Merge pull request #47 from NIRALUser/master

Release 1.2.9

Author: juanprietob

CMake/ITKSetStandardCompilerFlags.cmake

@@ -281,13 +281,7 @@ endmacro()#End the platform check function
 
 #-----------------------------------------------------------------------------
 #Check the set of warning flags the compiler supports
-check_compiler_warning_flags(C_WARNING_FLAGS CXX_WARNING_FLAGS)
-
-# Append ITK warnings to the CMake flags.
-# We do not set them in ITK_REQUIRED FLAGS because all project which
-# use ITK don't require these flags .
-set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${C_WARNING_FLAGS}")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_WARNING_FLAGS}")
+check_compiler_warning_flags(ITK_C_WARNING_FLAGS ITK_CXX_WARNING_FLAGS)
 
 #-----------------------------------------------------------------------------
 #Check the set of platform flags the compiler supports

CMakeLists.txt

@@ -1,5 +1,4 @@
-cmake_minimum_required(VERSION 2.8.9)
-cmake_policy(VERSION 2.8.9)
+cmake_minimum_required(VERSION 3.5)
 
 set(LOCAL_PROJECT_NAME DTIPrepTools)
 project(${LOCAL_PROJECT_NAME})

Common.cmake

@@ -29,9 +29,6 @@ if(${ITK_VERSION_MAJOR} STREQUAL "3")
   set(USE_ITKv4 OFF)
 endif()
 
-#CMAKE_DEPENDENT_OPTION(
-#  USE_DTIPrep                         "Build DTIPrep"                                ON "${LOCAL_PROJECT_NAME}_USE_QT" ON)
-
 set(${LOCAL_PROJECT_NAME}_USE_QT ON)
 if(${LOCAL_PROJECT_NAME}_USE_QT AND NOT DTIPrep_BUILD_SLICER_EXTENSION )
   if(NOT QT4_FOUND)
@@ -121,22 +118,14 @@ SETIFEMPTY(DTIPrepTools_CLI_INSTALL_RUNTIME_DESTINATION ${CMAKE_INSTALL_RUNTIME_
 #-------------------------------------------------------------------------
 include(ITKSetStandardCompilerFlags)
 if(CMAKE_BUILD_TYPE STREQUAL "Debug")
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${C_DEBUG_DESIRED_FLAGS}" )
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_DEBUG_DESIRED_FLAGS}" )
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_INIT} ${ITK_C_WARNING_FLAGS} ${C_DEBUG_DESIRED_FLAGS}" )
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_INIT} ${ITK_CXX_WARNING_FLAGS} ${CXX_DEBUG_DESIRED_FLAGS}" )
 else() # Release, or anything else
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${C_RELEASE_DESIRED_FLAGS}" )
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_RELEASE_DESIRED_FLAGS}" )
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_INIT} ${ITK_C_WARNING_FLAGS} ${C_RELEASE_DESIRED_FLAGS}" )
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_INIT} ${ITK_CXX_WARNING_FLAGS} ${CXX_RELEASE_DESIRED_FLAGS}" )
 endif()
 
-#-----------------------------------------------------------------------------
-# Add needed flag for gnu on linux like enviroments to build static common libs
-# suitable for linking with shared object libs.
-if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-  if(NOT "${CMAKE_CXX_FLAGS}" MATCHES "-fPIC")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
-  endif()
-  if(NOT "${CMAKE_C_FLAGS}" MATCHES "-fPIC")
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
-  endif()
-endif()
+set(CMAKE_POSITION_INDEPENDENT_CODE 1)
+set(CMAKE_CXX_VISIBILITY_PRESET hidden)
+set(CMAKE_VISIBILITY_INLINES_HIDDEN 1)
 

DTIPrepTools.cmake

@@ -42,7 +42,6 @@ set( ITKModules
   ITKRegistrationCommon
   ITKOptimizersv4
   ITKConnectedComponents
-  ITKV3Compatibility
   ITKMathematicalMorphology
   ITKBinaryMathematicalMorphology
   ITKRegionGrowing
@@ -193,7 +192,7 @@ if( DTIPrep_BUILD_SLICER_EXTENSION )
   set(EXTENSION_HOMEPAGE "https://www.nitrc.org/projects/dtiprep/")
   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_DESCRIPTION "DTIPrep performs a 'Study-specific Protocol' based automatic pipeline for DWI/DTI quality control and preparation")
   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
@@ -222,7 +221,8 @@ if(USE_DTIProcess)
   )
   list( APPEND ToolsPaths ${SUPERBUILD_BINARY_DIR}/DTIProcess-install/bin/ )
 endif()
-if(USE_NIRALUtilities)
+
+if(USE_niral_utilities)
   list(APPEND NotCLIToolsList
     ImageMath
     convertITKformats
@@ -235,8 +235,7 @@ if( DTIPrep_BUILD_SLICER_EXTENSION )
   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 )
+else()
   if( NOT APPLE )
     INSTALL_EXECUTABLE( OUTPUT_DIR bin LIST_EXEC ${NotCLIToolsList} PATHS ${ToolsPaths} )
   else()

