Merge pull request #2630 from gdevenyi/nifticlib3.0

Modules/ThirdParty/NIFTI/UpdateFromUpstream.sh

@@ -8,17 +8,16 @@ readonly name="nifti"
 readonly ownership="NIFTI Upstream <[email protected]>"
 readonly subtree="Modules/ThirdParty/NIFTI/src/nifti"
 readonly repo="https://github.com/NIFTI-Imaging/nifti_clib.git"
-readonly tag="master"
+readonly tag="v3.0.1"
 readonly shortlog=false
 readonly paths="
 CMakeLists.txt
 CTestConfig.cmake
 LICENSE
-README
+README.md
 cmake
 znzlib
 niftilib
-nifti2
 "
 
 extract_source () {

Modules/ThirdParty/NIFTI/src/CMakeLists.txt

@@ -13,6 +13,7 @@ set(NIFTI_USE_PACKAGING OFF CACHE BOOL "Do not use packaging from nifti when inc
 set(NIFTI_BUILD_APPLICATIONS OFF CACHE BOOL "Do not build applications provided by NIFTI" FORCE)
 # Testing is not compatible with ITK at the moment
 set(NIFTI_BUILD_TESTING OFF) # "Do not build nifit testing applications"
+set(DOWNLOAD_TEST_DATA OFF) # Don't download testing data
 
 add_definitions(-DITKZLIB)
 set(NIFTI_INSTALL_EXPORT_NAME ${ITKNIFTI-targets}) # "Set the nifti package export target name"

Modules/ThirdParty/NIFTI/src/nifti/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.16.3 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.10.2 FATAL_ERROR)
 
 set(NIFTI_MAX_VALIDATED_CMAKE_VERSION "3.13.1")
 if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "${NIFTI_MAX_VALIDATED_CMAKE_VERSION}")
@@ -11,106 +11,150 @@ endif()
 cmake_policy(VERSION ${NIFTI_CMAKE_POLICY_VERSION})
 
 set(NIFTI_HOMEPAGE_URL "https://nifti-imaging.github.io")
+execute_process(COMMAND git "describe" "--tags"
+  OUTPUT_VARIABLE GIT_REPO_VERSION_UNCLEANED
+  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+
+#Extract the GIT_REPO_VERSION as composed of non-negative integer components,
+# i.e. <major>[.<minor>[.<patch>[.<tweak>]]]
+string(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+((beta.*)?(alpha.*)?\\.[0-9]+(\\.g[0-9a-f]+)?)?"
+ GIT_REPO_VERSION  "${GIT_REPO_VERSION_UNCLEANED}")
+
+if( NOT GIT_REPO_VERSION )
+  message(NOTE "Invalid git tag does not match required regular expression, "
+               "can not extract version information from '${GIT_REPO_VERSION_UNCLEANED}'")
+  # NOTE: cmake -DGIT_REPO_VERSION:STRING=<major>[.<minor>[.<patch>[.<tweak>]]] can be used
+  #       to set the repo string for non-git repos.
+  set(GIT_REPO_VERSION "0.0.0.0") #Manually set the version string for testing purposes
+endif()
 project(NIFTI
-        VERSION 2.1.0
+        VERSION ${GIT_REPO_VERSION}
         DESCRIPTION "Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images."
         LANGUAGES C)
 
-macro(set_if_not_defined var defaultvalue)
-# Macro allowing to set a variable to its default value if not already defined.
-# The default value is set with:
-#  (1) if set, the value environment variable <var>.
-#  (2) if set, the value of local variable variable <var>.
-#  (3) if none of the above, the value passed as a parameter.
-# Setting the optional parameter 'OBFUSCATE' will display 'OBFUSCATED' instead of the real value.
-  set(_obfuscate FALSE)
-  foreach(arg ${ARGN})
-    if(arg STREQUAL "OBFUSCATE")
-      set(_obfuscate TRUE)
-    endif()
-  endforeach()
-  if(DEFINED ENV{${var}} AND NOT DEFINED ${var})
-    set(_value "$ENV{${var}}")
-    if(_obfuscate)
-      set(_value "OBFUSCATED")
-    endif()
-    message(STATUS "Setting '${var}' variable with environment variable value '${_value}'")
-    set(${var} $ENV{${var}})
-  endif()
-  if(NOT DEFINED ${var})
-    set(_value "${defaultvalue}")
-    if(_obfuscate)
-      set(_value "OBFUSCATED")
-    endif()
-    message(STATUS "Setting '${var}' variable with default value '${_value}'")
-    set(${var} "${defaultvalue}")
-  endif()
-endmacro()
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake)
+include(nifti_macros)
+
+set_property(GLOBAL PROPERTY nifti_installed_targets)
 
