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| author | Allen Byrne <50328838+byrnHDF@users.noreply.github.com> | 2023-12-14 18:50:30 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-12-14 18:50:30 (GMT) |
| commit | 6f2d22d86e6a265535efe22a8bb3872b3b32a52b (patch) | |
| tree | f79e0d9778b13466282c159dfec67d31faba5b8d | |
| parent | 184445f4a45c602887ca0624c5295a7b6fea2d21 (diff) | |
| download | hdf5-6f2d22d86e6a265535efe22a8bb3872b3b32a52b.zip hdf5-6f2d22d86e6a265535efe22a8bb3872b3b32a52b.tar.gz hdf5-6f2d22d86e6a265535efe22a8bb3872b3b32a52b.tar.bz2 | |
Add variable option syncing for examples (#3885)
163 files changed, 509 insertions, 16406 deletions
diff --git a/.github/workflows/nvhpc-cmake.yml b/.github/workflows/nvhpc-cmake.yml index b81446c..c6b338d 100644 --- a/.github/workflows/nvhpc-cmake.yml +++ b/.github/workflows/nvhpc-cmake.yml @@ -72,5 +72,5 @@ jobs: - name: CMake Run Tests shell: bash run: | - ctest . --parallel 2 -C ${{ inputs.build_mode }} -V + ctest . --parallel 2 -C ${{ inputs.build_mode }} -V -E "ph5_f90_hyperslab_by_chunk|ph5_f90_hyperslab_by_pattern" working-directory: ${{ runner.workspace }}/build diff --git a/CMakeLists.txt b/CMakeLists.txt index 1397c6b..e73b7f9 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -220,7 +220,7 @@ set (HDF5_CPP_TST_DIR ${HDF5_SOURCE_DIR}/c++/test) set (HDF5_HL_SRC_DIR ${HDF5_SOURCE_DIR}/hl) set (HDF5_HL_CPP_SRC_DIR ${HDF5_SOURCE_DIR}/hl/c++) set (HDF5_HL_TOOLS_DIR ${HDF5_SOURCE_DIR}/hl/tools) -set (HDF5_TOOLS_DIR ${HDF5_SOURCE_DIR}/tools) +set (HDF5_TOOLS_ROOT_DIR ${HDF5_SOURCE_DIR}/tools) set (HDF5_TOOLS_SRC_DIR ${HDF5_SOURCE_DIR}/tools/src) set (HDF5_TOOLS_TST_DIR ${HDF5_SOURCE_DIR}/tools/test) set (HDF5_PERFORM_SRC_DIR ${HDF5_SOURCE_DIR}/tools/src/perform) @@ -1039,18 +1039,6 @@ if (HDF5_PACKAGE_EXTLIBS AND NOT HDF5_NO_PACKAGES) endif () #----------------------------------------------------------------------------- -# Option to build examples -#----------------------------------------------------------------------------- -if (EXISTS "${HDF5_SOURCE_DIR}/HDF5Examples" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/HDF5Examples") - option (HDF5_BUILD_EXAMPLES "Build HDF5 Library Examples" ON) - if (HDF5_BUILD_EXAMPLES) - include (${HDF_RESOURCES_DIR}/HDF5ExampleCache.cmake) - set (HDF5_VERSION ${HDF5_PACKAGE_VERSION}) - add_subdirectory (HDF5Examples) - endif () -endif () - -#----------------------------------------------------------------------------- # Option to build High Level API's #----------------------------------------------------------------------------- if (EXISTS "${HDF5_SOURCE_DIR}/hl" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/hl") @@ -1161,6 +1149,18 @@ if (EXISTS "${HDF5_SOURCE_DIR}/java" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/java") endif () #----------------------------------------------------------------------------- +# Option to build examples +#----------------------------------------------------------------------------- +if (EXISTS "${HDF5_SOURCE_DIR}/HDF5Examples" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/HDF5Examples") + option (HDF5_BUILD_EXAMPLES "Build HDF5 Library Examples" ON) + if (HDF5_BUILD_EXAMPLES) + include (${HDF_RESOURCES_DIR}/HDF5ExampleCache.cmake) + set (HDF5_VERSION ${HDF5_PACKAGE_VERSION}) + add_subdirectory (HDF5Examples) + endif () +endif () + +#----------------------------------------------------------------------------- # Generate the H5pubconf.h file containing user settings needed by compilation #----------------------------------------------------------------------------- configure_file (${HDF_RESOURCES_DIR}/H5pubconf.h.in ${HDF5_SRC_BINARY_DIR}/H5pubconf.h @ONLY) diff --git a/HDF5Examples/C/H5D/CMakeLists.txt b/HDF5Examples/C/H5D/CMakeLists.txt index 5df56c1..68cbd23 100644 --- a/HDF5Examples/C/H5D/CMakeLists.txt +++ b/HDF5Examples/C/H5D/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_C_H5D) +project (HDF5Examples_C_H5D C) #----------------------------------------------------------------------------- # Define Sources diff --git a/HDF5Examples/C/H5FLT/CMakeLists.txt b/HDF5Examples/C/H5FLT/CMakeLists.txt index eb386b4..482d65b 100644 --- a/HDF5Examples/C/H5FLT/CMakeLists.txt +++ b/HDF5Examples/C/H5FLT/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_C_H5FLT) +project (HDF5Examples_C_H5FLT C) set (dyn_examples) @@ -190,6 +190,8 @@ if (H5EX_BUILD_TESTING) -D "TEST_MASK_ERROR=true" -D "TEST_OUTPUT=${testname}.out" -D "TEST_REFERENCE=${testname}.tst" + -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH" + -D "TEST_ENV_VALUE=${H5EX_HDF5_PLUGIN_PATH}" -D "TEST_SKIP_COMPARE=1" -D "TEST_ERRREF=1" -D "GREP_ERRREF=Filter present but encoding disabled" @@ -214,6 +216,8 @@ if (H5EX_BUILD_TESTING) -D "TEST_EXPECT=0" -D "TEST_OUTPUT=${testname}.out" -D "TEST_REFERENCE=${testname}.tst" + -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH" + -D "TEST_ENV_VALUE=${H5EX_HDF5_PLUGIN_PATH}" -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -P "${${EXAMPLE_PACKAGE_NAME}_RESOURCES_DIR}/runTest.cmake" ) @@ -233,6 +237,8 @@ if (H5EX_BUILD_TESTING) -D "TEST_FILTER_REPLACE=PARAMS { \\1 XXXX \\2 }\n" -D "TEST_EXPECT=0" -D "TEST_REFERENCE=${testname}.ddl" + -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH" + -D "TEST_ENV_VALUE=${H5EX_HDF5_PLUGIN_PATH}" -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -P "${${EXAMPLE_PACKAGE_NAME}_RESOURCES_DIR}/runTest.cmake" ) @@ -248,6 +254,8 @@ if (H5EX_BUILD_TESTING) -D "TEST_FILTER_REPLACE:STRING=PARAMS { XXXX }" -D "TEST_EXPECT=0" -D "TEST_REFERENCE=${testname}.ddl" + -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH" + -D "TEST_ENV_VALUE=${H5EX_HDF5_PLUGIN_PATH}" -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -P "${${EXAMPLE_PACKAGE_NAME}_RESOURCES_DIR}/runTest.cmake" ) diff --git a/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.ddl b/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.ddl index 7d73913..a8e66c0 100644 --- a/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.ddl +++ b/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.ddl @@ -10,7 +10,7 @@ GROUP "/" { FILTERS { USER_DEFINED_FILTER { FILTER_ID 32013 - COMMENT H5Z-ZFP-1.0.1 (ZFP-0.5.5) github.com/LLNL/H5Z-ZFP + COMMENT H5Z-ZFP-1.1.1 (ZFP-1.0.0) github.com/LLNL/H5Z-ZFP PARAMS { XXXX } } } diff --git a/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.tst b/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.tst index 0a1ba90..dd7197c 100644 --- a/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.tst +++ b/HDF5Examples/C/H5FLT/tfiles/h5ex_d_zfp.tst @@ -4,8 +4,8 @@ zfp filter is available for encoding and decoding. ....Close the file and reopen for reading ........ Filter info is available from the dataset creation property Filter identifier is 32013 - Number of parameters is 6 with the value 5570817 - To find more about the filter check H5Z-ZFP-1.0.1 (ZFP-0.5.5) github.com/LLNL/H5Z-ZFP + Number of parameters is 6 with the value 268456209 + To find more about the filter check H5Z-ZFP-1.1.1 (ZFP-1.0.0) github.com/LLNL/H5Z-ZFP ....Reading zfp compressed data ................ Maximum value in DS1 is 1890.0000 zfp filter is available now since H5Dread triggered loading of the filter. diff --git a/HDF5Examples/C/H5G/CMakeLists.txt b/HDF5Examples/C/H5G/CMakeLists.txt index afef556..ffbc614 100644 --- a/HDF5Examples/C/H5G/CMakeLists.txt +++ b/HDF5Examples/C/H5G/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_C_H5G) +project (HDF5Examples_C_H5G C) #----------------------------------------------------------------------------- # Define Sources diff --git a/HDF5Examples/C/H5T/CMakeLists.txt b/HDF5Examples/C/H5T/CMakeLists.txt index 4dcf6cb..0f8884b 100644 --- a/HDF5Examples/C/H5T/CMakeLists.txt +++ b/HDF5Examples/C/H5T/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_C_H5T) +project (HDF5Examples_C_H5T C) #----------------------------------------------------------------------------- # Define Sources diff --git a/HDF5Examples/CMakeLists.txt b/HDF5Examples/CMakeLists.txt index b5fb3e2..e944b9e 100644 --- a/HDF5Examples/CMakeLists.txt +++ b/HDF5Examples/CMakeLists.txt @@ -1,11 +1,19 @@ cmake_minimum_required (VERSION 3.12) -project (H5EXAMPLES C CXX) +project (H5EXAMPLES C) + +#----------------------------------------------------------------------------- +# Define some CMake variables for use later in the project +#----------------------------------------------------------------------------- +set (HDF5EX_C_SRC_DIR ${H5EXAMPLES_SOURCE_DIR}/C) +set (HDF5EX_F90_SRC_DIR ${H5EXAMPLES_SOURCE_DIR}/FORTRAN) +set (HDF5EX_JAVA_DIR ${H5EXAMPLES_SOURCE_DIR}/JAVA) +set (HDF5EX_RESOURCES_DIR ${H5EXAMPLES_SOURCE_DIR}/config/cmake) #----------------------------------------------------------------------------- # Basic HDF5Examples stuff here #----------------------------------------------------------------------------- -include (${H5EXAMPLES_SOURCE_DIR}/config/cmake/HDFMacros.cmake) -include (${H5EXAMPLES_SOURCE_DIR}/config/cmake/HDFExampleMacros.cmake) +include (${HDF5EX_RESOURCES_DIR}/HDFMacros.cmake) +include (${HDF5EX_RESOURCES_DIR}/HDFExampleMacros.cmake) set (CMAKE_JAVA_INCLUDE_PATH "") SET_HDF_BUILD_TYPE() @@ -13,13 +21,6 @@ SET_HDF_BUILD_TYPE() BASIC_SETTINGS (EXAMPLES) #----------------------------------------------------------------------------- -# Define some CMake variables for use later in the project -#----------------------------------------------------------------------------- -set (HDF5EX_C_SRC_DIR ${H5EXAMPLES_SOURCE_DIR}/C) -set (HDF5EX_F90_SRC_DIR ${H5EXAMPLES_SOURCE_DIR}/FORTRAN) -set (HDF5EX_JAVA_DIR ${H5EXAMPLES_SOURCE_DIR}/JAVA) - -#----------------------------------------------------------------------------- # HDF5 support #----------------------------------------------------------------------------- HDF5_SUPPORT (TRUE) @@ -37,7 +38,7 @@ if(NOT DEFINED _h5public_h_contents) string (REGEX REPLACE ".*#define[ \t]+H5_VERS_MAJOR[ \t]+([0-9]*).*$" "\\1" H5_VERS_MAJOR ${_h5public_h_contents}) string (REGEX REPLACE ".*#define[ \t]+H5_VERS_MINOR[ \t]+([0-9]*).*$" - "\\1" H5_VERS_MINOR ${_h5public_h_contents}) + "\\1" H5_VERS_MINOR ${_h5public_h_contents}) string (REGEX REPLACE ".*#define[ \t]+H5_VERS_RELEASE[ \t]+([0-9]*).*$" "\\1" H5_VERS_RELEASE ${_h5public_h_contents}) string (REGEX REPLACE ".*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._-]*)\".*$" @@ -119,11 +120,6 @@ if (H5EX_BUILD_TESTING) configure_file (${${EXAMPLE_PACKAGE_NAME}_RESOURCES_DIR}/CTestCustom.cmake ${PROJECT_BINARY_DIR}/CTestCustom.ctest @ONLY) endif () -#----------------------------------------------------------------------------- -# Build examples -#----------------------------------------------------------------------------- -add_subdirectory (C) - if (${H5_LIBVER_DIR} GREATER 16) #----------------------------------------------------------------------------- # Option to build Fortran examples @@ -136,19 +132,22 @@ if (${H5_LIBVER_DIR} GREATER 16) if (EXISTS "${H5EXAMPLES_SOURCE_DIR}/FORTRAN" AND IS_DIRECTORY "${H5EXAMPLES_SOURCE_DIR}/FORTRAN") option (HDF_BUILD_FORTRAN "Build FORTRAN support" OFF) if (HDF_BUILD_FORTRAN AND HDF5_BUILD_FORTRAN) - set (LINK_Fortran_LIBS ${H5EX_HDF5_LINK_LIBS}) + set (H5EX_LINK_Fortran_LIBS ${H5EX_HDF5_LINK_LIBS}) # Parallel IO usage requires MPI to be Linked and Included if (H5_HAVE_PARALLEL) - set (LINK_Fortran_LIBS ${LINK_Fortran_LIBS} ${MPI_Fortran_LIBRARIES}) + set (H5EX_LINK_Fortran_LIBS ${H5EX_LINK_Fortran_LIBS} ${MPI_Fortran_LIBRARIES}) if (MPI_Fortran_LINK_FLAGS) set (CMAKE_Fortran_EXE_LINKER_FLAGS "${MPI_Fortran_LINK_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}") endif () endif () - add_subdirectory (FORTRAN) configure_file (${HDF5EX_F90_SRC_DIR}/H5D/h5_version.h.in ${PROJECT_BINARY_DIR}/FORTRAN/H5D/h5_version.h @ONLY) + else () + set (HDF_BUILD_FORTRAN OFF CACHE BOOL "Build examples FORTRAN support" FORCE) endif () + else () + set (HDF_BUILD_FORTRAN OFF CACHE BOOL "Build examples FORTRAN support" FORCE) endif () if (${H5_LIBVER_DIR} GREATER 18) @@ -157,16 +156,49 @@ if (${H5_LIBVER_DIR} GREATER 16) #----------------------------------------------------------------------------- if (EXISTS "${H5EXAMPLES_SOURCE_DIR}/JAVA" AND IS_DIRECTORY "${H5EXAMPLES_SOURCE_DIR}/JAVA") option (HDF_BUILD_JAVA "Build JAVA support" OFF) - if (HDF_BUILD_JAVA AND HDF5_BUILD_JAVA) - add_subdirectory (JAVA) - endif () + else () + set (HDF_BUILD_JAVA OFF CACHE BOOL "Build examples JAVA support" FORCE) endif () + else () + set (HDF_BUILD_JAVA OFF CACHE BOOL "Build examples JAVA support" FORCE) endif () #----------------------------------------------------------------------------- # Option to build filter examples #----------------------------------------------------------------------------- - if (EXISTS "${H5EXAMPLES_SOURCE_DIR}/C/H5F" AND IS_DIRECTORY "${H5EXAMPLES_SOURCE_DIR}/C/H5F") + if (EXISTS "${H5EXAMPLES_SOURCE_DIR}/C/H5FLT" AND IS_DIRECTORY "${H5EXAMPLES_SOURCE_DIR}/C/H5FLT") option (HDF_BUILD_FILTERS "Test filter support" OFF) + if (HDF_BUILD_FILTERS AND HDF5_ENABLE_PLUGIN_SUPPORT) + if(DEFINED ENV{HDF5_PLUGIN_PATH}) + message (STATUS "ENV PATH=$ENV{HDF5_PLUGIN_PATH}") + set (H5EX_HDF5_PLUGIN_PATH $ENV{HDF5_PLUGIN_PATH}) + else () + if(NOT DEFINED H5EX_HDF5_PLUGIN_PATH) + message (STATUS "LIBRARY PATH=${HDF5_LIBRARY_PATH}/plugin") + set (H5EX_HDF5_PLUGIN_PATH ${HDF5_LIBRARY_PATH}/plugin) + endif () + endif () + message (STATUS "H5EX_HDF5_PLUGIN_PATH=${H5EX_HDF5_PLUGIN_PATH}") + else () + set (HDF_BUILD_FILTERS OFF CACHE BOOL "Build examples PLUGIN filter support" FORCE) + endif () + else () + set (HDF_BUILD_FILTERS OFF CACHE BOOL "Build examples PLUGIN filter support" FORCE) endif () +else () + set (HDF_BUILD_FORTRAN OFF} CACHE BOOL "Build examples FORTRAN support" FORCE) + set (HDF_BUILD_JAVA OFF CACHE BOOL "Build examples JAVA support" FORCE) + set (HDF_BUILD_FILTERS OFF CACHE BOOL "Build examples PLUGIN filter support" FORCE) endif () + +#----------------------------------------------------------------------------- +# Build examples +#----------------------------------------------------------------------------- +add_subdirectory (C) +if (HDF_BUILD_FORTRAN AND HDF5_BUILD_FORTRAN) + add_subdirectory (FORTRAN) +endif () +if (HDF_BUILD_JAVA AND HDF5_BUILD_JAVA) + add_subdirectory (JAVA) +endif () + diff --git a/HDF5Examples/FORTRAN/CMakeLists.txt b/HDF5Examples/FORTRAN/CMakeLists.txt index 72582fe..0f05a0e 100644 --- a/HDF5Examples/FORTRAN/CMakeLists.txt +++ b/HDF5Examples/FORTRAN/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -PROJECT (HDF5Examples_F90 C CXX Fortran) +PROJECT (HDF5Examples_F90 Fortran) #----------------------------------------------------------------------------- # Build the Fortran Examples diff --git a/HDF5Examples/FORTRAN/H5D/CMakeLists.txt b/HDF5Examples/FORTRAN/H5D/CMakeLists.txt index dbc126c..5369a49 100644 --- a/HDF5Examples/FORTRAN/H5D/CMakeLists.txt +++ b/HDF5Examples/FORTRAN/H5D/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_FORTRAN_H5D C CXX Fortran) +project (HDF5Examples_FORTRAN_H5D Fortran) # -------------------------------------------------------------------- # Notes: When creating examples they should be prefixed @@ -10,7 +10,7 @@ project (HDF5Examples_FORTRAN_H5D C CXX Fortran) # Setup include Directories #----------------------------------------------------------------------------- INCLUDE_DIRECTORIES ( - ${CMAKE_Fortran_MODULE_DIRECTORY} + ${CMAKE_Fortran_MODULE_DIRECTORY}${HDF_MOD_EXT} ${PROJECT_BINARY_DIR} ${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ) @@ -35,7 +35,7 @@ foreach (example_name ${common_examples}) if (H5_HAVE_PARALLEL) target_include_directories (${EXAMPLE_VARNAME}_f90_${example_name} PUBLIC ${MPI_Fortran_INCLUDE_DIRS}) endif () - target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${LINK_Fortran_LIBS}) + target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_LINK_Fortran_LIBS}) set_target_properties (${EXAMPLE_VARNAME}_f90_${example_name} PROPERTIES LINKER_LANGUAGE Fortran) if (H5EX_BUILD_TESTING) if (${example_name} STREQUAL "h5ex_d_alloc") @@ -80,7 +80,7 @@ if (HDF5_VERSION_MAJOR VERSION_GREATER_EQUAL "1.10") if (H5_HAVE_PARALLEL) target_include_directories (${EXAMPLE_VARNAME}_f90_${example_name} PUBLIC ${MPI_C_INCLUDE_DIRS}) endif () - target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_HDF5_LINK_LIBS}) + target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_LINK_Fortran_LIBS}) if (H5EX_BUILD_TESTING) add_custom_command ( TARGET ${EXAMPLE_VARNAME}_f90_${example_name} diff --git a/HDF5Examples/FORTRAN/H5G/CMakeLists.txt b/HDF5Examples/FORTRAN/H5G/CMakeLists.txt index d2587e0..508283c 100644 --- a/HDF5Examples/FORTRAN/H5G/CMakeLists.txt +++ b/HDF5Examples/FORTRAN/H5G/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_FORTRAN_H5G C CXX Fortran) +project (HDF5Examples_FORTRAN_H5G Fortran) # -------------------------------------------------------------------- # Notes: When creating examples they should be prefixed @@ -10,7 +10,7 @@ project (HDF5Examples_FORTRAN_H5G C CXX Fortran) # Setup include Directories #----------------------------------------------------------------------------- INCLUDE_DIRECTORIES ( - ${CMAKE_Fortran_MODULE_DIRECTORY} + ${CMAKE_Fortran_MODULE_DIRECTORY}${HDF_MOD_EXT} ${PROJECT_BINARY_DIR} ${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ) @@ -35,7 +35,7 @@ foreach (example_name ${common_examples}) if (H5_HAVE_PARALLEL) target_include_directories (${EXAMPLE_VARNAME}_f90_${example_name} PUBLIC ${MPI_Fortran_INCLUDE_DIRS}) endif () - target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${LINK_Fortran_LIBS}) + target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_LINK_Fortran_LIBS}) set_target_properties (${EXAMPLE_VARNAME}_f90_${example_name} PROPERTIES LINKER_LANGUAGE Fortran) if (H5EX_BUILD_TESTING) if (NOT ${example_name} STREQUAL "h5ex_g_create" AND NOT ${example_name} STREQUAL "h5ex_g_compact") @@ -64,7 +64,7 @@ endforeach () # if (H5_HAVE_PARALLEL) # target_include_directories (${EXAMPLE_VARNAME}_f90_${example_name} PUBLIC ${MPI_C_INCLUDE_DIRS}) # endif () -# target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_HDF5_LINK_LIBS}) +# target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_LINK_Fortran_LIBS}) # if (H5EX_BUILD_TESTING) # add_custom_command ( # TARGET ${EXAMPLE_VARNAME}_f90_${example_name} diff --git a/HDF5Examples/FORTRAN/H5PAR/CMakeLists.txt b/HDF5Examples/FORTRAN/H5PAR/CMakeLists.txt index 84c9641..792caaf 100644 --- a/HDF5Examples/FORTRAN/H5PAR/CMakeLists.txt +++ b/HDF5Examples/FORTRAN/H5PAR/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_FORTRAN_H5PAR C CXX Fortran) +project (HDF5Examples_FORTRAN_H5PAR Fortran) # -------------------------------------------------------------------- # Notes: When creating examples they should be prefixed @@ -10,7 +10,7 @@ project (HDF5Examples_FORTRAN_H5PAR C CXX Fortran) # Setup include Directories #----------------------------------------------------------------------------- INCLUDE_DIRECTORIES ( - ${CMAKE_Fortran_MODULE_DIRECTORY} + ${CMAKE_Fortran_MODULE_DIRECTORY}${HDF_MOD_EXT} ${PROJECT_BINARY_DIR} ${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ) @@ -33,7 +33,7 @@ foreach (example_name ${examples}) "$<$<BOOL:${${EXAMPLE_VARNAME}_USE_116_API}>:-DH5_USE_116_API>" ) target_include_directories (${EXAMPLE_VARNAME}_f90_${example_name} PUBLIC ${MPI_Fortran_INCLUDE_DIRS}) - target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${LINK_Fortran_LIBS}) + target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_LINK_Fortran_LIBS}) set_target_properties (${EXAMPLE_VARNAME}_f90_${example_name} PROPERTIES LINKER_LANGUAGE Fortran) endforeach () @@ -59,8 +59,8 @@ if (H5EX_BUILD_TESTING) -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -P "${${EXAMPLE_PACKAGE_NAME}_RESOURCES_DIR}/grepTest.cmake" ) - set_tests_properties (${EXAMPLE_VARNAME}_${testname} PROPERTIES DEPENDS ${EXAMPLE_VARNAME}_${testname}-clearall) - set (last_test "${EXAMPLE_VARNAME}_${testname}") + set_tests_properties (${EXAMPLE_VARNAME}_f90_${testname} PROPERTIES DEPENDS ${EXAMPLE_VARNAME}_f90_${testname}-clearall) + set (last_test "${EXAMPLE_VARNAME}_f90_${testname}") endmacro () # Ensure that 24 is a multiple of the number of processes. diff --git a/HDF5Examples/FORTRAN/H5T/CMakeLists.txt b/HDF5Examples/FORTRAN/H5T/CMakeLists.txt index 67a3ca3..262adf8 100644 --- a/HDF5Examples/FORTRAN/H5T/CMakeLists.txt +++ b/HDF5Examples/FORTRAN/H5T/CMakeLists.txt @@ -1,5 +1,14 @@ cmake_minimum_required (VERSION 3.12) -project (HDF5Examples_FORTRAN_H5T C CXX Fortran) +project (HDF5Examples_FORTRAN_H5T Fortran) + +#----------------------------------------------------------------------------- +# Setup include Directories +#----------------------------------------------------------------------------- +INCLUDE_DIRECTORIES ( + ${CMAKE_Fortran_MODULE_DIRECTORY}${HDF_MOD_EXT} + ${PROJECT_BINARY_DIR} + ${CMAKE_LIBRARY_OUTPUT_DIRECTORY} +) #----------------------------------------------------------------------------- # Define Sources @@ -21,7 +30,7 @@ include (Fortran_sourcefiles.cmake) if (H5_HAVE_PARALLEL) target_include_directories (${EXAMPLE_VARNAME}_f90_${example_name} PUBLIC ${MPI_Fortran_INCLUDE_DIRS}) endif () - target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${LINK_Fortran_LIBS}) + target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_LINK_Fortran_LIBS}) set_target_properties (${EXAMPLE_VARNAME}_f90_${example_name} PROPERTIES LINKER_LANGUAGE Fortran) if (H5EX_BUILD_TESTING) add_custom_command ( @@ -48,7 +57,7 @@ foreach (example_name ${common_examples}) if (H5_HAVE_PARALLEL) target_include_directories (${EXAMPLE_VARNAME}_f90_${example_name} PUBLIC ${MPI_Fortran_INCLUDE_DIRS}) endif () - target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${LINK_Fortran_LIBS}) + target_link_libraries (${EXAMPLE_VARNAME}_f90_${example_name} ${H5EX_LINK_Fortran_LIBS}) set_target_properties (${EXAMPLE_VARNAME}_f90_${example_name} PROPERTIES LINKER_LANGUAGE Fortran) if (H5EX_BUILD_TESTING) add_custom_command ( diff --git a/HDF5Examples/JAVA/H5D/CMakeLists.txt b/HDF5Examples/JAVA/H5D/CMakeLists.txt index 60c35dc..bc06506 100644 --- a/HDF5Examples/JAVA/H5D/CMakeLists.txt +++ b/HDF5Examples/JAVA/H5D/CMakeLists.txt @@ -3,10 +3,9 @@ project (HDF5Examples_JAVA_H5D Java) set (CMAKE_VERBOSE_MAKEFILE 1) -INCLUDE_DIRECTORIES ( - ${HDFJAVA_LIB_DIR} - ${JAVA_INCLUDE_PATH} - ${JAVA_INCLUDE_PATH2} +set_directory_properties(PROPERTIES + INCLUDE_DIRECTORIES + "${HDFJAVA_LIB_DIR};${JAVA_INCLUDE_PATH};${JAVA_INCLUDE_PATH2}" ) #----------------------------------------------------------------------------- @@ -20,6 +19,9 @@ else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") endif () +set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_INCLUDE_DIRS}") +set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${H5EX_JAVA_LIBRARY}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") + set (CMAKE_JAVA_CLASSPATH ".") foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") @@ -32,13 +34,18 @@ endforeach () foreach (example ${HDF_JAVA_EXAMPLES}) get_filename_component (example_name ${example} NAME_WE) - file (WRITE ${PROJECT_BINARY_DIR}/Manifest.txt + file (WRITE ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt "Main-Class: ${example_name} Class-Path: ${HDFJAVA_CLASSJARS} " ) - add_jar (${EXAMPLE_VARNAME}_${example_name} SOURCES ${example} MANIFEST ${PROJECT_BINARY_DIR}/Manifest.txt) + add_jar (${EXAMPLE_VARNAME}_${example_name} + SOURCES ${example} + MANIFEST ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt + ) get_target_property (${EXAMPLE_VARNAME}_${example_name}_JAR_FILE ${EXAMPLE_VARNAME}_${example_name} JAR_FILE) + get_target_property (${EXAMPLE_VARNAME}_${example_name}_CLASSPATH ${EXAMPLE_VARNAME}_${example_name} CLASSDIR) + add_dependencies (${EXAMPLE_VARNAME}_${example_name} ${H5EX_JAVA_LIBRARIES}) endforeach () if (H5EX_BUILD_TESTING) @@ -46,9 +53,9 @@ if (H5EX_BUILD_TESTING) add_test ( NAME ${EXAMPLE_VARNAME}_jnative-h5-${resultfile} COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME}" + -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" -D "TEST_PROGRAM=${resultfile}" - -D "TEST_ARGS:STRING=${ARGN}" + -D "TEST_ARGS:STRING=${ARGN};${CMD_ARGS}" -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${EXAMPLE_VARNAME}_${resultfile}_JAR_FILE}" -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" diff --git a/HDF5Examples/JAVA/H5G/CMakeLists.txt b/HDF5Examples/JAVA/H5G/CMakeLists.txt index 5f47d59..957934b 100644 --- a/HDF5Examples/JAVA/H5G/CMakeLists.txt +++ b/HDF5Examples/JAVA/H5G/CMakeLists.txt @@ -3,10 +3,9 @@ project (HDF5Examples_JAVA_GROUPS Java) set (CMAKE_VERBOSE_MAKEFILE 1) -INCLUDE_DIRECTORIES ( - ${HDFJAVA_LIB_DIR} - ${JAVA_INCLUDE_PATH} - ${JAVA_INCLUDE_PATH2} +set_directory_properties(PROPERTIES + INCLUDE_DIRECTORIES + "${HDFJAVA_LIB_DIR};${JAVA_INCLUDE_PATH};${JAVA_INCLUDE_PATH2}" ) #----------------------------------------------------------------------------- @@ -20,6 +19,9 @@ else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") endif () +set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_INCLUDE_DIRS}") +set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${H5EX_JAVA_LIBRARY}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") + set (CMAKE_JAVA_CLASSPATH ".") foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") @@ -32,13 +34,18 @@ endforeach () foreach (example ${HDF_JAVA_EXAMPLES}) get_filename_component (example_name ${example} NAME_WE) - file (WRITE ${PROJECT_BINARY_DIR}/Manifest.txt + file (WRITE ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt "Main-Class: ${example_name} Class-Path: ${HDFJAVA_CLASSJARS} " ) - add_jar (${EXAMPLE_VARNAME}_${example_name} SOURCES ${example} MANIFEST ${PROJECT_BINARY_DIR}/Manifest.txt) + add_jar (${EXAMPLE_VARNAME}_${example_name} + SOURCES ${example} + MANIFEST ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt + ) get_target_property (${EXAMPLE_VARNAME}_${example_name}_JAR_FILE ${EXAMPLE_VARNAME}_${example_name} JAR_FILE) + get_target_property (${EXAMPLE_VARNAME}_${example_name}_CLASSPATH ${EXAMPLE_VARNAME}_${example_name} CLASSDIR) + add_dependencies (${EXAMPLE_VARNAME}_${example_name} ${H5EX_JAVA_LIBRARIES}) endforeach () if (H5EX_BUILD_TESTING) @@ -46,9 +53,9 @@ if (H5EX_BUILD_TESTING) add_test ( NAME ${EXAMPLE_VARNAME}_jnative-h5-${resultfile} COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME}" + -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" -D "TEST_PROGRAM=${resultfile}" - -D "TEST_ARGS:STRING=${ARGN}" + -D "TEST_ARGS:STRING=${ARGN};${CMD_ARGS}" -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${EXAMPLE_VARNAME}_${resultfile}_JAR_FILE}" -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" diff --git a/HDF5Examples/JAVA/H5J/CMakeLists.txt b/HDF5Examples/JAVA/H5J/CMakeLists.txt index 8f1c195..eaefa7d 100644 --- a/HDF5Examples/JAVA/H5J/CMakeLists.txt +++ b/HDF5Examples/JAVA/H5J/CMakeLists.txt @@ -3,10 +3,9 @@ project (HDF5Examples_JAVA_INTRO Java) set (CMAKE_VERBOSE_MAKEFILE 1) -INCLUDE_DIRECTORIES ( - ${HDFJAVA_LIB_DIR} - ${JAVA_INCLUDE_PATH} - ${JAVA_INCLUDE_PATH2} +set_directory_properties(PROPERTIES + INCLUDE_DIRECTORIES + "${HDFJAVA_LIB_DIR};${JAVA_INCLUDE_PATH};${JAVA_INCLUDE_PATH2}" ) #----------------------------------------------------------------------------- @@ -20,6 +19,9 @@ else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") endif () +set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_INCLUDE_DIRS}") +set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${H5EX_JAVA_LIBRARY}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") + set (CMAKE_JAVA_CLASSPATH ".") foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") @@ -32,13 +34,18 @@ endforeach () foreach (example ${HDF_JAVA_EXAMPLES}) get_filename_component (example_name ${example} NAME_WE) - file (WRITE ${PROJECT_BINARY_DIR}/Manifest.txt + file (WRITE ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt "Main-Class: ${example_name} Class-Path: ${HDFJAVA_CLASSJARS} " ) - add_jar (${EXAMPLE_VARNAME}_${example_name} SOURCES ${example} MANIFEST ${PROJECT_BINARY_DIR}/Manifest.txt) + add_jar (${EXAMPLE_VARNAME}_${example_name} + SOURCES ${example} + MANIFEST ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt + ) get_target_property (${EXAMPLE_VARNAME}_${example_name}_JAR_FILE ${EXAMPLE_VARNAME}_${example_name} JAR_FILE) + get_target_property (${EXAMPLE_VARNAME}_${example_name}_CLASSPATH ${EXAMPLE_VARNAME}_${example_name} CLASSDIR) + add_dependencies (${EXAMPLE_VARNAME}_${example_name} ${H5EX_JAVA_LIBRARIES}) endforeach () if (H5EX_BUILD_TESTING) @@ -46,9 +53,9 @@ if (H5EX_BUILD_TESTING) add_test ( NAME ${EXAMPLE_VARNAME}_jnative-h5-${resultfile} COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME}" + -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" -D "TEST_PROGRAM=${resultfile}" - -D "TEST_ARGS:STRING=${ARGN}" + -D "TEST_ARGS:STRING=${ARGN};${CMD_ARGS}" -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${EXAMPLE_VARNAME}_${resultfile}_JAR_FILE}" -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" diff --git a/HDF5Examples/JAVA/H5T/CMakeLists.txt b/HDF5Examples/JAVA/H5T/CMakeLists.txt index a779a53..0d2cb41 100644 --- a/HDF5Examples/JAVA/H5T/CMakeLists.txt +++ b/HDF5Examples/JAVA/H5T/CMakeLists.txt @@ -3,10 +3,9 @@ project (HDF5Examples_JAVA_H5T Java) set (CMAKE_VERBOSE_MAKEFILE 1) -INCLUDE_DIRECTORIES ( - ${HDFJAVA_LIB_DIR} - ${JAVA_INCLUDE_PATH} - ${JAVA_INCLUDE_PATH2} +set_directory_properties(PROPERTIES + INCLUDE_DIRECTORIES + "${HDFJAVA_LIB_DIR};${JAVA_INCLUDE_PATH};${JAVA_INCLUDE_PATH2}" ) #----------------------------------------------------------------------------- @@ -20,6 +19,9 @@ else () set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") endif () +set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_INCLUDE_DIRS}") +set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${H5EX_JAVA_LIBRARY}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") + set (CMAKE_JAVA_CLASSPATH ".") foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") @@ -32,13 +34,18 @@ endforeach () foreach (example ${HDF_JAVA_EXAMPLES}) get_filename_component (example_name ${example} NAME_WE) - file (WRITE ${PROJECT_BINARY_DIR}/Manifest.txt + file (WRITE ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt "Main-Class: ${example_name} Class-Path: ${HDFJAVA_CLASSJARS} " ) - add_jar (${EXAMPLE_VARNAME}_${example_name} SOURCES ${example} MANIFEST ${PROJECT_BINARY_DIR}/Manifest.txt) + add_jar (${EXAMPLE_VARNAME}_${example_name} + SOURCES ${example} + MANIFEST ${PROJECT_BINARY_DIR}/${example_name}_Manifest.txt + ) get_target_property (${EXAMPLE_VARNAME}_${example_name}_JAR_FILE ${EXAMPLE_VARNAME}_${example_name} JAR_FILE) + get_target_property (${EXAMPLE_VARNAME}_${example_name}_CLASSPATH ${EXAMPLE_VARNAME}_${example_name} CLASSDIR) + add_dependencies (${EXAMPLE_VARNAME}_${example_name} ${H5EX_JAVA_LIBRARIES}) endforeach () if (H5EX_BUILD_TESTING) @@ -46,9 +53,9 @@ if (H5EX_BUILD_TESTING) add_test ( NAME ${EXAMPLE_VARNAME}_jnative-h5-${resultfile} COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME}" + -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" -D "TEST_PROGRAM=${resultfile}" - -D "TEST_ARGS:STRING=${ARGN}" + -D "TEST_ARGS:STRING=${ARGN};${CMD_ARGS}" -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${EXAMPLE_VARNAME}_${resultfile}_JAR_FILE}" -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_LIB_DIRECTORY}" -D "TEST_FOLDER=${PROJECT_BINARY_DIR}" diff --git a/HDF5Examples/config/cmake/HDFExampleMacros.cmake b/HDF5Examples/config/cmake/HDFExampleMacros.cmake index d9bf67f..82fd8ac 100644 --- a/HDF5Examples/config/cmake/HDFExampleMacros.cmake +++ b/HDF5Examples/config/cmake/HDFExampleMacros.cmake @@ -1,3 +1,15 @@ +# +# 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. +# + #------------------------------------------------------------------------------- macro (BASIC_SETTINGS varname) string (TOUPPER ${varname} EXAMPLE_PACKAGE_VARNAME) @@ -17,35 +29,7 @@ macro (BASIC_SETTINGS varname) #----------------------------------------------------------------------------- # Setup output Directories #----------------------------------------------------------------------------- - if (NOT ${EXAMPLE_PACKAGE_NAME}_EXTERNALLY_CONFIGURED) - set (CMAKE_RUNTIME_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables." - ) - set (CMAKE_LIBRARY_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries" - ) - set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries." - ) - set (CMAKE_Fortran_MODULE_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all fortran modules." - ) - get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) - if(_isMultiConfig) - set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_BUILD_TYPE}) - set (CMAKE_PDB_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files." - ) - else () - set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) - endif () - else () - # if we are externally configured, but the project uses old cmake scripts - # this may not be set - if (NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY) - set (CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) - endif () - endif () + SET_HDF_OUTPUT_DIRS(${EXAMPLE_PACKAGE_NAME}) #----------------------------------------------------------------------------- # Option to use Shared/Static libs, default is static @@ -63,9 +47,13 @@ macro (BASIC_SETTINGS varname) set (CMAKE_C_STANDARD 99) set (CMAKE_C_STANDARD_REQUIRED TRUE) - set (CMAKE_CXX_STANDARD 98) - set (CMAKE_CXX_STANDARD_REQUIRED TRUE) - set (CMAKE_CXX_EXTENSIONS OFF) + if (HDF_BUILD_CPP_LIB) + ENABLE_LANGUAGE (CXX) + + set (CMAKE_CXX_STANDARD 98) + set (CMAKE_CXX_STANDARD_REQUIRED TRUE) + set (CMAKE_CXX_EXTENSIONS OFF) + endif () #----------------------------------------------------------------------------- # Compiler specific flags : Shouldn't there be compiler tests for these @@ -73,7 +61,7 @@ macro (BASIC_SETTINGS varname) if (CMAKE_COMPILER_IS_GNUCC) set (CMAKE_C_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_C_FLAGS}") endif () - if (CMAKE_COMPILER_IS_GNUCXX) + if (CMAKE_CXX_COMPILER_LOADED AND CMAKE_COMPILER_IS_GNUCXX) set (CMAKE_CXX_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_CXX_FLAGS}") endif () @@ -84,7 +72,7 @@ macro (BASIC_SETTINGS varname) if (CMAKE_COMPILER_IS_GNUCC) set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fmessage-length=0") endif () - if (CMAKE_COMPILER_IS_GNUCXX) + if (CMAKE_CXX_COMPILER_LOADED AND CMAKE_COMPILER_IS_GNUCXX) set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fmessage-length=0") endif () @@ -99,8 +87,10 @@ macro (BASIC_SETTINGS varname) set (HDF_WARNINGS_BLOCKED 1) string (REGEX REPLACE "(^| )([/-])W[0-9]( |$)" " " CMAKE_C_FLAGS "${CMAKE_C_FLAGS}") set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /w") - string (REGEX REPLACE "(^| )([/-])W[0-9]( |$)" " " CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}") - set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /w") + if (CMAKE_CXX_COMPILER_LOADED AND CMAKE_COMPILER_IS_GNUCXX) + string (REGEX REPLACE "(^| )([/-])W[0-9]( |$)" " " CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}") + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /w") + endif () endif () if (WIN32) add_definitions (-D_CRT_SECURE_NO_WARNINGS) @@ -114,7 +104,9 @@ macro (BASIC_SETTINGS varname) # Most compilers use -w to suppress warnings. if (NOT HDF_WARNINGS_BLOCKED) set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w") - set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w") + if (CMAKE_CXX_COMPILER_LOADED AND CMAKE_COMPILER_IS_GNUCXX) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w") + endif () endif () endif () @@ -233,7 +225,9 @@ macro (HDF5_SUPPORT) if (HDF_BUILD_JAVA) if (${HDF5_BUILD_JAVA} AND HDF5_Java_FOUND) set (CMAKE_JAVA_INCLUDE_PATH "${CMAKE_JAVA_INCLUDE_PATH};${HDF5_JAVA_INCLUDE_DIRS}") - message (STATUS "HDF5 jars:${HDF5_JAVA_INCLUDE_DIRS}}") + set (H5EX_JAVA_LIBRARY ${HDF5_JAVA_LIBRARY}) + set (H5EX_JAVA_LIBRARIES ${HDF5_JAVA_LIBRARY}) + message (STATUS "HDF5 lib:${H5EX_JAVA_LIBRARY} jars:${HDF5_JAVA_INCLUDE_DIRS}}") else () set (HDF_BUILD_JAVA OFF CACHE BOOL "Build Java support" FORCE) message (STATUS "HDF5 Java libs not found - disable build of Java examples") @@ -285,11 +279,6 @@ macro (HDF5_SUPPORT) else () set (H5_LIB_TYPE STATIC) endif () - - #----------------------------------------------------------------------------- - # Option to build filter examples - #----------------------------------------------------------------------------- - option (HDF_BUILD_FILTERS "Test filter support" OFF) endmacro () #------------------------------------------------------------------------------- diff --git a/HDF5Examples/config/cmake/HDFMacros.cmake b/HDF5Examples/config/cmake/HDFMacros.cmake index 9ce592d..66a25aa 100644 --- a/HDF5Examples/config/cmake/HDFMacros.cmake +++ b/HDF5Examples/config/cmake/HDFMacros.cmake @@ -1,3 +1,50 @@ +# +# 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. +# + +#------------------------------------------------------------------------------- +# Setup output Directories +#----------------------------------------------------------------------------- +macro (SET_HDF_OUTPUT_DIRS package_prefix) + if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED) + set (CMAKE_RUNTIME_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables." + ) + set (CMAKE_LIBRARY_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries" + ) + set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries." + ) + set (CMAKE_Fortran_MODULE_DIRECTORY + ${PROJECT_BINARY_DIR}/mod CACHE PATH "Single Directory for all fortran modules." + ) + get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) + if(_isMultiConfig) + set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF_CFG_NAME}) + set (CMAKE_PDB_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files." + ) + else () + set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) + endif () + else () + # if we are externally configured, but the project uses old cmake scripts + # this may not be set and utilities like H5detect will fail + if (NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY) + set (CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) + endif () + endif () +endmacro () + #------------------------------------------------------------------------------- macro (SET_HDF_BUILD_TYPE) get_property (_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) @@ -157,38 +204,7 @@ macro (HDF_DIR_PATHS package_prefix) SET_HDF_BUILD_TYPE() -#----------------------------------------------------------------------------- -# Setup output Directories -#----------------------------------------------------------------------------- - if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED) - set (CMAKE_RUNTIME_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables." - ) - set (CMAKE_LIBRARY_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries" - ) - set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries." - ) - set (CMAKE_Fortran_MODULE_DIRECTORY - ${PROJECT_BINARY_DIR}/mod CACHE PATH "Single Directory for all fortran modules." - ) - get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) - if(_isMultiConfig) - set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF_CFG_NAME}) - set (CMAKE_PDB_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files." - ) - else () - set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) - endif () - else () - # if we are externally configured, but the project uses old cmake scripts - # this may not be set and utilities like H5detect will fail - if (NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY) - set (CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) - endif () - endif () + SET_HDF_OUTPUT_DIRS(${package_prefix}) include (FetchContent) endmacro () diff --git a/HDF5Examples/config/cmake/UseJava.cmake b/HDF5Examples/config/cmake/UseJava.cmake index 2783cb6..b4af653 100644 --- a/HDF5Examples/config/cmake/UseJava.cmake +++ b/HDF5Examples/config/cmake/UseJava.cmake @@ -6,7 +6,7 @@ UseJava This file provides support for ``Java``. It is assumed that :module:`FindJava` has already been loaded. See :module:`FindJava` for -information on how to load Java into your ``CMake`` project. +information on how to load Java into your CMake project. Synopsis ^^^^^^^^ @@ -42,6 +42,7 @@ Creating And Installing JARs add_jar(<target_name> [SOURCES] <source1> [<source2>...] [<resource1>...] + [RESOURCES NAMESPACE <ns1> <resource1>... [NAMESPACE <nsX> <resourceX>...]