SuperBuild.cmake

@@ -19,25 +19,57 @@ include(CTest)
 
 include(${CMAKE_CURRENT_LIST_DIR}/Common.cmake)
 
+option(USE_niral_utilities "Build niral_utilities" ON)
+
 if( DTIPrep_BUILD_SLICER_EXTENSION )
   set( EXTERNAL_SOURCE_IN_BINARY_DIR ON)
   set( USE_SYSTEM_VTK ON CACHE BOOL "Use system VTK" FORCE )
+  set( USE_SYSTEM_ITK ON CACHE BOOL "Use system ITK" FORCE )
+  set( USE_SYSTEM_SlicerExecutionModel ON CACHE BOOL "Use system SlicerExecutionModel" FORCE )
   #VTK_VERSION_MAJOR is define but not a CACHE variable
   set( VTK_VERSION_MAJOR ${VTK_VERSION_MAJOR} CACHE STRING "Choose the expected VTK major version to build Slicer (5, 6, 7).")
   set( USE_SYSTEM_DCMTK ON CACHE BOOL "Use system DCMTK" FORCE )
   set( USE_SYSTEM_Teem ON CACHE BOOL "Use system Teem" FORCE )
+  set( USE_SYSTEM_DTIProcess ON CACHE BOOL "Use system DTIProcess" FORCE )
   set( BUILD_SHARED_LIBS OFF CACHE BOOL "Use shared libraries" FORCE)
-  unsetForSlicer(NAMES CMAKE_MODULE_PATH CMAKE_C_COMPILER CMAKE_CXX_COMPILER DCMTK_DIR ITK_DIR SlicerExecutionModel_DIR VTK_DIR QT_QMAKE_EXECUTABLE ITK_VERSION_MAJOR CMAKE_CXX_FLAGS CMAKE_C_FLAGS Teem_DIR)
+  unsetForSlicer(NAMES
+    BRAINSCommonLib_DIR
+    CMAKE_MODULE_PATH
+    CMAKE_C_COMPILER
+    CMAKE_CXX_COMPILER
+    DCMTK_DIR
+    ITK_DIR
+    SlicerExecutionModel_DIR
+    VTK_DIR
+    QT_QMAKE_EXECUTABLE
+    ITK_VERSION_MAJOR
+    CMAKE_CXX_FLAGS
+    CMAKE_C_FLAGS
+    Teem_DIR
+    )
   find_package(Slicer REQUIRED)
-  unsetAllForSlicerBut( NAMES VTK_DIR QT_QMAKE_EXECUTABLE DCMTK_DIR Teem_DIR )
-  resetForSlicer(NAMES CMAKE_MODULE_PATH CMAKE_C_COMPILER CMAKE_CXX_COMPILER CMAKE_CXX_FLAGS CMAKE_C_FLAGS ITK_DIR SlicerExecutionModel_DIR  ITK_VERSION_MAJOR )
+  unsetAllForSlicerBut( NAMES
+    BRAINSCommonLib_DIR
+    SlicerExecutionModel_DIR
+    ITK_DIR
+    VTK_DIR
+    QT_QMAKE_EXECUTABLE
+    DCMTK_DIR
+    Teem_DIR
+    )
+  resetForSlicer(NAMES
+    CMAKE_MODULE_PATH
+    CMAKE_C_COMPILER
+    CMAKE_CXX_COMPILER
+    CMAKE_CXX_FLAGS
+    CMAKE_C_FLAGS
+    )
   if( APPLE )
     set( CMAKE_EXE_LINKER_FLAGS "${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()
 
@@ -141,7 +173,12 @@ option(USE_SYSTEM_niral_utilities "Build using external niral_utilities" OFF)
 #------------------------------------------------------------------------------
 # ${LOCAL_PROJECT_NAME} dependency list
 #------------------------------------------------------------------------------
-set( ${LOCAL_PROJECT_NAME}_DEPENDENCIES DCMTK ITKv4 SlicerExecutionModel VTK DTIProcess niral_utilities BRAINSTools)
+set( ${LOCAL_PROJECT_NAME}_DEPENDENCIES VTK DCMTK ITKv4 SlicerExecutionModel DTIProcess niral_utilities)
+if( NOT DTIPrep_BUILD_SLICER_EXTENSION )
+  list(APPEND ${LOCAL_PROJECT_NAME}_DEPENDENCIES
+    BRAINSTools
+    )
+endif()
 set( ${PROJECT_NAME}_BUILD_DICOM_SUPPORT ON )
 set( ${PROJECT_NAME}_BUILD_ZLIB_SUPPORT ON )
 if( UNIX )
@@ -237,6 +274,12 @@ if(${LOCAL_PROJECT_NAME}_USE_QT)
     )
 endif()
 
