Merge branch 'develop-1.9.17'

Author: vfonov

BEaST

@@ -27,7 +27,7 @@ ENDIF(COMMAND CMAKE_POLICY)
 SET(MINC_TOOLKIT_PACKAGE_VERSION_MAJOR 1)
 SET(MINC_TOOLKIT_PACKAGE_VERSION_MINOR 9)
 SET(MINC_TOOLKIT_PACKAGE_VERSION_PATCH 17)
-SET(MINC_TOOLKIT_RELEASE_DATE "20181127")
+SET(MINC_TOOLKIT_RELEASE_DATE "20190313")
 
 SET(MINC_TOOLKIT_VERSION_FULL "${MINC_TOOLKIT_PACKAGE_VERSION_MAJOR}.${MINC_TOOLKIT_PACKAGE_VERSION_MINOR}.${MINC_TOOLKIT_PACKAGE_VERSION_PATCH}-${MINC_TOOLKIT_RELEASE_DATE}")
 
@@ -153,6 +153,8 @@ INCLUDE(ExternalProject)
 INCLUDE(ConfigureExternalProjects)
 SET(SUPERBUILD_STAGING_PREFIX ${CMAKE_BINARY_DIR}/external)
 
+# Fix missing share directory
+file(MAKE_DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share)
 
 SET(MINC_TEST_ENVIRONMENT
  "PATH=${CMAKE_CURRENT_BINARY_DIR}:${CMAKE_CURRENT_BINARY_DIR}/N3:${CMAKE_CURRENT_BINARY_DIR}/classify:${CMAKE_CURRENT_BINARY_DIR}/minctools/progs:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/mincblur:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/make_phantom:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/minctracc:${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin:$ENV{PATH}" 
@@ -564,7 +566,6 @@ IF(MT_BUILD_VISUAL_TOOLS)
     ADD_DEPENDENCIES(Display FREEGLUT)
   ENDIF(NOT USE_SYSTEM_GLUT)
 
-  
   IF(MT_BUILD_SHARED_LIBS)
     ADD_DEPENDENCIES(ray_trace bicgl minc2_static bicpl_static)
     ADD_DEPENDENCIES(Display   bicgl minc2_static bicpl_static)
@@ -583,7 +584,6 @@ IF(MT_BUILD_VISUAL_TOOLS)
   ENDIF(X11_FOUND)
 ENDIF(MT_BUILD_VISUAL_TOOLS)
 
-
 IF(MT_BUILD_IM)
     message("Building minimal imagemagick, use with caution!")
     INCLUDE(BuildJPEG)
@@ -598,24 +598,22 @@ IF(MT_BUILD_IM)
     ADD_DEPENDENCIES(FREETYPE PNG)
     ADD_DEPENDENCIES(IM FREETYPE PNG JPEG)
 ENDIF(MT_BUILD_IM)
-# DO nothing?
-IF(USE_SUPERBUILD)
+
   #install external dependencies to final destination
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin
         DESTINATION .
         PATTERN *
         PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE GROUP_EXECUTE GROUP_READ WORLD_READ WORLD_EXECUTE )
 
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}
         DESTINATION .)
 
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/include
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/include
         DESTINATION .)
 
-  # do we really need to install share?
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share
+# share can be created by some packages
+INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share
         DESTINATION .)
-ENDIF(USE_SUPERBUILD)
 
 
 ADD_SUBDIRECTORY(man-pages)
@@ -634,8 +632,6 @@ ENDIF(APPLE)
 
 INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh DESTINATION .)
 