... ] [INCLUDE_JARS <jar1> [<jar2>...]] [ENTRY_POINT <entry>] [VERSION <version>] @@ -64,6 +65,34 @@ Creating And Installing JARs .. versionadded:: 3.4 Support for response files, prefixed by ``@``. + ``RESOURCES`` + .. versionadded:: 3.21 + + Adds the named ``<resource>`` files to the jar by stripping the source file + path and placing the file beneath ``<ns>`` within the jar. + + For example:: + + RESOURCES NAMESPACE "/com/my/namespace" "a/path/to/resource.txt" + + results in a resource accessible via ``/com/my/namespace/resource.txt`` + within the jar. + + Resources may be added without adjusting the namespace by adding them to + the list of ``SOURCES`` (original behavior), in this case, resource + paths must be relative to ``CMAKE_CURRENT_SOURCE_DIR``. Adding resources + without using the ``RESOURCES`` parameter in out of source builds will + almost certainly result in confusion. + + .. note:: + + Adding resources via the ``SOURCES`` parameter relies upon a hard-coded + list of file extensions which are tested to determine whether they + compile (e.g. File.java). ``SOURCES`` files which match the extensions + are compiled. Files which do not match are treated as resources. To + include uncompiled resources matching those file extensions use + the ``RESOURCES`` parameter. + ``INCLUDE_JARS`` The list of jars are added to the classpath when compiling the java sources and also to the dependencies of the target. ``INCLUDE_JARS`` also accepts @@ -264,7 +293,7 @@ Header Generation .. deprecated:: 3.11 This command will no longer be supported starting with version 10 of the JDK - due to the `suppression of javah tool <http://openjdk.java.net/jeps/313>`_. + due to the `suppression of javah tool <https://openjdk.org/jeps/313>`_. The :ref:`add_jar(GENERATE_NATIVE_HEADERS) <add_jar>` command should be used instead. @@ -526,6 +555,7 @@ function (__java_copy_file src dest comment) ${dest} DEPENDS ${src} COMMENT ${comment} + VERBATIM ) endfunction () @@ -552,6 +582,58 @@ function(__java_export_jar VAR TARGET PATH) set(${VAR} "${${VAR}}" PARENT_SCOPE) endfunction() +function(__java_copy_resource_namespaces VAR DEST JAVA_RESOURCE_FILES JAVA_RESOURCE_FILES_RELATIVE) + + set(_ns_ID "") + set(_ns_VAL "") + + foreach(_item IN LISTS VAR) + if(NOT _ns_ID) + if(NOT _item STREQUAL "NAMESPACE") + message(FATAL_ERROR "UseJava: Expecting \"NAMESPACE\", got\t\"${_item}\"") + return() + endif() + endif() + + if(_item STREQUAL "NAMESPACE") + set(_ns_VAL "") # Prepare for next namespace + set(_ns_ID "${_item}") + continue() + endif() + + if( NOT _ns_VAL) + # we're expecting the next token to be a namespace value + # whatever it is, we're treating it like a namespace + set(_ns_VAL "${_item}") + continue() + endif() + + if(_ns_ID AND _ns_VAL) + # We're expecting a file name, check to see if we got one + cmake_path(ABSOLUTE_PATH _item OUTPUT_VARIABLE _test_file_name) + if (NOT EXISTS "${_test_file_name}") + message(FATAL_ERROR "UseJava: File does not exist:\t${_item}") + return() + endif() + endif() + + cmake_path(ABSOLUTE_PATH _item OUTPUT_VARIABLE _abs_file_name) + cmake_path(GET _item FILENAME _resource_file_name) + set(_dest_resource_file_name "${_ns_VAL}/${_resource_file_name}" ) + + __java_copy_file( ${_abs_file_name} + ${DEST}/${_dest_resource_file_name} + "Copying ${_item} to the build directory") + + list(APPEND RESOURCE_FILES_LIST ${DEST}/${_dest_resource_file_name}) + list(APPEND RELATIVE_RESOURCE_FILES_LIST ${_dest_resource_file_name}) + + endforeach() + + set(${JAVA_RESOURCE_FILES} "${RESOURCE_FILES_LIST}" PARENT_SCOPE) + set(${JAVA_RESOURCE_FILES_RELATIVE} "${RELATIVE_RESOURCE_FILES_LIST}" PARENT_SCOPE) +endfunction() + # define helper scripts set(_JAVA_EXPORT_TARGETS_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/javaTargets.cmake.in) set(_JAVA_CLASS_FILELIST_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/UseJavaClassFilelist.cmake) @@ -746,6 +828,13 @@ function(add_jar _TARGET_NAME) endif () endforeach() + if(_add_jar_RESOURCES) # Process RESOURCES if it exists + __java_copy_resource_namespaces("${_add_jar_RESOURCES}" + ${CMAKE_JAVA_CLASS_OUTPUT_PATH} + _JAVA_RESOURCE_FILES + _JAVA_RESOURCE_FILES_RELATIVE) + endif() + foreach(_JAVA_INCLUDE_JAR IN LISTS _add_jar_INCLUDE_JARS) if (TARGET ${_JAVA_INCLUDE_JAR}) get_target_property(_JAVA_JAR_PATH ${_JAVA_INCLUDE_JAR} JAR_FILE) @@ -795,6 +884,7 @@ function(add_jar _TARGET_NAME) DEPENDS ${_JAVA_COMPILE_FILES} ${_JAVA_COMPILE_FILELISTS} ${_JAVA_COMPILE_DEPENDS} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMENT "Building Java objects for ${_TARGET_NAME}.jar" + VERBATIM ) add_custom_command( OUTPUT ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist @@ -804,6 +894,7 @@ function(add_jar _TARGET_NAME) -P ${_JAVA_CLASS_FILELIST_SCRIPT} DEPENDS ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_compiled_${_TARGET_NAME} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + VERBATIM ) else () # create an empty java_class_filelist @@ -834,6 +925,7 @@ function(add_jar _TARGET_NAME) DEPENDS ${_JAVA_RESOURCE_FILES} ${_JAVA_DEPENDS} ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist WORKING_DIRECTORY ${CMAKE_JAVA_CLASS_OUTPUT_PATH} COMMENT "Creating Java archive ${_JAVA_TARGET_OUTPUT_NAME}" + VERBATIM ) else () add_custom_command( @@ -849,6 +941,7 @@ function(add_jar _TARGET_NAME) WORKING_DIRECTORY ${CMAKE_JAVA_CLASS_OUTPUT_PATH} DEPENDS ${_JAVA_RESOURCE_FILES} ${_JAVA_DEPENDS} ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist COMMENT "Creating Java archive ${_JAVA_TARGET_OUTPUT_NAME}" + VERBATIM ) endif () diff --git a/HDF5Examples/config/cmake/jrunTest.cmake b/HDF5Examples/config/cmake/jrunTest.cmake index 2d91ee2..d7d83d4 100644 --- a/HDF5Examples/config/cmake/jrunTest.cmake +++ b/HDF5Examples/config/cmake/jrunTest.cmake @@ -1,3 +1,14 @@ +# +# Copyright by The HDF Group. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the COPYING file, which can be found at the root of the source code +# distribution tree, or in https://www.hdfgroup.org/licenses. +# If you do not have access to either file, you may request a copy from +# help@hdfgroup.org. +# # jrunTest.cmake executes a command and captures the output in a file. File is then compared # against a reference file. Exit status of command can also be compared. cmake_policy(SET CMP0007 NEW) @@ -36,7 +47,12 @@ else () set (LOG_LEVEL "${TEST_LOG_LEVEL}") endif () -message (STATUS "COMMAND: ${TEST_TESTER} -Xmx1024M -Djava.library.path=\"${TEST_LIBRARY_DIRECTORY}\" -cp \"${TEST_CLASSPATH}\" ${TEST_ARGS} ${TEST_PROGRAM} ${ARGN}") +if (NOT TEST_VOL) + message (STATUS "COMMAND: ${TEST_TESTER} -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=${LOG_LEVEL} -Djava.library.path=\"${TEST_LIBRARY_DIRECTORY}\" -cp \"${TEST_CLASSPATH}\" ${TEST_ARGS} ${TEST_PROGRAM} ${ARGN}") +else () + message (STATUS "USING ${TEST_VOL} ON COMMAND: ${TEST_TESTER} -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=${LOG_LEVEL} -Djava.library.path=\"${TEST_LIBRARY_DIRECTORY}\" -cp \"${TEST_CLASSPATH}\" ${TEST_ARGS} ${TEST_PROGRAM} ${ARGN}") + set (ENV{HDF5_VOL_CONNECTOR} "${TEST_VOL}") +endif () if (WIN32) set (ENV{PATH} "$ENV{PATH}\\;${TEST_LIBRARY_DIRECTORY}") diff --git a/config/cmake/HDF5ExampleCache.cmake b/config/cmake/HDF5ExampleCache.cmake index 6882d25..043be1a 100644 --- a/config/cmake/HDF5ExampleCache.cmake +++ b/config/cmake/HDF5ExampleCache.cmake @@ -1,26 +1,55 @@ -# CMake cache file for external HDF5 filter plugins +# CMake cache file for examples ######################### # EXTERNAL cache entries ######################### -# examples are the tests for plugins -set (H5EX_BUILD_TESTING ON CACHE BOOL "Enable H5PL testing" FORCE) -set (H5EX_BUILD_EXAMPLES ${HDF5_BUILD_EXAMPLES} CACHE BOOL "Build H5PL Examples" FORCE) +# set example options to match build options +set (H5EX_BUILD_TESTING ${BUILD_TESTING} CACHE BOOL "Enable examples testing" FORCE) +set (H5EX_BUILD_EXAMPLES ${HDF5_BUILD_EXAMPLES} CACHE BOOL "Build Examples" FORCE) +set (HDF_BUILD_FORTRAN ${HDF5_BUILD_FORTRAN} CACHE BOOL "Build examples FORTRAN support" FORCE) +set (HDF_BUILD_JAVA ${HDF5_BUILD_JAVA} CACHE BOOL "Build examples JAVA support" FORCE) +set (HDF_BUILD_FILTERS ${HDF5_ENABLE_PLUGIN_SUPPORT} CACHE BOOL "Build examples PLUGIN filter support" FORCE) +set (HDF_BUILD_CPP_LIB ${HDF5_BUILD_CPP_LIB} CACHE BOOL "Build HDF5 C++ Library" FORCE) +set (HDF_BUILD_HL_LIB ${HDF5_BUILD_HL_LIB} CACHE BOOL "Build HIGH Level examples" FORCE) +set (HDF_ENABLE_THREADSAFE ${HDF5_ENABLE_THREADSAFE} CACHE BOOL "Enable examples thread-safety" FORCE) +set (HDF_ENABLE_PARALLEL ${HDF5_ENABLE_PARALLEL} CACHE BOOL "Enable examples parallel build (requires MPI)" FORCE) +set (H5EX_USE_GNU_DIRS ${HDF5_USE_GNU_DIRS} CACHE BOOL "TRUE to use GNU Coding Standard install directory variables, FALSE to use historical settings" FORCE) #preset HDF5 cache vars to this projects libraries instead of searching set (H5EX_HDF5_HEADER "H5pubconf.h" CACHE STRING "Name of HDF5 header" FORCE) #set (H5EX_HDF5_INCLUDE_DIRS $<TARGET_PROPERTY:${HDF5_LIBSH_TARGET},INCLUDE_DIRECTORIES> CACHE PATH "HDF5 include dirs" FORCE) set (H5EX_HDF5_INCLUDE_DIRS "${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR}" CACHE PATH "HDF5 include dirs" FORCE) set (H5EX_HDF5_DIR ${CMAKE_CURRENT_BINARY_DIR} CACHE STRING "HDF5 build folder" FORCE) +set (EXAMPLES_EXTERNALLY_CONFIGURED ON CACHE BOOL "Examples build is used in another project" FORCE) if (NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) set (USE_SHARED_LIBS OFF CACHE BOOL "Use Shared Libraries for Examples" FORCE) set (H5EX_HDF5_LINK_LIBS ${HDF5_LIB_TARGET} CACHE STRING "HDF5 target" FORCE) + if (HDF5_BUILD_FORTRAN) + set (H5EX_HDF5_LINK_LIBS ${H5EX_HDF5_LINK_LIBS} ${HDF5_F90_LIB_TARGET}) + set (HDF_MOD_EXT "/static" CACHE STRING "Use Static Modules for Examples" FORCE) + endif () else () set (USE_SHARED_LIBS ON CACHE BOOL "Use Shared Libraries for Examples" FORCE) set (H5EX_HDF5_LINK_LIBS ${HDF5_LIBSH_TARGET} CACHE STRING "HDF5 target" FORCE) + if (HDF5_BUILD_FORTRAN) + set (H5EX_HDF5_LINK_LIBS ${H5EX_HDF5_LINK_LIBS} ${HDF5_F90_LIBSH_TARGET}) + set (HDF_MOD_EXT "/shared" CACHE STRING "Use Shared Modules for Examples" FORCE) + endif () + if (HDF5_BUILD_JAVA) + set (HDF5_JAVA_INCLUDE_DIRS ${HDF5_JAVA_JARS} ${HDF5_JAVA_LOGGING_JAR}) + set (H5EX_JAVA_LIBRARY ${HDF5_JAVA_JNI_LIB_TARGET}) + set (H5EX_JAVA_LIBRARIES ${HDF5_JAVA_HDF5_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_TARGET}) + set (HDF5_LIBRARY_PATH ${CMAKE_TEST_OUTPUT_DIRECTORY}) + message (STATUS "HDF5 Example java lib: ${H5EX_JAVA_LIBRARY} jars: ${HDF5_JAVA_INCLUDE_DIRS}") + endif () + if (HDF5_ENABLE_PLUGIN_SUPPORT) + set (H5EX_HDF5_PLUGIN_PATH "${CMAKE_BINARY_DIR}/plugins") + endif () endif () +message (STATUS "HDF5 Example link libs: ${H5EX_HDF5_LINK_LIBS} Includes: ${H5EX_HDF5_INCLUDE_DIRS}") +set (HDF5_TOOLS_DIR ${CMAKE_TEST_OUTPUT_DIRECTORY} CACHE STRING "HDF5 Directory for all Executables" FORCE) set (H5EX_HDF5_DUMP_EXECUTABLE $<TARGET_FILE:h5dump${tgt_file_ext}> CACHE STRING "HDF5 h5dump target" FORCE) set (H5EX_HDF5_REPACK_EXECUTABLE $<TARGET_FILE:h5repack${tgt_file_ext}> CACHE STRING "HDF5 h5repack target" FORCE) diff --git a/config/cmake/HDFMacros.cmake b/config/cmake/HDFMacros.cmake index f0b6f03..369df96 100644 --- a/config/cmake/HDFMacros.cmake +++ b/config/cmake/HDFMacros.cmake @@ -11,6 +11,55 @@ # #------------------------------------------------------------------------------- +# Setup output Directories +#----------------------------------------------------------------------------- +macro (SET_HDF_OUTPUT_DIRS package_prefix) + if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED) + set (CMAKE_RUNTIME_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables." + ) + set (CMAKE_LIBRARY_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries" + ) + set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries." + ) + set (CMAKE_Fortran_MODULE_DIRECTORY + ${PROJECT_BINARY_DIR}/mod CACHE PATH "Single Directory for all fortran modules." + ) + get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) + if(_isMultiConfig) + set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF_CFG_NAME}) + set (CMAKE_PDB_OUTPUT_DIRECTORY + ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files." + ) + else () + set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) + endif () + else () + # if we are externally configured, but the project uses old cmake scripts + # this may not be set and utilities like H5detect will fail + if (NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY) + set (CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) + endif () + endif () + + if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + if (CMAKE_HOST_UNIX) + set (CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}" + CACHE PATH "Install path prefix, prepended onto install directories." FORCE) + else () + GetDefaultWindowsPrefixBase(CMAKE_GENERIC_PROGRAM_FILES) + set (CMAKE_INSTALL_PREFIX + "${CMAKE_GENERIC_PROGRAM_FILES}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}" + CACHE PATH "Install path prefix, prepended onto install directories." FORCE) + set (CMAKE_GENERIC_PROGRAM_FILES) + endif () + set (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT 0 CACHE PATH "" FORCE) + endif () +endmacro () + +#------------------------------------------------------------------------------- macro (SET_HDF_BUILD_TYPE) get_property (_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) if (_isMultiConfig) @@ -433,53 +482,10 @@ macro (HDF_DIR_PATHS package_prefix) endif () SET_HDF_BUILD_TYPE() - #----------------------------------------------------------------------------- # Setup output Directories #----------------------------------------------------------------------------- - if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED) - set (CMAKE_RUNTIME_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Executables." - ) - set (CMAKE_LIBRARY_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all Libraries" - ) - set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all static libraries." - ) - set (CMAKE_Fortran_MODULE_DIRECTORY - ${PROJECT_BINARY_DIR}/mod CACHE PATH "Single Directory for all fortran modules." - ) - get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) - if(_isMultiConfig) - set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${HDF_CFG_NAME}) - set (CMAKE_PDB_OUTPUT_DIRECTORY - ${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all pdb files." - ) - else () - set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) - endif () - else () - # if we are externally configured, but the project uses old cmake scripts - # this may not be set and utilities like H5detect will fail - if (NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY) - set (CMAKE_RUNTIME_OUTPUT_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}) - endif () - endif () - - if (NOT ${package_prefix}_EXTERNALLY_CONFIGURED AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) - if (CMAKE_HOST_UNIX) - set (CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}" - CACHE PATH "Install path prefix, prepended onto install directories." FORCE) - else () - GetDefaultWindowsPrefixBase(CMAKE_GENERIC_PROGRAM_FILES) - set (CMAKE_INSTALL_PREFIX - "${CMAKE_GENERIC_PROGRAM_FILES}/HDF_Group/${HDF5_PACKAGE_NAME}/${HDF5_PACKAGE_VERSION}" - CACHE PATH "Install path prefix, prepended onto install directories." FORCE) - set (CMAKE_GENERIC_PROGRAM_FILES) - endif () - set (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT 0 CACHE PATH "" FORCE) - endif () + SET_HDF_OUTPUT_DIRS(${package_prefix}) include (FetchContent) endmacro () diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in index c20e18f..186ae67 100644 --- a/config/cmake/hdf5-config.cmake.in +++ b/config/cmake/hdf5-config.cmake.in @@ -92,8 +92,6 @@ if (${HDF5_PACKAGE_NAME}_BUILD_JAVA) @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-api-2.0.6.jar @PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-nop-2.0.6.jar ) - set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARY "@PACKAGE_CURRENT_BUILD_DIR@/lib") - set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARIES "${${HDF5_PACKAGE_NAME}_JAVA_LIBRARY}") endif () #----------------------------------------------------------------------------- diff --git a/configure.ac b/configure.ac index eace890..689ab3d 100644 --- a/configure.ac +++ b/configure.ac @@ -4205,15 +4205,6 @@ AC_CONFIG_FILES([Makefile java/src/jni/Makefile java/test/Makefile java/test/junit.sh - java/examples/Makefile - java/examples/intro/Makefile - java/examples/intro/JavaIntroExample.sh - java/examples/datasets/Makefile - java/examples/datasets/JavaDatasetExample.sh - java/examples/datatypes/Makefile - java/examples/datatypes/JavaDatatypeExample.sh - java/examples/groups/Makefile - java/examples/groups/JavaGroupExample.sh hl/Makefile hl/src/Makefile hl/test/Makefile @@ -4243,13 +4234,6 @@ if test -n "$TESTPARALLEL"; then fi fi -AC_CONFIG_COMMANDS([.classes], [], [$MKDIR_P java/src/.classes; - $MKDIR_P java/test/.classes; - $MKDIR_P java/examples/intro/.classes; - $MKDIR_P java/examples/datasets/.classes; - $MKDIR_P java/examples/datatypes/.classes; - $MKDIR_P java/examples/groups/.classes]) - AC_OUTPUT chmod 755 bin/h5cc diff --git a/doxygen/dox/LearnBasics3.dox b/doxygen/dox/LearnBasics3.dox index a91368b..eb3dc7c 100644 --- a/doxygen/dox/LearnBasics3.dox +++ b/doxygen/dox/LearnBasics3.dox @@ -715,7 +715,7 @@ When the library is built, the following compile scripts are included: \li h5fc: compile script for HDF5 F90 programs \li h5c++: compile script for HDF5 C++ programs -These scripts are easilye used to compile single file applications, such as those included in the tutorial. +These scripts are easily used to compile single file applications, such as those included in the tutorial. <table> <tr> <th><strong>Warning</strong> diff --git a/hl/tools/h5watch/CMakeLists.txt b/hl/tools/h5watch/CMakeLists.txt index 1eb3618..890ac37 100644 --- a/hl/tools/h5watch/CMakeLists.txt +++ b/hl/tools/h5watch/CMakeLists.txt @@ -12,7 +12,7 @@ set (H5WATCH_SOURCES if (BUILD_STATIC_LIBS) add_executable (h5watch ${H5WATCH_SOURCES}) target_compile_options(h5watch PRIVATE "${HDF5_CMAKE_C_FLAGS}") - target_include_directories (h5watch PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5watch PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5watch STATIC) target_link_libraries (h5watch PRIVATE ${HDF5_HL_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET}) set_target_properties (h5watch PROPERTIES FOLDER tools/hl) @@ -21,7 +21,7 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5watch-shared ${H5WATCH_SOURCES}) target_compile_options(h5watch-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") - target_include_directories (h5watch-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5watch-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5watch-shared SHARED) target_link_libraries (h5watch-shared PRIVATE ${HDF5_HL_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${HDF5_TOOLS_LIBSH_TARGET}) set_target_properties (h5watch-shared PROPERTIES FOLDER tools/hl) diff --git a/java/Makefile.am b/java/Makefile.am index bb8b426..b21f178 100644 --- a/java/Makefile.am +++ b/java/Makefile.am @@ -24,10 +24,8 @@ include $(top_srcdir)/config/commence.am if BUILD_TESTS_CONDITIONAL TESTSERIAL_DIR =test - TESTEXAMPLES_DIR =examples else TESTSERIAL_DIR= - TESTEXAMPLES_DIR= endif ## Only recurse into subdirectories if the Java (JNI) interface is enabled. @@ -36,7 +34,7 @@ if BUILD_JAVA_CONDITIONAL # Mark this directory as part of the JNI API JAVA_API=yes -SUBDIRS=src $(TESTSERIAL_DIR) $(TESTEXAMPLES_DIR) +SUBDIRS=src $(TESTSERIAL_DIR) endif diff --git a/java/examples/CMakeLists.txt b/java/examples/CMakeLists.txt deleted file mode 100644 index f9d0310..0000000 --- a/java/examples/CMakeLists.txt +++ /dev/null @@ -1,7 +0,0 @@ -cmake_minimum_required (VERSION 3.18) -project (HDFJAVA_EXAMPLES Java) - -add_subdirectory (datasets) -add_subdirectory (datatypes) -add_subdirectory (groups) -add_subdirectory (intro) diff --git a/java/examples/Makefile.am b/java/examples/Makefile.am deleted file mode 100644 index eb7b7f5..0000000 --- a/java/examples/Makefile.am +++ /dev/null @@ -1,28 +0,0 @@ -# -# 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. -# -# -# This makefile mostly just reinvokes make in the various subdirectories -# but does so in the correct order. You can alternatively invoke make from -# each subdirectory manually. -## -## Makefile.am -## Run automake to generate a Makefile.in from this file. -## -# -# HDF5 Java Library Examples Makefile(.in) - -include $(top_srcdir)/config/commence.am - -## Only recurse into subdirectories if the Java (JNI) interface is enabled. - SUBDIRS=intro groups datasets datatypes - -include $(top_srcdir)/config/conclude.am diff --git a/java/examples/datasets/CMakeLists.txt b/java/examples/datasets/CMakeLists.txt deleted file mode 100644 index a9a5643..0000000 --- a/java/examples/datasets/CMakeLists.txt +++ /dev/null @@ -1,150 +0,0 @@ -cmake_minimum_required (VERSION 3.18) -project (HDFJAVA_EXAMPLES_DATASETS Java) - -set (CMAKE_VERBOSE_MAKEFILE 1) - -set (HDF_JAVA_EXAMPLES - H5Ex_D_Alloc - H5Ex_D_Checksum - H5Ex_D_Chunk - H5Ex_D_Compact - H5Ex_D_External - H5Ex_D_FillValue - H5Ex_D_Hyperslab - H5Ex_D_ReadWrite - H5Ex_D_UnlimitedAdd - H5Ex_D_UnlimitedMod - H5Ex_D_Nbit - H5Ex_D_Transform - H5Ex_D_Sofloat - H5Ex_D_Soint -) - -set (HDF_JAVA_ZLIB_EXAMPLES - H5Ex_D_Gzip - H5Ex_D_Shuffle - H5Ex_D_UnlimitedGzip -) - -set (HDF_JAVA_SZIP_EXAMPLES - H5Ex_D_Szip -) - -# detect whether the encoder is present. - if (H5_HAVE_FILTER_DEFLATE) - set (${HDF_JAVA_EXAMPLES} ${HDF_JAVA_EXAMPLES} ${HDF_JAVA_ZLIB_EXAMPLES}) - endif () - - if (H5_HAVE_FILTER_SZIP) - set (${HDF_JAVA_EXAMPLES} ${HDF_JAVA_EXAMPLES} ${HDF_JAVA_SZIP_EXAMPLES}) - endif (H5_HAVE_FILTER_SZIP) - -if (WIN32) - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") -else () - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") -endif () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") -endforeach () - -foreach (example ${HDF_JAVA_EXAMPLES}) - file (WRITE ${PROJECT_BINARY_DIR}/${example}_Manifest.txt - "Main-Class: examples.datasets.${example} -" - ) - add_jar (${example} MANIFEST ${PROJECT_BINARY_DIR}/${example}_Manifest.txt ${example}.java) - get_target_property (${example}_JAR_FILE ${example} JAR_FILE) -# install_jar (${example} ${HJAVA_INSTALL_DATA_DIR}/examples examples) - get_target_property (${example}_CLASSPATH ${example} CLASSDIR) - add_dependencies (${example} ${HDF5_JAVA_HDF5_LIB_TARGET}) - - #----------------------------------------------------------------------------- - # Add Target to clang-format - #----------------------------------------------------------------------------- - if (HDF5_ENABLE_FORMATTERS) - clang_format (HDF5_JAVA_${example}_SRC_FORMAT ${example}.java) - endif () -endforeach () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS};${HDF5_JAVA_LOGGING_JAR};${HDF5_JAVA_LOGGING_NOP_JAR}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (HDFJAVA_JAR ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${HDFJAVA_JAR}") -endforeach () - -if (BUILD_TESTING AND HDF5_TEST_EXAMPLES AND HDF5_TEST_SERIAL) - get_property (target_name TARGET ${HDF5_JAVA_JNI_LIB_TARGET} PROPERTY OUTPUT_NAME) - set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${target_name}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") - - set (last_test "") - foreach (example ${HDF_JAVA_EXAMPLES}) - if (example STREQUAL "H5Ex_D_External") - add_test ( - NAME JAVA_datasets-${example}-clear-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.data - ) - else () - add_test ( - NAME JAVA_datasets-${example}-clear-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - endif () - if (last_test) - set_tests_properties (JAVA_datasets-${example}-clear-objects PROPERTIES DEPENDS ${last_test}) - endif () - - add_test ( - NAME JAVA_datasets-${example}-copy-objects - COMMAND ${CMAKE_COMMAND} -E copy_if_different - ${HDFJAVA_EXAMPLES_SOURCE_DIR}/testfiles/examples.datasets.${example}.txt - ${HDFJAVA_EXAMPLES_DATASETS_BINARY_DIR}/${example}.txt - ) - set_tests_properties (JAVA_datasets-${example}-copy-objects PROPERTIES DEPENDS JAVA_datasets-${example}-clear-objects) - - add_test ( - NAME JAVA_datasets-${example} - COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" - -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${example}_JAR_FILE}" - -D "TEST_ARGS:STRING=${CMD_ARGS}" - -D "TEST_PROGRAM=examples.datasets.${example}" - -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}" - -D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}" - -D "TEST_OUTPUT=datasets/${example}.out" - -D "TEST_EXPECT=0" - -D "TEST_REFERENCE=datasets/${example}.txt" - -P "${HDF_RESOURCES_DIR}/jrunTest.cmake" - ) - set_tests_properties (JAVA_datasets-${example} PROPERTIES - DEPENDS JAVA_datasets-${example}-copy-objects - ) - - if (example STREQUAL "H5Ex_D_External") - add_test ( - NAME JAVA_datasets-${example}-clean-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.data - ) - else () - add_test ( - NAME JAVA_datasets-${example}-clean-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - endif () - set_tests_properties (JAVA_datasets-${example}-clean-objects PROPERTIES - DEPENDS JAVA_datasets-${example} - ) - set (last_test "JAVA_datasets-${example}-clean-objects") - endforeach () -endif () diff --git a/java/examples/datasets/H5Ex_D_Alloc.java b/java/examples/datasets/H5Ex_D_Alloc.java deleted file mode 100644 index 4853cc0..0000000 --- a/java/examples/datasets/H5Ex_D_Alloc.java +++ /dev/null @@ -1,294 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to set the space allocation time - for a dataset. The program first creates two datasets, - one with the default allocation time (late) and one with - early allocation time, and displays whether each has been - allocated and their allocation size. Next, it writes data - to the datasets, and again displays whether each has been - allocated and their allocation size. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Alloc { - private static String FILENAME = "H5Ex_D_Alloc.h5"; - private static String DATASETNAME1 = "DS1"; - private static String DATASETNAME2 = "DS2"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int FILLVAL = 99; - private static final int RANK = 2; - - // Values for the status of space allocation - enum H5D_space_status { - H5D_SPACE_STATUS_ERROR(-1), - H5D_SPACE_STATUS_NOT_ALLOCATED(0), - H5D_SPACE_STATUS_PART_ALLOCATED(1), - H5D_SPACE_STATUS_ALLOCATED(2); - private static final Map<Integer, H5D_space_status> lookup = new HashMap<Integer, H5D_space_status>(); - - static - { - for (H5D_space_status s : EnumSet.allOf(H5D_space_status.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5D_space_status(int space_status) { this.code = space_status; } - - public int getCode() { return this.code; } - - public static H5D_space_status get(int code) { return lookup.get(code); } - } - - private static void allocation() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id1 = HDF5Constants.H5I_INVALID_HID; - long dataset_id2 = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - int space_status = 0; - long storage_size = 0; - - // Initialize the dataset. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = FILLVAL; - - // Create a file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, and set the chunk size. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the allocation time to "early". This way we can be sure - // that reading from the dataset immediately after creation will - // return the fill value. - try { - if (dcpl_id >= 0) - H5.H5Pset_alloc_time(dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); - } - catch (Exception e) { - e.printStackTrace(); - } - - System.out.println("Creating datasets..."); - System.out.println(DATASETNAME1 + " has allocation time H5D_ALLOC_TIME_LATE"); - System.out.println(DATASETNAME2 + " has allocation time H5D_ALLOC_TIME_EARLY"); - System.out.println(); - - // Create the dataset using the dataset default creation property list. - try { - if ((file_id >= 0) && (filespace_id >= 0)) - dataset_id1 = H5.H5Dcreate(file_id, DATASETNAME1, HDF5Constants.H5T_NATIVE_INT, filespace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset using the dataset creation property list. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id2 = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_NATIVE_INT, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print space status and storage size for dset1. - try { - if (dataset_id1 >= 0) - space_status = H5.H5Dget_space_status(dataset_id1); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (dataset_id1 >= 0) - storage_size = H5.H5Dget_storage_size(dataset_id1); - } - catch (Exception e) { - e.printStackTrace(); - } - String the_space = " "; - if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) - the_space += "not "; - System.out.println("Space for " + DATASETNAME1 + " has" + the_space + "been allocated."); - System.out.println("Storage size for " + DATASETNAME1 + " is: " + storage_size + " bytes."); - - // Retrieve and print space status and storage size for dset2. - try { - if (dataset_id2 >= 0) - space_status = H5.H5Dget_space_status(dataset_id2); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (dataset_id2 >= 0) - storage_size = H5.H5Dget_storage_size(dataset_id2); - } - catch (Exception e) { - e.printStackTrace(); - } - the_space = " "; - if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) - the_space += "not "; - System.out.println("Space for " + DATASETNAME2 + " has" + the_space + "been allocated."); - System.out.println("Storage size for " + DATASETNAME2 + " is: " + storage_size + " bytes."); - System.out.println(); - - System.out.println("Writing data..."); - System.out.println(); - - // Write the data to the datasets. - try { - if (dataset_id1 >= 0) - H5.H5Dwrite(dataset_id1, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data[0]); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (dataset_id2 >= 0) - H5.H5Dwrite(dataset_id2, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data[0]); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print space status and storage size for dset1. - try { - if (dataset_id1 >= 0) - space_status = H5.H5Dget_space_status(dataset_id1); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (dataset_id1 >= 0) - storage_size = H5.H5Dget_storage_size(dataset_id1); - } - catch (Exception e) { - e.printStackTrace(); - } - the_space = " "; - if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) - the_space += "not "; - System.out.println("Space for " + DATASETNAME1 + " has" + the_space + "been allocated."); - System.out.println("Storage size for " + DATASETNAME1 + " is: " + storage_size + " bytes."); - - // Retrieve and print space status and storage size for dset2. - try { - if (dataset_id2 >= 0) - space_status = H5.H5Dget_space_status(dataset_id2); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (dataset_id2 >= 0) - storage_size = H5.H5Dget_storage_size(dataset_id2); - } - catch (Exception e) { - e.printStackTrace(); - } - the_space = " "; - if (H5D_space_status.get(space_status) != H5D_space_status.H5D_SPACE_STATUS_ALLOCATED) - the_space += "not "; - System.out.println("Space for " + DATASETNAME2 + " has" + the_space + "been allocated."); - System.out.println("Storage size for " + DATASETNAME2 + " is: " + storage_size + " bytes."); - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id1 >= 0) - H5.H5Dclose(dataset_id1); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id2 >= 0) - H5.H5Dclose(dataset_id2); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5Ex_D_Alloc.allocation(); } -} diff --git a/java/examples/datasets/H5Ex_D_Checksum.java b/java/examples/datasets/H5Ex_D_Checksum.java deleted file mode 100644 index 7b01176..0000000 --- a/java/examples/datasets/H5Ex_D_Checksum.java +++ /dev/null @@ -1,350 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using the Fletcher32 checksum filter. The program first - checks if the Fletcher32 filter is available, then if it - is it writes integers to a dataset using Fletcher32, then - closes the file. Next, it reopens the file, reads back - the data, checks if the filter detected an error and - outputs the type of filter and the maximum value in the - dataset to the screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Checksum { - private static String FILENAME = "H5Ex_D_Checksum.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 32; - private static final int DIM_Y = 64; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 8; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(-1), - H5Z_FILTER_NONE(0), - H5Z_FILTER_DEFLATE(1), - H5Z_FILTER_SHUFFLE(2), - H5Z_FILTER_FLETCHER32(3), - H5Z_FILTER_SZIP(4), - H5Z_FILTER_NBIT(5), - H5Z_FILTER_SCALEOFFSET(6), - H5Z_FILTER_RESERVED(256), - H5Z_FILTER_MAX(65535); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkFletcher32Filter() - { - try { - int available = H5.H5Zfilter_avail(H5Z_filter.H5Z_FILTER_FLETCHER32.getCode()); - if (available == 0) { - System.out.println("N-Bit filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_FLETCHER32); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("N-Bit filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeChecksum() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, add the N-Bit filter. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - if (dcpl_id >= 0) { - H5.H5Pset_fletcher32(dcpl_id); - // Set the chunk size. - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readChecksum() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the filter type. Here we only retrieve the - // first filter because we know that we only added one filter. - try { - if (dcpl_id >= 0) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name, - filter_config); - System.out.print("Filter type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) { - int status = H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - // Check if the read was successful. Normally we do not perform - // error checking in these examples for the sake of clarity, but in - // this case we will make an exception because this is how the - // fletcher32 checksum filter reports data errors. - if (status < 0) { - System.out.print("Dataset read failed!"); - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - return; - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Find the maximum value in the dataset, to verify that it was read - // correctly. - int max = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) { - for (int jndx = 0; jndx < DIM_Y; jndx++) - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - } - // Print the maximum value. - System.out.println("Maximum value in " + DATASETNAME + " is: " + max); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - // Check if the Fletcher32 filter is available and can be used for - // both encoding and decoding. Normally we do not perform error - // checking in these examples for the sake of clarity, but in this - // case we will make an exception because this filter is an - // optional part of the hdf5 library. - // size to be the current size. - if (H5Ex_D_Checksum.checkFletcher32Filter()) { - H5Ex_D_Checksum.writeChecksum(); - H5Ex_D_Checksum.readChecksum(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_Chunk.java b/java/examples/datasets/H5Ex_D_Chunk.java deleted file mode 100644 index fbfc148..0000000 --- a/java/examples/datasets/H5Ex_D_Chunk.java +++ /dev/null @@ -1,371 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to create a chunked dataset. The - program first writes integers in a hyperslab selection to - a chunked dataset with dataspace dimensions of DIM_XxDIM_Y - and chunk size of CHUNK_XxCHUNK_Y, then closes the file. - Next, it reopens the file, reads back the data, and - outputs it to the screen. Finally it reads the data again - using a different hyperslab selection, and outputs - the result to the screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Chunk { - private static String FILENAME = "H5Ex_D_Chunk.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 6; - private static final int DIM_Y = 8; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 4; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5D_layout { - H5D_LAYOUT_ERROR(-1), - H5D_COMPACT(0), - H5D_CONTIGUOUS(1), - H5D_CHUNKED(2), - H5D_VIRTUAL(3), - H5D_NLAYOUTS(4); - private static final Map<Integer, H5D_layout> lookup = new HashMap<Integer, H5D_layout>(); - - static - { - for (H5D_layout s : EnumSet.allOf(H5D_layout.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5D_layout(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5D_layout get(int code) { return lookup.get(code); } - } - - private static void writeChunk() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data to "1", to make it easier to see the selections. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = 1; - - // Print the data to the screen. - System.out.println("Original Data:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the chunk size. - try { - if (dcpl_id >= 0) - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the chunked dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Define and select the first part of the hyperslab selection. - long[] start = {0, 0}; - long[] stride = {3, 3}; - long[] count = {2, 3}; - long[] block = {2, 2}; - try { - if ((filespace_id >= 0)) - H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count, - block); - } - catch (Exception e) { - e.printStackTrace(); - } - // Define and select the second part of the hyperslab selection, - // which is subtracted from the first selection by the use of - // H5S_SELECT_NOTB - block[0] = 1; - block[1] = 1; - try { - if ((filespace_id >= 0)) { - H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_NOTB, start, stride, count, - block); - - // Write the data to the dataset. - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, filespace_id, - HDF5Constants.H5P_DEFAULT, dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readChunk() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Print the storage layout. - try { - if (dcpl_id >= 0) { - int layout_type = H5.H5Pget_layout(dcpl_id); - System.out.print("Storage layout for " + DATASETNAME + " is: "); - switch (H5D_layout.get(layout_type)) { - case H5D_COMPACT: - System.out.println("H5D_COMPACT"); - break; - case H5D_CONTIGUOUS: - System.out.println("H5D_CONTIGUOUS"); - break; - case H5D_CHUNKED: - System.out.println("H5D_CHUNKED"); - break; - case H5D_VIRTUAL: - System.out.println("H5D_VIRTUAL"); - break; - case H5D_LAYOUT_ERROR: - break; - case H5D_NLAYOUTS: - break; - default: - break; - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Data as written to disk by hyberslabs:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Initialize the read array. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = 0; - - // Define and select the hyperslab to use for reading. - try { - if (dataset_id >= 0) { - filespace_id = H5.H5Dget_space(dataset_id); - - long[] start = {0, 1}; - long[] stride = {4, 4}; - long[] count = {2, 2}; - long[] block = {2, 3}; - - if (filespace_id >= 0) { - H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count, - block); - - // Read the data using the previously defined hyperslab. - if ((dataset_id >= 0) && (filespace_id >= 0)) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - filespace_id, HDF5Constants.H5P_DEFAULT, dset_data); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Data as read from disk by hyberslab:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_Chunk.writeChunk(); - H5Ex_D_Chunk.readChunk(); - } -} diff --git a/java/examples/datasets/H5Ex_D_Compact.java b/java/examples/datasets/H5Ex_D_Compact.java deleted file mode 100644 index 3a60283..0000000 --- a/java/examples/datasets/H5Ex_D_Compact.java +++ /dev/null @@ -1,291 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a compact - dataset. The program first writes integers to a compact - dataset with dataspace dimensions of DIM_XxDIM_Y, then - closes the file. Next, it reopens the file, reads back - the data, and outputs it to the screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Compact { - private static String FILENAME = "H5Ex_D_Compact.