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thewtex wants to merge 2 commits into from
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Libminc bump #756

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94758ec
MINC 2018-11-13 (bcbccf97)
vfonov Nov 13, 2018
9a97f5b
Merge branch 'upstream-minc' into libminc-bump
thewtex Apr 24, 2019
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91 changes: 48 additions & 43 deletions Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,13 +1,11 @@
# CMakeFiles.txt for the libminc library
#
# Andrew Janke - a.janke@gmail.com
# Vladimir S. FONOV - vladimir.fonov@gmail.com

PROJECT(LIBMINC)

SET(LIBMINC_PACKAGE_VERSION_MAJOR 2)
SET(LIBMINC_PACKAGE_VERSION_MINOR 4)
SET(LIBMINC_PACKAGE_VERSION_PATCH 03)
SET(LIBMINC_PACKAGE_VERSION_PATCH 04)

SET(LIBMINC_SOVERSION "5.2.0")

Expand Down Expand Up @@ -378,17 +376,36 @@ IF(LIBMINC_NIFTI_SUPPORT)
SET(NIFTI_LIBRARIES
${NIFTI_LIBRARY} ${ZNZ_LIBRARY}
)
get_filename_component(NIFTI_LIBRARY_NAME "${NIFTI_LIBRARY}" NAME)
get_filename_component(ZNZ_LIBRARY_NAME "${ZNZ_LIBRARY}" NAME)
ELSE(LIBMINC_NIFTI_SUPPORT)
SET(NIFTI_LIBRARIES )
SET(NIFTI_LIBRARY )
SET(ZNZ_LIBRARY )
SET(NIFTI_LIBRARY_NAME )
SET(ZNZ_LIBRARY_NAME )
ENDIF(LIBMINC_NIFTI_SUPPORT)

IF(NOT HDF5_LIBRARY AND HDF5_LIBRARIES)
SET(HDF5_LIBRARY ${HDF5_LIBRARIES})
ENDIF()

get_filename_component(HDF5_LIBRARY_NAME "${HDF5_LIBRARY}" NAME)
get_filename_component(ZLIB_LIBRARY_NAME "${ZLIB_LIBRARY}" NAME)

SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARY} ${HDF5_LIBRARIES} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY})
SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARIES} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY})
SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARY} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY})
SET(LIBMINC_LIBRARIES_CONFIG ${LIBMINC_LIBRARY} ${HDF5_LIBRARY_NAME} ${NIFTI_LIBRARY_NAME} ${ZNZ_LIBRARY_NAME} ${ZLIB_LIBRARY_NAME})
#message("LIBMINC_LIBRARIES_CONFIG=${LIBMINC_LIBRARIES_CONFIG}")

SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY})
SET(LIBMINC_STATIC_LIBRARIES_CONFIG ${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY_NAME} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY_NAME})

IF(UNIX)
SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARIES} m dl ${RT_LIBRARY})
SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_STATIC_LIBRARIES} m dl ${RT_LIBRARY})

SET(LIBMINC_LIBRARIES_CONFIG ${LIBMINC_LIBRARIES_CONFIG} m dl ${RT_LIBRARY_NAME})
SET(LIBMINC_STATIC_LIBRARIES_CONFIG ${LIBMINC_STATIC_LIBRARIES_CONFIG} m dl ${RT_LIBRARY_NAME})
ENDIF(UNIX)

SET(minc_LIB_SRCS ${minc2_LIB_SRCS} ${minc_common_SRCS})
Expand All @@ -411,11 +428,14 @@ IF(NIFTI_FOUND AND NOT LIBMINC_USE_SYSTEM_NIFTI)
ENDIF()


TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} ${HDF5_LIBRARIES} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY} ${RT_LIBRARY}) #
TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY} ${RT_LIBRARY}) #

IF(LIBMINC_MINC1_SUPPORT)
INCLUDE_DIRECTORIES(${NETCDF_INCLUDE_DIR})
TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} ${NETCDF_LIBRARY})
get_filename_component(NETCDF_LIBRARY_NAME "${NETCDF_LIBRARY}" NAME)
ELSE(LIBMINC_MINC1_SUPPORT)
SET(NETCDF_LIBRARY_NAME )
ENDIF(LIBMINC_MINC1_SUPPORT)

