nifti update

.pre-commit-config.yaml

@@ -98,8 +98,10 @@ repos:
       entry: 'Utilities/Hooks/kw-commit-msg'
       language: system
       stages: [commit-msg]
+      exclude: "\\/ThirdParty\\/"
     - id: kw-pre-commit
       name: 'kw-pre-commit'
       entry: 'Utilities/Hooks/kw-pre-commit'
       language: system
       stages: [pre-commit]
+      exclude: "\\/ThirdParty\\/"

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

@@ -54,6 +54,28 @@ endif()
 # current build behavior
 option( BUILD_SHARED_LIBS "Toggle building shared libraries." OFF)
 
+# Add options to mimic FSL features,  Can manually specify -DFSLSTYLE:BOOL=ON for parity support with makefile
+if(NOT FSLSTYLE)
+  # If FSL_STYLE is not defined, then
+  option( FSLSTYLE_NAME_CONFLICTS "FSL behavior for name conflicts (generate error if both img.nii and img.nii.gz exists)" OFF)
+  option( FSLSTYLE_PIGZ_SUPPORT   "PIGZ: Use PIGZ parallel compression if environment includes AFNI_COMPRESSOR=PIGZ" OFF)
+  option( FSLSTYLE_REJECT_COMPLEX "REJECT_COMPLEX: Generate error if file is complex datatype." OFF)
+else()
+  set(FSLSTYLE_NAME_CONFLICTS ON CACHE BOOL "FSL behavior for name conflicts (ambiguous files img.nii and img.nii.gz is an error)" FORCE)
+  set(FSLSTYLE_PIGZ_SUPPORT   ON CACHE BOOL "PIGZ support" FORCE)
+  set(FSLSTYLE_REJECT_COMPLEX ON CACHE BOOL "Reject complex images." FORCE)
+endif()
+
+if(FSLSTYLE_NAME_CONFLICTS)
+  ADD_DEFINITIONS(-DFSLSTYLE)
+endif()
+if(FSLSTYLE_PIGZ_SUPPORT)
+  ADD_DEFINITIONS(-DPIGZ)
+endif()
+if(FSLSTYLE_REJECT_COMPLEX)
+  ADD_DEFINITIONS(-DREJECT_COMPLEX)
+endif()
+
 # Include executables as part of the build
 option(NIFTI_BUILD_APPLICATIONS "Build various utility tools" ON)
 mark_as_advanced(NIFTI_BUILD_APPLICATIONS)
@@ -79,6 +101,7 @@ 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_INSTALL_MODULE_DIR share/cmake/${PACKAGE_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
@@ -141,9 +164,11 @@ if (NIFTI_BUILD_TESTING )
   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>).
+  cmake_policy(SET CMP0169 OLD)
   FetchContent_Declare( fetch_testing_data
           URL      https://github.com/NIFTI-Imaging/nifti-test-data/archive/v3.0.2.tar.gz
           URL_HASH SHA256=5dafec078151018da7aaf3c941bd31f246f590bc34fa3fef29ce77a773db16a6
+          DOWNLOAD_EXTRACT_TIMESTAMP TRUE
           )
   FetchContent_GetProperties(fetch_testing_data)
   if(NOT fetch_testing_data_POPULATED)
@@ -243,7 +268,7 @@ if(NIFTI_INSTALL_EXPORT_NAME STREQUAL "NIFTITargets")
   # NIFTI libraries into an external project
   include(CMakePackageConfigHelpers)
   set(CONFIG_SETUP_DIR ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME})
-  set(ConfigPackageLocation share/cmake/${PACKAGE_NAME})
+  set(ConfigPackageLocation ${NIFTI_INSTALL_MODULE_DIR})
 
   write_basic_package_version_file(
         ${CONFIG_SETUP_DIR}/${PACKAGE_NAME}ConfigVersion.cmake

Modules/ThirdParty/NIFTI/src/nifti/README.md

@@ -19,7 +19,7 @@ and, to contribute changes and enhancements to niftilib. Please contact us if
 you would like to contribute additional functionality to the i/o library.
 
 The main webpage for this project is [hosted on github](https://nifti-imaging.github.io/).
-This web site provde historical information.  Additional information from the [NIFTI DFWG](http://nifti.nimh.nih.gov)
+This web site provides historical information.  Additional information from the [NIFTI DFWG](http://nifti.nimh.nih.gov)
 
 The testing dashboard for monitoring the health of the libraries is at
 [my.cdash.org](https://my.cdash.org/index.php?project=nifti_clib).

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

@@ -113,7 +113,7 @@ function(install_nifti_target target_name)
   elseif(CMAKE_VER_AT_LEAST_3_13 AND NOT IS_PROJECT_DIR)
     # CMake >=3.13 has support for referencing targets in parent scopes of the
     # one in which the target is defined. This enables a central management of
-    # the installation process, along with installating an target export set.
+    # the installation process, along with installing an target export set.
     # No installation occurs from the directory in which the target is defined
     return()
   endif()
@@ -133,6 +133,9 @@ function(install_nifti_target target_name)
           PUBLIC_HEADER
             DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR}
             COMPONENT Development
+          PRIVATE_HEADER
+            DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR}
+            COMPONENT Development
           INCLUDES
             DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR}
           )

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

@@ -17,6 +17,8 @@ if(BUILD_SHARED_LIBS)
         VERSION ${NIFTI_VERSION}
         SOVERSION ${NIFTI_MAJOR_VERSION}
         )
+    target_compile_definitions(${NIFTI_NIFTILIB_NAME} PRIVATE NIFTIIO_BUILD_SHARED)
+    target_compile_definitions(${NIFTI_NIFTILIB_NAME} INTERFACE NIFTIIO_USE_SHARED)
 endif()
 install_nifti_target(${NIFTI_NIFTILIB_NAME})