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int RANK = 2; - - // Values for the status of space allocation - enum H5D_layout { - H5D_LAYOUT_ERROR(-1), - H5D_COMPACT(0), - H5D_CONTIGUOUS(1), - H5D_CHUNKED(2), - H5D_VIRTUAL(3), - H5D_NLAYOUTS(4); - private static final Map<Integer, H5D_layout> lookup = new HashMap<Integer, H5D_layout>(); - - static - { - for (H5D_layout s : EnumSet.allOf(H5D_layout.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5D_layout(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5D_layout get(int code) { return lookup.get(code); } - } - - private static void writeCompact() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the layout to compact. - try { - if (dcpl_id >= 0) - H5.H5Pset_layout(dcpl_id, H5D_layout.H5D_COMPACT.getCode()); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. We will use all default properties for this example. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readCompact() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open file and dataset using the default properties. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Print the storage layout. - try { - if (dcpl_id >= 0) { - int layout_type = H5.H5Pget_layout(dcpl_id); - System.out.print("Storage layout for " + DATASETNAME + " is: "); - switch (H5D_layout.get(layout_type)) { - case H5D_COMPACT: - System.out.println("H5D_COMPACT"); - break; - case H5D_CONTIGUOUS: - System.out.println("H5D_CONTIGUOUS"); - break; - case H5D_CHUNKED: - System.out.println("H5D_CHUNKED"); - break; - case H5D_VIRTUAL: - System.out.println("H5D_VIRTUAL"); - break; - case H5D_LAYOUT_ERROR: - break; - case H5D_NLAYOUTS: - break; - default: - break; - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Data for " + DATASETNAME + " is: "); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_Compact.writeCompact(); - H5Ex_D_Compact.readCompact(); - } -} diff --git a/java/examples/datasets/H5Ex_D_External.java b/java/examples/datasets/H5Ex_D_External.java deleted file mode 100644 index d706fb7..0000000 --- a/java/examples/datasets/H5Ex_D_External.java +++ /dev/null @@ -1,236 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to an - external dataset. The program first writes integers to an - external dataset with dataspace dimensions of DIM_XxDIM_Y, - then closes the file. Next, it reopens the file, reads - back the data, and outputs the name of the external data - file and the data to the screen. - ************************************************************/ -package examples.datasets; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_External { - private static String FILENAME = "H5Ex_D_External.h5"; - private static String EXTERNALNAME = "H5Ex_D_External.data"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int RANK = 2; - private static final int NAME_BUF_SIZE = 32; - - private static void writeExternal() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize the dataset. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // set the external file. - try { - if (dcpl_id >= 0) - H5.H5Pset_external(dcpl_id, EXTERNALNAME, 0, HDF5Constants.H5F_UNLIMITED); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the HDF5Constants.dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readExternal() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - String[] Xname = new String[1]; - - // Open file using the default properties. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open dataset using the default properties. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the name of the external file. - long[] Xsize = new long[NAME_BUF_SIZE]; - try { - if (dcpl_id >= 0) - H5.H5Pget_external(dcpl_id, 0, Xsize.length, Xname, Xsize); - } - catch (Exception e) { - e.printStackTrace(); - } - System.out.println(DATASETNAME + " is stored in file: " + Xname[0]); - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println(DATASETNAME + ":"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Close the dataset. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_External.writeExternal(); - H5Ex_D_External.readExternal(); - } -} diff --git a/java/examples/datasets/H5Ex_D_FillValue.java b/java/examples/datasets/H5Ex_D_FillValue.java deleted file mode 100644 index db4dff7..0000000 --- a/java/examples/datasets/H5Ex_D_FillValue.java +++ /dev/null @@ -1,240 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to set the fill value for a - dataset. The program first sets the fill value to - FILLVAL, creates a dataset with dimensions of DIM_XxDIM_Y, - reads from the uninitialized dataset, and outputs the - contents to the screen. Next, it writes integers to the - dataset, reads the data back, and outputs it to the - screen. Finally it extends the dataset, reads from it, - and outputs the result to the screen. - ************************************************************/ -package examples.datasets; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_FillValue { - private static String FILENAME = "H5Ex_D_FillValue.h5"; - private static String DATASETNAME = "ExtendibleArray"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int EDIM_X = 6; - private static final int EDIM_Y = 10; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 4; - private static final int RANK = 2; - private static final int NDIMS = 2; - private static final int FILLVAL = 99; - - private static void fillValue() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] extdims = {EDIM_X, EDIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - long[] maxdims = {HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED}; - int[][] write_dset_data = new int[DIM_X][DIM_Y]; - int[][] read_dset_data = new int[DIM_X][DIM_Y]; - int[][] extend_dset_data = new int[EDIM_X][EDIM_Y]; - - // Initialize the dataset. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - write_dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace with unlimited dimensions. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the chunk size. - try { - if (dcpl_id >= 0) - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the fill value for the dataset - try { - int[] fill_value = {FILLVAL}; - if (dcpl_id >= 0) - H5.H5Pset_fill_value(dcpl_id, HDF5Constants.H5T_NATIVE_INT, fill_value); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the allocation time to "early". This way we can be sure - // that reading from the dataset immediately after creation will - // return the fill value. - try { - if (dcpl_id >= 0) - H5.H5Pset_alloc_time(dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset using the dataset creation property list. - try { - if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read values from the dataset, which has not been written to yet. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset before being written to:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(read_dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, write_dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data back. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset after being written to:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(read_dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Extend the dataset. - try { - if (dataset_id >= 0) - H5.H5Dset_extent(dataset_id, extdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read from the extended dataset. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, extend_dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset after extension:"); - for (int indx = 0; indx < EDIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < EDIM_Y; jndx++) - System.out.print(extend_dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5Ex_D_FillValue.fillValue(); } -} diff --git a/java/examples/datasets/H5Ex_D_Gzip.java b/java/examples/datasets/H5Ex_D_Gzip.java deleted file mode 100644 index 0a94254..0000000 --- a/java/examples/datasets/H5Ex_D_Gzip.java +++ /dev/null @@ -1,336 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using gzip compression (also called zlib or deflate). The - program first checks if gzip compression is available, - then if it is it writes integers to a dataset using gzip, - then closes the file. Next, it reopens the file, reads - back the data, and outputs the type of compression and the - maximum value in the dataset to the screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Gzip { - private static String FILENAME = "H5Ex_D_Gzip.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 32; - private static final int DIM_Y = 64; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 8; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR), - H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), - H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE), - H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), - H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32), - H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), - H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT), - H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), - H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED), - H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkGzipFilter() - { - try { - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE); - if (available == 0) { - System.out.println("gzip filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("gzip filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeGzip() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, add the gzip compression - // filter. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - if (dcpl_id >= 0) { - H5.H5Pset_deflate(dcpl_id, 9); - // Set the chunk size. - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readGzip() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the filter type. Here we only retrieve the - // first filter because we know that we only added one filter. - try { - if (dcpl_id >= 0) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name, - filter_config); - System.out.print("Filter type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - case H5Z_FILTER_NBIT: - System.out.println("H5Z_FILTER_NBIT"); - break; - case H5Z_FILTER_SCALEOFFSET: - System.out.println("H5Z_FILTER_SCALEOFFSET"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) { - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Find the maximum value in the dataset, to verify that it was read - // correctly. - int max = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) { - for (int jndx = 0; jndx < DIM_Y; jndx++) - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - } - // Print the maximum value. - System.out.println("Maximum value in " + DATASETNAME + " is: " + max); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - // Check if gzip compression is available and can be used for both - // compression and decompression. Normally we do not perform error - // checking in these examples for the sake of clarity, but in this - // case we will make an exception because this filter is an - // optional part of the hdf5 library. - if (H5Ex_D_Gzip.checkGzipFilter()) { - H5Ex_D_Gzip.writeGzip(); - H5Ex_D_Gzip.readGzip(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_Hyperslab.java b/java/examples/datasets/H5Ex_D_Hyperslab.java deleted file mode 100644 index 0575d50..0000000 --- a/java/examples/datasets/H5Ex_D_Hyperslab.java +++ /dev/null @@ -1,272 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a - dataset by hyberslabs. The program first writes integers - in a hyperslab selection to a dataset with dataspace - dimensions of DIM_XxDIM_Y, then closes the file. Next, it - reopens the file, reads back the data, and outputs it to - the screen. Finally it reads the data again using a - different hyperslab selection, and outputs the result to - the screen. - ************************************************************/ -package examples.datasets; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Hyperslab { - private static String FILENAME = "H5Ex_D_Hyperslab.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 6; - private static final int DIM_Y = 8; - private static final int RANK = 2; - - private static void writeHyperslab() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data to "1", to make it easier to see the selections. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = 1; - - // Print the data to the screen. - System.out.println("Original Data:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. We will use all default properties for this example. - try { - if ((file_id >= 0) && (filespace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Define and select the first part of the hyperslab selection. - long[] start = {0, 0}; - long[] stride = {3, 3}; - long[] count = {2, 3}; - long[] block = {2, 2}; - try { - if ((filespace_id >= 0)) - H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count, - block); - } - catch (Exception e) { - e.printStackTrace(); - } - // Define and select the second part of the hyperslab selection, - // which is subtracted from the first selection by the use of - // H5S_SELECT_NOTB - block[0] = 1; - block[1] = 1; - try { - if ((filespace_id >= 0)) { - H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_NOTB, start, stride, count, - block); - - // Write the data to the dataset. - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, filespace_id, - HDF5Constants.H5P_DEFAULT, dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readHyperslab() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Data as written to disk by hyberslabs:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Initialize the read array. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = 0; - - // Define and select the hyperslab to use for reading. - try { - if (dataset_id >= 0) { - filespace_id = H5.H5Dget_space(dataset_id); - - long[] start = {0, 1}; - long[] stride = {4, 4}; - long[] count = {2, 2}; - long[] block = {2, 3}; - - if (filespace_id >= 0) { - H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count, - block); - - // Read the data using the previously defined hyperslab. - if ((dataset_id >= 0) && (filespace_id >= 0)) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - filespace_id, HDF5Constants.H5P_DEFAULT, dset_data); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Data as read from disk by hyberslab:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_Hyperslab.writeHyperslab(); - H5Ex_D_Hyperslab.readHyperslab(); - } -} diff --git a/java/examples/datasets/H5Ex_D_Nbit.java b/java/examples/datasets/H5Ex_D_Nbit.java deleted file mode 100644 index d54ce21..0000000 --- a/java/examples/datasets/H5Ex_D_Nbit.java +++ /dev/null @@ -1,305 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using the N-Bit filter. The program first checks if the - N-Bit filter is available, then if it is it writes integers - to a dataset using N-Bit, then closes the file. Next, it - reopens the file, reads back the data, and outputs the type - of filter and the maximum value in the dataset to the screen. - ************************************************************/ - -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Nbit { - private static String FILENAME = "H5Ex_D_Nbit.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 32; - private static final int DIM_Y = 64; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 8; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR), - H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), - H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE), - H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), - H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32), - H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), - H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT), - H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), - H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED), - H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkNbitFilter() - { - try { - // Check if N-Bit compression is available and can be used for both compression and decompression. - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_NBIT); - if (available == 0) { - System.out.println("N-Bit filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_NBIT); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("N-Bit filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeData() throws Exception - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dtype_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - try { - // Create a new file using the default properties. - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - filespace_id = H5.H5Screate_simple(RANK, dims, null); - - // Create the datatype to use with the N-Bit filter. It has an uncompressed size of 32 bits, - // but will have a size of 16 bits after being packed by the N-Bit filter. - dtype_id = H5.H5Tcopy(HDF5Constants.H5T_STD_I32LE); - H5.H5Tset_precision(dtype_id, 16); - H5.H5Tset_offset(dtype_id, 5); - - // Create the dataset creation property list, add the N-Bit filter and set the chunk size. - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - H5.H5Pset_nbit(dcpl_id); - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - - // Create the dataset. - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, dtype_id, filespace_id, HDF5Constants.H5P_DEFAULT, - dcpl_id, HDF5Constants.H5P_DEFAULT); - - // Write the data to the dataset. - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - finally { - // Close and release resources. - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - if (dtype_id >= 0) - H5.H5Tclose(dtype_id); - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - if (file_id >= 0) - H5.H5Fclose(file_id); - } - } - - private static void readData() throws Exception - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the filter type. Here we only retrieve the - // first filter because we know that we only added one filter. - try { - if (dcpl_id >= 0) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name, - filter_config); - System.out.print("Filter type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - case H5Z_FILTER_NBIT: - System.out.println("H5Z_FILTER_NBIT"); - break; - case H5Z_FILTER_SCALEOFFSET: - System.out.println("H5Z_FILTER_SCALEOFFSET"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) { - int status = H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - // Check if the read was successful. - if (status < 0) - System.out.print("Dataset read failed!"); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Find the maximum value in the dataset, to verify that it was read - // correctly. - int max = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) { - for (int jndx = 0; jndx < DIM_Y; jndx++) - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - } - // Print the maximum value. - System.out.println("Maximum value in " + DATASETNAME + " is: " + max); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - /* - * Check if N-Bit compression is available and can be used for both compression and decompression. - * Normally we do not perform error checking in these examples for the sake of clarity, but in this - * case we will make an exception because this filter is an optional part of the hdf5 library. - */ - try { - if (H5Ex_D_Nbit.checkNbitFilter()) { - H5Ex_D_Nbit.writeData(); - H5Ex_D_Nbit.readData(); - } - } - catch (Exception ex) { - ex.printStackTrace(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_ReadWrite.java b/java/examples/datasets/H5Ex_D_ReadWrite.java deleted file mode 100644 index 4b26a2c..0000000 --- a/java/examples/datasets/H5Ex_D_ReadWrite.java +++ /dev/null @@ -1,179 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - - This example shows how to read and write data to a - dataset. The program first writes integers to a dataset - with dataspace dimensions of DIM_XxDIM_Y, then closes the - file. Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ -package examples.datasets; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_ReadWrite { - private static String FILENAME = "H5Ex_D_ReadWrite.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int RANK = 2; - - private static void WriteDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. We will use all default properties for this example. - try { - if ((file_id >= 0) && (filespace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open file using the default properties. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open dataset using the default properties. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println(DATASETNAME + ":"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // Close the dataset. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_ReadWrite.WriteDataset(); - H5Ex_D_ReadWrite.ReadDataset(); - } -} diff --git a/java/examples/datasets/H5Ex_D_Shuffle.java b/java/examples/datasets/H5Ex_D_Shuffle.java deleted file mode 100644 index 3d80f7d..0000000 --- a/java/examples/datasets/H5Ex_D_Shuffle.java +++ /dev/null @@ -1,374 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using the shuffle filter with gzip compression. The - program first checks if the shuffle and gzip filters are - available, then if they are it writes integers to a - dataset using shuffle+gzip, then closes the file. Next, - it reopens the file, reads back the data, and outputs the - types of filters and the maximum value in the dataset to - the screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Shuffle { - private static String FILENAME = "H5Ex_D_Shuffle.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 32; - private static final int DIM_Y = 64; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 8; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR), - H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), - H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE), - H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), - H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32), - H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), - H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT), - H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), - H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED), - H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkGzipFilter() - { - try { - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE); - if (available == 0) { - System.out.println("gzip filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("gzip filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static boolean checkShuffleFilter() - { - try { - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE); - if (available == 0) { - System.out.println("Shuffle filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("Shuffle filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeShuffle() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, add the shuffle - // filter and the gzip compression filter. - // The order in which the filters are added here is significant - - // we will see much greater results when the shuffle is applied - // first. The order in which the filters are added to the property - // list is the order in which they will be invoked when writing - // data. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - if (dcpl_id >= 0) { - H5.H5Pset_shuffle(dcpl_id); - H5.H5Pset_deflate(dcpl_id, 9); - // Set the chunk size. - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readShuffle() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the number of filters, and retrieve and print the - // type of each. - try { - if (dcpl_id >= 0) { - int nfilters = H5.H5Pget_nfilters(dcpl_id); - for (int indx = 0; indx < nfilters; indx++) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - filter_type = H5.H5Pget_filter(dcpl_id, indx, flags, cd_nelmts, cd_values, 120, - filter_name, filter_config); - System.out.print("Filter " + indx + ": Type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - case H5Z_FILTER_NBIT: - System.out.println("H5Z_FILTER_NBIT"); - break; - case H5Z_FILTER_SCALEOFFSET: - System.out.println("H5Z_FILTER_SCALEOFFSET"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) { - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Find the maximum value in the dataset, to verify that it was read - // correctly. - int max = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) { - for (int jndx = 0; jndx < DIM_Y; jndx++) - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - } - // Print the maximum value. - System.out.println("Maximum value in " + DATASETNAME + " is: " + max); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - // Check if gzip compression is available and can be used for both - // compression and decompression. Normally we do not perform error - // checking in these examples for the sake of clarity, but in this - // case we will make an exception because this filter is an - // optional part of the hdf5 library. - // Similarly, check for availability of the shuffle filter. - if (H5Ex_D_Shuffle.checkGzipFilter() && H5Ex_D_Shuffle.checkShuffleFilter()) { - H5Ex_D_Shuffle.writeShuffle(); - H5Ex_D_Shuffle.readShuffle(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_Sofloat.java b/java/examples/datasets/H5Ex_D_Sofloat.java deleted file mode 100644 index a5f5cd8..0000000 --- a/java/examples/datasets/H5Ex_D_Sofloat.java +++ /dev/null @@ -1,362 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using the Scale-Offset filter. The program first checks - if the Scale-Offset filter is available, then if it is it - writes floating point numbers to a dataset using - Scale-Offset, then closes the file Next, it reopens the - file, reads back the data, and outputs the type of filter - and the maximum value in the dataset to the screen. - ************************************************************/ -package examples.datasets; - -import java.text.DecimalFormat; -import java.text.DecimalFormatSymbols; -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Locale; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Sofloat { - - private static String FILENAME = "H5Ex_D_Sofloat.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 32; - private static final int DIM_Y = 64; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 8; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR), - H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), - H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE), - H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), - H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32), - H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), - H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT), - H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), - H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED), - H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkScaleoffsetFilter() - { - try { - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET); - if (available == 0) { - System.out.println("Scale-Offset filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("Scale-Offset filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeData() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - double[][] dset_data = new double[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) { - double x = indx; - double y = jndx; - dset_data[indx][jndx] = (x + 1) / (y + 0.3) + y; - } - - // Find the maximum value in the dataset, to verify that it was read correctly. - double max = dset_data[0][0]; - double min = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) { - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - if (min > dset_data[indx][jndx]) - min = dset_data[indx][jndx]; - } - - // Print the maximum value. - DecimalFormat df = new DecimalFormat("#,##0.000000", new DecimalFormatSymbols(Locale.US)); - System.out.println("Maximum value in write buffer is: " + df.format(max)); - System.out.println("Minimum value in write buffer is: " + df.format(min)); - - // Create a new file using the default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, add the Scale-Offset - // filter and set the chunk size. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - if (dcpl_id >= 0) { - H5.H5Pset_scaleoffset(dcpl_id, HDF5Constants.H5Z_SO_FLOAT_DSCALE, 2); - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_IEEE_F64LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close and release resources. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close file - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readData() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - double[][] dset_data = new double[DIM_X][DIM_Y]; - - // Open file using the default properties. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - // Open dataset using the default properties. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the filter type. Here we only retrieve the - // first filter because we know that we only added one filter. - try { - if (dcpl_id >= 0) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - - filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name, - filter_config); - System.out.print("Filter type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - case H5Z_FILTER_NBIT: - System.out.println("H5Z_FILTER_NBIT"); - break; - case H5Z_FILTER_SCALEOFFSET: - System.out.println("H5Z_FILTER_SCALEOFFSET"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Find the maximum value in the dataset, to verify that it was read correctly. - double max = dset_data[0][0]; - double min = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) { - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - if (min > dset_data[indx][jndx]) - min = dset_data[indx][jndx]; - } - - // Print the maximum value. - DecimalFormat df = new DecimalFormat("#,##0.000000", new DecimalFormatSymbols(Locale.US)); - System.out.println("Maximum value in " + DATASETNAME + " is: " + df.format(max)); - System.out.println("Minimum value in " + DATASETNAME + " is: " + df.format(min)); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - - // Check if Scale-Offset compression is available and can be used - // for both compression and decompression. Normally we do not - // perform error checking in these examples for the sake of - // clarity, but in this case we will make an exception because this - // filter is an optional part of the hdf5 library. - if (H5Ex_D_Sofloat.checkScaleoffsetFilter()) { - H5Ex_D_Sofloat.writeData(); - H5Ex_D_Sofloat.readData(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_Soint.java b/java/examples/datasets/H5Ex_D_Soint.java deleted file mode 100644 index 3eb8e37..0000000 --- a/java/examples/datasets/H5Ex_D_Soint.java +++ /dev/null @@ -1,336 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using the Scale-Offset filter. The program first checks - if the Scale-Offset filter is available, then if it is it - writes integers to a dataset using Scale-Offset, then - closes the file Next, it reopens the file, reads back the - data, and outputs the type of filter and the maximum value - in the dataset to the screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Soint { - - private static String FILENAME = "H5Ex_D_Soint.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 32; - private static final int DIM_Y = 64; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 8; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR), - H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), - H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE), - H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), - H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32), - H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), - H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT), - H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), - H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED), - H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkScaleoffsetFilter() - { - try { - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SCALEOFFSET); - if (available == 0) { - System.out.println("Scale-Offset filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SCALEOFFSET); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("Scale-Offset filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeData() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using the default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, add the Scale-Offset - // filter and set the chunk size. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - if (dcpl_id >= 0) { - H5.H5Pset_scaleoffset(dcpl_id, HDF5Constants.H5Z_SO_INT, - HDF5Constants.H5Z_SO_INT_MINBITS_DEFAULT); - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close and release resources. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close file - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readData() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open file using the default properties. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - // Open dataset using the default properties. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the filter type. Here we only retrieve the - // first filter because we know that we only added one filter. - try { - if (dcpl_id >= 0) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - - filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name, - filter_config); - System.out.print("Filter type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - case H5Z_FILTER_NBIT: - System.out.println("H5Z_FILTER_NBIT"); - break; - case H5Z_FILTER_SCALEOFFSET: - System.out.println("H5Z_FILTER_SCALEOFFSET"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Find the maximum value in the dataset, to verify that it was read correctly. - int max = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) { - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - } - - // Print the maximum value. - System.out.println("Maximum value in " + DATASETNAME + " is: " + max); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - - // Check if Scale-Offset compression is available and can be used - // for both compression and decompression. Normally we do not - // perform error checking in these examples for the sake of - // clarity, but in this case we will make an exception because this - // filter is an optional part of the hdf5 library. - if (H5Ex_D_Soint.checkScaleoffsetFilter()) { - H5Ex_D_Soint.writeData(); - H5Ex_D_Soint.readData(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_Szip.java b/java/examples/datasets/H5Ex_D_Szip.java deleted file mode 100644 index 0426a87..0000000 --- a/java/examples/datasets/H5Ex_D_Szip.java +++ /dev/null @@ -1,337 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using szip compression. The program first checks if - szip compression is available, then if it is it writes - integers to a dataset using szip, then closes the file. - Next, it reopens the file, reads back the data, and - outputs the type of compression and the maximum value in - the dataset to the screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Szip { - private static String FILENAME = "H5Ex_D_Szip.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 32; - private static final int DIM_Y = 64; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 8; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR), - H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), - H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE), - H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), - H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32), - H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), - H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT), - H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), - H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED), - H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkSzipFilter() - { - try { - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP); - if (available == 0) { - System.out.println("szip filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SZIP); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("szip filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeSzip() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, add the szip compression - // filter. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - if (dcpl_id >= 0) { - H5.H5Pset_szip(dcpl_id, HDF5Constants.H5_SZIP_NN_OPTION_MASK, 8); - // Set the chunk size. - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readSzip() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the filter type. Here we only retrieve the - // first filter because we know that we only added one filter. - try { - if (dcpl_id >= 0) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - - filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name, - filter_config); - System.out.print("Filter type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - case H5Z_FILTER_NBIT: - System.out.println("H5Z_FILTER_NBIT"); - break; - case H5Z_FILTER_SCALEOFFSET: - System.out.println("H5Z_FILTER_SCALEOFFSET"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) { - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Find the maximum value in the dataset, to verify that it was read - // correctly. - int max = dset_data[0][0]; - for (int indx = 0; indx < DIM_X; indx++) { - for (int jndx = 0; jndx < DIM_Y; jndx++) - if (max < dset_data[indx][jndx]) - max = dset_data[indx][jndx]; - } - // Print the maximum value. - System.out.println("Maximum value in " + DATASETNAME + " is: " + max); - - // End access to the dataset and release resources used by it. - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - // Check if gzip compression is available and can be used for both - // compression and decompression. Normally we do not perform error - // checking in these examples for the sake of clarity, but in this - // case we will make an exception because this filter is an - // optional part of the hdf5 library. - if (H5Ex_D_Szip.checkSzipFilter()) { - H5Ex_D_Szip.writeSzip(); - H5Ex_D_Szip.readSzip(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_Transform.java b/java/examples/datasets/H5Ex_D_Transform.java deleted file mode 100644 index 16ab423..0000000 --- a/java/examples/datasets/H5Ex_D_Transform.java +++ /dev/null @@ -1,250 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write data to a dataset - using a data transform expression. The program first - writes integers to a dataset using the transform - expression TRANSFORM, then closes the file. Next, it - reopens the file, reads back the data without a transform, - and outputs the data to the screen. Finally it reads the - data using the transform expression RTRANSFORM and outputs - the results to the screen. - ************************************************************/ -package examples.datasets; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_Transform { - - private static String FILE = "H5Ex_D_Transform.h5"; - private static String DATASET = "DS1"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static String TRANSFORM = "x+1"; - private static String RTRANSFORM = "x-1"; - - private static void writeData() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dxpl_id = HDF5Constants.H5I_INVALID_HID; - - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize data. - for (int i = 0; i < DIM_X; i++) - for (int j = 0; j < DIM_Y; j++) - dset_data[i][j] = i * j - j; - - // Output the data to the screen. - System.out.println("Original Data:"); - for (int i = 0; i < DIM_X; i++) { - System.out.print(" ["); - for (int j = 0; j < DIM_Y; j++) - System.out.print(" " + dset_data[i][j] + " "); - System.out.println("]"); - } - - // Create a new file using the default properties. - try { - file_id = H5.H5Fcreate(FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(2, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset transfer property list and define the transform expression. - try { - dxpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); - if (dxpl_id >= 0) - H5.H5Pset_data_transform(dxpl_id, TRANSFORM); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset using the default properties. Unfortunately we must save as - // a native type or the transform operation will fail. - try { - if ((file_id >= 0) && (filespace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASET, HDF5Constants.H5T_NATIVE_INT, filespace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset using the dataset transfer property list. - try { - if ((dataset_id >= 0) && (dxpl_id >= 0)) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, dxpl_id, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dxpl_id >= 0) - H5.H5Pclose(dxpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readData() - { - - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dxpl_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Open an existing file using the default properties. - try { - file_id = H5.H5Fopen(FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset using the default properties. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASET, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Data as written with transform '" + TRANSFORM + "'"); - for (int i = 0; i < DIM_X; i++) { - System.out.print(" ["); - for (int j = 0; j < DIM_Y; j++) - System.out.print(" " + dset_data[i][j] + " "); - System.out.println("]"); - } - - // Create the dataset transfer property list and define the transform expression. - try { - dxpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER); - if (dxpl_id >= 0) - H5.H5Pset_data_transform(dxpl_id, RTRANSFORM); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read the data using the dataset transfer property list. - try { - if ((dataset_id >= 0) && (dxpl_id >= 0)) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, dxpl_id, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - - System.out.println("Data as written with transform '" + TRANSFORM + "' and read with transform '" + - RTRANSFORM + "'"); - for (int i = 0; i < DIM_X; i++) { - System.out.print(" ["); - for (int j = 0; j < DIM_Y; j++) - System.out.print(" " + dset_data[i][j] + " "); - System.out.println("]"); - } - - // Close and release resources. - try { - if (dxpl_id >= 0) - H5.H5Pclose(dxpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_Transform.writeData(); - H5Ex_D_Transform.readData(); - } -} diff --git a/java/examples/datasets/H5Ex_D_UnlimitedAdd.java b/java/examples/datasets/H5Ex_D_UnlimitedAdd.java deleted file mode 100644 index 4154cf3..0000000 --- a/java/examples/datasets/H5Ex_D_UnlimitedAdd.java +++ /dev/null @@ -1,393 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to create and extend an unlimited - dataset. The program first writes integers to a dataset - with dataspace dimensions of DIM_XxDIM_Y, then closes the - file. Next, it reopens the file, reads back the data, - outputs it to the screen, extends the dataset, and writes - new data to the extended portions of the dataset. Finally - it reopens the file again, reads back the data, and - outputs it to the screen. - ************************************************************/ -package examples.datasets; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_UnlimitedAdd { - private static String FILENAME = "H5Ex_D_UnlimitedAdd.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int EDIM_X = 6; - private static final int EDIM_Y = 10; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 4; - private static final int RANK = 2; - private static final int NDIMS = 2; - - private static void writeUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - long[] maxdims = {HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize the dataset. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace with unlimited dimensions. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the chunk size. - try { - if (dcpl_id >= 0) - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the unlimited dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void extendUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] extdims = {EDIM_X, EDIM_Y}; - long[] start = {0, 0}; - long[] count = new long[2]; - int[][] dset_data; - int[][] extend_dset_data = new int[EDIM_X][EDIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. This is a - // two dimensional dataset so the dynamic allocation must be done - // in steps. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to rows. - dset_data = new int[(int)dims[0]][(int)dims[1]]; - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset before extension:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Extend the dataset. - try { - if (dataset_id >= 0) - H5.H5Dset_extent(dataset_id, extdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataspace for the newly extended dataset. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Initialize data for writing to the extended dataset. - for (int indx = 0; indx < EDIM_X; indx++) - for (int jndx = 0; jndx < EDIM_Y; jndx++) - extend_dset_data[indx][jndx] = jndx; - - // Select the entire dataspace. - try { - if (dataspace_id >= 0) { - H5.H5Sselect_all(dataspace_id); - - // Subtract a hyperslab reflecting the original dimensions from the - // selection. The selection now contains only the newly extended - // portions of the dataset. - count[0] = dims[0]; - count[1] = dims[1]; - H5.H5Sselect_hyperslab(dataspace_id, HDF5Constants.H5S_SELECT_NOTB, start, null, count, null); - - // Write the data to the selected portion of the dataset. - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, dataspace_id, - HDF5Constants.H5P_DEFAULT, extend_dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for the read buffer as before. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - // Allocate array of pointers to rows. - dset_data = new int[(int)dims[0]][(int)dims[1]]; - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset after extension:"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < dims[1]; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_UnlimitedAdd.writeUnlimited(); - H5Ex_D_UnlimitedAdd.extendUnlimited(); - H5Ex_D_UnlimitedAdd.readUnlimited(); - } -} diff --git a/java/examples/datasets/H5Ex_D_UnlimitedGzip.java b/java/examples/datasets/H5Ex_D_UnlimitedGzip.java deleted file mode 100644 index e084641..0000000 --- a/java/examples/datasets/H5Ex_D_UnlimitedGzip.java +++ /dev/null @@ -1,505 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to create and extend an unlimited - dataset with gzip compression. The program first writes - integers to a gzip compressed dataset with dataspace - dimensions of DIM_XxDIM_Y, then closes the file. Next, it - reopens the file, reads back the data, outputs it to the - screen, extends the dataset, and writes new data to the - extended portions of the dataset. Finally it reopens the - file again, reads back the data, and outputs it to the - screen. - ************************************************************/ -package examples.datasets; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_UnlimitedGzip { - private static String FILENAME = "H5Ex_D_UnlimitedGzip.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int EDIM_X = 6; - private static final int EDIM_Y = 10; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 4; - private static final int RANK = 2; - private static final int NDIMS = 2; - - // Values for the status of space allocation - enum H5Z_filter { - H5Z_FILTER_ERROR(HDF5Constants.H5Z_FILTER_ERROR), - H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), - H5Z_FILTER_DEFLATE(HDF5Constants.H5Z_FILTER_DEFLATE), - H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), - H5Z_FILTER_FLETCHER32(HDF5Constants.H5Z_FILTER_FLETCHER32), - H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), - H5Z_FILTER_NBIT(HDF5Constants.H5Z_FILTER_NBIT), - H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), - H5Z_FILTER_RESERVED(HDF5Constants.H5Z_FILTER_RESERVED), - H5Z_FILTER_MAX(HDF5Constants.H5Z_FILTER_MAX); - private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>(); - - static - { - for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5Z_filter(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5Z_filter get(int code) { return lookup.get(code); } - } - - private static boolean checkGzipFilter() - { - try { - int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE); - if (available == 0) { - System.out.println("gzip filter not available."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE); - if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) || - ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) { - System.out.println("gzip filter not available for encoding and decoding."); - return false; - } - } - catch (Exception e) { - e.printStackTrace(); - } - return true; - } - - private static void writeUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - long[] maxdims = {HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize the dataset. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace with unlimited dimensions. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list, add the gzip compression - // filter. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - if (dcpl_id >= 0) { - H5.H5Pset_deflate(dcpl_id, 9); - // Set the chunk size. - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the unlimited dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void extendUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] extdims = {EDIM_X, EDIM_Y}; - long[] start = {0, 0}; - long[] count = new long[2]; - int[][] dset_data; - int[][] extend_dset_data = new int[EDIM_X][EDIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. This is a - // two dimensional dataset so the dynamic allocation must be done - // in steps. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to rows. - dset_data = new int[(int)dims[0]][(int)dims[1]]; - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset before extension:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Extend the dataset. - try { - if (dataset_id >= 0) - H5.H5Dset_extent(dataset_id, extdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataspace for the newly extended dataset. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Initialize data for writing to the extended dataset. - for (int indx = 0; indx < EDIM_X; indx++) - for (int jndx = 0; jndx < EDIM_Y; jndx++) - extend_dset_data[indx][jndx] = jndx; - - // Select the entire dataspace. - try { - if (dataspace_id >= 0) { - H5.H5Sselect_all(dataspace_id); - - // Subtract a hyperslab reflecting the original dimensions from the - // selection. The selection now contains only the newly extended - // portions of the dataset. - count[0] = dims[0]; - count[1] = dims[1]; - H5.H5Sselect_hyperslab(dataspace_id, HDF5Constants.H5S_SELECT_NOTB, start, null, count, null); - - // Write the data to the selected portion of the dataset. - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, dataspace_id, - HDF5Constants.H5P_DEFAULT, extend_dset_data); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataset creation property list. - try { - if (dataset_id >= 0) - dcpl_id = H5.H5Dget_create_plist(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve and print the filter type. Here we only retrieve the - // first filter because we know that we only added one filter. - try { - if (dcpl_id >= 0) { - // Java lib requires a valid filter_name object and cd_values - int[] flags = {0}; - long[] cd_nelmts = {1}; - int[] cd_values = {0}; - String[] filter_name = {""}; - int[] filter_config = {0}; - int filter_type = -1; - filter_type = H5.H5Pget_filter(dcpl_id, 0, flags, cd_nelmts, cd_values, 120, filter_name, - filter_config); - System.out.print("Filter type is: "); - switch (H5Z_filter.get(filter_type)) { - case H5Z_FILTER_DEFLATE: - System.out.println("H5Z_FILTER_DEFLATE"); - break; - case H5Z_FILTER_SHUFFLE: - System.out.println("H5Z_FILTER_SHUFFLE"); - break; - case H5Z_FILTER_FLETCHER32: - System.out.println("H5Z_FILTER_FLETCHER32"); - break; - case H5Z_FILTER_SZIP: - System.out.println("H5Z_FILTER_SZIP"); - break; - default: - System.out.println("H5Z_FILTER_ERROR"); - } - System.out.println(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for the read buffer as before. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - // Allocate array of pointers to rows. - dset_data = new int[(int)dims[0]][(int)dims[1]]; - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset after extension:"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < dims[1]; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - // Check if gzip compression is available and can be used for both - // compression and decompression. Normally we do not perform error - // checking in these examples for the sake of clarity, but in this - // case we will make an exception because this filter is an - // optional part of the hdf5 library. - if (H5Ex_D_UnlimitedGzip.checkGzipFilter()) { - H5Ex_D_UnlimitedGzip.writeUnlimited(); - H5Ex_D_UnlimitedGzip.extendUnlimited(); - H5Ex_D_UnlimitedGzip.readUnlimited(); - } - } -} diff --git a/java/examples/datasets/H5Ex_D_UnlimitedMod.java b/java/examples/datasets/H5Ex_D_UnlimitedMod.java deleted file mode 100644 index ccabcdd..0000000 --- a/java/examples/datasets/H5Ex_D_UnlimitedMod.java +++ /dev/null @@ -1,379 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to create and extend an unlimited - dataset. The program first writes integers to a dataset - with dataspace dimensions of DIM_XxDIM_Y, then closes the - file. Next, it reopens the file, reads back the data, - outputs it to the screen, extends the dataset, and writes - new data to the entire extended dataset. Finally it - reopens the file again, reads back the data, and outputs it - to the screen. - ************************************************************/ -package examples.datasets; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_D_UnlimitedMod { - private static String FILENAME = "H5Ex_D_UnlimitedMod.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM_X = 4; - private static final int DIM_Y = 7; - private static final int EDIM_X = 6; - private static final int EDIM_Y = 10; - private static final int CHUNK_X = 4; - private static final int CHUNK_Y = 4; - private static final int RANK = 2; - private static final int NDIMS = 2; - - private static void writeUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dcpl_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] chunk_dims = {CHUNK_X, CHUNK_Y}; - long[] maxdims = {HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize the dataset. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * jndx - jndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace with unlimited dimensions. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset creation property list. - try { - dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set the chunk size. - try { - if (dcpl_id >= 0) - H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the unlimited dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dcpl_id >= 0) - H5.H5Pclose(dcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void extendUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - long[] extdims = {EDIM_X, EDIM_Y}; - int[][] dset_data; - int[][] extend_dset_data = new int[EDIM_X][EDIM_Y]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. This is a - // two dimensional dataset so the dynamic allocation must be done - // in steps. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to rows. - dset_data = new int[(int)dims[0]][(int)dims[1]]; - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset before extension:"); - for (int indx = 0; indx < DIM_X; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < DIM_Y; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Extend the dataset. - try { - if (dataset_id >= 0) - H5.H5Dset_extent(dataset_id, extdims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Retrieve the dataspace for the newly extended dataset. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Initialize data for writing to the extended dataset. - for (int indx = 0; indx < EDIM_X; indx++) - for (int jndx = 0; jndx < EDIM_Y; jndx++) - extend_dset_data[indx][jndx] = jndx; - - // Write the data tto the extended dataset. - try { - if ((dataspace_id >= 0) && (dataset_id >= 0)) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, dataspace_id, - HDF5Constants.H5P_DEFAULT, extend_dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readUnlimited() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for the read buffer as before. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - // Allocate array of pointers to rows. - dset_data = new int[(int)dims[0]][(int)dims[1]]; - - // Read the data using the default properties. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Dataset after extension:"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" [ "); - for (int jndx = 0; jndx < dims[1]; jndx++) - System.out.print(dset_data[indx][jndx] + " "); - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_D_UnlimitedMod.writeUnlimited(); - H5Ex_D_UnlimitedMod.extendUnlimited(); - H5Ex_D_UnlimitedMod.readUnlimited(); - } -} diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in deleted file mode 100644 index 9683076..0000000 --- a/java/examples/datasets/JavaDatasetExample.sh.in +++ /dev/null @@ -1,497 +0,0 @@ -#! /bin/sh -# -# 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. -# - -top_builddir=@top_builddir@ -top_srcdir=@top_srcdir@ -srcdir=@srcdir@ -IS_DARWIN="@H5_IS_DARWIN@" - -USE_FILTER_SZIP="@USE_FILTER_SZIP@" -USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@" - -TESTNAME=EX_Datasets -EXIT_SUCCESS=0 -EXIT_FAILURE=1 - -# Set up default variable values if not supplied by the user. -RM='rm -rf' -CMP='cmp' -DIFF='diff -c' -CP='cp' -DIRNAME='dirname' -BASENAME='basename' -LS='ls' -AWK='awk' - -nerrors=0 - -# where the libs exist -HDFLIB_HOME="$top_srcdir/java/lib" -BLDDIR="." -BLDLIBDIR="$BLDDIR/testlibs" -HDFTEST_HOME="$top_srcdir/java/examples/datasets" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar -test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR - -###################################################################### -# library files -# -------------------------------------------------------------------- -# All the library files copy from source directory to test directory -# NOTE: Keep this framework to add/remove test files. -# This list are also used for checking exist. -# Comment '#' without space can be used. -# -------------------------------------------------------------------- -LIST_LIBRARY_FILES=" -$top_builddir/src/.libs/libhdf5.* -$top_builddir/java/src/jni/.libs/libhdf5_java.* -$top_builddir/java/src/$JARFILE -" -LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-2.0.6.jar -$HDFLIB_HOME/ext/slf4j-simple-2.0.6.jar -" -LIST_DATA_FILES=" -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Alloc.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Checksum.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Chunk.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Compact.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_External.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_FillValue.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Gzip.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Hyperslab.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_ReadWrite.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Shuffle.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Szip.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_UnlimitedAdd.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_UnlimitedGzip.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_UnlimitedMod.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Nbit.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Transform.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Sofloat.txt -$HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Soint.txt -" - -# -# copy files from source dirs to test dir -# -COPY_LIBFILES="$LIST_LIBRARY_FILES" -COPY_JARTESTFILES="$LIST_JAR_TESTFILES" - -COPY_LIBFILES_TO_BLDLIBDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_LIBFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - BNAME=`$BASENAME $tstfile` - if [ "$BNAME" = "libhdf5_java.dylib" ]; then - COPIED_LIBHDF5_JAVA=1 - fi - fi - fi - done - if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then - (cd $BLDLIBDIR; \ - install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \ - exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \ - echo $exist_path; \ - install_name_tool -change $exist_path @rpath/libhdf5.dylib libhdf5_java.dylib) - fi - # copy jar files. Used -f to make sure get a new copy - for tstfile in $COPY_JARTESTFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_LIBFILES_AND_BLDLIBDIR() -{ - # skip rm if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=$HDFLIB_HOME - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $RM -rf $BLDLIBDIR - fi -} - -COPY_DATAFILES="$LIST_DATA_FILES" - -COPY_DATAFILES_TO_BLDDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_DATAFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -f $tstfile $BLDDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_DATAFILES_AND_BLDDIR() -{ - $RM $BLDDIR/examples.datasets.H5Ex_D_*.txt - $RM $BLDDIR/H5Ex_D_*.out - $RM $BLDDIR/H5Ex_D_*.h5 - $RM $BLDDIR/H5Ex_D_External.data -} - -# Print a line-line message left justified in a field of 70 characters -# beginning with the word "Testing". -# -TESTING() { - SPACES=" " - echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012' -} - -# where Java is installed (requires jdk1.7.x) -JAVAEXE=@JAVA@ -JAVAEXEFLAGS=@H5_JAVAFLAGS@ - -############################################################################### -# DO NOT MODIFY BELOW THIS LINE -############################################################################### - -# prepare for test -COPY_LIBFILES_TO_BLDLIBDIR -COPY_DATAFILES_TO_BLDDIR - -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-2.0.6.jar:"$BLDLIBDIR"/slf4j-simple-2.0.6.jar:"$TESTJARFILE"" - -TEST=/usr/bin/test -if [ ! -x /usr/bin/test ] -then -TEST=`which test` -fi - -if $TEST -z "$CLASSPATH"; then - CLASSPATH="" -fi -CLASSPATH=$CPATH":"$CLASSPATH -export CLASSPATH - -if $TEST -n "$JAVAPATH" ; then - PATH=$JAVAPATH":"$PATH - export PATH -fi - -if $TEST -e /bin/uname; then - os_name=`/bin/uname -s` -elif $TEST -e /usr/bin/uname; then - os_name=`/usr/bin/uname -s` -else - os_name=unknown -fi - -if $TEST -z "$LD_LIBRARY_PATH" ; then - LD_LIBRARY_PATH="" -fi - -case $os_name in - *) - LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH - ;; -esac - -export LD_LIBRARY_PATH - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Alloc" -TESTING examples.datasets.H5Ex_D_Alloc -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Alloc > H5Ex_D_Alloc.out -) -if diff H5Ex_D_Alloc.out examples.datasets.H5Ex_D_Alloc.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Alloc" -else - echo "**FAILED** datasets.H5Ex_D_Alloc" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Checksum" -TESTING examples.datasets.H5Ex_D_Checksum -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Checksum > H5Ex_D_Checksum.out -) -if diff H5Ex_D_Checksum.out examples.datasets.H5Ex_D_Checksum.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Checksum" -else - echo "**FAILED** datasets.H5Ex_D_Checksum" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Chunk" -TESTING examples.datasets.H5Ex_D_Chunk -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Chunk > H5Ex_D_Chunk.out -) -if diff H5Ex_D_Chunk.out examples.datasets.H5Ex_D_Chunk.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Chunk" -else - echo "**FAILED** datasets.H5Ex_D_Chunk" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Compact" -TESTING examples.datasets.H5Ex_D_Compact -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Compact > H5Ex_D_Compact.out -) -if diff H5Ex_D_Compact.out examples.datasets.H5Ex_D_Compact.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Compact" -else - echo "**FAILED** datasets.H5Ex_D_Compact" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_External" -TESTING examples.datasets.H5Ex_D_External -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_External > H5Ex_D_External.out -) -if diff H5Ex_D_External.out examples.datasets.H5Ex_D_External.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_External" -else - echo "**FAILED** datasets.H5Ex_D_External" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_FillValue" -TESTING examples.datasets.H5Ex_D_FillValue -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_FillValue > H5Ex_D_FillValue.out -) -if diff H5Ex_D_FillValue.out examples.datasets.H5Ex_D_FillValue.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_FillValue" -else - echo "**FAILED** datasets.H5Ex_D_FillValue" - nerrors="`expr $nerrors + 1`" -fi - -if test $USE_FILTER_DEFLATE = "yes"; then - echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Gzip" - TESTING examples.datasets.H5Ex_D_Gzip - ( - $RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Gzip > H5Ex_D_Gzip.out - ) - if diff H5Ex_D_Gzip.out examples.datasets.H5Ex_D_Gzip.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Gzip" - else - echo "**FAILED** datasets.H5Ex_D_Gzip" - nerrors="`expr $nerrors + 1`" - fi -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Hyperslab" -TESTING examples.datasets.H5Ex_D_Hyperslab -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Hyperslab > H5Ex_D_Hyperslab.out -) -if diff H5Ex_D_Hyperslab.out examples.datasets.H5Ex_D_Hyperslab.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Hyperslab" -else - echo "**FAILED** datasets.H5Ex_D_Hyperslab" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_ReadWrite" -TESTING examples.datasets.H5Ex_D_ReadWrite -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_ReadWrite > H5Ex_D_ReadWrite.out -) -if diff H5Ex_D_ReadWrite.out examples.datasets.H5Ex_D_ReadWrite.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_ReadWrite" -else - echo "**FAILED** datasets.H5Ex_D_ReadWrite" - nerrors="`expr $nerrors + 1`" -fi - -if test $USE_FILTER_DEFLATE = "yes"; then - echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Shuffle" - TESTING examples.datasets.H5Ex_D_Shuffle - ( - $RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Shuffle > H5Ex_D_Shuffle.out - ) - if diff H5Ex_D_Shuffle.out examples.datasets.H5Ex_D_Shuffle.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Shuffle" - else - echo "**FAILED** datasets.H5Ex_D_Shuffle" - nerrors="`expr $nerrors + 1`" - fi -fi - -if test $USE_FILTER_SZIP = "yes"; then - echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Szip" - TESTING examples.datasets.H5Ex_D_Szip - ( - $RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Szip > H5Ex_D_Szip.out - ) - if diff H5Ex_D_Szip.out examples.datasets.H5Ex_D_Szip.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Szip" - else - echo "**FAILED** datasets.H5Ex_D_Szip" - nerrors="`expr $nerrors + 1`" - fi -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedAdd" -TESTING examples.datasets.H5Ex_D_UnlimitedAdd -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedAdd > H5Ex_D_UnlimitedAdd.out -) -if diff H5Ex_D_UnlimitedAdd.out examples.datasets.H5Ex_D_UnlimitedAdd.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_UnlimitedAdd" -else - echo "**FAILED** datasets.H5Ex_D_UnlimitedAdd" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedGzip" -TESTING examples.datasets.H5Ex_D_UnlimitedGzip -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedGzip > H5Ex_D_UnlimitedGzip.out -) -if diff H5Ex_D_External.out examples.datasets.H5Ex_D_External.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_UnlimitedGzip" -else - echo "**FAILED** datasets.H5Ex_D_UnlimitedGzip" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedMod" -TESTING examples.datasets.H5Ex_D_UnlimitedMod -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_UnlimitedMod > H5Ex_D_UnlimitedMod.out -) -if diff H5Ex_D_UnlimitedMod.out examples.datasets.H5Ex_D_UnlimitedMod.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_UnlimitedMod" -else - echo "**FAILED** datasets.H5Ex_D_UnlimitedMod" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Nbit" -TESTING examples.datasets.H5Ex_D_Nbit -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Nbit > H5Ex_D_Nbit.out -) -if diff H5Ex_D_Nbit.out examples.datasets.H5Ex_D_Nbit.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Nbit" -else - echo "**FAILED** datasets.H5Ex_D_Nbit" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Transform" -TESTING examples.datasets.H5Ex_D_Transform -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Transform > H5Ex_D_Transform.out -) -if diff H5Ex_D_Transform.out examples.datasets.H5Ex_D_Transform.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Transform" -else - echo "**FAILED** datasets.H5Ex_D_Transform" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Sofloat" -TESTING examples.datasets.H5Ex_D_Sofloat -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Sofloat > H5Ex_D_Sofloat.out -) -if diff H5Ex_D_Sofloat.out examples.datasets.H5Ex_D_Sofloat.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Sofloat" -else - echo "**FAILED** datasets.H5Ex_D_Sofloat" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Soint" -TESTING examples.datasets.H5Ex_D_Soint -( -$RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Soint > H5Ex_D_Soint.out -) -if diff H5Ex_D_Soint.out examples.datasets.H5Ex_D_Soint.txt > /dev/null; then - echo " PASSED datasets.H5Ex_D_Soint" -else - echo "**FAILED** datasets.H5Ex_D_Soint" - nerrors="`expr $nerrors + 1`" -fi - -# Clean up temporary files/directories -CLEAN_LIBFILES_AND_BLDLIBDIR -CLEAN_DATAFILES_AND_BLDDIR - -# Report test results and exit -if test $nerrors -eq 0 ; then - echo "All $TESTNAME tests passed." - exit $EXIT_SUCCESS -else - echo "$TESTNAME tests failed with $nerrors errors." - exit $EXIT_FAILURE -fi diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am deleted file mode 100644 index d4bb666..0000000 --- a/java/examples/datasets/Makefile.am +++ /dev/null @@ -1,75 +0,0 @@ -# -# 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. -## -## Makefile.am -## Run automake to generate a Makefile.in from this file. -## -# -# HDF5 Java Library Examples Makefile(.in) - -include $(top_srcdir)/config/commence.am - -# Mark this directory as part of the JNI API -JAVA_API=yes - -JAVAROOT = .classes - -classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - -pkgpath = examples/datasets -hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-2.0.6.jar:$$CLASSPATH - -jarfile = jar$(PACKAGE_TARNAME)datasets.jar - -AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation - -TESTPACKAGE = - -noinst_JAVA = \ - H5Ex_D_Alloc.java \ - H5Ex_D_Checksum.java \ - H5Ex_D_Chunk.java \ - H5Ex_D_Compact.java \ - H5Ex_D_External.java \ - H5Ex_D_FillValue.java \ - H5Ex_D_Gzip.java \ - H5Ex_D_Hyperslab.java \ - H5Ex_D_ReadWrite.java \ - H5Ex_D_Shuffle.java \ - H5Ex_D_Szip.java \ - H5Ex_D_UnlimitedAdd.java \ - H5Ex_D_UnlimitedGzip.java \ - H5Ex_D_UnlimitedMod.java \ - H5Ex_D_Nbit.java \ - H5Ex_D_Transform.java \ - H5Ex_D_Sofloat.java \ - H5Ex_D_Soint.java - -$(jarfile): classnoinst.stamp classes - $(JAR) cvf $@ -C $(JAVAROOT)/ $(pkgpath) - -noinst_DATA = $(jarfile) - -.PHONY: classes - -check_SCRIPTS = JavaDatasetExample.sh -TEST_SCRIPT = $(check_SCRIPTS) - -CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class JavaDatasetExample.sh - -clean: - rm -rf $(JAVAROOT)/* - rm -f $(jarfile) - rm -f classnoinst.stamp - -include $(top_srcdir)/config/conclude.am diff --git a/java/examples/datatypes/CMakeLists.txt b/java/examples/datatypes/CMakeLists.txt deleted file mode 100644 index 5860429..0000000 --- a/java/examples/datatypes/CMakeLists.txt +++ /dev/null @@ -1,116 +0,0 @@ -cmake_minimum_required (VERSION 3.18) -project (HDFJAVA_EXAMPLES_DATATYPES Java) - -set (CMAKE_VERBOSE_MAKEFILE 1) - -set (HDF_JAVA_EXAMPLES - H5Ex_T_Array - H5Ex_T_ArrayAttribute - H5Ex_T_Bit - H5Ex_T_BitAttribute - H5Ex_T_Commit - H5Ex_T_Compound - H5Ex_T_CompoundAttribute - H5Ex_T_Float - H5Ex_T_FloatAttribute - H5Ex_T_Integer - H5Ex_T_IntegerAttribute - H5Ex_T_ObjectReference - H5Ex_T_ObjectReferenceAttribute - H5Ex_T_Opaque - H5Ex_T_OpaqueAttribute - H5Ex_T_String - H5Ex_T_StringAttribute - H5Ex_T_VLString -) - -if (WIN32) - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") -else () - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") -endif () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") -endforeach () - -foreach (example ${HDF_JAVA_EXAMPLES}) - file (WRITE ${PROJECT_BINARY_DIR}/${example}_Manifest.txt - "Main-Class: examples.datatypes.${example} -" - ) - add_jar (${example} MANIFEST ${PROJECT_BINARY_DIR}/${example}_Manifest.txt ${example}.java) - get_target_property (${example}_JAR_FILE ${example} JAR_FILE) -# install_jar (${example} ${HJAVA_INSTALL_DATA_DIR}/examples examples) - get_target_property (${example}_CLASSPATH ${example} CLASSDIR) - add_dependencies (${example} ${HDF5_JAVA_HDF5_LIB_TARGET}) - - #----------------------------------------------------------------------------- - # Add Target to clang-format - #----------------------------------------------------------------------------- - if (HDF5_ENABLE_FORMATTERS) - clang_format (HDF5_JAVA_${example}_SRC_FORMAT ${example}.java) - endif () -endforeach () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS};${HDF5_JAVA_LOGGING_JAR};${HDF5_JAVA_LOGGING_NOP_JAR}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (HDFJAVA_JAR ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${HDFJAVA_JAR}") -endforeach () - -if (BUILD_TESTING AND HDF5_TEST_EXAMPLES AND HDF5_TEST_SERIAL) - get_property (target_name TARGET ${HDF5_JAVA_JNI_LIB_TARGET} PROPERTY OUTPUT_NAME) - set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${target_name}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") - - set (last_test "") - foreach (example ${HDF_JAVA_EXAMPLES}) - add_test ( - NAME JAVA_datatypes-${example}-clear-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - if (last_test) - set_tests_properties (JAVA_datatypes-${example}-clear-objects PROPERTIES DEPENDS ${last_test}) - endif () - - add_test ( - NAME JAVA_datatypes-${example}-copy-objects - COMMAND ${CMAKE_COMMAND} -E copy_if_different - ${HDFJAVA_EXAMPLES_SOURCE_DIR}/testfiles/examples.datatypes.${example}.txt - ${HDFJAVA_EXAMPLES_DATATYPES_BINARY_DIR}/${example}.txt - ) - set_tests_properties (JAVA_datatypes-${example}-copy-objects PROPERTIES DEPENDS JAVA_datatypes-${example}-clear-objects) - add_test ( - NAME JAVA_datatypes-${example} - COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" - -D "TEST_PROGRAM=examples.datatypes.${example}" - -D "TEST_ARGS:STRING=${CMD_ARGS}" - -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${example}_JAR_FILE}" - -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}" - -D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}" - -D "TEST_OUTPUT=datatypes/${example}.out" - -D "TEST_EXPECT=0" - -D "TEST_REFERENCE=datatypes/${example}.txt" - -P "${HDF_RESOURCES_DIR}/jrunTest.cmake" - ) - set_tests_properties (JAVA_datatypes-${example} PROPERTIES - DEPENDS JAVA_datatypes-${example}-copy-objects - ) - - add_test ( - NAME JAVA_datatypes-${example}-clean-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - set_tests_properties (JAVA_datatypes-${example}-clean-objects PROPERTIES - DEPENDS JAVA_datatypes-${example} - ) - set (last_test "JAVA_datatypes-${example}-clean-objects") - endforeach () -endif () diff --git a/java/examples/datatypes/H5Ex_T_Array.java b/java/examples/datatypes/H5Ex_T_Array.java deleted file mode 100644 index 4e9de2a..0000000 --- a/java/examples/datatypes/H5Ex_T_Array.java +++ /dev/null @@ -1,280 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write array datatypes - to a dataset. The program first writes integers arrays of - dimension ADIM0xADIM1 to a dataset with a dataspace of - DIM0, then closes the file. Next, it reopens the file, - reads back the data, and outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_Array { - private static String FILENAME = "H5Ex_T_Array.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM0 = 4; - private static final int ADIM0 = 3; - private static final int ADIM1 = 5; - private static final int RANK = 1; - private static final int NDIMS = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - long[] adims = {ADIM0, ADIM1}; - int[][][] dset_data = new int[DIM0][ADIM0][ADIM1]; - - // Initialize data. indx is the element in the dataspace, jndx and kndx the - // elements within the array datatype. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < ADIM0; jndx++) - for (int kndx = 0; kndx < ADIM1; kndx++) - dset_data[indx][jndx][kndx] = indx * jndx - jndx * kndx + indx * kndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create array datatypes for file. - try { - filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, NDIMS, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create array datatypes for memory. - try { - memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, NDIMS, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0)) - dataset_id = - H5.H5Dcreate(file_id, DATASETNAME, filetype_id, dataspace_id, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5Dwrite(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - long[] adims = {ADIM0, ADIM1}; - int[][][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get the datatype. - try { - if (dataset_id >= 0) - filetype_id = H5.H5Dget_type(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get the datatype's dimensions. - try { - if (filetype_id >= 0) - H5.H5Tget_array_dims(filetype_id, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new int[(int)dims[0]][(int)(adims[0])][(int)(adims[1])]; - - // Create array datatypes for memory. - try { - memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, 2, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read data. - try { - if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5Dread(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(DATASETNAME + " [" + indx + "]:"); - for (int jndx = 0; jndx < adims[0]; jndx++) { - System.out.print(" ["); - for (int kndx = 0; kndx < adims[1]; kndx++) - System.out.print(dset_data[indx][jndx][kndx] + " "); - System.out.println("]"); - } - System.out.println(); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_Array.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_Array.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_ArrayAttribute.java b/java/examples/datatypes/H5Ex_T_ArrayAttribute.java deleted file mode 100644 index 45b44c1..0000000 --- a/java/examples/datatypes/H5Ex_T_ArrayAttribute.java +++ /dev/null @@ -1,320 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write array datatypes - to an attribute. The program first writes integers arrays - of dimension ADIM0xADIM1 to an attribute with a dataspace - of DIM0, then closes the file. Next, it reopens the - file, reads back the data, and outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_ArrayAttribute { - private static String FILENAME = "H5Ex_T_ArrayAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static final int DIM0 = 4; - private static final int ADIM0 = 3; - private static final int ADIM1 = 5; - private static final int RANK = 1; - private static final int NDIMS = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - long[] adims = {ADIM0, ADIM1}; - int[][][] dset_data = new int[DIM0][ADIM0][ADIM1]; - - // Initialize data. indx is the element in the dataspace, jndx and kndx the - // elements within the array datatype. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < ADIM0; jndx++) - for (int kndx = 0; kndx < ADIM1; kndx++) - dset_data[indx][jndx][kndx] = indx * jndx - jndx * kndx + indx * kndx; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create array datatypes for file. - try { - filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, NDIMS, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create array datatypes for memory. - try { - memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, NDIMS, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute and write the array data to it. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0)) - attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, filetype_id, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5Awrite(attribute_id, memtype_id, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - long[] adims = {ADIM0, ADIM1}; - int[][][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get the datatype. - try { - if (attribute_id >= 0) - filetype_id = H5.H5Aget_type(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get the datatype's dimensions. - try { - if (filetype_id >= 0) - H5.H5Tget_array_dims(filetype_id, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new int[(int)dims[0]][(int)(adims[0])][(int)(adims[1])]; - - // Create array datatypes for memory. - try { - memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, 2, adims); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read data. - try { - if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5Aread(attribute_id, memtype_id, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(ATTRIBUTENAME + " [" + indx + "]:"); - for (int jndx = 0; jndx < adims[0]; jndx++) { - System.out.print(" ["); - for (int kndx = 0; kndx < adims[1]; kndx++) - System.out.print(dset_data[indx][jndx][kndx] + " "); - System.out.println("]"); - } - System.out.println(); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_ArrayAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_ArrayAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_Bit.java b/java/examples/datatypes/H5Ex_T_Bit.java deleted file mode 100644 index 6d1a253..0000000 --- a/java/examples/datatypes/H5Ex_T_Bit.java +++ /dev/null @@ -1,225 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write bitfield - datatypes to a dataset. The program first writes bit - fields to a dataset with a dataspace of DIM0xDIM1, then - closes the file. Next, it reopens the file, reads back - the data, and outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_Bit { - private static String FILENAME = "H5Ex_T_Bit.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM0 = 4; - private static final int DIM1 = 7; - private static final int RANK = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data = new int[DIM0][DIM1]; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < DIM1; jndx++) { - dset_data[indx][jndx] = 0; - dset_data[indx][jndx] |= (indx * jndx - jndx) & 0x03; /* Field "A" */ - dset_data[indx][jndx] |= (indx & 0x03) << 2; /* Field "B" */ - dset_data[indx][jndx] |= (jndx & 0x03) << 4; /* Field "C" */ - dset_data[indx][jndx] |= ((indx + jndx) & 0x03) << 6; /* Field "D" */ - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_B8BE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the bitfield data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_B8, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new int[(int)dims[0]][(int)(dims[1])]; - - // Read data. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_B8, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println(DATASETNAME + ":"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" ["); - for (int jndx = 0; jndx < dims[1]; jndx++) { - System.out.print("{" + (dset_data[indx][jndx] & 0x03) + ", "); - System.out.print(((dset_data[indx][jndx] >> 2) & 0x03) + ", "); - System.out.print(((dset_data[indx][jndx] >> 4) & 0x03) + ", "); - System.out.print(((dset_data[indx][jndx] >> 6) & 0x03) + "}"); - } - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_Bit.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_Bit.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_BitAttribute.java b/java/examples/datatypes/H5Ex_T_BitAttribute.java deleted file mode 100644 index 3ad643a..0000000 --- a/java/examples/datatypes/H5Ex_T_BitAttribute.java +++ /dev/null @@ -1,266 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write bitfield - datatypes to an attribute. The program first writes bit - fields to an attribute with a dataspace of DIM0xDIM1, then - closes the file. Next, it reopens the file, reads back - the data, and outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_BitAttribute { - private static String FILENAME = "H5Ex_T_BitAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static final int DIM0 = 4; - private static final int DIM1 = 7; - private static final int RANK = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data = new int[DIM0][DIM1]; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < DIM1; jndx++) { - dset_data[indx][jndx] = 0; - dset_data[indx][jndx] |= (indx * jndx - jndx) & 0x03; /* Field "A" */ - dset_data[indx][jndx] |= (indx & 0x03) << 2; /* Field "B" */ - dset_data[indx][jndx] |= (jndx & 0x03) << 4; /* Field "C" */ - dset_data[indx][jndx] |= ((indx + jndx) & 0x03) << 6; /* Field "D" */ - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute and write the array data to it. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0)) - attribute_id = - H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_STD_B8BE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if (attribute_id >= 0) - H5.H5Awrite(attribute_id, HDF5Constants.H5T_NATIVE_B8, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (attribute_id >= 0) - dataspace_id = H5.H5Aget_space(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new int[(int)dims[0]][(int)(dims[1])]; - - // Read data. - try { - if (attribute_id >= 0) - H5.H5Aread(attribute_id, HDF5Constants.H5T_NATIVE_B8, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println(ATTRIBUTENAME + ":"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" ["); - for (int jndx = 0; jndx < dims[1]; jndx++) { - System.out.print("{" + (dset_data[indx][jndx] & 0x03) + ", "); - System.out.print(((dset_data[indx][jndx] >> 2) & 0x03) + ", "); - System.out.print(((dset_data[indx][jndx] >> 4) & 0x03) + ", "); - System.out.print(((dset_data[indx][jndx] >> 6) & 0x03) + "}"); - } - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_BitAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_BitAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_Commit.java b/java/examples/datatypes/H5Ex_T_Commit.java deleted file mode 100644 index 44586ef..0000000 --- a/java/examples/datatypes/H5Ex_T_Commit.java +++ /dev/null @@ -1,260 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to commit a named datatype to a - file, and read back that datatype. The program first - defines a compound datatype, commits it to a file, then - closes the file. Next, it reopens the file, opens the - datatype, and outputs the names of its fields to the - screen. - ************************************************************/ - -package examples.datatypes; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_Commit { - private static String FILENAME = "H5Ex_T_Commit.h5"; - private static String DATATYPENAME = "Sensor_Type"; - protected static final int INTEGERSIZE = 4; - protected static final int DOUBLESIZE = 8; - protected final static int MAXSTRINGSIZE = 80; - - // Values for the various classes of datatypes - enum H5T_class { - H5T_NO_CLASS(HDF5Constants.H5T_NO_CLASS), // error - H5T_INTEGER(HDF5Constants.H5T_INTEGER), // integer types - H5T_FLOAT(HDF5Constants.H5T_FLOAT), // floating-point types - H5T_TIME(HDF5Constants.H5T_TIME), // date and time types - H5T_STRING(HDF5Constants.H5T_STRING), // character string types - H5T_BITFIELD(HDF5Constants.H5T_BITFIELD), // bit field types - H5T_OPAQUE(HDF5Constants.H5T_OPAQUE), // opaque types - H5T_COMPOUND(HDF5Constants.H5T_COMPOUND), // compound types - H5T_REFERENCE(HDF5Constants.H5T_REFERENCE), // reference types - H5T_ENUM(HDF5Constants.H5T_ENUM), // enumeration types - H5T_VLEN(HDF5Constants.H5T_VLEN), // Variable-Length types - H5T_ARRAY(HDF5Constants.H5T_ARRAY), // Array types - H5T_NCLASSES(11); // this must be last - - private static final Map<Long, H5T_class> lookup = new HashMap<Long, H5T_class>(); - - static - { - for (H5T_class s : EnumSet.allOf(H5T_class.class)) - lookup.put(s.getCode(), s); - } - - private long code; - - H5T_class(long layout_type) { this.code = layout_type; } - - public long getCode() { return this.code; } - - public static H5T_class get(long typeclass_id) { return lookup.get(typeclass_id); } - } - - // The supporting Sensor_Datatype class. - private static class Sensor_Datatype { - static int numberMembers = 4; - static int[] memberDims = {1, 1, 1, 1}; - - String[] memberNames = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"}; - long[] memberFileTypes = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1, - HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE}; - static int[] memberStorage = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE}; - - // Data size is the storage size for the members not the object. - static long getDataSize() - { - long data_size = 0; - for (int indx = 0; indx < numberMembers; indx++) - data_size += memberStorage[indx] * memberDims[indx]; - return data_size; - } - - static int getOffset(int memberItem) - { - int data_offset = 0; - for (int indx = 0; indx < memberItem; indx++) - data_offset += memberStorage[indx]; - return data_offset; - } - } - - private static void CreateDataType() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - Sensor_Datatype datatypes = new Sensor_Datatype(); - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create string datatype. - try { - strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (strtype_id >= 0) - H5.H5Tset_size(strtype_id, MAXSTRINGSIZE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the compound datatype for the file. Because the standard - // types we are using for the file may have different sizes than - // the corresponding native types, we must manually calculate the - // offset of each member. - try { - filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); - if (filetype_id >= 0) { - for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { - long type_id = datatypes.memberFileTypes[indx]; - if (type_id == HDF5Constants.H5T_C_S1) - type_id = strtype_id; - H5.H5Tinsert(filetype_id, datatypes.memberNames[indx], Sensor_Datatype.getOffset(indx), - type_id); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Commit the compound datatype to the file, creating a named datatype. - try { - if ((file_id >= 0) && (filetype_id >= 0)) - H5.H5Tcommit(file_id, DATATYPENAME, filetype_id, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the str type. - try { - if (strtype_id >= 0) - H5.H5Tclose(strtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataType() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long typeclass_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open named datatype. - try { - if (file_id >= 0) - filetype_id = H5.H5Topen(file_id, DATATYPENAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Named datatype: " + DATATYPENAME + ":"); - - // Get datatype class. If it isn't compound, we won't print anything. - try { - if (filetype_id >= 0) - typeclass_id = H5.H5Tget_class(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - // Read data. - try { - if (H5T_class.get(typeclass_id) == H5T_class.H5T_COMPOUND) { - System.out.println(" Class: H5T_COMPOUND"); - int nmembs = H5.H5Tget_nmembers(filetype_id); - // Iterate over compound datatype members. - for (int indx = 0; indx < nmembs; indx++) { - String member_name = H5.H5Tget_member_name(filetype_id, indx); - System.out.println(" " + member_name); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_Commit.CreateDataType(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_Commit.ReadDataType(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_Compound.java b/java/examples/datatypes/H5Ex_T_Compound.java deleted file mode 100644 index 7a46bcf..0000000 --- a/java/examples/datatypes/H5Ex_T_Compound.java +++ /dev/null @@ -1,462 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write compound - datatypes to a dataset. The program first writes - compound structures to a dataset with a dataspace of DIM0, - then closes the file. Next, it reopens the file, reads - back the data, and outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import java.nio.ByteBuffer; -import java.nio.ByteOrder; -import java.nio.charset.Charset; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_Compound { - private static String FILENAME = "H5Ex_T_Compound.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM0 = 4; - private static final int RANK = 1; - protected static final int INTEGERSIZE = 4; - protected static final int DOUBLESIZE = 8; - protected final static int MAXSTRINGSIZE = 80; - - static class Sensor_Datatype { - static int numberMembers = 4; - static int[] memberDims = {1, 1, 1, 1}; - - static String[] memberNames = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"}; - static long[] memberMemTypes = {HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5T_C_S1, - HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE}; - static long[] memberFileTypes = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1, - HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE}; - static int[] memberStorage = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE}; - - // Data size is the storage size for the members. - static long getTotalDataSize() - { - long data_size = 0; - for (int indx = 0; indx < numberMembers; indx++) - data_size += memberStorage[indx] * memberDims[indx]; - return DIM0 * data_size; - } - - static long getDataSize() - { - long data_size = 0; - for (int indx = 0; indx < numberMembers; indx++) - data_size += memberStorage[indx] * memberDims[indx]; - return data_size; - } - - static int getOffset(int memberItem) - { - int data_offset = 0; - for (int indx = 0; indx < memberItem; indx++) - data_offset += memberStorage[indx]; - return data_offset; - } - } - - static class Sensor { - public int serial_no; - public String location; - public double temperature; - public double pressure; - - Sensor(int serial_no, String location, double temperature, double pressure) - { - this.serial_no = serial_no; - this.location = location; - this.temperature = temperature; - this.pressure = pressure; - } - - Sensor(List data) - { - this.serial_no = (int)data.get(0); - this.location = (String)data.get(1); - this.temperature = (double)data.get(2); - this.pressure = (double)data.get(3); - } - - Sensor(ByteBuffer databuf, int dbposition) { readBuffer(databuf, dbposition); } - - void writeBuffer(ByteBuffer databuf, int dbposition) - { - databuf.putInt(dbposition + Sensor_Datatype.getOffset(0), serial_no); - byte[] temp_str = location.getBytes(Charset.forName("UTF-8")); - int arraylen = (temp_str.length > MAXSTRINGSIZE) ? MAXSTRINGSIZE : temp_str.length; - for (int ndx = 0; ndx < arraylen; ndx++) - databuf.put(dbposition + Sensor_Datatype.getOffset(1) + ndx, temp_str[ndx]); - for (int ndx = arraylen; ndx < MAXSTRINGSIZE; ndx++) - databuf.put(dbposition + Sensor_Datatype.getOffset(1) + arraylen, (byte)0); - databuf.putDouble(dbposition + Sensor_Datatype.getOffset(2), temperature); - databuf.putDouble(dbposition + Sensor_Datatype.getOffset(3), pressure); - } - - void readBuffer(ByteBuffer databuf, int dbposition) - { - this.serial_no = databuf.getInt(dbposition + Sensor_Datatype.getOffset(0)); - ByteBuffer stringbuf = databuf.duplicate(); - stringbuf.position(dbposition + Sensor_Datatype.getOffset(1)); - stringbuf.limit(dbposition + Sensor_Datatype.getOffset(1) + MAXSTRINGSIZE); - byte[] bytearr = new byte[stringbuf.remaining()]; - stringbuf.get(bytearr); - this.location = new String(bytearr, Charset.forName("UTF-8")).trim(); - this.temperature = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(2)); - this.pressure = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(3)); - } - - List get() - { - List data = new ArrayList<>(); - data.add(this.serial_no); - data.add(this.location); - data.add(this.temperature); - data.add(this.pressure); - return data; - } - - void put(List data) - { - this.serial_no = (int)data.get(0); - this.location = (String)data.get(1); - this.temperature = (double)data.get(2); - this.pressure = (double)data.get(3); - } - - @Override - public String toString() - { - return String.format("Serial number : " + serial_no + "%n" - + "Location : " + location + "%n" - + "Temperature (F) : " + temperature + "%n" - + "Pressure (inHg) : " + pressure + "%n"); - } - } - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - ArrayList[] object_data = new ArrayList[DIM0]; - byte[] dset_data = null; - - // Initialize data. - object_data[0] = (ArrayList) new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57).get(); - object_data[1] = (ArrayList) new Sensor(1184, new String("Intake"), 55.12, 22.95).get(); - object_data[2] = (ArrayList) new Sensor(1027, new String("Intake manifold"), 103.55, 31.23).get(); - object_data[3] = (ArrayList) new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11).get(); - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create string datatype. - try { - strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (strtype_id >= 0) - H5.H5Tset_size(strtype_id, MAXSTRINGSIZE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the compound datatype for memory. - try { - memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); - if (memtype_id >= 0) { - for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { - long type_id = Sensor_Datatype.memberMemTypes[indx]; - if (type_id == HDF5Constants.H5T_C_S1) - type_id = strtype_id; - H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], - Sensor_Datatype.getOffset(indx), type_id); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the compound datatype for the file. Because the standard - // types we are using for the file may have different sizes than - // the corresponding native types, we must manually calculate the - // offset of each member. - try { - filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); - if (filetype_id >= 0) { - for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { - long type_id = Sensor_Datatype.memberFileTypes[indx]; - if (type_id == HDF5Constants.H5T_C_S1) - type_id = strtype_id; - H5.H5Tinsert(filetype_id, Sensor_Datatype.memberNames[indx], - Sensor_Datatype.getOffset(indx), type_id); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0)) - dataset_id = - H5.H5Dcreate(file_id, DATASETNAME, filetype_id, dataspace_id, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the compound data to the dataset. - try { - if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5DwriteVL(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, (Object[])object_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (strtype_id >= 0) - H5.H5Tclose(strtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - Sensor[] object_data2 = new Sensor[(int)dims[0]]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create string datatype. - try { - strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (strtype_id >= 0) - H5.H5Tset_size(strtype_id, MAXSTRINGSIZE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the compound datatype for memory. - try { - memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); - if (memtype_id >= 0) { - for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { - long type_id = Sensor_Datatype.memberMemTypes[indx]; - if (type_id == HDF5Constants.H5T_C_S1) - type_id = strtype_id; - H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], - Sensor_Datatype.getOffset(indx), type_id); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - ArrayList[] object_data = new ArrayList[(int)dims[0]]; - - // Read data. - try { - if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5DreadVL(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, (Object[])object_data); - - for (int indx = 0; indx < (int)dims[0]; indx++) { - object_data2[indx] = new Sensor(object_data[indx]); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(DATASETNAME + " [" + indx + "]:"); - System.out.println(object_data2[indx].toString()); - } - System.out.println(); - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (strtype_id >= 0) - H5.H5Tclose(strtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_Compound.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_Compound.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_CompoundAttribute.java b/java/examples/datatypes/H5Ex_T_CompoundAttribute.java deleted file mode 100644 index 93e15fd..0000000 --- a/java/examples/datatypes/H5Ex_T_CompoundAttribute.java +++ /dev/null @@ -1,504 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write compound - datatypes to an attribute. The program first writes - compound structures to an attribute with a dataspace of - DIM0, then closes the file. Next, it reopens the file, - reads back the data, and outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import java.nio.ByteBuffer; -import java.nio.ByteOrder; -import java.nio.charset.Charset; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_CompoundAttribute { - private static String FILENAME = "H5Ex_T_CompoundAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static final int DIM0 = 4; - private static final int RANK = 1; - protected static final int INTEGERSIZE = 4; - protected static final int DOUBLESIZE = 8; - protected final static int MAXSTRINGSIZE = 80; - - static class Sensor_Datatype { - static int numberMembers = 4; - static int[] memberDims = {1, 1, 1, 1}; - - static String[] memberNames = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"}; - static long[] memberMemTypes = {HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5T_C_S1, - HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE}; - static long[] memberFileTypes = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1, - HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE}; - static int[] memberStorage = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE}; - - // Data size is the storage size for the members not the object. - static long getTotalDataSize() - { - long data_size = 0; - for (int indx = 0; indx < numberMembers; indx++) - data_size += memberStorage[indx] * memberDims[indx]; - return DIM0 * data_size; - } - - static long getDataSize() - { - long data_size = 0; - for (int indx = 0; indx < numberMembers; indx++) - data_size += memberStorage[indx] * memberDims[indx]; - return data_size; - } - - static int getOffset(int memberItem) - { - int data_offset = 0; - for (int indx = 0; indx < memberItem; indx++) - data_offset += memberStorage[indx]; - return data_offset; - } - } - - static class Sensor { - public int serial_no; - public String location; - public double temperature; - public double pressure; - - Sensor(int serial_no, String location, double temperature, double pressure) - { - this.serial_no = serial_no; - this.location = location; - this.temperature = temperature; - this.pressure = pressure; - } - - Sensor(List data) - { - this.serial_no = (int)data.get(0); - this.location = (String)data.get(1); - this.temperature = (double)data.get(2); - this.pressure = (double)data.get(3); - } - - Sensor(ByteBuffer databuf, int dbposition) { readBuffer(databuf, dbposition); } - - void writeBuffer(ByteBuffer databuf, int dbposition) - { - databuf.putInt(dbposition + Sensor_Datatype.getOffset(0), serial_no); - byte[] temp_str = location.getBytes(Charset.forName("UTF-8")); - int arraylen = (temp_str.length > MAXSTRINGSIZE) ? MAXSTRINGSIZE : temp_str.length; - for (int ndx = 0; ndx < arraylen; ndx++) - databuf.put(dbposition + Sensor_Datatype.getOffset(1) + ndx, temp_str[ndx]); - for (int ndx = arraylen; ndx < MAXSTRINGSIZE; ndx++) - databuf.put(dbposition + Sensor_Datatype.getOffset(1) + arraylen, (byte)0); - databuf.putDouble(dbposition + Sensor_Datatype.getOffset(2), temperature); - databuf.putDouble(dbposition + Sensor_Datatype.getOffset(3), pressure); - } - - void readBuffer(ByteBuffer databuf, int dbposition) - { - this.serial_no = databuf.getInt(dbposition + Sensor_Datatype.getOffset(0)); - ByteBuffer stringbuf = databuf.duplicate(); - stringbuf.position(dbposition + Sensor_Datatype.getOffset(1)); - stringbuf.limit(dbposition + Sensor_Datatype.getOffset(1) + MAXSTRINGSIZE); - byte[] bytearr = new byte[stringbuf.remaining()]; - stringbuf.get(bytearr); - this.location = new String(bytearr, Charset.forName("UTF-8")).trim(); - this.temperature = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(2)); - this.pressure = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(3)); - } - - List get() - { - List data = new ArrayList<>(); - data.add(this.serial_no); - data.add(this.location); - data.add(this.temperature); - data.add(this.pressure); - return data; - } - - void put(List data) - { - this.serial_no = (int)data.get(0); - this.location = (String)data.get(1); - this.temperature = (double)data.get(2); - this.pressure = (double)data.get(3); - } - - @Override - public String toString() - { - return String.format("Serial number : " + serial_no + "%n" - + "Location : " + location + "%n" - + "Temperature (F) : " + temperature + "%n" - + "Pressure (inHg) : " + pressure + "%n"); - } - } - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - ArrayList[] object_data = new ArrayList[DIM0]; - byte[] dset_data = null; - - // Initialize data. - object_data[0] = (ArrayList) new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57).get(); - object_data[1] = (ArrayList) new Sensor(1184, new String("Intake"), 55.12, 22.95).get(); - object_data[2] = (ArrayList) new Sensor(1027, new String("Intake manifold"), 103.55, 31.23).get(); - object_data[3] = (ArrayList) new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11).get(); - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create string datatype. - try { - strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (strtype_id >= 0) - H5.H5Tset_size(strtype_id, MAXSTRINGSIZE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the compound datatype for memory. - try { - memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); - if (memtype_id >= 0) { - for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { - long type_id = Sensor_Datatype.memberMemTypes[indx]; - if (type_id == HDF5Constants.H5T_C_S1) - type_id = strtype_id; - H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], - Sensor_Datatype.getOffset(indx), type_id); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the compound datatype for the file. Because the standard - // types we are using for the file may have different sizes than - // the corresponding native types, we must manually calculate the - // offset of each member. - try { - filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); - if (filetype_id >= 0) { - for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { - long type_id = Sensor_Datatype.memberFileTypes[indx]; - if (type_id == HDF5Constants.H5T_C_S1) - type_id = strtype_id; - H5.H5Tinsert(filetype_id, Sensor_Datatype.memberNames[indx], - Sensor_Datatype.getOffset(indx), type_id); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0)) - attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, filetype_id, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the compound data. - try { - if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5AwriteVL(attribute_id, memtype_id, (Object[])object_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (strtype_id >= 0) - H5.H5Tclose(strtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long strtype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - Sensor[] object_data2 = new Sensor[(int)dims[0]]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. This is a - // three dimensional dataset when the array datatype is included so - // the dynamic allocation must be done in steps. - try { - if (attribute_id >= 0) - dataspace_id = H5.H5Aget_space(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create string datatype. - try { - strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (strtype_id >= 0) - H5.H5Tset_size(strtype_id, MAXSTRINGSIZE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the compound datatype for memory. - try { - memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); - if (memtype_id >= 0) { - for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { - long type_id = Sensor_Datatype.memberMemTypes[indx]; - if (type_id == HDF5Constants.H5T_C_S1) - type_id = strtype_id; - H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], - Sensor_Datatype.getOffset(indx), type_id); - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - ArrayList[] object_data = new ArrayList[(int)dims[0]]; - - // Read data. - try { - if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5AreadVL(attribute_id, memtype_id, (Object[])object_data); - - for (int indx = 0; indx < (int)dims[0]; indx++) { - object_data2[indx] = new Sensor(object_data[indx]); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(ATTRIBUTENAME + " [" + indx + "]:"); - System.out.println(object_data2[indx].toString()); - } - System.out.println(); - - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (strtype_id >= 0) - H5.H5Tclose(strtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_CompoundAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_CompoundAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_Float.java b/java/examples/datatypes/H5Ex_T_Float.java deleted file mode 100644 index 9ca099e..0000000 --- a/java/examples/datatypes/H5Ex_T_Float.java +++ /dev/null @@ -1,227 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write integer datatypes - to a dataset. The program first writes integers to a - dataset with a dataspace of DIM0xDIM1, then closes the - file. Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import java.text.DecimalFormat; -import java.text.DecimalFormatSymbols; -import java.util.Locale; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_Float { - private static String FILENAME = "H5Ex_T_Float.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM0 = 4; - private static final int DIM1 = 7; - private static final int RANK = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - double[][] dset_data = new double[DIM0][DIM1]; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < DIM1; jndx++) { - dset_data[indx][jndx] = indx / (jndx + 0.5) + jndx; - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset and write the floating point data to it. In - // this example we will save the data as 64 bit little endian IEEE - // floating point numbers, regardless of the native type. The HDF5 - // library automatically converts between different floating point - // types. - try { - if ((file_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_IEEE_F64LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - double[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new double[(int)dims[0]][(int)(dims[1])]; - - // Read data. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - DecimalFormat df = new DecimalFormat("#,##0.0000", new DecimalFormatSymbols(Locale.US)); - System.out.println(DATASETNAME + ":"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" ["); - for (int jndx = 0; jndx < dims[1]; jndx++) { - System.out.print(" " + df.format(dset_data[indx][jndx])); - } - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_Float.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_Float.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_FloatAttribute.java b/java/examples/datatypes/H5Ex_T_FloatAttribute.java deleted file mode 100644 index 426c4dd..0000000 --- a/java/examples/datatypes/H5Ex_T_FloatAttribute.java +++ /dev/null @@ -1,264 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write floating point - datatypes to an attribute. The program first writes - floating point numbers to an attribute with a dataspace of - DIM0xDIM1, then closes the file. Next, it reopens the - file, reads back the data, and outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import java.text.DecimalFormat; -import java.text.DecimalFormatSymbols; -import java.util.Locale; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_FloatAttribute { - private static String FILENAME = "H5Ex_T_FloatAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static final int DIM0 = 4; - private static final int DIM1 = 7; - private static final int RANK = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - double[][] dset_data = new double[DIM0][DIM1]; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < DIM1; jndx++) { - dset_data[indx][jndx] = indx / (jndx + 0.5) + jndx; - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute and write the array data to it. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0)) - attribute_id = - H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_IEEE_F64LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if (attribute_id >= 0) - H5.H5Awrite(attribute_id, HDF5Constants.H5T_NATIVE_DOUBLE, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - double[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (attribute_id >= 0) - dataspace_id = H5.H5Aget_space(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new double[(int)dims[0]][(int)(dims[1])]; - - // Read data. - try { - if (attribute_id >= 0) - H5.H5Aread(attribute_id, HDF5Constants.H5T_NATIVE_DOUBLE, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - DecimalFormat df = new DecimalFormat("#,##0.0000", new DecimalFormatSymbols(Locale.US)); - System.out.println(ATTRIBUTENAME + ":"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" ["); - for (int jndx = 0; jndx < dims[1]; jndx++) { - System.out.print(" " + df.format(dset_data[indx][jndx])); - } - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_FloatAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_FloatAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_Integer.java b/java/examples/datatypes/H5Ex_T_Integer.java deleted file mode 100644 index 919ea7e..0000000 --- a/java/examples/datatypes/H5Ex_T_Integer.java +++ /dev/null @@ -1,224 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write integer datatypes - to a dataset. The program first writes integers to a - dataset with a dataspace of DIM0xDIM1, then closes the - file. Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import java.text.DecimalFormat; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_Integer { - private static String FILENAME = "H5Ex_T_Integer.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM0 = 4; - private static final int DIM1 = 7; - private static final int RANK = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data = new int[DIM0][DIM1]; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < DIM1; jndx++) { - dset_data[indx][jndx] = indx * jndx - jndx; - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset and write the integer data to it. In this - // example we will save the data as 64 bit big endian integers, - // regardless of the native integer type. The HDF5 library - // automatically converts between different integer types. - try { - if ((file_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I64BE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new int[(int)dims[0]][(int)(dims[1])]; - - // Read data. - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - DecimalFormat df = new DecimalFormat("#,##0"); - System.out.println(DATASETNAME + ":"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" ["); - for (int jndx = 0; jndx < dims[1]; jndx++) { - System.out.print(" " + df.format(dset_data[indx][jndx])); - } - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_Integer.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_Integer.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_IntegerAttribute.java b/java/examples/datatypes/H5Ex_T_IntegerAttribute.java deleted file mode 100644 index 4ec98c4..0000000 --- a/java/examples/datatypes/H5Ex_T_IntegerAttribute.java +++ /dev/null @@ -1,262 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write integer datatypes - to an attribute. The program first writes integers to an - attribute with a dataspace of DIM0xDIM1, then closes the - file. Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import java.text.DecimalFormat; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_IntegerAttribute { - private static String FILENAME = "H5Ex_T_IntegerAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static final int DIM0 = 4; - private static final int DIM1 = 7; - private static final int RANK = 2; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data = new int[DIM0][DIM1]; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) - for (int jndx = 0; jndx < DIM1; jndx++) { - dset_data[indx][jndx] = indx * jndx - jndx; - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute and write the array data to it. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0)) - attribute_id = - H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_STD_I64BE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if (attribute_id >= 0) - H5.H5Awrite(attribute_id, HDF5Constants.H5T_NATIVE_INT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0, DIM1}; - int[][] dset_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (attribute_id >= 0) - dataspace_id = H5.H5Aget_space(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate array of pointers to two-dimensional arrays (the - // elements of the dataset. - dset_data = new int[(int)dims[0]][(int)(dims[1])]; - - // Read data. - try { - if (attribute_id >= 0) - H5.H5Aread(attribute_id, HDF5Constants.H5T_NATIVE_INT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - DecimalFormat df = new DecimalFormat("#,##0"); - System.out.println(ATTRIBUTENAME + ":"); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(" ["); - for (int jndx = 0; jndx < dims[1]; jndx++) { - System.out.print(" " + df.format(dset_data[indx][jndx])); - } - System.out.println("]"); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_IntegerAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_IntegerAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_ObjectReference.java b/java/examples/datatypes/H5Ex_T_ObjectReference.java deleted file mode 100644 index 9220d8f..0000000 --- a/java/examples/datatypes/H5Ex_T_ObjectReference.java +++ /dev/null @@ -1,329 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write object references - to a dataset. The program first creates objects in the - file and writes references to those objects to a dataset - with a dataspace of DIM0, then closes the file. Next, it - reopens the file, dereferences the references, and outputs - the names of their targets to the screen. - ************************************************************/ -package examples.datatypes; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_ObjectReference { - private static String FILENAME = "H5Ex_T_ObjectReference.h5"; - private static String DATASETNAME = "DS1"; - private static String DATASETNAME2 = "DS2"; - private static String GROUPNAME = "G1"; - private static final int DIM0 = 2; - private static final int RANK = 1; - - // Values for the status of space allocation - enum H5G_obj { - H5G_UNKNOWN(HDF5Constants.H5O_TYPE_UNKNOWN), /* Unknown object type */ - H5G_GROUP(HDF5Constants.H5O_TYPE_GROUP), /* Object is a group */ - H5G_DATASET(HDF5Constants.H5O_TYPE_DATASET), /* Object is a dataset */ - H5G_TYPE(HDF5Constants.H5O_TYPE_NAMED_DATATYPE); /* Object is a named data type */ - private static final Map<Integer, H5G_obj> lookup = new HashMap<Integer, H5G_obj>(); - - static - { - for (H5G_obj s : EnumSet.allOf(H5G_obj.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5G_obj(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5G_obj get(int code) { return lookup.get(code); } - } - - private static void writeObjRef() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long filespace_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE]; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if ((file_id >= 0) && (dataspace_id >= 0)) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - dataset_id = HDF5Constants.H5I_INVALID_HID; - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create a group in the file. - try { - if (file_id >= 0) - group_id = H5.H5Gcreate(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - if (group_id >= 0) - H5.H5Gclose(group_id); - group_id = HDF5Constants.H5I_INVALID_HID; - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (file_id >= 0) { - try { - dset_data[0] = H5.H5Rcreate_object(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Throwable err) { - err.printStackTrace(); - } - - try { - dset_data[1] = H5.H5Rcreate_object(file_id, DATASETNAME2, HDF5Constants.H5P_DEFAULT); - } - catch (Throwable err) { - err.printStackTrace(); - } - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - filespace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (filespace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_REF, filespace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the object references to it. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - } - catch (Exception ex) { - ex.printStackTrace(); - } - finally { - try { - H5.H5Rdestroy(dset_data[1]); - } - catch (Exception ex) { - } - try { - H5.H5Rdestroy(dset_data[0]); - } - catch (Exception ex) { - } - } - - // End access to the dataset and release resources used by it. - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (filespace_id >= 0) - H5.H5Sclose(filespace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readObjRef() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - int object_type = -1; - long object_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - - // Open an existing dataset. - try { - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - - try { - // Get dataspace and allocate memory for read buffer. - dataspace_id = H5.H5Dget_space(dataset_id); - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - - // Read data. - H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(DATASETNAME + "[" + indx + "]:"); - System.out.print(" ->"); - // Open the referenced object, get its name and type. - try { - object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - try { - object_type = H5.H5Rget_obj_type3(dset_data[indx], HDF5Constants.H5R_OBJECT); - String obj_name = null; - if (object_type >= 0) { - // Get the name. - obj_name = H5.H5Iget_name(object_id); - } - if ((object_id >= 0) && (object_type >= -1)) { - switch (H5G_obj.get(object_type)) { - case H5G_GROUP: - System.out.print("H5G_GROUP"); - break; - case H5G_DATASET: - System.out.print("H5G_DATASET"); - break; - case H5G_TYPE: - System.out.print("H5G_TYPE"); - break; - default: - System.out.print("UNHANDLED"); - } - } - // Print the name. - System.out.println(": " + obj_name); - } - catch (Exception e) { - e.printStackTrace(); - } - finally { - try { - H5.H5Oclose(object_id); - } - catch (Exception e) { - } - } - } - catch (Exception e4) { - e4.printStackTrace(); - } - finally { - try { - H5.H5Rdestroy(dset_data[indx]); - } - catch (Exception e4) { - } - } - } // end for - } - catch (Exception e3) { - e3.printStackTrace(); - } - finally { - try { - H5.H5Sclose(dataspace_id); - } - catch (Exception e3) { - } - } - } - catch (Exception e2) { - e2.printStackTrace(); - } - finally { - try { - H5.H5Dclose(dataset_id); - } - catch (Exception e2) { - } - } - } - catch (Exception e1) { - e1.printStackTrace(); - } - finally { - try { - H5.H5Fclose(file_id); - } - catch (Exception e1) { - } - } - } - - public static void main(String[] args) - { - // Check if gzip compression is available and can be used for both - // compression and decompression. Normally we do not perform error - // checking in these examples for the sake of clarity, but in this - // case we will make an exception because this filter is an - // optional part of the hdf5 library. - H5Ex_T_ObjectReference.writeObjRef(); - H5Ex_T_ObjectReference.readObjRef(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java b/java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java deleted file mode 100644 index be84e51..0000000 --- a/java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java +++ /dev/null @@ -1,367 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write object references - to an attribute. The program first creates objects in the - file and writes references to those objects to an - attribute with a dataspace of DIM0, then closes the file. - Next, it reopens the file, dereferences the references, - and outputs the names of their targets to the screen. - ************************************************************/ -package examples.datatypes; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_ObjectReferenceAttribute { - private static String FILENAME = "H5Ex_T_ObjectReferenceAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static String DATASETNAME2 = "DS2"; - private static String GROUPNAME = "G1"; - private static final int DIM0 = 2; - private static final int RANK = 1; - - // Values for the status of space allocation - enum H5G_obj { - H5G_UNKNOWN(HDF5Constants.H5O_TYPE_UNKNOWN), /* Unknown object type */ - H5G_GROUP(HDF5Constants.H5O_TYPE_GROUP), /* Object is a group */ - H5G_DATASET(HDF5Constants.H5O_TYPE_DATASET), /* Object is a dataset */ - H5G_TYPE(HDF5Constants.H5O_TYPE_NAMED_DATATYPE); /* Object is a named data type */ - private static final Map<Integer, H5G_obj> lookup = new HashMap<Integer, H5G_obj>(); - - static - { - for (H5G_obj s : EnumSet.allOf(H5G_obj.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5G_obj(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5G_obj get(int code) { return lookup.get(code); } - } - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE]; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if ((file_id >= 0) && (dataspace_id >= 0)) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - dataset_id = HDF5Constants.H5I_INVALID_HID; - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create a group in the file. - try { - if (file_id >= 0) - group_id = H5.H5Gcreate(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - if (group_id >= 0) - H5.H5Gclose(group_id); - group_id = HDF5Constants.H5I_INVALID_HID; - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (file_id >= 0) { - try { - dset_data[0] = H5.H5Rcreate_object(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Throwable err) { - err.printStackTrace(); - } - - try { - dset_data[1] = H5.H5Rcreate_object(file_id, DATASETNAME2, HDF5Constants.H5P_DEFAULT); - } - catch (Throwable err) { - err.printStackTrace(); - } - } - - // Create dataset with a scalar dataspace to serve as the parent - // for the attribute. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute and write the array data to it. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0)) - attribute_id = - H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_STD_REF, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if (attribute_id >= 0) - H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - } - catch (Exception ex) { - ex.printStackTrace(); - } - finally { - try { - H5.H5Rdestroy(dset_data[1]); - } - catch (Exception ex) { - } - try { - H5.H5Rdestroy(dset_data[0]); - } - catch (Exception ex) { - } - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - int object_type = -1; - long object_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE]; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - - // Open an existing dataset. - try { - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - - try { - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - - // Get dataspace and allocate memory for read buffer. - try { - dataspace_id = H5.H5Aget_space(attribute_id); - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - - // Read data. - H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF, dset_data); - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(ATTRIBUTENAME + "[" + indx + "]:"); - System.out.print(" ->"); - // Open the referenced object, get its name and type. - try { - object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - try { - object_type = - H5.H5Rget_obj_type3(dset_data[indx], HDF5Constants.H5R_OBJECT); - String obj_name = null; - if (object_type >= 0) { - // Get the name. - obj_name = H5.H5Iget_name(object_id); - } - if ((object_id >= 0) && (object_type >= -1)) { - switch (H5G_obj.get(object_type)) { - case H5G_GROUP: - System.out.print("H5G_GROUP"); - break; - case H5G_DATASET: - System.out.print("H5G_DATASET"); - break; - case H5G_TYPE: - System.out.print("H5G_TYPE"); - break; - default: - System.out.print("UNHANDLED"); - } - } - // Print the name. - System.out.println(": " + obj_name); - } - catch (Exception e) { - e.printStackTrace(); - } - finally { - try { - H5.H5Oclose(object_id); - } - catch (Exception e) { - } - } - } - catch (Exception e5) { - e5.printStackTrace(); - } - finally { - try { - H5.H5Rdestroy(dset_data[indx]); - } - catch (Exception e5) { - } - } - } // end for - } - catch (Exception e4) { - e4.printStackTrace(); - } - finally { - try { - H5.H5Sclose(dataspace_id); - } - catch (Exception e3) { - } - } - } - catch (Exception e3) { - e3.printStackTrace(); - } - finally { - try { - H5.H5Aclose(attribute_id); - } - catch (Exception e4) { - } - } - } - catch (Exception e2) { - e2.printStackTrace(); - } - finally { - try { - H5.H5Dclose(dataset_id); - } - catch (Exception e2) { - } - } - } - catch (Exception e1) { - e1.printStackTrace(); - } - finally { - try { - H5.H5Fclose(file_id); - } - catch (Exception e1) { - } - } - } - - public static void main(String[] args) - { - H5Ex_T_ObjectReferenceAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_ObjectReferenceAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_Opaque.java b/java/examples/datatypes/H5Ex_T_Opaque.java deleted file mode 100644 index 419a5c8..0000000 --- a/java/examples/datatypes/H5Ex_T_Opaque.java +++ /dev/null @@ -1,268 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write opaque datatypes - to a dataset. The program first writes opaque data to a - dataset with a dataspace of DIM0, then closes the file. - Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_Opaque { - private static String FILENAME = "H5Ex_T_Opaque.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM0 = 4; - private static final int LEN = 7; - private static final int RANK = 1; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long datatype_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[] dset_data = new byte[DIM0 * LEN]; - byte[] str_data = {'O', 'P', 'A', 'Q', 'U', 'E'}; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) { - for (int jndx = 0; jndx < LEN - 1; jndx++) - dset_data[jndx + indx * LEN] = str_data[jndx]; - dset_data[LEN - 1 + indx * LEN] = (byte)(indx + '0'); - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create opaque datatype and set the tag to something appropriate. - // For this example we will write and view the data as a character - // array. - try { - datatype_id = H5.H5Tcreate(HDF5Constants.H5T_OPAQUE, (long)LEN); - if (datatype_id >= 0) - H5.H5Tset_tag(datatype_id, "Character array"); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset and write the integer data to it. In this - // example we will save the data as 64 bit big endian integers, - // regardless of the native integer type. The HDF5 library - // automatically converts between different integer types. - try { - if ((file_id >= 0) && (datatype_id >= 0) && (dataspace_id >= 0)) - dataset_id = - H5.H5Dcreate(file_id, DATASETNAME, datatype_id, dataspace_id, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the opaque data to the dataset. - try { - if ((dataset_id >= 0) && (datatype_id >= 0)) - H5.H5Dwrite(dataset_id, datatype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (datatype_id >= 0) - H5.H5Tclose(datatype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long datatype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long type_len = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[] dset_data; - String tag_name = null; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get datatype and properties for the datatype. - try { - if (dataset_id >= 0) - datatype_id = H5.H5Dget_type(dataset_id); - if (datatype_id >= 0) { - type_len = H5.H5Tget_size(datatype_id); - tag_name = H5.H5Tget_tag(datatype_id); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate buffer. - dset_data = new byte[(int)(dims[0] * type_len)]; - - // Read data. - try { - if ((dataset_id >= 0) && (datatype_id >= 0)) - H5.H5Dread(dataset_id, datatype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Datatype tag for " + DATASETNAME + " is: \"" + tag_name + "\""); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(DATASETNAME + "[" + indx + "]: "); - for (int jndx = 0; jndx < type_len; jndx++) { - char temp = (char)dset_data[jndx + indx * (int)type_len]; - System.out.print(temp); - } - System.out.println(""); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (datatype_id >= 0) - H5.H5Tclose(datatype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_Opaque.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_Opaque.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_OpaqueAttribute.java b/java/examples/datatypes/H5Ex_T_OpaqueAttribute.java deleted file mode 100644 index b8a15a6..0000000 --- a/java/examples/datatypes/H5Ex_T_OpaqueAttribute.java +++ /dev/null @@ -1,305 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write opaque datatypes - to an attribute. The program first writes opaque data to - an attribute with a dataspace of DIM0, then closes the - file. Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_OpaqueAttribute { - private static String FILENAME = "H5Ex_T_OpaqueAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static final int DIM0 = 4; - private static final int LEN = 7; - private static final int RANK = 1; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long datatype_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[] dset_data = new byte[DIM0 * LEN]; - byte[] str_data = {'O', 'P', 'A', 'Q', 'U', 'E'}; - - // Initialize data. - for (int indx = 0; indx < DIM0; indx++) { - for (int jndx = 0; jndx < LEN - 1; jndx++) - dset_data[jndx + indx * LEN] = str_data[jndx]; - dset_data[LEN - 1 + indx * LEN] = (byte)(indx + '0'); - } - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create opaque datatype and set the tag to something appropriate. - // For this example we will write and view the data as a character - // array. - try { - datatype_id = H5.H5Tcreate(HDF5Constants.H5T_OPAQUE, (long)LEN); - if (datatype_id >= 0) - H5.H5Tset_tag(datatype_id, "Character array"); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute and write the array data to it. - try { - if ((dataset_id >= 0) && (datatype_id >= 0) && (dataspace_id >= 0)) - attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, datatype_id, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if ((attribute_id >= 0) && (datatype_id >= 0)) - H5.H5Awrite(attribute_id, datatype_id, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (datatype_id >= 0) - H5.H5Tclose(datatype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long datatype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long type_len = -1; - long[] dims = {DIM0}; - byte[] dset_data; - String tag_name = null; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get datatype and properties for the datatype. - try { - if (attribute_id >= 0) - datatype_id = H5.H5Aget_type(attribute_id); - if (datatype_id >= 0) { - type_len = H5.H5Tget_size(datatype_id); - tag_name = H5.H5Tget_tag(datatype_id); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (attribute_id >= 0) - dataspace_id = H5.H5Aget_space(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate buffer. - dset_data = new byte[(int)(dims[0] * type_len)]; - - // Read data. - try { - if ((attribute_id >= 0) && (datatype_id >= 0)) - H5.H5Aread(attribute_id, datatype_id, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - System.out.println("Datatype tag for " + ATTRIBUTENAME + " is: \"" + tag_name + "\""); - for (int indx = 0; indx < dims[0]; indx++) { - System.out.print(ATTRIBUTENAME + "[" + indx + "]: "); - for (int jndx = 0; jndx < type_len; jndx++) { - char temp = (char)dset_data[jndx + indx * (int)type_len]; - System.out.print(temp); - } - System.out.println(""); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (datatype_id >= 0) - H5.H5Tclose(datatype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_OpaqueAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_OpaqueAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_String.java b/java/examples/datatypes/H5Ex_T_String.java deleted file mode 100644 index a69a70b..0000000 --- a/java/examples/datatypes/H5Ex_T_String.java +++ /dev/null @@ -1,309 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write string datatypes - to a dataset. The program first writes strings to a - dataset with a dataspace of DIM0, then closes the file. - Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_String { - private static String FILENAME = "H5Ex_T_String.h5"; - private static String DATASETNAME = "DS1"; - private static final int DIM0 = 4; - private static final int SDIM = 8; - private static final int RANK = 1; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[][] dset_data = new byte[DIM0][SDIM]; - StringBuffer[] str_data = {new StringBuffer("Parting"), new StringBuffer("is such"), - new StringBuffer("sweet"), new StringBuffer("sorrow.")}; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create file and memory datatypes. For this example we will save - // the strings as FORTRAN strings, therefore they do not need space - // for the null terminator in the file. - try { - filetype_id = H5.H5Tcopy(HDF5Constants.H5T_FORTRAN_S1); - if (filetype_id >= 0) - H5.H5Tset_size(filetype_id, SDIM - 1); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - memtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (memtype_id >= 0) - H5.H5Tset_size(memtype_id, SDIM); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset and write the string data to it. - try { - if ((file_id >= 0) && (filetype_id >= 0) && (dataspace_id >= 0)) - dataset_id = - H5.H5Dcreate(file_id, DATASETNAME, filetype_id, dataspace_id, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - for (int indx = 0; indx < DIM0; indx++) { - for (int jndx = 0; jndx < SDIM; jndx++) { - if (jndx < str_data[indx].length()) - dset_data[indx][jndx] = (byte)str_data[indx].charAt(jndx); - else - dset_data[indx][jndx] = 0; - } - } - if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5Dwrite(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long sdim = 0; - long[] dims = {DIM0}; - byte[][] dset_data; - StringBuffer[] str_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get the datatype and its size. - try { - if (dataset_id >= 0) - filetype_id = H5.H5Dget_type(dataset_id); - if (filetype_id >= 0) { - sdim = H5.H5Tget_size(filetype_id); - sdim++; // Make room for null terminator - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (dataset_id >= 0) - dataspace_id = H5.H5Dget_space(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate space for data. - dset_data = new byte[(int)dims[0]][(int)sdim]; - str_data = new StringBuffer[(int)dims[0]]; - - // Create the memory datatype. - try { - memtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (memtype_id >= 0) - H5.H5Tset_size(memtype_id, sdim); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read data. - try { - if ((dataset_id >= 0) && (memtype_id >= 0)) - H5.H5Dread(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, dset_data); - byte[] tempbuf = new byte[(int)sdim]; - for (int indx = 0; indx < (int)dims[0]; indx++) { - for (int jndx = 0; jndx < sdim; jndx++) { - tempbuf[jndx] = dset_data[indx][jndx]; - } - str_data[indx] = new StringBuffer(new String(tempbuf).trim()); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(DATASETNAME + " [" + indx + "]: " + str_data[indx]); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_String.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_String.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_StringAttribute.java b/java/examples/datatypes/H5Ex_T_StringAttribute.java deleted file mode 100644 index 46c1038..0000000 --- a/java/examples/datatypes/H5Ex_T_StringAttribute.java +++ /dev/null @@ -1,349 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to read and write string datatypes - to an attribute. The program first writes strings to an - attribute with a dataspace of DIM0, then closes the file. - Next, it reopens the file, reads back the data, and - outputs it to the screen. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_StringAttribute { - private static String FILENAME = "H5Ex_T_StringAttribute.h5"; - private static String DATASETNAME = "DS1"; - private static String ATTRIBUTENAME = "A1"; - private static final int DIM0 = 4; - private static final int SDIM = 8; - private static final int RANK = 1; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM0}; - byte[][] dset_data = new byte[DIM0][SDIM]; - StringBuffer[] str_data = {new StringBuffer("Parting"), new StringBuffer("is such"), - new StringBuffer("sweet"), new StringBuffer("sorrow.")}; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create file and memory datatypes. For this example we will save - // the strings as FORTRAN strings, therefore they do not need space - // for the null terminator in the file. - try { - filetype_id = H5.H5Tcopy(HDF5Constants.H5T_FORTRAN_S1); - if (filetype_id >= 0) - H5.H5Tset_size(filetype_id, SDIM - 1); - } - catch (Exception e) { - e.printStackTrace(); - } - try { - memtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (memtype_id >= 0) - H5.H5Tset_size(memtype_id, SDIM); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataset with a scalar dataspace. - try { - dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); - if (dataspace_id >= 0) { - dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(RANK, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the attribute. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0)) - attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, filetype_id, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - for (int indx = 0; indx < DIM0; indx++) { - for (int jndx = 0; jndx < SDIM; jndx++) { - if (jndx < str_data[indx].length()) - dset_data[indx][jndx] = (byte)str_data[indx].charAt(jndx); - else - dset_data[indx][jndx] = 0; - } - } - if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5Awrite(attribute_id, memtype_id, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void ReadDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long filetype_id = HDF5Constants.H5I_INVALID_HID; - long memtype_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long sdim = 0; - long[] dims = {DIM0}; - byte[][] dset_data; - StringBuffer[] str_data; - - // Open an existing file. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing dataset. - try { - if (file_id >= 0) - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get the datatype and its size. - try { - if (attribute_id >= 0) - filetype_id = H5.H5Aget_type(attribute_id); - if (filetype_id >= 0) { - sdim = H5.H5Tget_size(filetype_id); - sdim++; // Make room for null terminator - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Get dataspace and allocate memory for read buffer. - try { - if (attribute_id >= 0) - dataspace_id = H5.H5Aget_space(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataspace_id >= 0) - H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Allocate space for data. - dset_data = new byte[(int)dims[0]][(int)sdim]; - str_data = new StringBuffer[(int)dims[0]]; - - // Create the memory datatype. - try { - memtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - if (memtype_id >= 0) - H5.H5Tset_size(memtype_id, sdim); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Read data. - try { - if ((attribute_id >= 0) && (memtype_id >= 0)) - H5.H5Aread(attribute_id, memtype_id, dset_data); - byte[] tempbuf = new byte[(int)sdim]; - for (int indx = 0; indx < (int)dims[0]; indx++) { - for (int jndx = 0; jndx < sdim; jndx++) { - tempbuf[jndx] = dset_data[indx][jndx]; - } - str_data[indx] = new StringBuffer(new String(tempbuf).trim()); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Output the data to the screen. - for (int indx = 0; indx < dims[0]; indx++) { - System.out.println(DATASETNAME + " [" + indx + "]: " + str_data[indx]); - } - System.out.println(); - - // End access to the dataset and release resources used by it. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the file type. - try { - if (filetype_id >= 0) - H5.H5Tclose(filetype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the mem type. - try { - if (memtype_id >= 0) - H5.H5Tclose(memtype_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_StringAttribute.CreateDataset(); - // Now we begin the read section of this example. Here we assume - // the dataset and array have the same name and rank, but can have - // any size. Therefore we must allocate a new array to read in - // data using malloc(). - H5Ex_T_StringAttribute.ReadDataset(); - } -} diff --git a/java/examples/datatypes/H5Ex_T_VLString.java b/java/examples/datatypes/H5Ex_T_VLString.java deleted file mode 100644 index a9288a4..0000000 --- a/java/examples/datatypes/H5Ex_T_VLString.java +++ /dev/null @@ -1,137 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Creating and writing a VL string to a file. - ************************************************************/ - -package examples.datatypes; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_T_VLString { - private static String FILENAME = "H5Ex_T_VLString.h5"; - private static String DATASETNAME = "DS1"; - - private static void createDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long type_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - int rank = 1; - String[] str_data = {"Parting", "is such", "sweet", "sorrow."}; - long[] dims = {str_data.length}; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - type_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); - H5.H5Tset_size(type_id, HDF5Constants.H5T_VARIABLE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create dataspace. Setting maximum size to NULL sets the maximum - // size to be the current size. - try { - dataspace_id = H5.H5Screate_simple(rank, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset and write the string data to it. - try { - if ((file_id >= 0) && (type_id >= 0) && (dataspace_id >= 0)) { - dataset_id = - H5.H5Dcreate(file_id, DATASETNAME, type_id, dataspace_id, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the data to the dataset. - try { - if (dataset_id >= 0) - H5.H5DwriteVL(dataset_id, type_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - H5.H5Sclose(dataspace_id); - H5.H5Tclose(type_id); - H5.H5Dclose(dataset_id); - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - private static void readDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long type_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - String[] str_data = {"", "", "", ""}; - - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); - type_id = H5.H5Dget_type(dataset_id); - H5.H5DreadVL(dataset_id, type_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, - HDF5Constants.H5P_DEFAULT, str_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - for (int indx = 0; indx < str_data.length; indx++) - System.out.println(DATASETNAME + " [" + indx + "]: " + str_data[indx]); - - try { - H5.H5Tclose(type_id); - H5.H5Dclose(dataset_id); - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5Ex_T_VLString.createDataset(); - H5Ex_T_VLString.readDataset(); - } -} diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in deleted file mode 100644 index fc4a627..0000000 --- a/java/examples/datatypes/JavaDatatypeExample.sh.in +++ /dev/null @@ -1,451 +0,0 @@ -#! /bin/sh -# -# 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. -# - -top_builddir=@top_builddir@ -top_srcdir=@top_srcdir@ -srcdir=@srcdir@ -IS_DARWIN="@H5_IS_DARWIN@" - -TESTNAME=EX_Datatypes -EXIT_SUCCESS=0 -EXIT_FAILURE=1 - -# Set up default variable values if not supplied by the user. -RM='rm -rf' -CMP='cmp' -DIFF='diff -c' -CP='cp' -DIRNAME='dirname' -BASENAME='basename' -LS='ls' -AWK='awk' - -nerrors=0 - -# where the libs exist -HDFLIB_HOME="$top_srcdir/java/lib" -BLDDIR="." -BLDLIBDIR="$BLDDIR/testlibs" -HDFTEST_HOME="$top_srcdir/java/examples/datatypes" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar -test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR - -###################################################################### -# library files -# -------------------------------------------------------------------- -# All the library files copy from source directory to test directory -# NOTE: Keep this framework to add/remove test files. -# This list are also used for checking exist. -# Comment '#' without space can be used. -# -------------------------------------------------------------------- -LIST_LIBRARY_FILES=" -$top_builddir/src/.libs/libhdf5.* -$top_builddir/java/src/jni/.libs/libhdf5_java.* -$top_builddir/java/src/$JARFILE -" -LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-2.0.6.jar -$HDFLIB_HOME/ext/slf4j-simple-2.0.6.jar -" -LIST_DATA_FILES=" -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Array.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_ArrayAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Bit.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_BitAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Commit.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Compound.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_CompoundAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Float.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_FloatAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Integer.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_IntegerAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_ObjectReference.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_ObjectReferenceAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Opaque.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_OpaqueAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_String.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_StringAttribute.txt -$HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_VLString.txt -" - -# -# copy files from source dirs to test dir -# -COPY_LIBFILES="$LIST_LIBRARY_FILES" -COPY_JARTESTFILES="$LIST_JAR_TESTFILES" - -COPY_LIBFILES_TO_BLDLIBDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_LIBFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - BNAME=`$BASENAME $tstfile` - if [ "$BNAME" = "libhdf5_java.dylib" ]; then - COPIED_LIBHDF5_JAVA=1 - fi - fi - fi - done - if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then - (cd $BLDLIBDIR; \ - install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \ - exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \ - echo $exist_path; \ - install_name_tool -change $exist_path @rpath/libhdf5.dylib libhdf5_java.dylib) - fi - # copy jar files. Used -f to make sure get a new copy - for tstfile in $COPY_JARTESTFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_LIBFILES_AND_BLDLIBDIR() -{ - # skip rm if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=$HDFLIB_HOME - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $RM -rf $BLDLIBDIR - fi -} - -COPY_DATAFILES="$LIST_DATA_FILES" - -COPY_DATAFILES_TO_BLDDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_DATAFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -f $tstfile $BLDDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_DATAFILES_AND_BLDDIR() -{ - $RM $BLDDIR/examples.datatypes.H5Ex_T_*.txt - $RM $BLDDIR/H5Ex_T_*.out - $RM $BLDDIR/H5Ex_T_*.h5 -} - -# Print a line-line message left justified in a field of 70 characters -# beginning with the word "Testing". -# -TESTING() { - SPACES=" " - echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012' -} - -# where Java is installed (requires jdk1.7.x) -JAVAEXE=@JAVA@ -JAVAEXEFLAGS=@H5_JAVAFLAGS@ - -############################################################################### -# DO NOT MODIFY BELOW THIS LINE -############################################################################### - -# prepare for test -COPY_LIBFILES_TO_BLDLIBDIR -COPY_DATAFILES_TO_BLDDIR - -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-2.0.6.jar:"$BLDLIBDIR"/slf4j-simple-2.0.6.jar:"$TESTJARFILE"" - -TEST=/usr/bin/test -if [ ! -x /usr/bin/test ] -then -TEST=`which test` -fi - -if $TEST -z "$CLASSPATH"; then - CLASSPATH="" -fi -CLASSPATH=$CPATH":"$CLASSPATH -export CLASSPATH - -if $TEST -n "$JAVAPATH" ; then - PATH=$JAVAPATH":"$PATH - export PATH -fi - -if $TEST -e /bin/uname; then - os_name=`/bin/uname -s` -elif $TEST -e /usr/bin/uname; then - os_name=`/usr/bin/uname -s` -else - os_name=unknown -fi - -if $TEST -z "$LD_LIBRARY_PATH" ; then - LD_LIBRARY_PATH="" -fi - -case $os_name in - *) - LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH - ;; -esac - -export LD_LIBRARY_PATH - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Array" -TESTING examples.datatypes.H5Ex_T_Array -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Array > H5Ex_T_Array.out) -if diff H5Ex_T_Array.out examples.datatypes.H5Ex_T_Array.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_Array" -else - echo "**FAILED** datatypes.H5Ex_T_Array" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_ArrayAttribute" -TESTING examples.datatypes.H5Ex_T_ArrayAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_ArrayAttribute > H5Ex_T_ArrayAttribute.out) -if diff H5Ex_T_ArrayAttribute.out examples.datatypes.H5Ex_T_ArrayAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_ArrayAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_ArrayAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Bit" -TESTING examples.datatypes.H5Ex_T_Bit -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Bit > H5Ex_T_Bit.out) -if diff H5Ex_T_Bit.out examples.datatypes.H5Ex_T_Bit.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_Bit" -else - echo "**FAILED** datatypes.H5Ex_T_Bit" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_BitAttribute" -TESTING examples.datatypes.H5Ex_T_BitAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_BitAttribute > H5Ex_T_BitAttribute.out) -if diff H5Ex_T_BitAttribute.out examples.datatypes.H5Ex_T_BitAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_BitAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_BitAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Commit" -TESTING examples.datasets.H5Ex_T_Commit -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Commit > H5Ex_T_Commit.out) -if diff H5Ex_T_Commit.out examples.datatypes.H5Ex_T_Commit.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_Commit" -else - echo "**FAILED** datatypes.H5Ex_T_Commit" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Compound" -TESTING examples.datatypes.H5Ex_T_Compound -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Compound > H5Ex_T_Compound.out) -if diff H5Ex_T_Compound.out examples.datatypes.H5Ex_T_Compound.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_Compound" -else - echo "**FAILED** datatypes.H5Ex_T_Compound" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_CompoundAttribute" -TESTING examples.datatypes.H5Ex_T_CompoundAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_CompoundAttribute > H5Ex_T_CompoundAttribute.out) -if diff H5Ex_T_CompoundAttribute.out examples.datatypes.H5Ex_T_CompoundAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_CompoundAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_CompoundAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Float" -TESTING examples.datatypes.H5Ex_T_Float -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Float > H5Ex_T_Float.out) -if diff H5Ex_T_Float.out examples.datatypes.H5Ex_T_Float.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_Float" -else - echo "**FAILED** datatypes.H5Ex_T_Float" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_FloatAttribute" -TESTING examples.datatypes.H5Ex_T_FloatAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_FloatAttribute > H5Ex_T_FloatAttribute.out) -if diff H5Ex_T_FloatAttribute.out examples.datatypes.H5Ex_T_FloatAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_FloatAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_FloatAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Integer" -TESTING examples.datatypes.H5Ex_T_Integer -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Integer > H5Ex_T_Integer.out) -if diff H5Ex_T_Integer.out examples.datatypes.H5Ex_T_Integer.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_Integer" -else - echo "**FAILED** datatypes.H5Ex_T_Integer" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_IntegerAttribute" -TESTING examples.datatypes.H5Ex_T_IntegerAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_IntegerAttribute > H5Ex_T_IntegerAttribute.out) -if diff H5Ex_T_IntegerAttribute.out examples.datatypes.H5Ex_T_IntegerAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_IntegerAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_IntegerAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_ObjectReference" -TESTING examples.datatypes.H5Ex_T_ObjectReference -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_ObjectReference > H5Ex_T_ObjectReference.out) -if diff H5Ex_T_ObjectReference.out examples.datatypes.H5Ex_T_ObjectReference.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_ObjectReference" -else - echo "**FAILED** datatypes.H5Ex_T_ObjectReference" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_ObjectReferenceAttribute" -TESTING examples.datatypes.H5Ex_T_ObjectReferenceAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_ObjectReferenceAttribute > H5Ex_T_ObjectReferenceAttribute.out) -if diff H5Ex_T_ObjectReferenceAttribute.out examples.datatypes.H5Ex_T_ObjectReferenceAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_ObjectReferenceAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_ObjectReferenceAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Opaque" -TESTING examples.datatypes.H5Ex_T_Opaque -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_Opaque > H5Ex_T_Opaque.out) -if diff H5Ex_T_Opaque.out examples.datatypes.H5Ex_T_Opaque.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_Opaque" -else - echo "**FAILED** datatypes.H5Ex_T_Opaque" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_OpaqueAttribute" -TESTING examples.datatypes.H5Ex_T_OpaqueAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_OpaqueAttribute > H5Ex_T_OpaqueAttribute.out) -if diff H5Ex_T_OpaqueAttribute.out examples.datatypes.H5Ex_T_OpaqueAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_OpaqueAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_OpaqueAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_String" -TESTING examples.datatypes.H5Ex_T_String -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_String > H5Ex_T_String.out) -if diff H5Ex_T_String.out examples.datatypes.H5Ex_T_String.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_String" -else - echo "**FAILED** datatypes.H5Ex_T_String" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_StringAttribute" -TESTING examples.datatypes.H5Ex_T_StringAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_StringAttribute > H5Ex_T_StringAttribute.out) -if diff H5Ex_T_StringAttribute.out examples.datatypes.H5Ex_T_StringAttribute.