_MAJOR}.${G4VERSION_MINOR} EQUAL 11.2)
  MESSAGE("Warning! This GATE version is not validated for Geant4 ${G4VERSION_MAJOR}.${G4VERSION_MINOR} distribution. Please use Geant4 11.2 distribution instead.")
ENDIF()

#=========================================================
# Option for Root use
SET(GATE_USE_ROOT ON)
SET(GATE_ANALYSIS_USE_GENERAL ON)
SET(GATE_ANALYSIS_USE_FILE ON)

OPTION(GATE_USE_OPTICAL "Gate use optical photon" ON)
OPTION(GATE_USE_XRAYLIB "Option for XRAYLIB use" OFF)
OPTION(GATE_USE_DAVIS "Gate use Davis LUT model" OFF)
OPTION(GATE_USE_LMF "Gate use LMF" OFF)
OPTION(GATE_USE_ECAT7 "Gate use ECAT7" OFF)
OPTION(GATE_USE_SYSTEM_CLHEP "If 'ON', Gate does not use the standard CLHEP of GEANT4. Use OFF if you compile G4 with embedded CLHEP" OFF)

#=========================================================
# Option for libTorch
OPTION(GATE_USE_TORCH "Gate use libTorch" OFF)

#=========================================================
# RTK / ITK
option(GATE_USE_RTK "Use the Reconstruction Toolkit (RTK, requires also ITK)" OFF)
option(GATE_USE_ITK "Use the Insight Toolkit (ITK, required by RTK, DICOM reader and thermal therapy capability)" OFF)

#=========================================================
# ROOT
IF(GATE_USE_ROOT)
  FIND_PACKAGE(ROOT REQUIRED)
  include(${ROOT_USE_FILE})
  get_target_property(ROOT_INTERFACE_COMPILE_FEATURES ROOT::Core INTERFACE_COMPILE_FEATURES)
  IF(NOT "${ROOT_INTERFACE_COMPILE_FEATURES}" STREQUAL cxx_std_${Geant4_CXX_STANDARD})
    MESSAGE(FATAL_ERROR "ROOT has been compiled with ${ROOT_INTERFACE_COMPILE_FEATURES}, please use cxx_std_${Geant4_CXX_STANDARD} as your Geant4.")
  ENDIF()
ENDIF()

#=========================================================
# Option for Optical Photon use
IF(GATE_USE_OPTICAL)
  FIND_PACKAGE(LibXml2 REQUIRED)
  INCLUDE_DIRECTORIES(${LIBXML2_INCLUDE_DIR})
  SET(LINK_DIRECTORIES ${LIBXML2_LIBRARIES})
ENDIF(GATE_USE_OPTICAL)

#=========================================================
# Option for XRAYLIB use
IF(GATE_USE_XRAYLIB)
  FIND_PACKAGE(LIBXRL REQUIRED)
  INCLUDE_DIRECTORIES(${LIBXRL_INCLUDE_DIR})
  SET(LINK_DIRECTORIES ${LIBXRL_LIBRARIES})
  IF(NOT LIBXRL_INCLUDE_DIR)
    MESSAGE("xraylib not found! Please install xraylib and make it available in PATH or manually set the LIBXRL_LIBRARY and LIBXRL_INCLUDE variables.")
  ENDIF()
ENDIF(GATE_USE_XRAYLIB)

#=========================================================
# Option for Clhep use
IF(GATE_USE_SYSTEM_CLHEP)
  FIND_PACKAGE(CLHEP REQUIRED)
  INCLUDE_DIRECTORIES(${CLHEP_INCLUDE_DIR})
  SET(LINK_DIRECTORIES ${CLHEP_LIBRARIES})
  MESSAGE("Your current CLHEP version is ${CLHEP_VERSION}")
  MESSAGE("Please refer to http://geant4.web.cern.ch/geant4/support/ReleaseNotes4.${G4VERSION_MAJOR}.${G4VERSION_MINOR}.html to verify that your CLHEP version is supported by Geant4.")

  #MESSAGE("Found Clhep in ${CLHEP_INCLUDE_DIR} ${CLHEP_LIBRARY}")
ENDIF()

#=========================================================
# Option for LMF use
IF(GATE_USE_LMF)
  ADD_SUBDIRECTORY(${PROJECT_SOURCE_DIR}/source/externals/lmf ${PROJECT_BINARY_DIR}/lmf)
  SET(LMF_LIBRARY "-L${PROJECT_BINARY_DIR}/lmf -lLMF")
  INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/source/externals/lmf ${PROJECT_SOURCE_DIR}/source/externals/lmf/lmf_v3.0/includes )
ENDIF(GATE_USE_LMF)
#IF(GATE_USE_LMF)
#  FIND_PATH(LMF_HOME lmf /usr /usr/local)
#  SET(LMF_INCLUDE_DIR "${LMF_HOME}/includes")
#  SET(LMF_LIBRARIES "${LMF_HOME}/lib")
#  SET(LMF_LIBRARY "-L${LMF_LIBRARIES} -lLMF")
#  INCLUDE_DIRECTORIES(${LMF_INCLUDE_DIR})
#  SET(LINK_DIRECTORIES ${LMF_LIBRARIES})
#  #MESSAGE("Found Lmf in ${LMF_INCLUDE_DIR} ${LMF_LIBRARIES} ${LMF_LIBRARY}")
#ENDIF(GATE_USE_LMF)

