DTIPrepTools.cmake

set(MODULE_NAME ${EXTENSION_NAME}) # Do not use 'project()'
set(MODULE_TITLE ${MODULE_NAME})

macro(INSTALL_EXECUTABLE)
  set(options )
  set( oneValueArgs OUTPUT_DIR )
  set(multiValueArgs LIST_EXEC PATHS)
  CMAKE_PARSE_ARGUMENTS(LOCAL
    "${options}"
    "${oneValueArgs}"
    "${multiValueArgs}"
    ${ARGN}
    )
  foreach( tool ${LOCAL_LIST_EXEC})
     find_program( programPATH NAMES ${tool} PATHS ${LOCAL_PATHS} NO_DEFAULT_PATH NO_CMAKE_ENVIRONMENT_PATH NO_SYSTEM_ENVIRONMENT_PATH NO_CMAKE_PATH NO_CMAKE_SYSTEM_PATH )
     install(PROGRAMS ${programPATH} DESTINATION ${LOCAL_OUTPUT_DIR} )
     unset( programPATH CACHE )
  endforeach()
endmacro()

#-----------------------------------------------------------------------------
# Update CMake module path
#------------------------------------------------------------------------------
set(CMAKE_MODULE_PATH
  ${${PROJECT_NAME}_SOURCE_DIR}/CMake
  ${${PROJECT_NAME}_BINARY_DIR}/CMake
  ${CMAKE_MODULE_PATH}
  )

find_package(SlicerExecutionModel REQUIRED)

find_package(GenerateCLP REQUIRED)
if(GenerateCLP_FOUND)
  include(${GenerateCLP_USE_FILE})
endif()

#-----------------------------------------------------------------------------
find_package(ITK COMPONENTS
  ITKDiffusionTensorImage
  ITKRegistrationCommon
  ITKOptimizersv4
  ITKConnectedComponents
  ITKV3Compatibility
  ITKMathematicalMorphology
  ITKBinaryMathematicalMorphology
  ITKRegionGrowing
  ITKMetricsv4
  ITKRegistrationMethodsv4
  ITKDistanceMap
  ITKVTK
  ITKTransform
  ITKIOImageBase
  ITKIONRRD
  ITKImageCompare
  ITKIOBMP
  ITKIOBioRad
  ITKIOCSV
  ITKIODCMTK
  ITKIOGDCM
  ITKIOGE
  ITKIOGIPL
  ITKIOHDF5
  ITKIOIPL
  ITKIOImageBase
  ITKIOJPEG
  ITKIOLSM
  MGHIO
  ITKIOMRC
  ITKIOMesh
  ITKIOMeta
  ITKIONIFTI
  ITKIONRRD
  ITKIOPNG
  ITKIORAW
  ITKIOSiemens
  ITKIOSpatialObjects
  ITKIOStimulate
  ITKIOTIFF
  ITKIOTransformBase
  ITKIOTransformHDF5
  ITKIOTransformInsightLegacy
  ITKIOTransformMatlab
  ITKIOVTK
  ITKIOXML
  REQUIRED)

include(${ITK_USE_FILE})

#-----------------------------------------------------------------------------
set(VTK_FOUND OFF)
find_package(VTK COMPONENTS
      vtkCommonSystem
      vtkCommonCore
      vtkCommonSystem
      vtkCommonMath
      vtkCommonMisc
      vtkCommonTransforms
      vtkIOLegacy
      vtkIOXML
      vtkGUISupportQt
      vtkInteractionImage
      REQUIRED)
if(VTK_USE_FILE)
  include(${VTK_USE_FILE})
endif()


#-----------------------------------------------------------------------------
find_package(SlicerExecutionModel NO_MODULE REQUIRED GenerateCLP)
include(${GenerateCLP_USE_FILE})
include(${SlicerExecutionModel_USE_FILE})
include(${SlicerExecutionModel_CMAKE_DIR}/SEMMacroBuildCLI.cmake)

include(${CMAKE_CURRENT_LIST_DIR}/Common.cmake)

if(USE_ANTS)
  # find ANTS includes
  message("ANTs_SOURCE_DIR=${ANTs_SOURCE_DIR}")
  include_directories(${BOOST_INCLUDE_DIR})
  include_directories(${ANTs_SOURCE_DIR}/Temporary)
  include_directories(${ANTs_SOURCE_DIR}/Tensor)
  include_directories(${ANTs_SOURCE_DIR}/Utilities)
  include_directories(${ANTs_SOURCE_DIR}/Examples)
  include_directories(${ANTs_SOURCE_DIR}/ImageRegistration)
  link_directories(${BRAINSTools_LIBRARY_PATH} ${BRAINSTools_CLI_ARCHIVE_OUTPUT_DIRECTORY} ${ANTs_LIBRARY_DIR})
  set(ANTS_LIBS antsUtilities)
endif()

message("BRAINSCommonLib_DIR=${BRAINSCommonLib_DIR}")

find_package(BRAINSCommonLib NO_MODULE REQUIRED)
include(${BRAINSCommonLib_USE_FILE})
include_directories(${BRAINSCommonLib_INCLUDE_DIRS})
link_directories(${BRAINSCommonLib_LIBRARY_DIRS})


