ENH: Various changes after merging new HDF5

- Fixed various merge conflicts
- Had to add/remove a few files.
- Improved comments that specify ITK-specific changes

Modules/ThirdParty/HDF5/src/itkhdf5/CMakeInstallation.cmake

@@ -23,7 +23,9 @@ if (WIN32)
   find_program (WIX_EXECUTABLE candle  PATHS "${CPACK_WIX_ROOT}/bin")
 endif ()
 
+# ITK --start
 if(0) # Skip for ITK internal build
+# ITK --stop
 
 #-----------------------------------------------------------------------------
 # Add Target(s) to CMake Install for import into other projects
@@ -114,7 +116,9 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
       COMPONENT configinstall
   )
 endif ()
+# ITK --start
 endif() # Skip for ITK internal build
+# ITK --stop
 
 #-----------------------------------------------------------------------------
 # Configure the libhdf5.settings file for the lib info

Modules/ThirdParty/HDF5/src/itkhdf5/CMakeLists.txt

@@ -502,12 +502,10 @@ option (BUILD_STATIC_LIBS "Build Static Libraries" ON)
 set (H5_ENABLE_STATIC_LIB NO)
 option (BUILD_SHARED_LIBS "Build Shared Libraries" ON)
 set (H5_ENABLE_SHARED_LIB NO)
-
 # ITK --start
 option (ONLY_SHARED_LIBS "Only Build Shared Libraries" ${BUILD_SHARED_LIBS})
-#option (ONLY_SHARED_LIBS "Only Build Shared Libraries" OFF)
-mark_as_advanced (ONLY_SHARED_LIBS)
 # ITK --stop
+mark_as_advanced (ONLY_SHARED_LIBS)
 
 if (BUILD_STATIC_LIBS)
   set (H5_ENABLE_STATIC_LIB YES)
@@ -1186,4 +1184,3 @@ option (HDF5_USE_PREGEN "Use pre-generated Files" OFF)
 option (HDF5_BATCH_H5DETECT "Use a batch command for running h5detect" OFF)
 
 include (CMakeInstallation.cmake)
-

Modules/ThirdParty/HDF5/src/itkhdf5/CMakePlugins.cmake

@@ -0,0 +1,56 @@
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+
+include (ExternalProject)
+#option (HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)" "NO")
+set (HDF5_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)")
+set_property (CACHE HDF5_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ)
+if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+  option (PLUGIN_USE_EXTERNAL "Use External Library Building for filter PLUGIN" 1)
+  if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT")
+    set (PLUGIN_URL ${PLUGIN_GIT_URL} CACHE STRING "Path to PLUGIN git repository")
+    set (PLUGIN_BRANCH ${PLUGIN_GIT_BRANCH})
+  elseif (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+    if (NOT TGZPATH)
+      set (TGZPATH ${HDF5_SOURCE_DIR})
+    endif ()
+    set (PLUGIN_URL ${TGZPATH}/${PLUGIN_TGZ_NAME})
+    if (NOT EXISTS "${PLUGIN_URL}")
+      set (HDF5_ENABLE_PLUGIN_SUPPORT OFF CACHE BOOL "" FORCE)
+      message (STATUS "Filter PLUGIN file ${PLUGIN_URL} not found")
+    endif ()
+  else ()
+    set (PLUGIN_USE_EXTERNAL 0)
+  endif ()
+endif ()
+
+#-----------------------------------------------------------------------------
+# Option for PLUGIN support
+#-----------------------------------------------------------------------------
+option (HDF5_ENABLE_PLUGIN_SUPPORT "Enable PLUGIN Filters" OFF)
+if (HDF5_ENABLE_PLUGIN_SUPPORT)
+  if (NOT PLUGIN_USE_EXTERNAL)
+    find_package (PLUGIN NAMES ${PLUGIN_PACKAGE_NAME}${HDF_PACKAGE_EXT})
+    if (NOT PLUGIN_FOUND)
+      find_package (PLUGIN) # Legacy find
+    endif ()
+  endif ()
+  if (NOT PLUGIN_FOUND)
+    if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+      EXTERNAL_PLUGIN_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT})
+      message (STATUS "Filter PLUGIN is built")
+    else ()
+      message (FATAL_ERROR " PLUGIN is Required for PLUGIN support in HDF5")
+    endif ()
+  endif ()
+  message (STATUS "Filter PLUGIN is ON")
+endif ()

Modules/ThirdParty/HDF5/src/itkhdf5/CTestConfig.cmake

@@ -43,12 +43,16 @@ set (UPDATE_TYPE git)
 set (VALGRIND_COMMAND "/usr/bin/valgrind")
 set (VALGRIND_COMMAND_OPTIONS "-v --tool=memcheck --leak-check=full --track-fds=yes --num-callers=50 --show-reachable=yes --track-origins=yes --malloc-fill=0xff --free-fill=0xfe")
 
+# ITK --start
 if(FALSE) # ITK commented out
+# ITK --stop
 set (CTEST_TEST_TIMEOUT 1200 CACHE STRING
     "Maximum time allowed before CTest will kill the test.")
 set (DART_TESTING_TIMEOUT 1200 CACHE STRING
     "Maximum time allowed before CTest will kill the test." FORCE)
 
 set (CTEST_SUBMIT_RETRY_DELAY 20 CACHE STRING
     "How long to wait between timed-out CTest submissions.")
+# ITK --start
 endif() # ITK commented out
+# ITK --stop

Modules/ThirdParty/HDF5/src/itkhdf5/c++/CMakeLists.txt

@@ -13,6 +13,9 @@ endif ()
 #-----------------------------------------------------------------------------
 # Build the CPP unit tests
 #-----------------------------------------------------------------------------
-#ITK REMOVED if (BUILD_TESTING)
-#ITK REMOVED  add_subdirectory (test)
-#ITK REMOVEDendif ()
+# ITK --start
+# ITK removed
+#if (BUILD_TESTING)
+#  add_subdirectory (test)
+#endif ()
+# ITK --stop