#=========================================================
# Option for ECAT7 use
IF(GATE_USE_ECAT7)
  ADD_SUBDIRECTORY(${PROJECT_SOURCE_DIR}/source/externals/ecat ${PROJECT_BINARY_DIR}/ecat)
  SET(ECAT7_LIBRARY "-L${PROJECT_BINARY_DIR}/ecat -lecat")
  INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/source/externals/ecat/src )
ENDIF(GATE_USE_ECAT7)
#IF(GATE_USE_ECAT7)
#  FIND_PATH(ECAT7_HOME ecat /usr /usr/local)
#  SET(ECAT7_INCLUDE_DIR "${ECAT7_HOME}/include")
#  SET(ECAT7_LIBRARIES "${ECAT7_HOME}/lib")
#  SET(ECAT7_LIBRARY "-L${ECAT7_LIBRARIES} -lecat")
#  INCLUDE_DIRECTORIES(${ECAT7_INCLUDE_DIR})
#  SET(LINK_DIRECTORIES ${ECAT7_LIBRARIES})
#  #MESSAGE("Found Ecat in ${ECAT7_INCLUDE_DIR} ${ECAT7_LIBRARIES} ${ECAT7_LIBRARY}")
#ENDIF(GATE_USE_ECAT7)

#=========================================================
# Create configuration file
CONFIGURE_FILE(GateConfiguration.h.in ${PROJECT_BINARY_DIR}/GateConfiguration.h)
INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR})

#=========================================================
# Setup Geant4 include directories and compile definitions
# Setup include directory for this project
INCLUDE(${Geant4_USE_FILE})
INCLUDE_DIRECTORIES(
  ${PROJECT_SOURCE_DIR}/source/io/include
  ${PROJECT_SOURCE_DIR}/source/arf/include
  ${PROJECT_SOURCE_DIR}/source/geometry/include
  ${PROJECT_SOURCE_DIR}/source/physics/include
  ${PROJECT_SOURCE_DIR}/source/digits_hits/include
  ${PROJECT_SOURCE_DIR}/source/general/include
  ${PROJECT_SOURCE_DIR}/source/externals/clhep/include)

#=========================================================
# Locate sources and headers for this project
FILE(GLOB sources
  ${PROJECT_SOURCE_DIR}/source/io/src/*.cc
  ${PROJECT_SOURCE_DIR}/source/arf/src/*.cc
  ${PROJECT_SOURCE_DIR}/source/geometry/src/*.cc
  ${PROJECT_SOURCE_DIR}/source/digits_hits/src/*.cc
  ${PROJECT_SOURCE_DIR}/source/physics/src/*.cc
  ${PROJECT_SOURCE_DIR}/source/general/src/*.cc
  ${PROJECT_SOURCE_DIR}/source/externals/clhep/src/CLHEP/Matrix/*.cc
  ${PROJECT_SOURCE_DIR}/source/externals/clhep/src/CLHEP/RandomObjects/*.cc)

FILE(GLOB headers
  ${PROJECT_SOURCE_DIR}/source/io/include/*.hh
  ${PROJECT_SOURCE_DIR}/source/arf/include/*.hh
  ${PROJECT_SOURCE_DIR}/source/geometry/include/*.hh
  ${PROJECT_SOURCE_DIR}/source/physics/include/*.hh
  ${PROJECT_SOURCE_DIR}/source/digits_hits/include/*.hh
  ${PROJECT_SOURCE_DIR}/source/general/include/*.hh
  ${PROJECT_SOURCE_DIR}/source/externals/clhep/include/*.hh)

#=========================================================
IF(GATE_USE_TORCH)
  FIND_PACKAGE(Torch REQUIRED)
  INCLUDE_DIRECTORIES(${TORCH_INCLUDE_DIRS})
ENDIF()

#=========================================================
# RTK
IF(GATE_USE_RTK OR GATE_USE_ITK)
  SET(ITK_MINIMAL_VERSION 5.1)
  SET(ITK_COMPONENTS ITKIOImageBase;ITKGDCM;ITKIOGDCM;ITKThresholding;ITKFFT;ITKImageCompose;ITKSmoothing)
  IF(GATE_USE_RTK)
    LIST(APPEND ITK_COMPONENTS RTK)
    SET(ITK_MINIMAL_VERSION 4.12)
  ENDIF()
  FIND_PACKAGE(ITK ${ITK_MINIMAL_VERSION} REQUIRED COMPONENTS ${ITK_COMPONENTS})
  IF(GATE_USE_RTK AND "${RTK_VERSION_MAJOR}.${RTK_VERSION_MINOR}" VERSION_LESS 2.0)
    MESSAGE(FATAL_ERROR "RTK version 2.0 is required")
  ENDIF()
  INCLUDE(${ITK_USE_FILE})
  STRING(REPLACE "-pedantic" "" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
ELSE()
  ADD_SUBDIRECTORY(source/externals/itk-mhd ${PROJECT_BINARY_DIR}/itk-mhd)
  SET(ITK_LIBRARIES MetaIO itkzlib)
  INCLUDE_DIRECTORIES(
    ${PROJECT_SOURCE_DIR}/source/externals/itk-mhd/
    ${PROJECT_SOURCE_DIR}/source/externals/itk-mhd/itkzlib
    ${PROJECT_SOURCE_DIR}/source/externals/itk-mhd/src
    ${PROJECT_BINARY_DIR}/itk-mhd/)
  SET(ITKMHD_LIBS MetaIO itkzlib)
ENDIF()

