ENH: Update SuperBuild process and package extension for SLICER

jcfr · Aug 14, 2016 · 2ea5e5b · 2ea5e5b
1 parent 590f70b
commit 2ea5e5b
Show file tree

Hide file tree

Showing 8 changed files with 87 additions and 60 deletions.
diff --git a/CMakeFiles/cmake.check_cache b/CMakeFiles/cmake.check_cache
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -22,7 +22,6 @@ project(${LOCAL_PROJECT_NAME})
 #-----------------------------------------------------------------------------
 option(${LOCAL_PROJECT_NAME}_SUPERBUILD "Build ${LOCAL_PROJECT_NAME} and the projects it depends on via SuperBuild.cmake." ON)
 mark_as_advanced(${LOCAL_PROJECT_NAME}_SUPERBUILD)
-
 #-----------------------------------------------------------------------------
 # Superbuild script
 #-----------------------------------------------------------------------------

diff --git a/Common.cmake b/Common.cmake
@@ -2,22 +2,6 @@
 include(CMakeDependentOption)
 
 
-#Declare DTIPrep extension variables
-set(EXTENSION_NAME DTIPrep)
-set(EXTENSION_HOMEPAGE "http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DTIPrep")
-set(EXTENSION_CATEGORY "Diffusion")
-set(EXTENSION_CONTRIBUTORS "Francois Budin (UNC)")
-set(EXTENSION_DESCRIPTION "This extension provides the tool DTIPrep integrated in Slicer")
-set(EXTENSION_ICONURL "http://www.nitrc.org/project/screenshot.php?group_id=283&screenshot_id=608")
-set(EXTENSION_SCREENSHOTURLS "http://www.nitrc.org/project/screenshot.php?group_id=283&screenshot_id=609 http://www.nitrc.org/project/screenshot.php?group_id=283&screenshot_id=610")
-set(EXTENSION_STATUS "Beta")
-set(EXTENSION_DEPENDS "DTIProcess" ) # Specified as a space separated list or 'NA' if any
-set(EXTENSION_BUILD_SUBDIRECTORY DTIPrepTools-build )
-
-
-
-
-
 #-----------------------------------------------------------------------------
 # Build option(s)
 #-----------------------------------------------------------------------------

diff --git a/DTIPrepTools.cmake b/DTIPrepTools.cmake
@@ -1,3 +1,5 @@
+include(${CMAKE_CURRENT_LIST_DIR}/Common.cmake)
+
 set(MODULE_NAME ${EXTENSION_NAME}) # Do not use 'project()'
 set(MODULE_TITLE ${MODULE_NAME})
 
@@ -117,8 +119,6 @@ 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}")
@@ -194,9 +194,10 @@ if( DTIPrep_BUILD_SLICER_EXTENSION )
   set(EXTENSION_CATEGORY "DWI/DTI Quality Control")
   set(EXTENSION_CONTRIBUTORS "Joy Matsui, Zhexing Liu, Clement Vachet, David Welch, Guido Gerig, kent williams, Mahshid Farzinfar, Sylvain Gouttard, Vincent Magnotta, Hans Johnson, Martin Styner, Francois Budin, Juan Prieto")
   set(EXTENSION_DESCRIPTION "DTIPrep performs a "Study-specific Protocol" based automatic pipeline for DWI/DTI quality control and preparation")
-  set(EXTENSION_ICONURL "https://www.nitrc.org/project/list_screenshots.php?group_id=283&screenshot_id=216")
+  set(EXTENSION_ICONURL "http://www.nitrc.org/project/screenshot.php?group_id=283&screenshot_id=608")
+  set(EXTENSION_SCREENSHOTURLS "http://www.nitrc.org/project/screenshot.php?group_id=283&screenshot_id=609 http://www.nitrc.org/project/screenshot.php?group_id=283&screenshot_id=610")
   set(EXTENSION_DEPENDS "NA") # Specified as a space separated list or 'NA' if any
-  set(EXTENSION_BUILD_SUBDIRECTORY ".")
+  set(EXTENSION_BUILD_SUBDIRECTORY ".")  
 