-
-
 # setup additional variables for making Debian package
 INCLUDE(DebianPackageAddons)
 

CMakeLists.txt

@@ -0,0 +1,26 @@
+From c3e30b2bc2234dfafc9e674c8ab5723fabeb04c5 Mon Sep 17 00:00:00 2001
+From: Sacha <[email protected]>
+Date: Wed, 13 Mar 2019 23:21:54 +1000
+Subject: [PATCH] Change 64-bit detection as explained in #2056
+
+---
+ cmake/system_check.cmake | 6 +++++-
+ 1 file changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/cmake/system_check.cmake b/cmake/system_check.cmake
+index 88bb081a6..f30a946b4 100644
+--- a/cmake/system_check.cmake
++++ b/cmake/system_check.cmake
+@@ -39,7 +39,11 @@ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc.*|power.*|Power.*")
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "mips64.*")
+   set(MIPS64 1)
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64.*|x86_64.*|AMD64.*")
+-  set(X86_64 1)
++  if("${CMAKE_SIZEOF_VOID_P}" EQUAL "8")
++    set(X86_64 1)
++  else()
++    set(X86 1)
++  endif()
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "i686.*|i386.*|x86.*|amd64.*|AMD64.*")
+   set(X86 1)
+ elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(arm.*|ARM.*)")

EZminc

@@ -0,0 +1,25 @@
+From 89af9b2694715bf8204993e032fa132f80cf37bd Mon Sep 17 00:00:00 2001
+From: Martino Pilia <[email protected]>
+Date: Fri, 1 Jun 2018 18:17:57 +0200
+Subject: [PATCH] BUG: fix a bug in
+ ImageSegmentation/antsAtroposSegmentationImageFilter.h
+
+This should be pretty obvious, the return type of a getter method was
+wrong.
+---
+ ImageSegmentation/antsAtroposSegmentationImageFilter.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ImageSegmentation/antsAtroposSegmentationImageFilter.h b/ImageSegmentation/antsAtroposSegmentationImageFilter.h
+index e4b32a0cf..adeb4baad 100644
+--- a/ImageSegmentation/antsAtroposSegmentationImageFilter.h
++++ b/ImageSegmentation/antsAtroposSegmentationImageFilter.h
+@@ -518,7 +518,7 @@ class AtroposSegmentationImageFilter :
+   /**
+    * Get the prior label parameters.
+    */
+-  void GetPriorLabelParameterMap()
++  LabelParameterMapType GetPriorLabelParameterMap()
+   {
+     return this->m_PriorLabelParameterMap;
+   }

ILT

@@ -62,6 +62,7 @@ macro(build_ANTS install_prefix staging_prefix itk_dir ) #boost_dir
     #UPDATE_COMMAND ""
     SOURCE_DIR ${CMAKE_SOURCE_DIR}/ANTs
     BINARY_DIR ANTS-build
+    PATCH_COMMAND patch -p1 -t -N -i ${CMAKE_SOURCE_DIR}/cmake-modules/89af9b2694715bf8204993e032fa132f80cf37bd.patch
     #PATCH_COMMAND ${PATCH_QUIET}
     LIST_SEPARATOR :::  
     CMAKE_GENERATOR ${CMAKE_GEN}

cmake-modules/0001-Fix-1705-where-we-incorrectly-calculate-page-locatio.patch

@@ -17,17 +17,17 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
   LIST(APPEND EXT_CMAKE_C_FLAGS -D_XOPEN_SOURCE=600)
   LIST(APPEND EXT_CMAKE_CXX_FLAGS -D_XOPEN_SOURCE=600)
   ENDIF(NOT APPLE)
-  
+
   set(CMAKE_EXTERNAL_PROJECT_ARGS
         -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
         -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
         -DCMAKE_LINKER:FILEPATH=${CMAKE_LINKER}
-        -DCMAKE_CXX_FLAGS:STRING=${EXT_CMAKE_CXX_FLAGS} 
+        -DCMAKE_CXX_FLAGS:STRING=${EXT_CMAKE_CXX_FLAGS}
         -DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
         -DCMAKE_CXX_FLAGS_MINSIZEREL:STRING=${CMAKE_CXX_FLAGS_MINSIZEREL}
         -DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
         -DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-        -DCMAKE_C_FLAGS:STRING=${EXT_CMAKE_C_FLAGS} 
+        -DCMAKE_C_FLAGS:STRING=${EXT_CMAKE_C_FLAGS}
         -DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
         -DCMAKE_C_FLAGS_MINSIZEREL:STRING=${CMAKE_C_FLAGS_MINSIZEREL}
         -DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
@@ -78,16 +78,16 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
   #endif(MT_BUILD_QUIET)
 