IF(NOT LIBMINC_USE_SYSTEM_NIFTI AND NOT LIBMINC_EXTERNALLY_CONFIGURED)
Expand All @@ -425,7 +445,7 @@ ENDIF(NOT LIBMINC_USE_SYSTEM_NIFTI AND NOT LIBMINC_EXTERNALLY_CONFIGURED)
#EXPORT(TARGETS ${LIBMINC_LIBRARY} FILE "${LIBMINC_EXPORTED_TARGETS}.cmake")

IF(UNIX)
TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} m dl )
TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} m dl )

#ITK: Skip static library build
IF(0)
Expand All @@ -447,6 +467,9 @@ SET_TARGET_PROPERTIES(${LIBMINC_LIBRARY}
IF(LIBMINC_MINC1_SUPPORT)
SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARIES} ${NETCDF_LIBRARY} )
SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_STATIC_LIBRARIES} ${NETCDF_LIBRARY} )

SET(LIBMINC_LIBRARIES_CONFIG ${LIBMINC_LIBRARIES_CONFIG} ${NETCDF_LIBRARY_NAME} )
SET(LIBMINC_STATIC_LIBRARIES_CONFIG ${LIBMINC_STATIC_LIBRARIES_CONFIG} ${NETCDF_LIBRARY_NAME} )
ENDIF(LIBMINC_MINC1_SUPPORT)

IF( LIBMINC_INSTALL_LIB_DIR )
Expand All @@ -470,7 +493,23 @@ IF(LIBMINC_MINC1_SUPPORT)
ADD_SUBDIRECTORY( ezminc )
ENDIF(LIBMINC_MINC1_SUPPORT)

# config for the build directory
SET(EZMINC_LIBRARIES minc_io ${LIBMINC_LIBRARIES})
SET(EZMINC_LIBRARIES_CONFIG minc_io ${LIBMINC_LIBRARIES_CONFIG})

# config for install dir
SET(LIBMINC_USE_FILE_CONFIG "\${LIBMINC_INSTALL_PREFIX}/lib/UseLIBMINC.cmake" )
SET(LIBMINC_INCLUDE_DIRS_CONFIG "\${LIBMINC_INSTALL_PREFIX}/include" )
SET(LIBMINC_LIBRARY_DIRS_CONFIG "\${LIBMINC_INSTALL_PREFIX}/lib" )
SET(LIBMINC_STATIC_LIBRARIES_CONFIG "" )
SET(VOLUME_IO_LIBRARY_STATIC "")

configure_file(LIBMINCConfig.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINCConfig.cmake @ONLY )

configure_file(UseLIBMINC.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake @ONLY)

# configure for build dir
SET(LIBMINC_USE_FILE_CONFIG ${CMAKE_CURRENT_BINARY_DIR}/UseLIBMINC.cmake)

SET(LIBMINC_INCLUDE_DIRS_CONFIG
Expand All @@ -479,7 +518,6 @@ SET(LIBMINC_INCLUDE_DIRS_CONFIG
${CMAKE_CURRENT_SOURCE_DIR}/libsrc2
${CMAKE_CURRENT_SOURCE_DIR}/volume_io/Include
)

IF(LIBMINC_MINC1_SUPPORT)
SET(LIBMINC_INCLUDE_DIRS_CONFIG
${LIBMINC_INCLUDE_DIRS_CONFIG}
Expand All @@ -488,10 +526,10 @@ IF(LIBMINC_MINC1_SUPPORT)
)
ENDIF(LIBMINC_MINC1_SUPPORT)

SET(EZMINC_LIBRARIES minc_io ${LIBMINC_LIBRARIES})
SET(LIBMINC_LIBRARY_DIRS_CONFIG ${CMAKE_CURRENT_BINARY_DIR})
SET(LIBMINC_LIBRARIES_CONFIG ${LIBMINC_LIBRARIES})
SET(LIBMINC_STATIC_LIBRARIES_CONFIG ${LIBMINC_STATIC_LIBRARIES})
SET(EZMINC_LIBRARIES_CONFIG ${EZMINC_LIBRARIES})