   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)

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
@@ -12,33 +12,12 @@ enable_testing()
 include(CTest)
 
 #-----------------------------------------------------------------------------
-include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake)
+
 #-----------------------------------------------------------------------------
 #If it is build as an extension
 #-----------------------------------------------------------------------------
-if( DTIPrep_BUILD_SLICER_EXTENSION )
-  set( EXTERNAL_SOURCE_IN_BINARY_DIR ON)
-  set( USE_SYSTEM_VTK ON CACHE BOOL "Use system VTK" FORCE )
-  #VTK_VERSION_MAJOR is define but not a CACHE variable
-  set( VTK_VERSION_MAJOR ${VTK_VERSION_MAJOR} CACHE STRING "Choose the expected VTK major version to build Slicer (5 or 6).")
-  set( USE_SYSTEM_DCMTK ON CACHE BOOL "Use system DCMTK" FORCE )
-  set( USE_SYSTEM_Teem ON CACHE BOOL "Use system Teem" FORCE )
-  set( BUILD_SHARED_LIBS OFF CACHE BOOL "Use shared libraries" FORCE)
-  unsetForSlicer(NAMES CMAKE_MODULE_PATH CMAKE_C_COMPILER CMAKE_CXX_COMPILER DCMTK_DIR ITK_DIR SlicerExecutionModel_DIR VTK_DIR QT_QMAKE_EXECUTABLE ITK_VERSION_MAJOR CMAKE_CXX_FLAGS CMAKE_C_FLAGS Teem_DIR)
-  find_package(Slicer REQUIRED)
-  unsetAllForSlicerBut( NAMES VTK_DIR QT_QMAKE_EXECUTABLE DCMTK_DIR Teem_DIR )
-  resetForSlicer(NAMES CMAKE_MODULE_PATH CMAKE_C_COMPILER CMAKE_CXX_COMPILER CMAKE_CXX_FLAGS CMAKE_C_FLAGS ITK_DIR SlicerExecutionModel_DIR  ITK_VERSION_MAJOR )
-  if( APPLE )
-    set( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-rpath,@loader_path/../../../../../")
-  endif()
-  find_package(Subversion REQUIRED )
-else()
-  set( USE_ITK_Module_MGHIO ON )
-  set( SUPERBUILD_NOT_EXTENSION TRUE )
-  option(USE_DTIProcess "Build DTIProcess" ON)
-endif()
-option(USE_NIRALUtilities "Build NIRALUtilities" ON)
 
+include(${CMAKE_CURRENT_LIST_DIR}/Common.cmake)
 
 if( EXTERNAL_SOURCE_IN_BINARY_DIR )
   set( EXTERNAL_SOURCE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} )
@@ -133,12 +112,14 @@ option(USE_SYSTEM_Teem "Build using external Teem" OFF)
 option(USE_SYSTEM_zlib "Build using external zlib" OFF)
 option(USE_ANTs "Build BRAINSTools with ANTs" OFF)
 option(${PROJECT_NAME}_BUILD_FFTW_SUPPORT "Build external FFTW" OFF)
+option(USE_SYSTEM_DTIProcess "Build using external DTIProcess" OFF)
+option(USE_SYSTEM_niral_utilities "Build using external niral_utilities" OFF)
 #option(${PROJECT_NAME}_BUILD_DICOM_SUPPORT "Build Dicom Support" ON)
 
 #------------------------------------------------------------------------------
 # ${LOCAL_PROJECT_NAME} dependency list
 #------------------------------------------------------------------------------
-set( ${LOCAL_PROJECT_NAME}_DEPENDENCIES DCMTK ITKv4 SlicerExecutionModel VTK BRAINSTools )
+set( ${LOCAL_PROJECT_NAME}_DEPENDENCIES DCMTK ITKv4 SlicerExecutionModel VTK DTIProcess niral_utilities BRAINSTools)
 set( ${PROJECT_NAME}_BUILD_DICOM_SUPPORT ON )
 set( ${PROJECT_NAME}_BUILD_ZLIB_SUPPORT ON )
 if( UNIX )
@@ -311,17 +292,6 @@ if(verbose)
   endforeach()
 endif()
 