   SET(HDF5_LIB_SUFFIX ".a")
-  
-  IF(MT_BUILD_SHARED_LIBS) 
+
+  IF(MT_BUILD_SHARED_LIBS)
     SET(ITK_SHARED_LIBRARY "ON")
-    
+
     IF(APPLE)
         SET(HDF5_LIB_SUFFIX ".dylib")
     ELSE(APPLE)
         SET(HDF5_LIB_SUFFIX ".so")
     ENDIF(APPLE)
-    
+
   ELSE(MT_BUILD_SHARED_LIBS)
       SET(HDF5_LIB_SUFFIX    ".a")
       SET(ITK_SHARED_LIBRARY "OFF")
@@ -136,13 +136,13 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
   message("HDF5_HL_CPP_LIBRARY=${HDF5_HL_CPP_LIBRARY}")
   message("HDF5_BIN_DIR=${HDF5_BIN_DIR}")
 
-  GET_PACKAGE("https://sourceforge.net/projects/itk/files/itk/4.13/InsightToolkit-4.13.0.tar.xz" "3badf70cfb0093054453f66c5974c5a4" "InsightToolkit-4.13.0.tar.xz" ITKv4_PATH ) 
-  
+  GET_PACKAGE("https://github.com/InsightSoftwareConsortium/ITK/releases/download/v4.13.1/InsightToolkit-4.13.1.tar.xz" "bc7296e7faccdcb5656a7669d4d875d2" "InsightToolkit-4.13.1.tar.xz" ITKv4_PATH )
+
 
 
   ExternalProject_Add(ITKv4
     URL "${ITKv4_PATH}"
-    URL_MD5 "3badf70cfb0093054453f66c5974c5a4"
+    URL_MD5 "bc7296e7faccdcb5656a7669d4d875d2"
     UPDATE_COMMAND ""
     SOURCE_DIR ITKv4
     BINARY_DIR ITKv4-build
@@ -195,19 +195,19 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
     INSTALL_DIR ${staging_prefix}/${install_prefix}
     STEP_TARGETS PatchInstall
   )
-  
-  ExternalProject_Add_Step(ITKv4 PatchInstall 
+
+  ExternalProject_Add_Step(ITKv4 PatchInstall
     COMMAND ${CMAKE_COMMAND} -Dstaging_prefix=${staging_prefix} -Dminc_dir=${minc_dir} -Dinstall_prefix=${install_prefix} -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake-modules/PatchITKv4.cmake
     COMMENT "Patching ITKv4 Build"
     DEPENDEES install
     )
-  
+
   # let's patch targets to remove staging directory
-  
-  
+
+
   SET(ITK_DIR ${CMAKE_CURRENT_BINARY_DIR}/ITKv4-build)
-  
-  SET(ITK_INCLUDE_DIRS 
+
+  SET(ITK_INCLUDE_DIRS
         ${CMAKE_CURRENT_BINARY_DIR}/ITKv4-build
         ${CMAKE_CURRENT_BINARY_DIR}/ITKv4/Code/Algorithms
         ${CMAKE_CURRENT_BINARY_DIR}/ITKv4/Code/BasicFilters
@@ -242,18 +242,18 @@ macro(build_itkv4 install_prefix staging_prefix minc_dir)
 
 # The ITK library directories.
   SET(ITK_LIBRARY_DIRS "${CMAKE_CURRENT_BINARY_DIR}/ITKv4-build/bin")
-  
-  SET(ITK_LIBRARIES  
-          ITKAlgorithms ITKStatistics 
-          ITKNumerics 
-          ITKFEM ITKQuadEdgeMesh 
-          ITKBasicFilters  ITKIO ITKNrrdIO 
+
+  SET(ITK_LIBRARIES
+          ITKAlgorithms ITKStatistics
+          ITKNumerics
+          ITKFEM ITKQuadEdgeMesh
+          ITKBasicFilters  ITKIO ITKNrrdIO
           ITKSpatialObject ITKMetaIO
           ITKDICOMParser ITKEXPAT
-          ITKniftiio ITKTransformIOReview  ITKCommon ITKznz 
-          itkgdcm itkpng itktiff itkzlib itkvcl 
-          itkvcl 
-          itkv3p_lsqr  itkvnl_algo itkvnl_inst itkvnl itkv3p_netlib 
+          ITKniftiio ITKTransformIOReview  ITKCommon ITKznz
+          itkgdcm itkpng itktiff itkzlib itkvcl
+          itkvcl
+          itkv3p_lsqr  itkvnl_algo itkvnl_inst itkvnl itkv3p_netlib
           itksys itkjpeg8 itkjpeg12 itkjpeg16 itkopenjpeg  hdf5_cpp hdf5
           ${CMAKE_THREAD_LIBS_INIT}
           )