+# Disable the "You are in 'detached HEAD' state." warning.
+set(git_config_arg)
+if(CMAKE_VERSION VERSION_GREATER "3.7.2")
+  set(git_config_arg GIT_CONFIG "advice.detachedHead=false")
+endif()
+
 _expand_external_project_vars()
 set(COMMON_EXTERNAL_PROJECT_ARGS ${${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_ARGS})
 set(extProjName ${LOCAL_PROJECT_NAME})
@@ -290,10 +333,6 @@ if( DTIPrep_BUILD_SLICER_EXTENSION )
     Slicer_DIR:PATH
     DTIPrep_BUILD_SLICER_EXTENSION:BOOL
     )
-else()
-  list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS
-    SUPERBUILD_NOT_EXTENSION:BOOL
-    )
 endif()
 _expand_external_project_vars()
 set(COMMON_EXTERNAL_PROJECT_ARGS ${${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_ARGS})
@@ -322,15 +361,18 @@ ExternalProject_Add(${proj}
   DEPENDS ${${LOCAL_PROJECT_NAME}_DEPENDENCIES}
   DOWNLOAD_COMMAND ""
   SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
-  BINARY_DIR ${LOCAL_PROJECT_NAME}-build
+  BINARY_DIR ${LOCAL_PROJECT_NAME}-build  
   CMAKE_GENERATOR ${gen}
   CMAKE_ARGS
     --no-warn-unused-cli # HACK Only expected variables should be passed down.
     ${CMAKE_OSX_EXTERNAL_PROJECT_ARGS}
     ${COMMON_EXTERNAL_PROJECT_ARGS}
     -D${LOCAL_PROJECT_NAME}_SUPERBUILD:BOOL=OFF
     -DBUILD_TESTING:BOOL=${BUILD_TESTING}
-  INSTALL_COMMAND ""
+    -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/${LOCAL_PROJECT_NAME}-install
+    -DUSE_niral_utilities=${USE_niral_utilities}
+    -DUSE_DTIProcess=${USE_DTIProcess}
+  #INSTALL_COMMAND ""
   )
 
 ## Force rebuilding of the main subproject every time building from super structure

SuperBuild/External_ANTs.cmake

@@ -86,6 +86,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}"
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}
+    ${git_config_arg}
     SOURCE_DIR ${EXTERNAL_SOURCE_DIRECTORY}/${proj}
     BINARY_DIR ${proj}-build
     LOG_CONFIGURE 0  # Wrap configure in script to ignore log output from dashboards

SuperBuild/External_BRAINSTools.cmake

@@ -242,6 +242,7 @@ if(NOT ( DEFINED "${extProjName}_SOURCE_DIR" OR ( DEFINED "USE_SYSTEM_${extProjN
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}
+    ${git_config_arg}
     SOURCE_DIR ${EXTERNAL_SOURCE_DIRECTORY}/${proj}
     BINARY_DIR ${proj}-build
     LOG_CONFIGURE 0  # Wrap configure in script to ignore log output from dashboards

SuperBuild/External_BatchMake.cmake

@@ -69,6 +69,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}"
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}
+    ${git_config_arg}
     SOURCE_DIR ${EXTERNAL_SOURCE_DIRECTORY}/${proj}
     BINARY_DIR ${proj}-build
     LOG_CONFIGURE 0  # Wrap configure in script to ignore log output from dashboards

SuperBuild/External_Cppcheck.cmake

@@ -60,6 +60,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}"
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}
+    ${git_config_arg}
     SOURCE_DIR ${EXTERNAL_SOURCE_DIRECTORY}/${proj}
     BUILD_IN_SOURCE 1
     LOG_CONFIGURE 0  # Wrap configure in script to ignore log output from dashboards

SuperBuild/External_DCMTK.cmake

@@ -119,6 +119,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}"
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}
+    ${git_config_arg}
     SOURCE_DIR ${EXTERNAL_SOURCE_DIRECTORY}/${proj}
     BINARY_DIR ${EXTERNAL_BINARY_DIRECTORY}/${proj}-build
     INSTALL_DIR ${EXTERNAL_BINARY_DIRECTORY}/${proj}-install