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
 set(CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
+include(CMakeDependentOption)
 
+if("${CMAKE_VERSION}" VERSION_GREATER_EQUAL "3.13")
+set(CMAKE_VER_AT_LEAST_3_13 1 CACHE BOOL "Is set for cmake >=3.13")
+endif()
 
 # add option to build shared libraries. The default is OFF to maintain the
 # current build behavior
 option( BUILD_SHARED_LIBS "Toggle building shared libraries." OFF)
 
+# Include executables as part of the build
+option(NIFTI_BUILD_APPLICATIONS "Build various utility tools" ON)
+mark_as_advanced(NIFTI_BUILD_APPLICATIONS)
+
 #When including nifti as a subpackage, a prefix is often needed to avoid conflicts with sytem installed libraries.
 set_if_not_defined(NIFTI_PACKAGE_PREFIX "")
+set(PACKAGE_NAME ${NIFTI_PACKAGE_PREFIX}NIFTI)
+set_if_not_defined(NIFTI_INSTALL_EXPORT_NAME ${PACKAGE_NAME}Targets)
 
 # Set default shared library version
 # This library version will be applied to all libraries in the package
 # unless it is not explicitely for a certain lib.
-set(NIFTI_SHAREDLIB_VERSION ${NIFTI_VERSION_MAJOR}.${NIFTI_VERSION_MINOR}.${NIFTI_VERSION_PATCH} )
-string( REGEX MATCH "^[0-9]+" NIFTI_SHAREDLIB_SOVERSION ${NIFTI_SHAREDLIB_VERSION})
+set(NIFTI_SHAREDLIB_VERSION ${GIT_REPO_VERSION} )
 if(BUILD_SHARED_LIBS AND NOT NIFTI_LIBRARY_PROPERTIES)
   set(NIFTI_LIBRARY_PROPERTIES ${DEFAULT_SHARED_LIBS}
-    BUILD_SHARED_LIBS TRUE POSITION_INDEPENDENT_CODE TRUE VERSION ${NIFTI_SHAREDLIB_VERSION} SOVERSION ${NIFTI_SHAREDLIB_SOVERSION}
+    BUILD_SHARED_LIBS TRUE POSITION_INDEPENDENT_CODE TRUE
   )
 endif()
 
-set_if_not_defined(NIFTI_INSTALL_RUNTIME_DIR "${CMAKE_INSTALL_PREFIX}/bin")
-set_if_not_defined(NIFTI_INSTALL_LIBRARY_DIR "${CMAKE_INSTALL_PREFIX}/lib")
-set_if_not_defined(NIFTI_INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_PREFIX}/include/nifti")
+set_if_not_defined(NIFTI_INSTALL_RUNTIME_DIR bin)
+set_if_not_defined(NIFTI_INSTALL_LIBRARY_DIR lib)
+set_if_not_defined(NIFTI_INSTALL_ARCHIVE_DIR ${NIFTI_INSTALL_LIBRARY_DIR})
+set_if_not_defined(NIFTI_INSTALL_INCLUDE_DIR include/nifti)
+set_if_not_defined(NIFTI_INSTALL_MAN_DIR share/man/man1)
+set_if_not_defined(NIFTI_INSTALL_DOC_DIR share/doc/${PROJECT_NAME})
 set_if_not_defined(NIFTI_ZLIB_LIBRARIES "")
+set_if_not_defined(ZNZ_COMPILE_DEF "")
 if(NOT NIFTI_ZLIB_LIBRARIES) # If using a custom zlib library, skip the find package
   ###  USE AS STAND ALONE PACKAGE
   find_package(ZLIB REQUIRED)
   set(NIFTI_ZLIB_LIBRARIES ${ZLIB_LIBRARIES})
 endif()
 #message(STATUS "---------------------ZLIB -${NIFTI_ZLIB_LIBRARIES}--")
 add_definitions(-DHAVE_ZLIB)
-# Modern CMake install COMPONENTS is being considered in upstream NIFTI
-# Setting NIFTI_INSTALL_NO_DEVELOPMENT & NIFTI_INSTALL_NO_LIBRARIES to
-# FALSE to make explicit that the development and libraries
-# can not be skipped for installation.  Use the install COMPONENTS
-# features instead.
-set(NIFTI_INSTALL_NO_DEVELOPMENT FALSE)
-set(NIFTI_INSTALL_NO_LIBRARIES FALSE)
 