cmake-modules/2058.patch

@@ -3,7 +3,7 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
   if(NOT CMAKE_Fortran_COMPILER)
     message("Fortran compiler not found! OpenBLAS will not work as expected!")
   endif(NOT CMAKE_Fortran_COMPILER)
-  
+
   if(CMAKE_EXTRA_GENERATOR)
     set(CMAKE_GEN "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}")
   else()
@@ -52,26 +52,26 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
         -DCMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO}
         -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
   )
-  
+
   if(APPLE)
     list(APPEND CMAKE_EXTERNAL_PROJECT_ARGS
       -DCMAKE_OSX_ARCHITECTURES:STRING=${CMAKE_OSX_ARCHITECTURES}
       -DCMAKE_OSX_SYSROOT:STRING=${CMAKE_OSX_SYSROOT}
       -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=${CMAKE_OSX_DEPLOYMENT_TARGET}
     )
   endif()
-  
-  
-  
+
+
+
 
-  GET_PACKAGE("https://github.com/xianyi/OpenBLAS/archive/v0.3.2.tar.gz" "686f30a234f81fd768dbad5bbd41ca4f" "openblas_v0.3.2.tar.gz" OPENBLAS_PATH ) 
-  
+  GET_PACKAGE("https://github.com/xianyi/OpenBLAS/archive/v0.3.5.tar.gz" "579bda57f68ea6e9074bf5780e8620bb" "openblas_v0.3.5.tar.gz" OPENBLAS_PATH )
+
   ExternalProject_Add(OpenBLAS
         URL "${OPENBLAS_PATH}"
-        URL_MD5 "686f30a234f81fd768dbad5bbd41ca4f"
+        URL_MD5 "579bda57f68ea6e9074bf5780e8620bb"
         SOURCE_DIR OpenBLAS
         BINARY_DIR OpenBLAS-build
-        PATCH_COMMAND patch -p1 -t -N -i ${CMAKE_SOURCE_DIR}/cmake-modules/0001-Fix-1705-where-we-incorrectly-calculate-page-locatio.patch
+        PATCH_COMMAND patch -p1 -t -N -i ${CMAKE_SOURCE_DIR}/cmake-modules/2058.patch
         LIST_SEPARATOR :::
         CMAKE_GENERATOR ${CMAKE_GEN}
         CMAKE_ARGS
@@ -89,15 +89,14 @@ macro(build_open_blas install_prefix staging_prefix build_parallel)
         ${CMAKE_EXTERNAL_PROJECT_ARGS}
         "-DCMAKE_CXX_FLAGS:STRING=-fPIC ${CMAKE_CXX_FLAGS}"
         "-DCMAKE_C_FLAGS:STRING=-fPIC ${CMAKE_C_FLAGS}"
-        -DCMAKE_INSTALL_LIBDIR:PATH=${install_prefix}/lib${LIB_SUFFIX} 
+        -DCMAKE_INSTALL_LIBDIR:PATH=${install_prefix}/lib${LIB_SUFFIX}
             INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
             INSTALL_DIR ${staging_prefix}/${install_prefix}
       )
-  
+
   SET(OpenBLAS_INCLUDE_DIRS ${staging_prefix}/${install_prefix}/include )
   SET(OpenBLAS_LIBRARIES    ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libopenblas.so  )
   SET(OpenBLAS_DIR          ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/cmake/openblas )
   SET(OpenBLAS_FOUND        ON)
 
 endmacro(build_open_blas)
-