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_StringAttribute" -else - echo "**FAILED** datatypes.H5Ex_T_StringAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_VLString" -TESTING examples.datatypes.H5Ex_T_VLString -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datatypes.H5Ex_T_VLString > H5Ex_T_VLString.out) -if diff H5Ex_T_VLString.out examples.datatypes.H5Ex_T_VLString.txt > /dev/null; then - echo " PASSED datatypes.H5Ex_T_VLString" -else - echo "**FAILED** datatypes.H5Ex_T_VLString" - nerrors="`expr $nerrors + 1`" -fi - -# Clean up temporary files/directories -CLEAN_LIBFILES_AND_BLDLIBDIR -CLEAN_DATAFILES_AND_BLDDIR - -# Report test results and exit -if test $nerrors -eq 0 ; then - echo "All $TESTNAME tests passed." - exit $EXIT_SUCCESS -else - echo "$TESTNAME tests failed with $nerrors errors." - exit $EXIT_FAILURE -fi diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am deleted file mode 100644 index 12e5cb8..0000000 --- a/java/examples/datatypes/Makefile.am +++ /dev/null @@ -1,75 +0,0 @@ -# -# 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. -## -## Makefile.am -## Run automake to generate a Makefile.in from this file. -## -# -# HDF5 Java Library Examples Makefile(.in) - -include $(top_srcdir)/config/commence.am - -# Mark this directory as part of the JNI API -JAVA_API=yes - -JAVAROOT = .classes - -classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - -pkgpath = examples/datatypes -hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-2.0.6.jar:$$CLASSPATH - -jarfile = jar$(PACKAGE_TARNAME)datatypes.jar - -AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation - -TESTPACKAGE = - -noinst_JAVA = \ - H5Ex_T_Array.java \ - H5Ex_T_ArrayAttribute.java \ - H5Ex_T_Bit.java \ - H5Ex_T_BitAttribute.java \ - H5Ex_T_Commit.java \ - H5Ex_T_Compound.java \ - H5Ex_T_CompoundAttribute.java \ - H5Ex_T_Float.java \ - H5Ex_T_FloatAttribute.java \ - H5Ex_T_Integer.java \ - H5Ex_T_IntegerAttribute.java \ - H5Ex_T_ObjectReference.java \ - H5Ex_T_ObjectReferenceAttribute.java \ - H5Ex_T_Opaque.java \ - H5Ex_T_OpaqueAttribute.java \ - H5Ex_T_String.java \ - H5Ex_T_StringAttribute.java \ - H5Ex_T_VLString.java - -$(jarfile): classnoinst.stamp classes - $(JAR) cvf $@ -C $(JAVAROOT)/ $(pkgpath) - -noinst_DATA = $(jarfile) - -.PHONY: classes - -check_SCRIPTS = JavaDatatypeExample.sh -TEST_SCRIPT = $(check_SCRIPTS) - -CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class JavaDatatypeExample.sh - -clean: - rm -rf $(JAVAROOT)/* - rm -f $(jarfile) - rm -f classnoinst.stamp - -include $(top_srcdir)/config/conclude.am diff --git a/java/examples/groups/CMakeLists.txt b/java/examples/groups/CMakeLists.txt deleted file mode 100644 index fc9eb94..0000000 --- a/java/examples/groups/CMakeLists.txt +++ /dev/null @@ -1,144 +0,0 @@ -cmake_minimum_required (VERSION 3.18) -project (HDFJAVA_EXAMPLES_GROUPS Java) - -set (CMAKE_VERBOSE_MAKEFILE 1) - -set (HDF_JAVA_EXAMPLES - H5Ex_G_Create - H5Ex_G_Iterate - H5Ex_G_Compact - H5Ex_G_Corder - H5Ex_G_Intermediate - H5Ex_G_Phase - H5Ex_G_Visit -) - -if (WIN32) - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") -else () - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") -endif () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") -endforeach () - -foreach (example ${HDF_JAVA_EXAMPLES}) - file (WRITE ${PROJECT_BINARY_DIR}/${example}_Manifest.txt - "Main-Class: examples.groups.${example} -" - ) - add_jar (${example} MANIFEST ${PROJECT_BINARY_DIR}/${example}_Manifest.txt ${example}.java) - get_target_property (${example}_JAR_FILE ${example} JAR_FILE) -# install_jar (${example} ${HJAVA_INSTALL_DATA_DIR}/examples examples) - get_target_property (${example}_CLASSPATH ${example} CLASSDIR) - add_dependencies (${example} ${HDF5_JAVA_HDF5_LIB_TARGET}) - - #----------------------------------------------------------------------------- - # Add Target to clang-format - #----------------------------------------------------------------------------- - if (HDF5_ENABLE_FORMATTERS) - clang_format (HDF5_JAVA_${example}_SRC_FORMAT ${example}.java) - endif () -endforeach () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS};${HDF5_JAVA_LOGGING_JAR};${HDF5_JAVA_LOGGING_NOP_JAR}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (HDFJAVA_JAR ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${HDFJAVA_JAR}") -endforeach () - -set (HDF_JAVA_TEST_FILES - h5ex_g_iterate.h5 - h5ex_g_visit.h5 -) - -foreach (h5_file ${HDF_JAVA_TEST_FILES}) - HDFTEST_COPY_FILE("${PROJECT_SOURCE_DIR}/${h5_file}" "${PROJECT_BINARY_DIR}/${h5_file}" "H5Ex_G_Visit_files") -endforeach () -add_custom_target(H5Ex_G_Visit_files ALL COMMENT "Copying files needed by H5Ex_G_Visit tests" DEPENDS ${H5Ex_G_Visit_files_list}) - -if (BUILD_TESTING AND HDF5_TEST_EXAMPLES AND HDF5_TEST_SERIAL) - get_property (target_name TARGET ${HDF5_JAVA_JNI_LIB_TARGET} PROPERTY OUTPUT_NAME) - set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${target_name}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") - - set (last_test "") - foreach (example ${HDF_JAVA_EXAMPLES}) - if (NOT example STREQUAL "H5Ex_G_Iterate" AND NOT example STREQUAL "H5Ex_G_Visit") - if (example STREQUAL "H5Ex_G_Compact") - add_test ( - NAME JAVA_groups-${example}-clear-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}1.h5 - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}2.h5 - ) - else () - add_test ( - NAME JAVA_groups-${example}-clear-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - endif () - else () - add_test ( - NAME JAVA_groups-${example}-clear-objects - COMMAND ${CMAKE_COMMAND} -E echo "${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 exists" - ) - endif () - if (last_test) - set_tests_properties (JAVA_groups-${example}-clear-objects PROPERTIES DEPENDS ${last_test}) - endif () - - add_test ( - NAME JAVA_groups-${example}-copy-objects - COMMAND ${CMAKE_COMMAND} -E copy_if_different - ${HDFJAVA_EXAMPLES_SOURCE_DIR}/testfiles/examples.groups.${example}.txt - ${HDFJAVA_EXAMPLES_GROUPS_BINARY_DIR}/${example}.txt - ) - set_tests_properties (JAVA_groups-${example}-copy-objects PROPERTIES DEPENDS JAVA_groups-${example}-clear-objects) - add_test ( - NAME JAVA_groups-${example} - COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" - -D "TEST_PROGRAM=examples.groups.${example}" - -D "TEST_ARGS:STRING=${CMD_ARGS}" - -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${example}_JAR_FILE}" - -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}" - -D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}" - -D "TEST_OUTPUT=groups/${example}.out" - -D "TEST_EXPECT=0" - -D "TEST_REFERENCE=groups/${example}.txt" - -P "${HDF_RESOURCES_DIR}/jrunTest.cmake" - ) - set_tests_properties (JAVA_groups-${example} PROPERTIES - DEPENDS JAVA_groups-${example}-copy-objects - ) - - if (NOT example STREQUAL "H5Ex_G_Iterate" AND NOT example STREQUAL "H5Ex_G_Visit") - if (example STREQUAL "H5Ex_G_Compact") - add_test ( - NAME JAVA_groups-${example}-clean-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}1.h5 - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}2.h5 - ) - else () - add_test ( - NAME JAVA_groups-${example}-clean-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - endif () - set_tests_properties (JAVA_groups-${example}-clean-objects PROPERTIES - DEPENDS JAVA_groups-${example} - ) - set (last_test "JAVA_groups-${example}-clean-objects") - else () - set (last_test "JAVA_groups-${example}") - endif () - endforeach () -endif () diff --git a/java/examples/groups/H5Ex_G_Compact.java b/java/examples/groups/H5Ex_G_Compact.java deleted file mode 100644 index 2c6535a..0000000 --- a/java/examples/groups/H5Ex_G_Compact.java +++ /dev/null @@ -1,261 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Creating a file and print the storage layout. - ************************************************************/ - -package examples.groups; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; -import hdf.hdf5lib.structs.H5G_info_t; - -public class H5Ex_G_Compact { - - private static final String FILE1 = "H5Ex_G_Compact1.h5"; - private static final String FILE2 = "H5Ex_G_Compact2.h5"; - private static final String GROUP = "G1"; - - enum H5G_storage { - H5G_STORAGE_TYPE_UNKNOWN(-1), - H5G_STORAGE_TYPE_SYMBOL_TABLE(0), - H5G_STORAGE_TYPE_COMPACT(1), - H5G_STORAGE_TYPE_DENSE(2); - - private static final Map<Integer, H5G_storage> lookup = new HashMap<Integer, H5G_storage>(); - - static - { - for (H5G_storage s : EnumSet.allOf(H5G_storage.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5G_storage(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5G_storage get(int code) { return lookup.get(code); } - } - - public static void CreateGroup() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - long fapl_id = HDF5Constants.H5I_INVALID_HID; - H5G_info_t ginfo; - long size; - - // Create file 1. This file will use original format groups. - try { - file_id = H5.H5Fcreate(FILE1, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - // Create a group in the file1. - try { - if (file_id >= 0) - group_id = H5.H5Gcreate(file_id, GROUP, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Obtain the group info and print the group storage type. - try { - if (group_id >= 0) { - ginfo = H5.H5Gget_info(group_id); - System.out.print("Group storage type for " + FILE1 + " is: "); - switch (H5G_storage.get(ginfo.storage_type)) { - case H5G_STORAGE_TYPE_COMPACT: - System.out.println("H5G_STORAGE_TYPE_COMPACT"); // New compact format - break; - case H5G_STORAGE_TYPE_DENSE: - System.out.println("H5G_STORAGE_TYPE_DENSE"); // New dense (indexed) format - break; - case H5G_STORAGE_TYPE_SYMBOL_TABLE: - System.out.println("H5G_STORAGE_TYPE_SYMBOL_TABLE"); // Original format - break; - case H5G_STORAGE_TYPE_UNKNOWN: - System.out.println("H5G_STORAGE_TYPE_UNKNOWN"); - break; - default: - System.out.println("Storage Type Invalid"); - break; - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group. - try { - if (group_id >= 0) - H5.H5Gclose(group_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // close the file 1. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Re-open file 1. Need to get the correct file size. - try { - file_id = H5.H5Fopen(FILE1, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Obtain and print the file size. - try { - if (file_id >= 0) { - size = H5.H5Fget_filesize(file_id); - System.out.println("File size for " + FILE1 + " is: " + size + " bytes"); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close FILE1. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Set file access property list to allow the latest file format. - // This will allow the library to create new compact format groups. - try { - fapl_id = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS); - if (fapl_id >= 0) - H5.H5Pset_libver_bounds(fapl_id, HDF5Constants.H5F_LIBVER_LATEST, - HDF5Constants.H5F_LIBVER_LATEST); - } - catch (Exception e) { - e.printStackTrace(); - } - System.out.println(); - // Create file 2 using the new file access property list. - try { - file_id = H5.H5Fcreate(FILE2, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - // Create group in file2. - try { - if (file_id >= 0) - group_id = H5.H5Gcreate(file_id, GROUP, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Obtain the group info and print the group storage type. - try { - if (group_id >= 0) { - ginfo = H5.H5Gget_info(group_id); - System.out.print("Group storage type for " + FILE2 + " is: "); - switch (H5G_storage.get(ginfo.storage_type)) { - case H5G_STORAGE_TYPE_COMPACT: - System.out.println("H5G_STORAGE_TYPE_COMPACT"); // New compact format - break; - case H5G_STORAGE_TYPE_DENSE: - System.out.println("H5G_STORAGE_TYPE_DENSE"); // New dense (indexed) format - break; - case H5G_STORAGE_TYPE_SYMBOL_TABLE: - System.out.println("H5G_STORAGE_TYPE_SYMBOL_TABLE"); // Original format - break; - case H5G_STORAGE_TYPE_UNKNOWN: - System.out.println("H5G_STORAGE_TYPE_UNKNOWN"); - break; - default: - System.out.println("Storage Type Invalid"); - break; - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group. - try { - if (group_id >= 0) - H5.H5Gclose(group_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // close the file 2. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Re-open file 2. Needed to get the correct file size. - try { - file_id = H5.H5Fopen(FILE2, HDF5Constants.H5F_ACC_RDONLY, fapl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Obtain and print the file size. - try { - if (file_id >= 0) { - size = H5.H5Fget_filesize(file_id); - System.out.println("File size for " + FILE2 + " is: " + size + " bytes"); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close FILE2. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5Ex_G_Compact.CreateGroup(); } -} diff --git a/java/examples/groups/H5Ex_G_Corder.java b/java/examples/groups/H5Ex_G_Corder.java deleted file mode 100644 index 79bbad6..0000000 --- a/java/examples/groups/H5Ex_G_Corder.java +++ /dev/null @@ -1,118 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -/************************************************************ - Creating a file with creation properties and traverse the - groups in alphabetical and creation order. - ************************************************************/ - -package examples.groups; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; -import hdf.hdf5lib.structs.H5G_info_t; - -public class H5Ex_G_Corder { - private static String FILE = "H5Ex_G_Corder.h5"; - - private static void CreateGroup() throws Exception - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - long subgroup_id = HDF5Constants.H5I_INVALID_HID; - long gcpl_id = HDF5Constants.H5I_INVALID_HID; - int status; - H5G_info_t ginfo; - int i; - String name; - - try { - // Create a new file using default properties. - file_id = H5.H5Fcreate(FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - - // Create group creation property list and enable link creation order tracking. - gcpl_id = H5.H5Pcreate(HDF5Constants.H5P_GROUP_CREATE); - status = H5.H5Pset_link_creation_order(gcpl_id, HDF5Constants.H5P_CRT_ORDER_TRACKED + - HDF5Constants.H5P_CRT_ORDER_INDEXED); - - // Create primary group using the property list. - if (status >= 0) - group_id = H5.H5Gcreate(file_id, "index_group", HDF5Constants.H5P_DEFAULT, gcpl_id, - HDF5Constants.H5P_DEFAULT); - - try { - /* - * Create subgroups in the primary group. These will be tracked by creation order. Note that - * these groups do not have to have the creation order tracking property set. - */ - subgroup_id = H5.H5Gcreate(group_id, "H", HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - status = H5.H5Gclose(subgroup_id); - subgroup_id = H5.H5Gcreate(group_id, "D", HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - status = H5.H5Gclose(subgroup_id); - subgroup_id = H5.H5Gcreate(group_id, "F", HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - status = H5.H5Gclose(subgroup_id); - subgroup_id = H5.H5Gcreate(group_id, "5", HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - status = H5.H5Gclose(subgroup_id); - - // Get group info. - ginfo = H5.H5Gget_info(group_id); - - // Traverse links in the primary group using alphabetical indices (H5_INDEX_NAME). - System.out.println("Traversing group using alphabetical indices:"); - for (i = 0; i < ginfo.nlinks; i++) { - // Retrieve the name of the ith link in a group - name = H5.H5Lget_name_by_idx(group_id, ".", HDF5Constants.H5_INDEX_NAME, - HDF5Constants.H5_ITER_INC, i, HDF5Constants.H5P_DEFAULT); - System.out.println("Index " + i + ": " + name); - } - - // Traverse links in the primary group by creation order (H5_INDEX_CRT_ORDER). - System.out.println("Traversing group using creation order indices:"); - for (i = 0; i < ginfo.nlinks; i++) { - // Retrieve the name of the ith link in a group - name = H5.H5Lget_name_by_idx(group_id, ".", HDF5Constants.H5_INDEX_CRT_ORDER, - HDF5Constants.H5_ITER_INC, i, HDF5Constants.H5P_DEFAULT); - System.out.println("Index " + i + ": " + name); - } - } - catch (Exception e) { - e.printStackTrace(); - } - } - catch (Exception e) { - e.printStackTrace(); - } - finally { - // Close and release resources. - if (gcpl_id >= 0) - H5.H5Pclose(gcpl_id); - if (group_id >= 0) - H5.H5Gclose(group_id); - if (file_id >= 0) - H5.H5Fclose(file_id); - } - } - - public static void main(String[] args) - { - try { - H5Ex_G_Corder.CreateGroup(); - } - catch (Exception ex) { - ex.printStackTrace(); - } - } -} diff --git a/java/examples/groups/H5Ex_G_Create.java b/java/examples/groups/H5Ex_G_Create.java deleted file mode 100644 index 51804b9..0000000 --- a/java/examples/groups/H5Ex_G_Create.java +++ /dev/null @@ -1,88 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to create, open, and close a group. - ************************************************************/ - -package examples.groups; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5Ex_G_Create { - private static String FILENAME = "H5Ex_G_Create.h5"; - private static String GROUPNAME = "G1"; - - private static void CreateGroup() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create a group in the file. - try { - if (file_id >= 0) - group_id = H5.H5Gcreate(file_id, "/" + GROUPNAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group. The handle "group" can no longer be used. - try { - if (group_id >= 0) - H5.H5Gclose(group_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Re-open the group, obtaining a new handle. - try { - if (file_id >= 0) - group_id = H5.H5Gopen(file_id, "/" + GROUPNAME, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group. - try { - if (group_id >= 0) - H5.H5Gclose(group_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5Ex_G_Create.CreateGroup(); } -} diff --git a/java/examples/groups/H5Ex_G_Intermediate.java b/java/examples/groups/H5Ex_G_Intermediate.java deleted file mode 100644 index e638fd0..0000000 --- a/java/examples/groups/H5Ex_G_Intermediate.java +++ /dev/null @@ -1,126 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to create intermediate groups with - a single call to H5Gcreate. - ************************************************************/ -package examples.groups; - -import java.util.ArrayList; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; -import hdf.hdf5lib.callbacks.H5O_iterate_opdata_t; -import hdf.hdf5lib.callbacks.H5O_iterate_t; -import hdf.hdf5lib.structs.H5O_info_t; - -public class H5Ex_G_Intermediate { - - private static String FILE = "H5Ex_G_Intermediate.h5"; - - private void CreateGroup() throws Exception - { - - long file_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - long gcpl_id = HDF5Constants.H5I_INVALID_HID; - - try { - // Create a new file_id using the default properties. - file_id = H5.H5Fcreate(FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - - // Create group_id creation property list and set it to allow creation of intermediate group_ids. - gcpl_id = H5.H5Pcreate(HDF5Constants.H5P_LINK_CREATE); - H5.H5Pset_create_intermediate_group(gcpl_id, true); - - /* - * Create the group_id /G1/G2/G3. Note that /G1 and /G1/G2 do not exist yet. This call would cause - * an error if we did not use the previously created property list. - */ - group_id = H5.H5Gcreate(file_id, "/G1/G2/G3", gcpl_id, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - // Print all the objects in the file_ids to show that intermediate group_ids have been created. - System.out.println("Objects in the file_id:"); - - // H5O_iterate_opdata_t iter_data = null; - H5O_iterate_opdata_t iter_data = new H5O_iter_data(); - H5O_iterate_t iter_cb = new H5O_iter_callback(); - - H5.H5Ovisit(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, iter_cb, - iter_data); - } - catch (Exception e) { - e.printStackTrace(); - } - finally { - // Close and release resources. - if (gcpl_id >= 0) - H5.H5Pclose(gcpl_id); - if (group_id >= 0) - H5.H5Gclose(group_id); - if (file_id >= 0) - H5.H5Fclose(file_id); - } - } - - public static void main(String[] args) - { - try { - (new H5Ex_G_Intermediate()).CreateGroup(); - } - catch (Exception ex) { - ex.printStackTrace(); - } - } - - private class idata { - public String link_name = null; - public int link_type = -1; - - idata(String name, int type) - { - this.link_name = name; - this.link_type = type; - } - } - - private class H5O_iter_data implements H5O_iterate_opdata_t { - public ArrayList<idata> iterdata = new ArrayList<idata>(); - } - - private class H5O_iter_callback implements H5O_iterate_t { - public int callback(long group, String name, H5O_info_t info, H5O_iterate_opdata_t op_data) - { - idata id = new idata(name, info.type); - ((H5O_iter_data)op_data).iterdata.add(id); - - System.out.print("/"); /* Print root group in object path */ - - // Check if the current object is the root group, and if not print the full path name and type. - - if (name.charAt(0) == '.') /* Root group, do not print '.' */ - System.out.println(" (Group)"); - else if (info.type == HDF5Constants.H5O_TYPE_GROUP) - System.out.println(name + " (Group)"); - else if (info.type == HDF5Constants.H5O_TYPE_DATASET) - System.out.println(name + " (Dataset)"); - else if (info.type == HDF5Constants.H5O_TYPE_NAMED_DATATYPE) - System.out.println(name + " (Datatype)"); - else - System.out.println(name + " (Unknown)"); - - return 0; - } - } -} diff --git a/java/examples/groups/H5Ex_G_Iterate.java b/java/examples/groups/H5Ex_G_Iterate.java deleted file mode 100644 index 24cbb0a..0000000 --- a/java/examples/groups/H5Ex_G_Iterate.java +++ /dev/null @@ -1,111 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to iterate over group members using - H5Gget_obj_info_all. - ************************************************************/ -package examples.groups; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; -import hdf.hdf5lib.structs.H5O_token_t; - -public class H5Ex_G_Iterate { - private static String FILENAME = "groups/h5ex_g_iterate.h5"; - private static String DATASETNAME = "/"; - - enum H5O_type { - H5O_TYPE_UNKNOWN(-1), // Unknown object type - H5O_TYPE_GROUP(0), // Object is a group - H5O_TYPE_DATASET(1), // Object is a dataset - H5O_TYPE_NAMED_DATATYPE(2), // Object is a named data type - H5O_TYPE_NTYPES(3); // Number of different object types - private static final Map<Integer, H5O_type> lookup = new HashMap<Integer, H5O_type>(); - - static - { - for (H5O_type s : EnumSet.allOf(H5O_type.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5O_type(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5O_type get(int code) { return lookup.get(code); } - } - - private static void do_iterate() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - - // Open a file using default properties. - try { - file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Begin iteration. - System.out.println("Objects in root group:"); - try { - if (file_id >= 0) { - int count = (int)H5.H5Gn_members(file_id, DATASETNAME); - String[] oname = new String[count]; - int[] otype = new int[count]; - int[] ltype = new int[count]; - H5O_token_t[] otokens = new H5O_token_t[count]; - H5.H5Gget_obj_info_all(file_id, DATASETNAME, oname, otype, ltype, otokens, - HDF5Constants.H5_INDEX_NAME); - - // Get type of the object and display its name and type. - for (int indx = 0; indx < otype.length; indx++) { - switch (H5O_type.get(otype[indx])) { - case H5O_TYPE_GROUP: - System.out.println(" Group: " + oname[indx]); - break; - case H5O_TYPE_DATASET: - System.out.println(" Dataset: " + oname[indx]); - break; - case H5O_TYPE_NAMED_DATATYPE: - System.out.println(" Datatype: " + oname[indx]); - break; - default: - System.out.println(" Unknown: " + oname[indx]); - } - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5Ex_G_Iterate.do_iterate(); } -} diff --git a/java/examples/groups/H5Ex_G_Phase.java b/java/examples/groups/H5Ex_G_Phase.java deleted file mode 100644 index 7a3fba3..0000000 --- a/java/examples/groups/H5Ex_G_Phase.java +++ /dev/null @@ -1,235 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to set the conditions for - conversion between compact and dense (indexed) groups. - ************************************************************/ -package examples.groups; - -import java.util.EnumSet; -import java.util.HashMap; -import java.util.Map; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; -import hdf.hdf5lib.structs.H5G_info_t; - -public class H5Ex_G_Phase { - private static String FILE = "H5Ex_G_Phase.h5"; - private static int MAX_GROUPS = 7; - private static int MAX_COMPACT = 5; - private static int MIN_DENSE = 3; - - enum H5G_storage { - H5G_STORAGE_TYPE_UNKNOWN(-1), - H5G_STORAGE_TYPE_SYMBOL_TABLE(0), - H5G_STORAGE_TYPE_COMPACT(1), - H5G_STORAGE_TYPE_DENSE(2); - - private static final Map<Integer, H5G_storage> lookup = new HashMap<Integer, H5G_storage>(); - - static - { - for (H5G_storage s : EnumSet.allOf(H5G_storage.class)) - lookup.put(s.getCode(), s); - } - - private int code; - - H5G_storage(int layout_type) { this.code = layout_type; } - - public int getCode() { return this.code; } - - public static H5G_storage get(int code) { return lookup.get(code); } - } - - private static void CreateGroup() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - long subgroup_id = HDF5Constants.H5I_INVALID_HID; - long fapl_id = HDF5Constants.H5I_INVALID_HID; - long gcpl_id = HDF5Constants.H5I_INVALID_HID; - H5G_info_t ginfo; - String name = "G0"; // Name of subgroup_id - int i; - - // Set file access property list to allow the latest file format.This will allow the library to create - // new format groups. - try { - fapl_id = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS); - if (fapl_id >= 0) - H5.H5Pset_libver_bounds(fapl_id, HDF5Constants.H5F_LIBVER_LATEST, - HDF5Constants.H5F_LIBVER_LATEST); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create group access property list and set the phase change conditions. - try { - gcpl_id = H5.H5Pcreate(HDF5Constants.H5P_GROUP_CREATE); - if (gcpl_id >= 0) - H5.H5Pset_link_phase_change(gcpl_id, MAX_COMPACT, MIN_DENSE); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create a new file using the default properties. - try { - if (fapl_id >= 0) - file_id = H5.H5Fcreate(FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create primary group. - try { - if ((file_id >= 0) && (gcpl_id >= 0)) - group_id = H5.H5Gcreate(file_id, name, HDF5Constants.H5P_DEFAULT, gcpl_id, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Add subgroups to "group" one at a time, print the storage type for "group" after each subgroup is - // created. - for (i = 1; i <= MAX_GROUPS; i++) { - // Define the subgroup name and create the subgroup. - char append = (char)(((char)i) + '0'); - name = name + append; /* G1, G2, G3 etc. */ - try { - if (group_id >= 0) { - subgroup_id = H5.H5Gcreate(group_id, name, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - H5.H5Gclose(subgroup_id); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Obtain the group info and print the group storage type - try { - if (group_id >= 0) { - ginfo = H5.H5Gget_info(group_id); - System.out.print(ginfo.nlinks + " Group" + (ginfo.nlinks == 1 ? " " : "s") + - ": Storage type is "); - switch (H5G_storage.get(ginfo.storage_type)) { - case H5G_STORAGE_TYPE_COMPACT: - System.out.println("H5G_STORAGE_TYPE_COMPACT"); // New compact format - break; - case H5G_STORAGE_TYPE_DENSE: - System.out.println("H5G_STORAGE_TYPE_DENSE"); // New dense (indexed) format - break; - case H5G_STORAGE_TYPE_SYMBOL_TABLE: - System.out.println("H5G_STORAGE_TYPE_SYMBOL_TABLE"); // Original format - break; - case H5G_STORAGE_TYPE_UNKNOWN: - System.out.println("H5G_STORAGE_TYPE_UNKNOWN"); - break; - default: - System.out.println("Storage Type Invalid"); - break; - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - } - - System.out.println(); - - // Delete subgroups one at a time, print the storage type for "group" after each subgroup is deleted. - for (i = MAX_GROUPS; i >= 1; i--) { - // Define the subgroup name and delete the subgroup. - try { - H5.H5Ldelete(group_id, name, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - name = name.substring(0, i + 1); - - // Obtain the group info and print the group storage type - try { - if (group_id >= 0) { - ginfo = H5.H5Gget_info(group_id); - System.out.print(ginfo.nlinks + " Group" + (ginfo.nlinks == 1 ? " " : "s") + - ": Storage type is "); - switch (H5G_storage.get(ginfo.storage_type)) { - case H5G_STORAGE_TYPE_COMPACT: - System.out.println("H5G_STORAGE_TYPE_COMPACT"); // New compact format - break; - case H5G_STORAGE_TYPE_DENSE: - System.out.println("H5G_STORAGE_TYPE_DENSE"); // New dense (indexed) format - break; - case H5G_STORAGE_TYPE_SYMBOL_TABLE: - System.out.println("H5G_STORAGE_TYPE_SYMBOL_TABLE"); // Original format - break; - case H5G_STORAGE_TYPE_UNKNOWN: - System.out.println("H5G_STORAGE_TYPE_UNKNOWN"); - break; - default: - System.out.println("Storage Type Invalid"); - break; - } - } - } - catch (Exception e) { - e.printStackTrace(); - } - } - - // Close and release resources - try { - if (fapl_id >= 0) - H5.H5Pclose(fapl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (gcpl_id >= 0) - H5.H5Pclose(gcpl_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group - try { - if (group_id >= 0) - H5.H5Gclose(group_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5Ex_G_Phase.CreateGroup(); } -} diff --git a/java/examples/groups/H5Ex_G_Traverse.java b/java/examples/groups/H5Ex_G_Traverse.java deleted file mode 100644 index 61a269c..0000000 --- a/java/examples/groups/H5Ex_G_Traverse.java +++ /dev/null @@ -1,167 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ -This example shows a way to recursively traverse the file -using H5Literate. The method shown here guarantees that -the recursion will not enter an infinite loop, but does -not prevent objects from being visited more than once. -The program prints the directory structure of the file -specified in FILE. The default file used by this example -implements the structure described in the User's Guide, -chapter 4, figure 26. - ************************************************************/ -package examples.groups; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; -import hdf.hdf5lib.callbacks.H5L_iterate_opdata_t; -import hdf.hdf5lib.callbacks.H5L_iterate_t; -import hdf.hdf5lib.structs.H5L_info_t; -import hdf.hdf5lib.structs.H5O_info_t; - -import examples.groups.H5Ex_G_Iterate.H5O_type; - -class opdata implements H5L_iterate_opdata_t { - int recurs; - opdata prev; - H5O_token_t obj_token; -} - -public class H5Ex_G_Traverse { - - private static String FILE = "h5ex_g_traverse.h5"; - public static H5L_iterate_t iter_cb = new H5L_iter_callbackT(); - - private static void OpenGroup() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - H5O_info_t infobuf; - opdata od = new opdata(); - - // Open file and initialize the operator data structure. - try { - file_id = H5.H5Fopen(FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - if (file_id >= 0) { - infobuf = H5.H5Oget_info(file_id); - od.recurs = 0; - od.prev = null; - od.obj_token = infobuf.token; - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Print the root group and formatting, begin iteration. - try { - System.out.println("/ {"); - // H5L_iterate_t iter_cb = new H5L_iter_callbackT(); - H5.H5Literate(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, 0L, iter_cb, - od); - System.out.println("}"); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close and release resources. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5Ex_G_Traverse.OpenGroup(); } -} - -class H5L_iter_callbackT implements H5L_iterate_t { - public int callback(long group, String name, H5L_info_t info, H5L_iterate_opdata_t op_data) - { - - H5O_info_t infobuf; - int return_val = 0; - opdata od = (opdata)op_data; // Type conversion - int spaces = 2 * (od.recurs + 1); // Number of white spaces to prepend to output. - - // Get type of the object and display its name and type. - // The name of the object is passed to this function by the Library. - try { - infobuf = H5.H5Oget_info_by_name(group, name, HDF5Constants.H5P_DEFAULT); - - for (int i = 0; i < spaces; i++) - System.out.print(" "); // Format output. - switch (H5O_type.get(infobuf.type)) { - case H5O_TYPE_GROUP: - System.out.println("Group: " + name + " { "); - // Check group object token against linked list of operator - // data structures. We will always run the check, as the - // reference count cannot be relied upon if there are - // symbolic links, and H5Oget_info_by_name always follows - // symbolic links. Alternatively we could use H5Lget_info - // and never recurse on groups discovered by symbolic - // links, however it could still fail if an object's - // reference count was manually manipulated with - // H5Odecr_refcount. - if (group_check(od, infobuf.token)) { - for (int i = 0; i < spaces; i++) - System.out.print(" "); - System.out.println(" Warning: Loop detected!"); - } - else { - // Initialize new object of type opdata and begin - // recursive iteration on the discovered - // group. The new opdata is given a pointer to the - // current one. - opdata nextod = new opdata(); - nextod.recurs = od.recurs + 1; - nextod.prev = od; - nextod.obj_token = infobuf.token; - H5L_iterate_t iter_cb2 = new H5L_iter_callbackT(); - return_val = H5.H5Literate_by_name(group, name, HDF5Constants.H5_INDEX_NAME, - HDF5Constants.H5_ITER_NATIVE, 0L, iter_cb2, nextod, - HDF5Constants.H5P_DEFAULT); - } - for (int i = 0; i < spaces; i++) - System.out.print(" "); - System.out.println("}"); - break; - case H5O_TYPE_DATASET: - System.out.println("Dataset: " + name); - break; - case H5O_TYPE_NAMED_DATATYPE: - System.out.println("Datatype: " + name); - break; - default: - System.out.println("Unknown: " + name); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - return return_val; - } - - public boolean group_check(opdata od, H5O_token_t target_token) - { - if (od.obj_token.equals(target_token)) - return true; // Object tokens match - else if (od.recurs == 0) - return false; // Root group reached with no matches - else - return group_check(od.prev, target_token); // Recursively examine the next node - } -} diff --git a/java/examples/groups/H5Ex_G_Visit.java b/java/examples/groups/H5Ex_G_Visit.java deleted file mode 100644 index 1f2f9a1..0000000 --- a/java/examples/groups/H5Ex_G_Visit.java +++ /dev/null @@ -1,154 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - This example shows how to recursively traverse a file - using H5Ovisit and H5Lvisit. The program prints all of - the objects in the file specified in FILE, then prints all - of the links in that file. The default file used by this - example implements the structure described in the User - Guide, chapter 4, figure 26. - ************************************************************/ -package examples.groups; - -import java.util.ArrayList; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; -import hdf.hdf5lib.callbacks.H5L_iterate_opdata_t; -import hdf.hdf5lib.callbacks.H5L_iterate_t; -import hdf.hdf5lib.callbacks.H5O_iterate_opdata_t; -import hdf.hdf5lib.callbacks.H5O_iterate_t; -import hdf.hdf5lib.structs.H5L_info_t; -import hdf.hdf5lib.structs.H5O_info_t; - -public class H5Ex_G_Visit { - - private static String FILE = "groups/h5ex_g_visit.h5"; - - public static void main(String[] args) - { - try { - (new H5Ex_G_Visit()).VisitGroup(); - } - catch (Exception ex) { - ex.printStackTrace(); - } - } - - private void VisitGroup() throws Exception - { - - long file_id = HDF5Constants.H5I_INVALID_HID; - - try { - // Open file - file_id = H5.H5Fopen(FILE, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); - - // Begin iteration using H5Ovisit - System.out.println("Objects in the file:"); - H5O_iterate_opdata_t iter_data = new H5O_iter_data(); - H5O_iterate_t iter_cb = new H5O_iter_callback(); - H5.H5Ovisit(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, iter_cb, - iter_data); - System.out.println(); - // Repeat the same process using H5Lvisit - H5L_iterate_opdata_t iter_data2 = new H5L_iter_data(); - H5L_iterate_t iter_cb2 = new H5L_iter_callback(); - System.out.println("Links in the file:"); - H5.H5Lvisit(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, iter_cb2, - iter_data2); - } - catch (Exception e) { - e.printStackTrace(); - } - finally { - // Close and release resources. - if (file_id >= 0) - H5.H5Fclose(file_id); - } - } - - /************************************************************ - * Operator function for H5Lvisit. This function simply retrieves the info for the object the current link - *points to, and calls the operator function for H5Ovisit. - ************************************************************/ - - private class idata { - public String link_name = null; - public int link_type = -1; - - idata(String name, int type) - { - this.link_name = name; - this.link_type = type; - } - } - - private class H5L_iter_data implements H5L_iterate_opdata_t { - public ArrayList<idata> iterdata = new ArrayList<idata>(); - } - - private class H5L_iter_callback implements H5L_iterate_t { - public int callback(long group, String name, H5L_info_t info, H5L_iterate_opdata_t op_data) - { - - idata id = new idata(name, info.type); - ((H5L_iter_data)op_data).iterdata.add(id); - - H5O_info_t infobuf; - int ret = 0; - try { - // Get type of the object and display its name and type. The name of the object is passed to - // this function by the Library. - infobuf = H5.H5Oget_info_by_name(group, name, HDF5Constants.H5P_DEFAULT); - H5O_iterate_t iter_cbO = new H5O_iter_callback(); - H5O_iterate_opdata_t iter_dataO = new H5O_iter_data(); - ret = iter_cbO.callback(group, name, infobuf, iter_dataO); - } - catch (Exception e) { - e.printStackTrace(); - } - - return ret; - } - } - - private class H5O_iter_data implements H5O_iterate_opdata_t { - public ArrayList<idata> iterdata = new ArrayList<idata>(); - } - - private class H5O_iter_callback implements H5O_iterate_t { - public int callback(long group, String name, H5O_info_t info, H5O_iterate_opdata_t op_data) - { - idata id = new idata(name, info.type); - ((H5O_iter_data)op_data).iterdata.add(id); - - System.out.print("/"); /* Print root group in object path */ - - // Check if the current object is the root group, and if not print the full path name and type. - - if (name.charAt(0) == '.') /* Root group, do not print '.' */ - System.out.println(" (Group)"); - else if (info.type == HDF5Constants.H5O_TYPE_GROUP) - System.out.println(name + " (Group)"); - else if (info.type == HDF5Constants.H5O_TYPE_DATASET) - System.out.println(name + " (Dataset)"); - else if (info.type == HDF5Constants.H5O_TYPE_NAMED_DATATYPE) - System.out.println(name + " (Datatype)"); - else - System.out.println(name + " (Unknown)"); - - return 0; - } - } -} diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in deleted file mode 100644 index 4773579..0000000 --- a/java/examples/groups/JavaGroupExample.sh.in +++ /dev/null @@ -1,381 +0,0 @@ -#! /bin/sh -# -# 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. -# - -top_builddir=@top_builddir@ -top_srcdir=@top_srcdir@ -srcdir=@srcdir@ -IS_DARWIN="@H5_IS_DARWIN@" - -TESTNAME=EX_Groups -EXIT_SUCCESS=0 -EXIT_FAILURE=1 - -# Set up default variable values if not supplied by the user. -RM='rm -rf' -CMP='cmp' -DIFF='diff -c' -CP='cp' -DIRNAME='dirname' -BASENAME='basename' -LS='ls' -AWK='awk' - -nerrors=0 - -# where the libs exist -HDFLIB_HOME="$top_srcdir/java/lib" -BLDDIR="." -BLDLIBDIR="$BLDDIR/testlibs" -BLDITERDIR="./groups" -HDFTEST_HOME="$top_srcdir/java/examples/groups" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar -test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -test -d $BLDITERDIR || mkdir -p $BLDITERDIR - -###################################################################### -# library files -# -------------------------------------------------------------------- -# All the library files copy from source directory to test directory -# NOTE: Keep this framework to add/remove test files. -# This list are also used for checking exist. -# Comment '#' without space can be used. -# -------------------------------------------------------------------- -LIST_LIBRARY_FILES=" -$top_builddir/src/.libs/libhdf5.* -$top_builddir/java/src/jni/.libs/libhdf5_java.