+set_if_not_defined(NIFTI_INSTALL_NO_DOCS TRUE)
+
+# Include test to verify linking in installed executables
+# The test should only be added when applications are built, and no prefix string is set.
+cmake_dependent_option(
+  TEST_INSTALL "Add a test to check that linking to SO libraries occurs correctly during installation." ON
+  "${NIFTI_PACKAGE_PREFIX};${NIFTI_BUILD_APPLICATIONS};${BUILD_SHARED_LIBS};${NIFTI_BUILD_TESTING}" OFF
+)
+
+# Add a default attempt at setting the run path correctly for binaries
+if(NOT CMAKE_SKIP_INSTALL_RPATH)
+  file(
+    RELATIVE_PATH
+    relDir
+    ${CMAKE_INSTALL_PREFIX}/${NIFTI_INSTALL_RUNTIME_DIR}
+    ${CMAKE_INSTALL_PREFIX}/${NIFTI_INSTALL_LIBRARY_DIR}
+  )
+  if(APPLE)
+    set_if_not_defined(CMAKE_INSTALL_RPATH  "@loader_path/${relDir}")
+  else()
+    set_if_not_defined(CMAKE_INSTALL_RPATH   "\$ORIGIN/${relDir}")
+  endif()
+endif()
+
+if(NOT NIFTI_INSTALL_NO_DOCS)
+      find_program(HELP2MAN help2man REQUIRED)
+      set(MAN_DIR ${PROJECT_BINARY_DIR}/manpages)
+      file(MAKE_DIRECTORY ${MAN_DIR})
+endif()
 #######################################################################
-enable_testing()
-include(CTest)
-#Needs an if clause and more work before testing can take place.
+
+set_if_not_defined(BUILD_TESTING ON)
 set_if_not_defined(NIFTI_BUILD_TESTING ${BUILD_TESTING})
-if (NIFTI_BUILD_TESTING AND CMAKE_VERSION GREATER_EQUAL 3.11.0) # CMAKE VERSION 3.11.0 needed for fetching data with cmake
+if (NIFTI_BUILD_TESTING )
+  include(CTest)
+  enable_testing()
+  #Needs an if clause and more work before testing can take place.
+  option(
+    DOWNLOAD_TEST_DATA
+    "Allow download of data used for some tests. Can be used in conjunction with ctest label filter '-LE NEEDS_DATA'"
+    ON
+    )
+  set_if_not_defined(NIFTI_SHELL_SCRIPT_TESTS "ON")
+  if(DOWNLOAD_TEST_DATA)
+  if ( CMAKE_VERSION VERSION_LESS 3.11.0 )
+    # CMAKE VERSION 3.11.0 needed for fetching data with cmake
+    message(FATAL_ERROR "ERROR:  The testing framework for nifti_clib requires CMake version 3.11.0 or greater")
+  endif()
 
   include(FetchContent) # fetch data a configure time to simplify tests
   # If new or changed data is needed, add that data to the https://github.com/NIFTI-Imaging/nifti-test-data repo
   # make a new release, and then update the URL and hash (shasum -a 256 <downloaded tarball>).
   FetchContent_Declare( fetch_testing_data
-          URL      https://github.com/NIFTI-Imaging/nifti-test-data/archive/v3.0.0.tar.gz
-          URL_HASH SHA256=8a22554ca196f707f7c8cdc102e1a30117cd67da41d269390952683076ffcac8
+          URL      https://github.com/NIFTI-Imaging/nifti-test-data/archive/v3.0.2.tar.gz
+          URL_HASH SHA256=5dafec078151018da7aaf3c941bd31f246f590bc34fa3fef29ce77a773db16a6
           )
   FetchContent_GetProperties(fetch_testing_data)
-  if(NOT fetch_testing_data)
+  if(NOT fetch_testing_data_POPULATED)
     set(FETCHCONTENT_QUIET OFF)
-    message(STATUS "Downloading testing data... please wait")
     FetchContent_Populate( fetch_testing_data )
-    message(STATUS "download complete.")
+  endif()
   endif()
 endif()
 
+#######################################################################
+# Find unix math libraries
+if(NOT WIN32)
+    find_library(NIFTI_SYSTEM_MATH_LIB m)
+else()
+    set(NIFTI_SYSTEM_MATH_LIB "")
+endif()
 #######################################################################
 add_subdirectory(znzlib)
 add_subdirectory(niftilib)
@@ -121,12 +165,8 @@ if(USE_NIFTICDF_CODE)
     add_subdirectory(nifticdf)
 endif()
 
-option(NIFTI_BUILD_APPLICATIONS "Build various utility tools" ON)
-mark_as_advanced(NIFTI_BUILD_APPLICATIONS)
-
 option(USE_NIFTI2_CODE "Build the nifti2 library and tools" ON)
 mark_as_advanced(USE_NIFTI2_CODE)
-include(CMakeDependentOption)
 cmake_dependent_option(USE_CIFTI_CODE "Build the cifti library and tools" OFF "USE_NIFTI2_CODE" OFF)
 mark_as_advanced(USE_CIFTI_CODE)
 