#find_package(MultiImageRegistration NO_MODULE REQUIRED)
#include(${MultiImageRegistration_USE_FILE})

# Use the include path and library for Qt that is used by VTK.
#include_directories(
#  ${CMAKE_CURRENT_BINARY_DIR}
#  ${CMAKE_CURRENT_SOURCE_DIR}
#  ${VTK_INCLUDE_DIR}
#  ${ITK_INCLUDE_DIR}
#  ${QT_INCLUDE_DIR}
#)

# No need to add with nothing to compile. add_subdirectory(BRAINSFit_Common)
##HACK:
#set(BRAINSFit_SOURCE_DIR  ${CMAKE_CURRENT_SOURCE_DIR}/BRAINSFit)
#include_directories(${BRAINSFit_SOURCE_DIR})
#include_directories(${BRAINSFit_SOURCE_DIR}/BRAINSFit_Common)
#include_directories(${BRAINSFit_SOURCE_DIR}/LargestForegroundFilledMaskImageFilter)
#include_directories(${BRAINSFit_SOURCE_DIR}/FindCenterOfBrainFilter)
#include_directories(${CMAKE_INSTALL_PREFIX}/MultiImageRegistration/Source)
#include_directories(${CMAKE_INSTALL_PREFIX}/MultiImageRegistration/Source/Common)

#-----------------------------------------------------------------------
# Setup locations to find externally maintained test data.
#-----------------------------------------------------------------------
list(APPEND ExternalData_URL_TEMPLATES
  # Local data store populated by the ITK pre-commit hook
  "file:///${${PROJECT_NAME}_SOURCE_DIR}/.ExternalData/%(algo)/%(hash)"
  # Data published by Iowa Psychiatry web interface
  ## This server is now obsolete "http://www.psychiatry.uiowa.edu/users/brainstestdata/ctestdata/%(algo)/%(hash)"
  ## The primary new home for data
  "http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=%(hash)"
  # Data published by MIDAS
  "http://midas.kitware.com/api/rest/midas.bitstream.by.hash?hash=%(hash)&algorithm=%(algo)"
  # Data published by developers using git-gerrit-push.
  "http://www.itk.org/files/ExternalData/%(algo)/%(hash)"
)

# Tell ExternalData commands to transform raw files to content links.
# TODO: Condition this feature on presence of our pre-commit hook.
#set(ExternalData_LINK_CONTENT MD5)
#set(ExternalData_SOURCE_ROOT ${${PROJECT_NAME}_SOURCE_DIR})
#include(ExternalData)

set(TestData_DIR ${CMAKE_CURRENT_SOURCE_DIR}/TestData)

if( DTIPrep_BUILD_SLICER_EXTENSION )
  unsetForSlicer( NAMES SlicerExecutionModel_DIR ITK_DIR VTK_DIR CMAKE_C_COMPILER CMAKE_CXX_COMPILER CMAKE_CXX_FLAGS CMAKE_C_FLAGS ITK_LIBRARIES )
  find_package(Slicer REQUIRED)
  include(${Slicer_USE_FILE})
  resetForSlicer( NAMES ITK_DIR SlicerExecutionModel_DIR CMAKE_C_COMPILER CMAKE_CXX_COMPILER CMAKE_CXX_FLAGS CMAKE_C_FLAGS ITK_LIBRARIES )
endif()

#-----------------------------------------------------------------------------
# Add module sub-directory if USE_<MODULENAME> is both defined and true
#-----------------------------------------------------------------------------
add_subdirectory(src)

IF(BUILD_TESTING)
  include(CTest)
  ADD_SUBDIRECTORY(Testing)
ENDIF(BUILD_TESTING)

if(USE_DTIProcess)
  set( NotCLIToolsList
    dtiestim
    dtiprocess
  )
  list( APPEND ToolsPaths ${SUPERBUILD_BINARY_DIR}/DTIProcess-install/bin/ )
endif()
if(USE_NIRALUtilities)
  list(APPEND NotCLIToolsList
    ImageMath
    convertITKformats
  )
  list( APPEND ToolsPaths ${SUPERBUILD_BINARY_DIR}/niral_utilities-install/bin/ )
endif()

if( DTIPrep_BUILD_SLICER_EXTENSION )
  set(NOCLI_INSTALL_DIR ${Slicer_INSTALL_CLIMODULES_BIN_DIR}/../ExternalBin)
  INSTALL_EXECUTABLE( OUTPUT_DIR ${NOCLI_INSTALL_DIR} LIST_EXEC ${NotCLIToolsList} PATHS ${ToolsPaths} )
  set(CPACK_INSTALL_CMAKE_PROJECTS "${CPACK_INSTALL_CMAKE_PROJECTS};${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/")
  include(${Slicer_EXTENSION_CPACK})
endif()
if( SUPERBUILD_NOT_EXTENSION )
  if( NOT APPLE )
    INSTALL_EXECUTABLE( OUTPUT_DIR bin LIST_EXEC ${NotCLIToolsList} PATHS ${ToolsPaths} )
  else()
    INSTALL_EXECUTABLE( OUTPUT_DIR ${CMAKE_INSTALL_PREFIX}/bin/DTIPrep.app/Contents/ExternalBin LIST_EXEC ${NotCLIToolsList} PATHS ${ToolsPaths} )
  endif()
endif()