IF(LIBMINC_MINC1_SUPPORT)
SET(LIBMINC_LIBRARY_DIRS_CONFIG ${LIBMINC_LIBRARY_DIRS_CONFIG} ${CMAKE_CURRENT_BINARY_DIR}/ezminc)
Expand All @@ -503,48 +541,15 @@ configure_file(LIBMINCConfig.cmake.in
configure_file(UseLIBMINC.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/UseLIBMINC.cmake @ONLY)

# config for install dir
SET(LIBMINC_USE_FILE_CONFIG "${CMAKE_INSTALL_PREFIX}/${LIBMINC_INSTALL_LIB_DIR}/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake")
SET(LIBMINC_INCLUDE_DIRS_CONFIG ${CMAKE_INSTALL_PREFIX}/${LIBMINC_INSTALL_INCLUDE_DIR} )
SET(LIBMINC_LIBRARY_DIRS_CONFIG ${CMAKE_INSTALL_PREFIX}/${LIBMINC_INSTALL_LIB_DIR})
SET(LIBMINC_STATIC_LIBRARIES_CONFIG "")
SET(VOLUME_IO_LIBRARY_STATIC "")

#fix for superbuild install
IF(SUPERBUILD_STAGING_PREFIX)
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" LIBMINC_INCLUDE_DIRS_CONFIG "${LIBMINC_INCLUDE_DIRS_CONFIG}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" LIBMINC_LIBRARY_DIRS_CONFIG "${LIBMINC_LIBRARY_DIRS_CONFIG}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" LIBMINC_LIBRARIES_CONFIG "${LIBMINC_LIBRARIES_CONFIG}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" EZMINC_LIBRARIES "${EZMINC_LIBRARIES}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NETCDF_INCLUDE_DIR "${NETCDF_INCLUDE_DIR}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_INCLUDE_DIR "${HDF5_INCLUDE_DIR}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_INCLUDE_DIRS "${HDF5_INCLUDE_DIRS}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NIFTI_INCLUDE_DIR "${NIFTI_INCLUDE_DIR}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NETCDF_LIBRARY "${NETCDF_LIBRARY}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_LIBRARY "${HDF5_LIBRARY}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_LIBRARIES "${HDF5_LIBRARIES}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NIFTI_LIBRARY "${NIFTI_LIBRARY}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" ZNZ_LIBRARY "${ZNZ_LIBRARY}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" ZLIB_LIBRARY "${ZLIB_LIBRARY}")
STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" ZLIB_LIBRARIES "${ZLIB_LIBRARIES}")
ENDIF(SUPERBUILD_STAGING_PREFIX)

configure_file(LIBMINCConfig.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINCConfig.cmake @ONLY )

configure_file(UseLIBMINC.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake @ONLY)

IF(LIBMINC_INSTALL_LIB_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT)

INSTALL(
FILES
${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake
${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINCConfig.cmake
DESTINATION
${LIBMINC_INSTALL_LIB_DIR}
COMPONENT Development)

ENDIF(LIBMINC_INSTALL_LIB_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT)

# testing
Expand Down
33 changes: 17 additions & 16 deletions Modules/ThirdParty/MINC/src/libminc/LIBMINCConfig.cmake.in
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Original file line number Diff line number Diff line change
@@ -1,34 +1,35 @@
# LIBMINC CMake configuration file


get_filename_component(LIBMINC_INSTALL_PREFIX "${CMAKE_CURRENT_LIST_DIR}/../" ABSOLUTE)
get_filename_component(LIBMINC_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH )
get_filename_component(LIBMINC_INSTALL_PREFIX "${LIBMINC_CMAKE_DIR}" PATH)

set(HAVE_MINC2 1)
set(HAVE_EZMINC @LIBMINC_MINC1_SUPPORT@)
set(HAVE_MINC1 @LIBMINC_MINC1_SUPPORT@)

set(LIBMINC_NIFTI_SUPPORT @LIBMINC_NIFTI_SUPPORT@)

set(NETCDF_INCLUDE_DIR "@NETCDF_INCLUDE_DIR@")
set(HDF5_INCLUDE_DIR "@HDF5_INCLUDE_DIR@")
set(NIFTI_INCLUDE_DIR "@NIFTI_INCLUDE_DIR@")
#set(NETCDF_INCLUDE_DIR "@NETCDF_INCLUDE_DIR@")
#set(HDF5_INCLUDE_DIR "@HDF5_INCLUDE_DIR@")
#set(NIFTI_INCLUDE_DIR "@NIFTI_INCLUDE_DIR@")