#=========================================================
# Add the executable, and link it to the Geant4/ROOT/CLHEP/ITK libraries
ADD_LIBRARY(GateLib OBJECT ${sources} ${headers})
TARGET_LINK_LIBRARIES(GateLib ${Geant4_LIBRARIES} ${ROOT_LIBRARIES} ${CLHEP_LIBRARIES} ${LIBXML2_LIBRARIES} ${LIBXRL_LIBRARIES} ${LMF_LIBRARY} ${ECAT7_LIBRARY} ${TORCH_LIBRARIES} ${ITK_LIBRARIES} pthread)
ADD_EXECUTABLE(Gate Gate.cc $<TARGET_OBJECTS:GateLib> )
TARGET_LINK_LIBRARIES(Gate GateLib)

#=========================================================
INSTALL(TARGETS Gate DESTINATION bin)

OPTION(GATE_COMPILE_GATEDIGIT "Build GateDigit tools" OFF)
IF(GATE_COMPILE_GATEDIGIT)
    ADD_EXECUTABLE(GateDigit_singles_sorter ${PROJECT_SOURCE_DIR}/source/bin/GateDigit_singles_sorter.cc $<TARGET_OBJECTS:GateLib> )
    ADD_EXECUTABLE(GateDigit_hits_digitizer ${PROJECT_SOURCE_DIR}/source/bin/GateDigit_hits_digitizer.cc  $<TARGET_OBJECTS:GateLib>)
    ADD_EXECUTABLE(GateDigit_coincidence_processor ${PROJECT_SOURCE_DIR}/source/bin/GateDigit_coincidence_processor.cc $<TARGET_OBJECTS:GateLib>)
    ADD_EXECUTABLE(GateDigit_seqCoinc2Cones ${PROJECT_SOURCE_DIR}/source/bin/GateDigit_seqCoinc2Cones.cc $<TARGET_OBJECTS:GateLib>)
    ADD_EXECUTABLE(Convert_CCMod2PETCoinc ${PROJECT_SOURCE_DIR}/source/bin/Convert_CCMod2PETCoinc.cc $<TARGET_OBJECTS:GateLib>)
    TARGET_LINK_LIBRARIES(GateDigit_singles_sorter GateLib)
    TARGET_LINK_LIBRARIES(GateDigit_hits_digitizer GateLib)
    TARGET_LINK_LIBRARIES(GateDigit_coincidence_processor GateLib)
    TARGET_LINK_LIBRARIES(GateDigit_seqCoinc2Cones GateLib)
    TARGET_LINK_LIBRARIES(Convert_CCMod2PETCoinc GateLib)
    INSTALL(TARGETS GateDigit_singles_sorter DESTINATION bin)
    INSTALL(TARGETS GateDigit_hits_digitizer DESTINATION bin)
    INSTALL(TARGETS GateDigit_coincidence_processor DESTINATION bin)
    INSTALL(TARGETS GateDigit_seqCoinc2Cones DESTINATION bin)
    INSTALL(TARGETS Convert_CCMod2PETCoinc DESTINATION bin)
ENDIF(GATE_COMPILE_GATEDIGIT)

#=========================================================
# We remove the warning option "shadow", because there are tons of
# such warning related to clhep/g4 system of units.
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-shadow")
#=========================================================

#=========================================================
# Display Geant4 version
MESSAGE("Your current Geant4 version is ${Geant4_VERSION}")

#=========================================================
# Display message about this version
MESSAGE("IMPORTANT! This version of GATE (9.4) has still some traces of passage for new digitizer.")
MESSAGE("Please, be aware that some of functionalities are NOT YET re-implemented: ")
MESSAGE("- Coincidence digitizer modules (combining of several Coincidence Sorters)")
MESSAGE("- Output: Sinogram, Ecat7, LMF")
MESSAGE("- ARF may work not properly yet")
MESSAGE("We apologize for this inconvenience and kindly ask for your patience.")
MESSAGE("This functionalities will be added during 2024.")
MESSAGE("Meanwhile, please, use Gate 9.3")


#=========================================================
# Add gprof to RELWITHDEBINFO target
IF(NOT APPLE)
  SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -pg")
  SET(CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO "${CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO} -pg")
  SET(CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO "${CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO} -pg")
ENDIF()
#=========================================================