@@ -146,40 +186,81 @@ if(USE_FSL_CODE)
   add_subdirectory(fsliolib)
 endif()
 
-set_if_not_defined(NIFTI_INSTALL_EXPORT_NAME "NIFTITargets")
-if(NIFTI_INSTALL_EXPORT_NAME EQUAL "NIFTITargets")
+# Allow an uninstall (with some risk of messiness)
+
+if(NOT TARGET uninstall)
+  configure_file(
+    "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
+    "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake" IMMEDIATE @ONLY
+  )
+
+  add_custom_target(
+    uninstall COMMAND ${CMAKE_COMMAND} -P
+                      ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake
+  )
+endif()
+
+# Report installed targets
+get_property(nifti_installed_targets GLOBAL PROPERTY nifti_installed_targets)
+message("nifti_installed_targets: ${nifti_installed_targets}")
+
+if(CMAKE_VER_AT_LEAST_3_13)
+  # Target installation for CMake versions >=3.13
+  foreach(targ ${nifti_installed_targets})
+    install_nifti_target(${targ})
+  endforeach()
+endif()
+
+if(NOT NIFTI_INSTALL_NO_DOCS)
+  install(
+      DIRECTORY ${MAN_DIR}/
+      DESTINATION ${NIFTI_INSTALL_MAN_DIR}
+      FILES_MATCHING REGEX ".*.1.gz"
+      PERMISSIONS OWNER_READ WORLD_READ
+      )
+  install(
+    FILES ${PROJECT_SOURCE_DIR}/README.md
+    DESTINATION ${NIFTI_INSTALL_DOC_DIR}
+    )
+  install(
+    DIRECTORY ${PROJECT_SOURCE_DIR}/real_easy/
+    DESTINATION ${NIFTI_INSTALL_DOC_DIR}/examples
+    )
+endif()
+
+if(NIFTI_INSTALL_EXPORT_NAME STREQUAL "NIFTITargets")
   #######################################################################
   # CMake itself and can use some CMake facilities for creating the package files.
   # This allows for find_package(NIFTI 2.1.0 NO_MODULE) to work for pulling in
   # NIFTI libraries into an external project
   include(CMakePackageConfigHelpers)
+  set(CONFIG_SETUP_DIR ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME})
+  set(ConfigPackageLocation share/cmake/${PACKAGE_NAME})
 
   write_basic_package_version_file(
-        "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTIConfigVersion.cmake"
-        VERSION ${NIFTI_VERSION}
+        ${CONFIG_SETUP_DIR}/${PACKAGE_NAME}ConfigVersion.cmake
+        VERSION ${GIT_REPO_VERSION}
         COMPATIBILITY AnyNewerVersion
   )
 
-  export(EXPORT NIFTITargets
-        FILE "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTITargets.cmake"
-        NAMESPACE ${NIFTI_PACKAGE_PREFIX}NIFTI::
-        )
   configure_file(cmake/NIFTIConfig.cmake
-        "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTIConfig.cmake"
+        ${CONFIG_SETUP_DIR}/${PACKAGE_NAME}Config.cmake
         COPYONLY
         )
 
-  set(ConfigPackageLocation lib/cmake/NIFTI)
-  install(EXPORT NIFTITargets
-        FILE          NIFTITargets.cmake
-        NAMESPACE     ${NIFTI_PACKAGE_PREFIX}NIFTI::
+
+  install(EXPORT ${NIFTI_INSTALL_EXPORT_NAME}
+        FILE NIFTITargets.cmake
+        NAMESPACE     ${PACKAGE_NAME}::
         DESTINATION   ${ConfigPackageLocation}
+        COMPONENT     Development
         )
+
   install(FILES
-           cmake/NIFTIConfig.cmake
-           "${CMAKE_CURRENT_BINARY_DIR}/NIFTI/NIFTIConfigVersion.cmake"
-        DESTINATION   ${ConfigPackageLocation}
+           ${CONFIG_SETUP_DIR}/${PACKAGE_NAME}Config.cmake
+           ${CONFIG_SETUP_DIR}/${PACKAGE_NAME}ConfigVersion.cmake
         COMPONENT     Development
+        DESTINATION   ${ConfigPackageLocation}
   )
 endif()
 

Modules/ThirdParty/NIFTI/src/nifti/CTestConfig.cmake

@@ -9,7 +9,7 @@
 set(CTEST_PROJECT_NAME "NIFTI")
 set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
 
-set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_METHOD "https")
 set(CTEST_DROP_SITE "my.cdash.org")
 set(CTEST_DROP_LOCATION "/submit.php?project=nifti_clib")
 set(CTEST_DROP_SITE_CDASH TRUE)