-
-if(USE_DTIProcess)
-  include(${CMAKE_CURRENT_LIST_DIR}/SuperBuild/External_DTIProcess.cmake)
-  list( APPEND ${LOCAL_PROJECT_NAME}_DEPENDENCIES DTIProcess )
-endif()
-
-if(USE_NIRALUtilities)
-  include(${CMAKE_CURRENT_LIST_DIR}/SuperBuild/External_niral_utilities.cmake)
-  list( APPEND ${LOCAL_PROJECT_NAME}_DEPENDENCIES niral_utilities )
-endif()
-
 #------------------------------------------------------------------------------
 # Configure and build
 #------------------------------------------------------------------------------
@@ -338,8 +308,6 @@ ExternalProject_Add(${proj}
     ${COMMON_EXTERNAL_PROJECT_ARGS}
     -D${LOCAL_PROJECT_NAME}_SUPERBUILD:BOOL=OFF
     -DBUILD_TESTING:BOOL=${BUILD_TESTING}
-    -DUSE_NIRALUtilities:BOOL=${USE_NIRALUtilities}
-    -DUSE_DTIProcess:BOOL=${USE_DTIProcess}
   INSTALL_COMMAND ""
   )
 

diff --git a/SuperBuild/External_BRAINSTools.cmake b/SuperBuild/External_BRAINSTools.cmake
@@ -61,6 +61,77 @@ if(NOT ( DEFINED "${extProjName}_SOURCE_DIR" OR ( DEFINED "USE_SYSTEM_${extProjN
   # Set CMake OSX variable to pass down the external project
   set(CMAKE_OSX_EXTERNAL_PROJECT_ARGS)
   if(APPLE)
+                      #This code was taken from BRAINSTools, for some reason is not working when doing the superbuild but if done here it works
+                      # Waiting universal binaries are supported and tested, complain if
+                      # multiple architectures are specified.
+                      if(NOT "${CMAKE_OSX_ARCHITECTURES}" STREQUAL "")
+                        list(LENGTH CMAKE_OSX_ARCHITECTURES arch_count)
+                        if(arch_count GREATER 1)
+                          message(FATAL_ERROR "error: Only one value (i386 or x86_64) should be associated with CMAKE_OSX_ARCHITECTURES.")
+                        endif()
+                      endif()
+
+                      # See CMake/Modules/Platform/Darwin.cmake)
+                      #   8.x == Mac OSX 10.4 (Tiger)
+                      #   9.x == Mac OSX 10.5 (Leopard)
+                      #  10.x == Mac OSX 10.6 (Snow Leopard)
+                      #  11.x == Mac OSX 10.7 (Lion)
+                      #  12.x == Mac OSX 10.8 (Mountain Lion)
+                      #  13.x == Mac OSX 10.9 (Mavericks)
+                      #  14.x == Mac OSX 10.10 (Yosemite)
+                      set(OSX_SDK_104_NAME "Tiger")
+                      set(OSX_SDK_105_NAME "Leopard")
+                      set(OSX_SDK_106_NAME "Snow Leopard")
+                      set(OSX_SDK_107_NAME "Lion")
+                      set(OSX_SDK_108_NAME "Mountain Lion")
+                      set(OSX_SDK_109_NAME "Mavericks")
+                      set(OSX_SDK_1010_NAME "Yosemite")
+                      set(OSX_SDK_1011_NAME "El Capitan")
+
+                      set(OSX_SDK_ROOTS
+                        /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs
+                        /Developer/SDKs
+                        )
+
+                      # Explicitly set the OSX_SYSROOT to the latest one, as its required
+                      #       when the SX_DEPLOYMENT_TARGET is explicitly set
+                      foreach(SDK_ROOT ${OSX_SDK_ROOTS})
+                        if( "x${CMAKE_OSX_SYSROOT}x" STREQUAL "xx")
+                          file(GLOB SDK_SYSROOTS "${SDK_ROOT}/MacOSX*.sdk")
+
+                          if(NOT "x${SDK_SYSROOTS}x" STREQUAL "xx")
+                            set(SDK_SYSROOT_NEWEST "")
+                            set(CMAKE_OSX_DEPLOYMENT_TARGET "0")
+                            # find the latest SDK
+                            foreach(SDK_ROOT_I ${SDK_SYSROOTS})
+                              # extract version from SDK
+                              string(REGEX MATCH "MacOSX([0-9]+\\.[0-9]+)\\.sdk" _match "${SDK_ROOT_I}")
+                              if("${CMAKE_MATCH_1}" VERSION_GREATER "${CMAKE_OSX_DEPLOYMENT_TARGET}")
+                                set(SDK_SYSROOT_NEWEST "${SDK_ROOT_I}")
+                                set(CMAKE_OSX_DEPLOYMENT_TARGET "${CMAKE_MATCH_1}")
+                              endif()
+                            endforeach()
+
+                            if(NOT "x${SDK_SYSROOT_NEWEST}x" STREQUAL "xx")
+                              string(REPLACE "." "" sdk_version_no_dot ${CMAKE_OSX_DEPLOYMENT_TARGET})
+                              set(OSX_NAME ${OSX_SDK_${sdk_version_no_dot}_NAME})
+                              set(CMAKE_OSX_ARCHITECTURES "x86_64" CACHE STRING "Force build for 64-bit ${OSX_NAME}." FORCE)
+                              set(CMAKE_OSX_SYSROOT "${SDK_SYSROOT_NEWEST}" CACHE PATH "Force build for 64-bit ${OSX_NAME}." FORCE)
+                              set(CMAKE_OSX_DEPLOYMENT_TARGET "${CMAKE_OSX_DEPLOYMENT_TARGET}" CACHE PATH "Force Deployment Target ${OSX_NAME}." FORCE)
+                              message(STATUS "Setting OSX_ARCHITECTURES to '${CMAKE_OSX_ARCHITECTURES}' as none was specified.")
+                              message(STATUS "Setting OSX_SYSROOT to latest '${CMAKE_OSX_SYSROOT}' as none was specified.")
+                              message(STATUS "Setting OSX_DEPLOYMENT_TARGET to latest '${CMAKE_OSX_DEPLOYMENT_TARGET}' as none was specified.")
+                            endif()
+                          endif()
+                        endif()
+                      endforeach()
+
+                      if(NOT "${CMAKE_OSX_SYSROOT}" STREQUAL "")
+                        if(NOT EXISTS "${CMAKE_OSX_SYSROOT}")
+                          message(FATAL_ERROR "error: CMAKE_OSX_SYSROOT='${CMAKE_OSX_SYSROOT}' does not exist")
+                        endif()
+                      endif()
+
     list(APPEND CMAKE_OSX_EXTERNAL_PROJECT_ARGS
       -DCMAKE_OSX_ARCHITECTURES=${CMAKE_OSX_ARCHITECTURES}
       -DCMAKE_OSX_SYSROOT=${CMAKE_OSX_SYSROOT}
@@ -167,7 +238,7 @@ if(NOT ( DEFINED "${extProjName}_SOURCE_DIR" OR ( DEFINED "USE_SYSTEM_${extProjN
 