set(NETCDF_LIBRARY "@NETCDF_LIBRARY@")
set(HDF5_LIBRARY "@HDF5_LIBRARY@")
set(ZLIB_LIBRARY "@ZLIB_LIBRARY@")
set(ZLIB_LIBRARIES "@ZLIB_LIBRARY@")
set(NIFTI_LIBRARIES "@NIFTI_LIBRARIES@")
#set(NETCDF_LIBRARY "@NETCDF_LIBRARY@")
#set(HDF5_LIBRARY "@HDF5_LIBRARY@")
#set(ZLIB_LIBRARY "@ZLIB_LIBRARY@")
#set(ZLIB_LIBRARIES "@ZLIB_LIBRARY@")
#set(NIFTI_LIBRARIES "@NIFTI_LIBRARIES@")

set(LIBMINC_INCLUDE_DIRS "@LIBMINC_INCLUDE_DIRS_CONFIG@")
set(LIBMINC_LIBRARY_DIRS "@LIBMINC_LIBRARY_DIRS_CONFIG@")
set(LIBMINC_USE_FILE "@LIBMINC_USE_FILE_CONFIG@")
set(LIBMINC_LIBRARIES "@LIBMINC_LIBRARIES_CONFIG@")
set(LIBMINC_INCLUDE_DIRS "@LIBMINC_INCLUDE_DIRS_CONFIG@") # ${LIBMINC_INSTALL_PREFIX}/include
set(LIBMINC_LIBRARY_DIRS "@LIBMINC_LIBRARY_DIRS_CONFIG@") # ${LIBMINC_INSTALL_PREFIX}/lib
set(LIBMINC_USE_FILE "@LIBMINC_USE_FILE_CONFIG@") # ${LIBMINC_INSTALL_PREFIX}/lib/UseLIBMINC.cmake

set(EZMINC_LIBRARIES "@EZMINC_LIBRARIES@")
set(VOLUME_IO_LIBRARIES "@VOLUME_IO_LIBRARY@")
set(LIBMINC_LIBRARIES "@LIBMINC_LIBRARIES_CONFIG@")
set(VOLUME_IO_LIBRARIES "@LIBMINC_LIBRARIES_CONFIG@")
set(EZMINC_LIBRARIES "@EZMINC_LIBRARIES_CONFIG@")

set(LIBMINC_STATIC_LIBRARIES "@LIBMINC_STATIC_LIBRARIES_CONFIG@")
set(VOLUME_IO_STATIC_LIBRARIES "@VOLUME_IO_LIBRARY_STATIC@")
set(VOLUME_IO_STATIC_LIBRARIES "@LIBMINC_STATIC_LIBRARIES_CONFIG@")

set( LIBMINC_FOUND 1 )

Expand Down
3 changes: 3 additions & 0 deletions Modules/ThirdParty/MINC/src/libminc/libsrc/hdf_convenience.c
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,9 @@
/* Make 1.8.x compatible files if building with 1.10.x */
#if (H5_VERS_MAJOR==1)&&(H5_VERS_MINOR<10)
#define H5F_LIBVER_V18 H5F_LIBVER_LATEST
#elif (H5_VERS_MAJOR==1)&&(H5_VERS_MINOR==10)&&(H5_VERS_RELEASE<2)
#error The selected version of HDF5 library does not support setting backwards compatibility at run-time.\
Please use a different version of HDF5
#endif

/************************************************************************
Expand Down
3 changes: 3 additions & 0 deletions Modules/ThirdParty/MINC/src/libminc/libsrc2/volume.c
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,9 @@
/* Build with 1.8.x support if using 1.10.x */
#if (H5_VERS_MAJOR==1)&&(H5_VERS_MINOR<10)
#define H5F_LIBVER_V18 H5F_LIBVER_LATEST
#elif (H5_VERS_MAJOR==1)&&(H5_VERS_MINOR==10)&&(H5_VERS_RELEASE<2)
#error The selected version of HDF5 library does not support setting backwards compatibility at run-time.\
Please use a different version of HDF5
#endif

/*Used to optimize chunking size for faster MINC1 API access*/
Expand Down