   ### --- End Project specific additions
   set(${proj}_REPOSITORY "${git_protocol}://github.com/BRAINSia/BRAINSTools.git")
-  set(${proj}_GIT_TAG 98fe1ad2b9297e444d662d09dc83a9409fcf520a )
+  set(${proj}_GIT_TAG b0b4a0950b9cfa3abb7c6dd7f8314d15f2aa2a21 )
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}

diff --git a/SuperBuild/External_DTIProcess.cmake b/SuperBuild/External_DTIProcess.cmake
@@ -70,6 +70,9 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}"
     -DUSE_SYSTEM_ITK:BOOL=ON
     -DUSE_SYSTEM_VTK:BOOL=ON
     -DUSE_SYSTEM_SlicerExecutionModel:BOOL=ON
+    -DITK_DIR=${ITK_DIR}
+    -DVTK_DIR=${VTK_DIR}
+    -DSlicerExecutionModel_DIR=${SlicerExecutionModel_DIR}
     -DDTIProcess_SUPERBUILD:BOOL=OFF
     -DEXECUTABLES_ONLY:BOOL=ON
     -DSubversion_SVN_EXECUTABLE:PATH=${SVNCOMMAND}

diff --git a/SuperBuild/External_niral_utilities.cmake b/SuperBuild/External_niral_utilities.cmake
@@ -72,6 +72,8 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}"
     -DUSE_SYSTEM_SlicerExecutionModel:BOOL=ON
     -DUSE_SYSTEM_ITK:BOOL=ON
     -DUSE_SYSTEM_VTK:BOOL=ON
+    -DITK_DIR=${ITK_DIR}
+    -DVTK_DIR=${VTK_DIR}
     -DITK_VERSION_MAJOR:STRING=${ITK_VERSION_MAJOR}
     )