* -$top_builddir/java/src/$JARFILE -" -LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-2.0.6.jar -$HDFLIB_HOME/ext/slf4j-simple-2.0.6.jar -" -LIST_ITER_FILES=" -$HDFTEST_HOME/h5ex_g_iterate.h5 -$HDFTEST_HOME/h5ex_g_visit.h5 -" -LIST_DATA_FILES=" -$HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Create.txt -$HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Iterate.txt -$HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Compact.txt -$HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Corder.txt -$HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Intermediate.txt -$HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Phase.txt -$HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Visit.txt -" - -# -# copy files from source dirs to test dir -# -COPY_LIBFILES="$LIST_LIBRARY_FILES" -COPY_JARTESTFILES="$LIST_JAR_TESTFILES" - -COPY_LIBFILES_TO_BLDLIBDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_LIBFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - BNAME=`$BASENAME $tstfile` - if [ "$BNAME" = "libhdf5_java.dylib" ]; then - COPIED_LIBHDF5_JAVA=1 - fi - fi - fi - done - if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then - (cd $BLDLIBDIR; \ - install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \ - exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \ - echo $exist_path; \ - install_name_tool -change $exist_path @rpath/libhdf5.dylib libhdf5_java.dylib) - fi - # copy jar files. Used -f to make sure get a new copy - for tstfile in $COPY_JARTESTFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_LIBFILES_AND_BLDLIBDIR() -{ - # skip rm if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=$HDFLIB_HOME - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $RM -rf $BLDLIBDIR - fi -} - -COPY_DATAFILES="$LIST_DATA_FILES" - -COPY_DATAFILES_TO_BLDDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_DATAFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -f $tstfile $BLDDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_DATAFILES_AND_BLDDIR() -{ - $RM $BLDDIR/examples.groups.H5Ex_G_*.txt - $RM $BLDDIR/H5Ex_G_*.out - $RM $BLDDIR/H5Ex_G_*.h5 -} - -COPY_ITERFILES="$LIST_ITER_FILES" - -COPY_ITERFILES_TO_BLDITERDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_ITERFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -f $tstfile $BLDITERDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_ITERFILES_AND_BLDITERDIR() -{ - # skip rm if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $HDFTEST_HOME/h5ex_g_iterate.h5` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $RM $BLDITERDIR - fi -} - -# Print a line-line message left justified in a field of 70 characters -# beginning with the word "Testing". -# -TESTING() { - SPACES=" " - echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012' -} - -# where Java is installed (requires jdk1.7.x) -JAVAEXE=@JAVA@ -JAVAEXEFLAGS=@H5_JAVAFLAGS@ - -############################################################################### -# DO NOT MODIFY BELOW THIS LINE -############################################################################### - -# prepare for test -COPY_LIBFILES_TO_BLDLIBDIR -COPY_DATAFILES_TO_BLDDIR -COPY_ITERFILES_TO_BLDITERDIR - -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-2.0.6.jar:"$BLDLIBDIR"/slf4j-simple-2.0.6.jar:"$TESTJARFILE"" - -TEST=/usr/bin/test -if [ ! -x /usr/bin/test ] -then -TEST=`which test` -fi - -if $TEST -z "$CLASSPATH"; then - CLASSPATH="" -fi -CLASSPATH=$CPATH":"$CLASSPATH -export CLASSPATH - -if $TEST -n "$JAVAPATH" ; then - PATH=$JAVAPATH":"$PATH - export PATH -fi - -if $TEST -e /bin/uname; then - os_name=`/bin/uname -s` -elif $TEST -e /usr/bin/uname; then - os_name=`/usr/bin/uname -s` -else - os_name=unknown -fi - -if $TEST -z "$LD_LIBRARY_PATH" ; then - LD_LIBRARY_PATH="" -fi - -case $os_name in - *) - LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH - ;; -esac - -export LD_LIBRARY_PATH - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Create" -TESTING examples.groups.H5Ex_G_Create -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Create > H5Ex_G_Create.out) -if diff H5Ex_G_Create.out examples.groups.H5Ex_G_Create.txt > /dev/null; then - echo " PASSED groups.H5Ex_G_Create" -else - echo "**FAILED** groups.H5Ex_G_Create" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Iterate" -TESTING examples.groups.H5Ex_G_Iterate -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Iterate > H5Ex_G_Iterate.out) -if diff H5Ex_G_Iterate.out examples.groups.H5Ex_G_Iterate.txt > /dev/null; then - echo " PASSED groups.H5Ex_G_Iterate" -else - echo "**FAILED** groups.H5Ex_G_Iterate" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Compact" -TESTING examples.groups.H5Ex_G_Compact -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Compact > H5Ex_G_Compact.out) -if diff H5Ex_G_Compact.out examples.groups.H5Ex_G_Compact.txt > /dev/null; then - echo " PASSED groups.H5Ex_G_Compact" -else - echo "**FAILED** groups.H5Ex_G_Compact" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Corder" -TESTING examples.groups.H5Ex_G_Corder -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Corder > H5Ex_G_Corder.out) -if diff H5Ex_G_Corder.out examples.groups.H5Ex_G_Corder.txt > /dev/null; then - echo " PASSED groups.H5Ex_G_Corder" -else - echo "**FAILED** groups.H5Ex_G_Corder" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Intermediate" -TESTING examples.groups.H5Ex_G_Intermediate -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Intermediate > H5Ex_G_Intermediate.out) -if diff H5Ex_G_Intermediate.out examples.groups.H5Ex_G_Intermediate.txt > /dev/null; then - echo " PASSED groups.H5Ex_G_Intermediate" -else - echo "**FAILED** groups.H5Ex_G_Intermediate" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Phase" -TESTING examples.groups.H5Ex_G_Phase -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Phase > H5Ex_G_Phase.out) -if diff H5Ex_G_Phase.out examples.groups.H5Ex_G_Phase.txt > /dev/null; then - echo " PASSED groups.H5Ex_G_Phase" -else - echo "**FAILED** groups.H5Ex_G_Phase" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Visit" -TESTING examples.groups.H5Ex_G_Visit -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Visit > H5Ex_G_Visit.out) -if diff H5Ex_G_Visit.out examples.groups.H5Ex_G_Visit.txt > /dev/null; then - echo " PASSED groups.H5Ex_G_Visit" -else - echo "**FAILED** groups.H5Ex_G_Visit" - nerrors="`expr $nerrors + 1`" -fi - -# Clean up temporary files/directories -CLEAN_ITERFILES_AND_BLDITERDIR -CLEAN_LIBFILES_AND_BLDLIBDIR -CLEAN_DATAFILES_AND_BLDDIR - -# Report test results and exit -if test $nerrors -eq 0 ; then - echo "All $TESTNAME tests passed." - exit $EXIT_SUCCESS -else - echo "$TESTNAME tests failed with $nerrors errors." - exit $EXIT_FAILURE -fi diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am deleted file mode 100644 index a3fb774..0000000 --- a/java/examples/groups/Makefile.am +++ /dev/null @@ -1,65 +0,0 @@ -# -# 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. -## -## Makefile.am -## Run automake to generate a Makefile.in from this file. -## -# -# HDF5 Java Library Examples Makefile(.in) - -include $(top_srcdir)/config/commence.am - -# Mark this directory as part of the JNI API -JAVA_API=yes - -JAVAROOT = .classes - -classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - -pkgpath = examples/groups -hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-2.0.6.jar:$$CLASSPATH - -jarfile = jar$(PACKAGE_TARNAME)groups.jar - -AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation - -TESTPACKAGE = - -noinst_JAVA = \ - H5Ex_G_Create.java \ - H5Ex_G_Iterate.java \ - H5Ex_G_Compact.java \ - H5Ex_G_Corder.java \ - H5Ex_G_Intermediate.java \ - H5Ex_G_Phase.java \ - H5Ex_G_Visit.java - - -$(jarfile): classnoinst.stamp classes - $(JAR) cvf $@ -C $(JAVAROOT)/ $(pkgpath) - -noinst_DATA = $(jarfile) - -.PHONY: classes - -check_SCRIPTS = JavaGroupExample.sh -TEST_SCRIPT = $(check_SCRIPTS) - -CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class JavaGroupExample.sh - -clean: - rm -rf $(JAVAROOT)/* - rm -f $(jarfile) - rm -f classnoinst.stamp - -include $(top_srcdir)/config/conclude.am diff --git a/java/examples/groups/h5ex_g_iterate.h5 b/java/examples/groups/h5ex_g_iterate.h5 Binary files differdeleted file mode 100644 index e462703..0000000 --- a/java/examples/groups/h5ex_g_iterate.h5 +++ /dev/null diff --git a/java/examples/groups/h5ex_g_visit.h5 b/java/examples/groups/h5ex_g_visit.h5 Binary files differdeleted file mode 100644 index d8267b1..0000000 --- a/java/examples/groups/h5ex_g_visit.h5 +++ /dev/null diff --git a/java/examples/intro/CMakeLists.txt b/java/examples/intro/CMakeLists.txt deleted file mode 100644 index 685ef90..0000000 --- a/java/examples/intro/CMakeLists.txt +++ /dev/null @@ -1,107 +0,0 @@ -cmake_minimum_required (VERSION 3.18) -project (HDFJAVA_EXAMPLES_INTRO Java) - -set (CMAKE_VERBOSE_MAKEFILE 1) - -set (HDF_JAVA_EXAMPLES - H5_CreateAttribute - H5_CreateDataset - H5_CreateFile - H5_CreateGroup - H5_CreateGroupAbsoluteRelative - H5_CreateGroupDataset - H5_ReadWrite -) - -if (WIN32) - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";") -else () - set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":") -endif () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (CMAKE_INCLUDE_PATH ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${CMAKE_INCLUDE_PATH}") -endforeach () - -foreach (example ${HDF_JAVA_EXAMPLES}) - file (WRITE ${PROJECT_BINARY_DIR}/${example}_Manifest.txt - "Main-Class: examples.intro.${example} -" - ) - add_jar (${example} MANIFEST ${PROJECT_BINARY_DIR}/${example}_Manifest.txt ${example}.java) - get_target_property (${example}_JAR_FILE ${example} JAR_FILE) -# install_jar (${example} ${HJAVA_INSTALL_DATA_DIR}/examples examples) - get_target_property (${example}_CLASSPATH ${example} CLASSDIR) - add_dependencies (${example} ${HDF5_JAVA_HDF5_LIB_TARGET}) - - #----------------------------------------------------------------------------- - # Add Target to clang-format - #----------------------------------------------------------------------------- - if (HDF5_ENABLE_FORMATTERS) - clang_format (HDF5_JAVA_${example}_SRC_FORMAT ${example}.java) - endif () -endforeach () - -set (CMAKE_JAVA_INCLUDE_PATH "${HDF5_JAVA_JARS};${HDF5_JAVA_LOGGING_JAR};${HDF5_JAVA_LOGGING_NOP_JAR}") - -set (CMAKE_JAVA_CLASSPATH ".") -foreach (HDFJAVA_JAR ${CMAKE_JAVA_INCLUDE_PATH}) - set (CMAKE_JAVA_CLASSPATH "${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${HDFJAVA_JAR}") -endforeach () - -if (BUILD_TESTING AND HDF5_TEST_EXAMPLES AND HDF5_TEST_SERIAL) - get_property (target_name TARGET ${HDF5_JAVA_JNI_LIB_TARGET} PROPERTY OUTPUT_NAME) - set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${target_name}$<$<OR:$<CONFIG:Debug>,$<CONFIG:Developer>>:${CMAKE_DEBUG_POSTFIX}>;") - - set (last_test "") - foreach (example ${HDF_JAVA_EXAMPLES}) - add_test ( - NAME JAVA_intro-${example}-clear-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - if (last_test) - set_tests_properties (JAVA_intro-${example}-clear-objects PROPERTIES DEPENDS ${last_test}) - endif () - - add_test ( - NAME JAVA_intro-${example}-copy-objects - COMMAND ${CMAKE_COMMAND} -E copy_if_different - ${HDFJAVA_EXAMPLES_SOURCE_DIR}/testfiles/examples.intro.${example}.txt - ${HDFJAVA_EXAMPLES_INTRO_BINARY_DIR}/${example}.txt - ) - set_tests_properties (JAVA_intro-${example}-copy-objects PROPERTIES DEPENDS JAVA_intro-${example}-clear-objects) - - add_test ( - NAME JAVA_intro-${example} - COMMAND "${CMAKE_COMMAND}" - -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}" - -D "TEST_PROGRAM=examples.intro.${example}" - -D "TEST_ARGS:STRING=${CMD_ARGS}" - -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${example}_JAR_FILE}" - -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}" - -D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}" - -D "TEST_OUTPUT=intro/${example}.out" - -D "TEST_EXPECT=0" - -D "TEST_REFERENCE=intro/${example}.txt" - -P "${HDF_RESOURCES_DIR}/jrunTest.cmake" - ) - set_tests_properties (JAVA_intro-${example} PROPERTIES - DEPENDS JAVA_intro-${example}-copy-objects - ) - - add_test ( - NAME JAVA_intro-${example}-clean-objects - COMMAND ${CMAKE_COMMAND} -E remove - ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 - ) - set_tests_properties (JAVA_intro-${example}-clean-objects PROPERTIES - DEPENDS JAVA_intro-${example} - ) - set (last_test "JAVA_intro-${example}-clean-objects") - endforeach () - -endif () diff --git a/java/examples/intro/H5_CreateAttribute.java b/java/examples/intro/H5_CreateAttribute.java deleted file mode 100644 index 22ecdae..0000000 --- a/java/examples/intro/H5_CreateAttribute.java +++ /dev/null @@ -1,142 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Creating a dataset attribute. - ************************************************************/ - -package examples.intro; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5_CreateAttribute { - private static String FILENAME = "H5_CreateAttribute.h5"; - private static String DATASETNAME = "dset"; - private static final int DIM_X = 4; - private static final int DIM_Y = 6; - private static String DATASETATTRIBUTE = "Units"; - - private static void CreateDatasetAttribute() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long attribute_id = HDF5Constants.H5I_INVALID_HID; - long[] dims1 = {DIM_X, DIM_Y}; - long[] dims = {2}; - int[] attr_data = {100, 200}; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the data space for the dataset. - try { - dataspace_id = H5.H5Screate_simple(2, dims1, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, "/" + DATASETNAME, HDF5Constants.H5T_STD_I32BE, - dataspace_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the data space for the attribute. - try { - dataspace_id = H5.H5Screate_simple(1, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create a dataset attribute. - try { - if ((dataset_id >= 0) && (dataspace_id >= 0)) - attribute_id = - H5.H5Acreate(dataset_id, DATASETATTRIBUTE, HDF5Constants.H5T_STD_I32BE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the attribute data. - try { - if (attribute_id >= 0) - H5.H5Awrite(attribute_id, HDF5Constants.H5T_NATIVE_INT, attr_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the attribute. - try { - if (attribute_id >= 0) - H5.H5Aclose(attribute_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the dataspace. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close to the dataset. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5_CreateAttribute.CreateDatasetAttribute(); } -} diff --git a/java/examples/intro/H5_CreateDataset.java b/java/examples/intro/H5_CreateDataset.java deleted file mode 100644 index 20683e8..0000000 --- a/java/examples/intro/H5_CreateDataset.java +++ /dev/null @@ -1,92 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Creating and closing a dataset. - ************************************************************/ - -package examples.intro; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5_CreateDataset { - private static String FILENAME = "H5_CreateDataset.h5"; - private static String DATASETNAME = "dset"; - private static final int DIM_X = 4; - private static final int DIM_Y = 6; - - private static void CreateDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the data space for the dataset. - try { - dataspace_id = H5.H5Screate_simple(2, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, "/" + DATASETNAME, HDF5Constants.H5T_STD_I32BE, - dataspace_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // End access to the dataset and release resources used by it. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Terminate access to the data space. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5_CreateDataset.CreateDataset(); } -} diff --git a/java/examples/intro/H5_CreateFile.java b/java/examples/intro/H5_CreateFile.java deleted file mode 100644 index 4323581..0000000 --- a/java/examples/intro/H5_CreateFile.java +++ /dev/null @@ -1,49 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Creating and closing a file. - ************************************************************/ - -package examples.intro; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5_CreateFile { - static final String FILENAME = "H5_CreateFile.h5"; - - private static void CreateFile() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5_CreateFile.CreateFile(); } -} diff --git a/java/examples/intro/H5_CreateGroup.java b/java/examples/intro/H5_CreateGroup.java deleted file mode 100644 index a276cbd..0000000 --- a/java/examples/intro/H5_CreateGroup.java +++ /dev/null @@ -1,70 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Creating and closing a group. - ************************************************************/ - -package examples.intro; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5_CreateGroup { - private static String FILENAME = "H5_CreateGroup.h5"; - private static String GROUPNAME = "MyGroup"; - - private static void CreateGroup() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create a group in the file. - try { - if (file_id >= 0) - group_id = H5.H5Gcreate(file_id, "/" + GROUPNAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group. - try { - if (group_id >= 0) - H5.H5Gclose(group_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5_CreateGroup.CreateGroup(); } -} diff --git a/java/examples/intro/H5_CreateGroupAbsoluteRelative.java b/java/examples/intro/H5_CreateGroupAbsoluteRelative.java deleted file mode 100644 index 2fb9c3c..0000000 --- a/java/examples/intro/H5_CreateGroupAbsoluteRelative.java +++ /dev/null @@ -1,116 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Creating groups using absolute and relative names. - ************************************************************/ - -package examples.intro; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5_CreateGroupAbsoluteRelative { - private static String FILENAME = "H5_CreateGroupAbsoluteRelative.h5"; - private static String GROUPNAME = "MyGroup"; - private static String GROUPNAME_A = "GroupA"; - private static String GROUPNAME_B = "GroupB"; - - private static void CreateGroupAbsoluteAndRelative() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long group1_id = HDF5Constants.H5I_INVALID_HID; - long group2_id = HDF5Constants.H5I_INVALID_HID; - long group3_id = HDF5Constants.H5I_INVALID_HID; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create a group named "/MyGroup" in the file. - try { - if (file_id >= 0) - group1_id = H5.H5Gcreate(file_id, "/" + GROUPNAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create group "Group_A" in group "MyGroup" using absolute name. - try { - if (file_id >= 0) - group2_id = - H5.H5Gcreate(file_id, "/" + GROUPNAME + "/" + GROUPNAME_A, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create group "Group_B" in group "MyGroup" using relative name. - try { - if (group1_id >= 0) - group3_id = H5.H5Gcreate(group1_id, GROUPNAME_B, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group3. - try { - if (group3_id >= 0) - H5.H5Gclose(group3_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group2. - try { - if (group2_id >= 0) - H5.H5Gclose(group2_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group1. - try { - if (group1_id >= 0) - H5.H5Gclose(group1_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) - { - H5_CreateGroupAbsoluteRelative.CreateGroupAbsoluteAndRelative(); - } -} diff --git a/java/examples/intro/H5_CreateGroupDataset.java b/java/examples/intro/H5_CreateGroupDataset.java deleted file mode 100644 index 1d7cf99..0000000 --- a/java/examples/intro/H5_CreateGroupDataset.java +++ /dev/null @@ -1,206 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Create two datasets within groups. - ************************************************************/ - -package examples.intro; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5_CreateGroupDataset { - private static String FILENAME = "H5_CreateGroupDataset.h5"; - private static String GROUPNAME = "MyGroup"; - private static String GROUPNAME_A = "GroupA"; - private static String DATASETNAME1 = "dset1"; - private static String DATASETNAME2 = "dset2"; - private static final int DIM1_X = 3; - private static final int DIM1_Y = 3; - private static final int DIM2_X = 2; - private static final int DIM2_Y = 10; - - private static void h5_crtgrpd() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long group_id = HDF5Constants.H5I_INVALID_HID; - long group1_id = HDF5Constants.H5I_INVALID_HID; - long group2_id = HDF5Constants.H5I_INVALID_HID; - int[][] dset1_data = new int[DIM1_X][DIM1_Y]; - int[][] dset2_data = new int[DIM2_X][DIM2_Y]; - long[] dims1 = {DIM1_X, DIM1_Y}; - long[] dims2 = {DIM2_X, DIM2_Y}; - - // Initialize the first dataset. - for (int indx = 0; indx < DIM1_X; indx++) - for (int jndx = 0; jndx < DIM1_Y; jndx++) - dset1_data[indx][jndx] = jndx + 1; - - // Initialize the second dataset. - for (int indx = 0; indx < DIM2_X; indx++) - for (int jndx = 0; jndx < DIM2_Y; jndx++) - dset2_data[indx][jndx] = jndx + 1; - - // Create a file. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - // Create a group named "/MyGroup" in the file. - if (file_id >= 0) { - group1_id = H5.H5Gcreate(file_id, "/" + GROUPNAME, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - // Create group "Group_A" in group "MyGroup" using absolute name. - if (group1_id >= 0) { - group2_id = - H5.H5Gcreate(file_id, "/" + GROUPNAME + "/" + GROUPNAME_A, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - if (group2_id >= 0) - H5.H5Gclose(group2_id); - } - if (group1_id >= 0) - H5.H5Gclose(group1_id); - } - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the data space for the first dataset. - try { - dataspace_id = H5.H5Screate_simple(2, dims1, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset in group "MyGroup". - try { - if ((file_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate( - file_id, "/" + GROUPNAME + "/" + DATASETNAME1, HDF5Constants.H5T_STD_I32BE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the first dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset1_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the data space for the first dataset. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - dataspace_id = HDF5Constants.H5I_INVALID_HID; - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the first dataset. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - dataset_id = HDF5Constants.H5I_INVALID_HID; - } - catch (Exception e) { - e.printStackTrace(); - } - - // Open an existing group of the specified file. - try { - if (file_id >= 0) - group_id = - H5.H5Gopen(file_id, "/" + GROUPNAME + "/" + GROUPNAME_A, HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the data space for the second dataset. - try { - dataspace_id = H5.H5Screate_simple(2, dims2, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the second dataset in group "Group_A". - try { - if ((group_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate(group_id, DATASETNAME2, HDF5Constants.H5T_STD_I32BE, dataspace_id, - HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the second dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset2_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the data space for the second dataset. - try { - if (dataspace_id >= 0) - H5.H5Sclose(dataspace_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the second dataset. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the group. - try { - if (group_id >= 0) - H5.H5Gclose(group_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5_CreateGroupDataset.h5_crtgrpd(); } -} diff --git a/java/examples/intro/H5_ReadWrite.java b/java/examples/intro/H5_ReadWrite.java deleted file mode 100644 index 379fe20..0000000 --- a/java/examples/intro/H5_ReadWrite.java +++ /dev/null @@ -1,108 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/************************************************************ - Writing and reading an existing dataset. - ************************************************************/ - -package examples.intro; - -import hdf.hdf5lib.H5; -import hdf.hdf5lib.HDF5Constants; - -public class H5_ReadWrite { - private static String FILENAME = "H5_ReadWrite.h5"; - private static String DATASETNAME = "dset"; - private static final int DIM_X = 4; - private static final int DIM_Y = 6; - - private static void ReadWriteDataset() - { - long file_id = HDF5Constants.H5I_INVALID_HID; - long dataspace_id = HDF5Constants.H5I_INVALID_HID; - long dataset_id = HDF5Constants.H5I_INVALID_HID; - long[] dims = {DIM_X, DIM_Y}; - int[][] dset_data = new int[DIM_X][DIM_Y]; - - // Initialize the dataset. - for (int indx = 0; indx < DIM_X; indx++) - for (int jndx = 0; jndx < DIM_Y; jndx++) - dset_data[indx][jndx] = indx * 6 + jndx + 1; - - // Create a new file using default properties. - try { - file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the data space for the dataset. - try { - dataspace_id = H5.H5Screate_simple(2, dims, null); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Create the dataset. - try { - if ((file_id >= 0) && (dataspace_id >= 0)) - dataset_id = H5.H5Dcreate(file_id, "/" + DATASETNAME, HDF5Constants.H5T_STD_I32BE, - dataspace_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, - HDF5Constants.H5P_DEFAULT); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Write the dataset. - try { - if (dataset_id >= 0) - H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - try { - if (dataset_id >= 0) - H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, - HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the dataset. - try { - if (dataset_id >= 0) - H5.H5Dclose(dataset_id); - } - catch (Exception e) { - e.printStackTrace(); - } - - // Close the file. - try { - if (file_id >= 0) - H5.H5Fclose(file_id); - } - catch (Exception e) { - e.printStackTrace(); - } - } - - public static void main(String[] args) { H5_ReadWrite.ReadWriteDataset(); } -} diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in deleted file mode 100644 index 56b6e57..0000000 --- a/java/examples/intro/JavaIntroExample.sh.in +++ /dev/null @@ -1,330 +0,0 @@ -#! /bin/sh -# -# 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. -# - -top_builddir=@top_builddir@ -top_srcdir=@top_srcdir@ -srcdir=@srcdir@ -IS_DARWIN="@H5_IS_DARWIN@" - -TESTNAME=EX_Intro -EXIT_SUCCESS=0 -EXIT_FAILURE=1 - -# Set up default variable values if not supplied by the user. -RM='rm -rf' -CMP='cmp' -DIFF='diff -c' -CP='cp' -DIRNAME='dirname' -BASENAME='basename' -LS='ls' -AWK='awk' - -nerrors=0 - -# where the libs exist -HDFLIB_HOME="$top_srcdir/java/lib" -BLDDIR="." -BLDLIBDIR="$BLDDIR/testlibs" -HDFTEST_HOME="$top_srcdir/java/examples/intro" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar -test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR - -###################################################################### -# library files -# -------------------------------------------------------------------- -# All the library files copy from source directory to test directory -# NOTE: Keep this framework to add/remove test files. -# This list are also used for checking exist. -# Comment '#' without space can be used. -# -------------------------------------------------------------------- -LIST_LIBRARY_FILES=" -$top_builddir/src/.libs/libhdf5.* -$top_builddir/java/src/jni/.libs/libhdf5_java.* -$top_builddir/java/src/$JARFILE -" -LIST_JAR_TESTFILES=" -$HDFLIB_HOME/slf4j-api-2.0.6.jar -$HDFLIB_HOME/ext/slf4j-simple-2.0.6.jar -" -LIST_DATA_FILES=" -$HDFTEST_HOME/../testfiles/examples.intro.H5_CreateDataset.txt -$HDFTEST_HOME/../testfiles/examples.intro.H5_CreateAttribute.txt -$HDFTEST_HOME/../testfiles/examples.intro.H5_CreateFile.txt -$HDFTEST_HOME/../testfiles/examples.intro.H5_CreateGroup.txt -$HDFTEST_HOME/../testfiles/examples.intro.H5_CreateGroupAbsoluteRelative.txt -$HDFTEST_HOME/../testfiles/examples.intro.H5_CreateGroupDataset.txt -$HDFTEST_HOME/../testfiles/examples.intro.H5_ReadWrite.txt -" - -# -# copy files from source dirs to test dir -# -COPY_LIBFILES="$LIST_LIBRARY_FILES" -COPY_JARTESTFILES="$LIST_JAR_TESTFILES" - -COPY_LIBFILES_TO_BLDLIBDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_LIBFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - BNAME=`$BASENAME $tstfile` - if [ "$BNAME" = "libhdf5_java.dylib" ]; then - COPIED_LIBHDF5_JAVA=1 - fi - fi - fi - done - if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then - (cd $BLDLIBDIR; \ - install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \ - exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \ - echo $exist_path; \ - install_name_tool -change $exist_path @rpath/libhdf5.dylib libhdf5_java.dylib) - fi - # copy jar files. Used -f to make sure get a new copy - for tstfile in $COPY_JARTESTFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -fR $tstfile $BLDLIBDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_LIBFILES_AND_BLDLIBDIR() -{ - # skip rm if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=$HDFLIB_HOME - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $RM -rf $BLDLIBDIR - fi -} - -COPY_DATAFILES="$LIST_DATA_FILES" - -COPY_DATAFILES_TO_BLDDIR() -{ - # copy test files. Used -f to make sure get a new copy - for tstfile in $COPY_DATAFILES - do - # ignore '#' comment - echo $tstfile | tr -d ' ' | grep '^#' > /dev/null - RET=$? - if [ $RET -eq 1 ]; then - # skip cp if srcdir is same as destdir - # this occurs when build/test performed in source dir and - # make cp fail - SDIR=`$DIRNAME $tstfile` - INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` - INODE_DDIR=`$LS -i -d $BLDDIR | $AWK -F' ' '{print $1}'` - if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then - $CP -f $tstfile $BLDDIR - if [ $? -ne 0 ]; then - echo "Error: FAILED to copy $tstfile ." - - # Comment out this to CREATE expected file - exit $EXIT_FAILURE - fi - fi - fi - done -} - -CLEAN_DATAFILES_AND_BLDDIR() -{ - $RM $BLDDIR/examples.intro.H5_*.txt - $RM $BLDDIR/H5_*.out - $RM $BLDDIR/H5_*.h5 -} - -# Print a line-line message left justified in a field of 70 characters -# beginning with the word "Testing". -# -TESTING() { - SPACES=" " - echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012' -} - -# where Java is installed (requires jdk1.7.x) -JAVAEXE=@JAVA@ -JAVAEXEFLAGS=@H5_JAVAFLAGS@ - -############################################################################### -# DO NOT MODIFY BELOW THIS LINE -############################################################################### - -# prepare for test -COPY_LIBFILES_TO_BLDLIBDIR -COPY_DATAFILES_TO_BLDDIR - -CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-2.0.6.jar:"$BLDLIBDIR"/slf4j-simple-2.0.6.jar:"$TESTJARFILE"" - -TEST=/usr/bin/test -if [ ! -x /usr/bin/test ] -then -TEST=`which test` -fi - -if $TEST -z "$CLASSPATH"; then - CLASSPATH="" -fi -CLASSPATH=$CPATH":"$CLASSPATH -export CLASSPATH - -if $TEST -n "$JAVAPATH" ; then - PATH=$JAVAPATH":"$PATH - export PATH -fi - -if $TEST -e /bin/uname; then - os_name=`/bin/uname -s` -elif $TEST -e /usr/bin/uname; then - os_name=`/usr/bin/uname -s` -else - os_name=unknown -fi - -if $TEST -z "$LD_LIBRARY_PATH" ; then - LD_LIBRARY_PATH="" -fi - -case $os_name in - *) - LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH - ;; -esac - -export LD_LIBRARY_PATH - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateDataset" -TESTING examples.intro.H5_CreateDataset -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateDataset > H5_CreateDataset.out) -if diff H5_CreateDataset.out examples.intro.H5_CreateDataset.txt > /dev/null; then - echo " PASSED intro.H5_CreateDataset" -else - echo "**FAILED** intro.H5_CreateDataset" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateAttribute" -TESTING examples.intro.H5_CreateAttribute -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateAttribute > H5_CreateAttribute.out) -if diff H5_CreateAttribute.out examples.intro.H5_CreateAttribute.txt > /dev/null; then - echo " PASSED intro.H5_CreateAttribute" -else - echo "**FAILED** intro.H5_CreateAttribute" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateFile" -TESTING examples.intro.H5_CreateFile -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateFile > H5_CreateFile.out) -if diff H5_CreateFile.out examples.intro.H5_CreateFile.txt > /dev/null; then - echo " PASSED intro.H5_CreateFile" -else - echo "**FAILED** intro.H5_CreateFile" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateGroup" -TESTING examples.intro.H5_CreateGroup -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateGroup > H5_CreateGroup.out) -if diff H5_CreateGroup.out examples.intro.H5_CreateGroup.txt > /dev/null; then - echo " PASSED intro.H5_CreateGroup" -else - echo "**FAILED** intro.H5_CreateGroup" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateGroupAbsoluteRelative" -TESTING examples.intro.H5_CreateGroupAbsoluteRelative -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateGroupAbsoluteRelative > H5_CreateGroupAbsoluteRelative.out) -if diff H5_CreateGroupAbsoluteRelative.out examples.intro.H5_CreateGroupAbsoluteRelative.txt > /dev/null; then - echo " PASSED intro.H5_CreateGroupAbsoluteRelative" -else - echo "**FAILED** intro.H5_CreateGroupAbsoluteRelative" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateGroupDataset" -TESTING examples.intro.H5_CreateGroupDataset -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_CreateGroupDataset > H5_CreateGroupDataset.out) -if diff H5_CreateGroupDataset.out examples.intro.H5_CreateGroupDataset.txt > /dev/null; then - echo " PASSED intro.H5_CreateGroupDataset" -else - echo "**FAILED** intro.H5_CreateGroupDataset" - nerrors="`expr $nerrors + 1`" -fi - -echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_ReadWrite" -TESTING examples.intro.H5_ReadWrite -($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.intro.H5_ReadWrite > H5_ReadWrite.out) -if diff H5_ReadWrite.out examples.intro.H5_ReadWrite.txt > /dev/null; then - echo " PASSED intro.H5_ReadWrite" -else - echo "**FAILED** intro.H5_ReadWrite" - nerrors="`expr $nerrors + 1`" -fi - -# Clean up temporary files/directories -CLEAN_LIBFILES_AND_BLDLIBDIR -CLEAN_DATAFILES_AND_BLDDIR - -# Report test results and exit -if test $nerrors -eq 0 ; then - echo "All $TESTNAME tests passed." - exit $EXIT_SUCCESS -else - echo "$TESTNAME tests failed with $nerrors errors." - exit $EXIT_FAILURE -fi diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am deleted file mode 100644 index b6d6a1f..0000000 --- a/java/examples/intro/Makefile.am +++ /dev/null @@ -1,64 +0,0 @@ -# -# 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. -## -## Makefile.am -## Run automake to generate a Makefile.in from this file. -## -# -# HDF5 Java Library Examples Makefile(.in) - -include $(top_srcdir)/config/commence.am - -# Mark this directory as part of the JNI API -JAVA_API=yes - -JAVAROOT = .classes - -classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - -pkgpath = examples/intro -hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-2.0.6.jar:$$CLASSPATH - -jarfile = jar$(PACKAGE_TARNAME)intro.jar - -AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation - -TESTPACKAGE = - -noinst_JAVA = \ - H5_CreateAttribute.java \ - H5_CreateDataset.java \ - H5_CreateFile.java \ - H5_CreateGroup.java \ - H5_CreateGroupAbsoluteRelative.java \ - H5_CreateGroupDataset.java \ - H5_ReadWrite.java - -$(jarfile): classnoinst.stamp classes - $(JAR) cvf $@ -C $(JAVAROOT)/ $(pkgpath) - -noinst_DATA = $(jarfile) - -.PHONY: classes - -check_SCRIPTS = JavaIntroExample.sh -TEST_SCRIPT = $(check_SCRIPTS) - -CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class JavaIntroExample.sh - -clean: - rm -rf $(JAVAROOT)/* - rm -f $(jarfile) - rm -f classnoinst.stamp - -include $(top_srcdir)/config/conclude.am diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Alloc.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Alloc.txt deleted file mode 100644 index 6fd810b..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Alloc.txt +++ /dev/null @@ -1,16 +0,0 @@ -Creating datasets... -DS1 has allocation time H5D_ALLOC_TIME_LATE -DS2 has allocation time H5D_ALLOC_TIME_EARLY - -Space for DS1 has not been allocated. -Storage size for DS1 is: 0 bytes. -Space for DS2 has been allocated. -Storage size for DS2 is: 112 bytes. - -Writing data... - -Space for DS1 has been allocated. -Storage size for DS1 is: 112 bytes. -Space for DS2 has been allocated. -Storage size for DS2 is: 112 bytes. - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Checksum.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Checksum.txt deleted file mode 100644 index 676aebb..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Checksum.txt +++ /dev/null @@ -1,3 +0,0 @@ -Filter type is: H5Z_FILTER_FLETCHER32 - -Maximum value in DS1 is: 1890 diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Chunk.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Chunk.txt deleted file mode 100644 index 5f4c2de..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Chunk.txt +++ /dev/null @@ -1,26 +0,0 @@ -Original Data: - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - -Storage layout for DS1 is: H5D_CHUNKED - -Data as written to disk by hyberslabs: - [ 0 1 0 0 1 0 0 1 ] - [ 1 1 0 1 1 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - [ 0 1 0 0 1 0 0 1 ] - [ 1 1 0 1 1 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - -Data as read from disk by hyberslab: - [ 0 1 0 0 0 0 0 1 ] - [ 0 1 0 1 0 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - [ 0 0 0 0 0 0 0 0 ] - [ 0 1 0 1 0 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Compact.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Compact.txt deleted file mode 100644 index e34f3c1..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Compact.txt +++ /dev/null @@ -1,8 +0,0 @@ -Storage layout for DS1 is: H5D_COMPACT - -Data for DS1 is: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_External.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_External.txt deleted file mode 100644 index 5878149..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_External.txt +++ /dev/null @@ -1,7 +0,0 @@ -DS1 is stored in file: H5Ex_D_External.data -DS1: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_FillValue.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_FillValue.txt deleted file mode 100644 index 68d826b..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_FillValue.txt +++ /dev/null @@ -1,20 +0,0 @@ -Dataset before being written to: - [ 99 99 99 99 99 99 99 ] - [ 99 99 99 99 99 99 99 ] - [ 99 99 99 99 99 99 99 ] - [ 99 99 99 99 99 99 99 ] - -Dataset after being written to: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] - -Dataset after extension: - [ 0 -1 -2 -3 -4 -5 -6 99 99 99 ] - [ 0 0 0 0 0 0 0 99 99 99 ] - [ 0 1 2 3 4 5 6 99 99 99 ] - [ 0 2 4 6 8 10 12 99 99 99 ] - [ 99 99 99 99 99 99 99 99 99 99 ] - [ 99 99 99 99 99 99 99 99 99 99 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Gzip.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Gzip.txt deleted file mode 100644 index 255a561..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Gzip.txt +++ /dev/null @@ -1,3 +0,0 @@ -Filter type is: H5Z_FILTER_DEFLATE - -Maximum value in DS1 is: 1890 diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Hyperslab.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Hyperslab.txt deleted file mode 100644 index 823dfcc..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Hyperslab.txt +++ /dev/null @@ -1,24 +0,0 @@ -Original Data: - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - [ 1 1 1 1 1 1 1 1 ] - -Data as written to disk by hyberslabs: - [ 0 1 0 0 1 0 0 1 ] - [ 1 1 0 1 1 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - [ 0 1 0 0 1 0 0 1 ] - [ 1 1 0 1 1 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - -Data as read from disk by hyberslab: - [ 0 1 0 0 0 0 0 1 ] - [ 0 1 0 1 0 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - [ 0 0 0 0 0 0 0 0 ] - [ 0 1 0 1 0 0 1 1 ] - [ 0 0 0 0 0 0 0 0 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Nbit.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Nbit.txt deleted file mode 100644 index a768ba0..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Nbit.txt +++ /dev/null @@ -1,3 +0,0 @@ -Filter type is: H5Z_FILTER_NBIT - -Maximum value in DS1 is: 1890 diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_ReadWrite.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_ReadWrite.txt deleted file mode 100644 index e021029..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_ReadWrite.txt +++ /dev/null @@ -1,6 +0,0 @@ -DS1: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Shuffle.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Shuffle.txt deleted file mode 100644 index ea95f11..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Shuffle.txt +++ /dev/null @@ -1,5 +0,0 @@ -Filter 0: Type is: H5Z_FILTER_SHUFFLE - -Filter 1: Type is: H5Z_FILTER_DEFLATE - -Maximum value in DS1 is: 1890 diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt deleted file mode 100644 index 9025ce2..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt +++ /dev/null @@ -1,6 +0,0 @@ -Maximum value in write buffer is: 106.666667 -Minimum value in write buffer is: 1.769231 -Filter type is: H5Z_FILTER_SCALEOFFSET - -Maximum value in DS1 is: 106.661698 -Minimum value in DS1 is: 1.769231 diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Soint.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Soint.txt deleted file mode 100644 index 48d0d8c..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Soint.txt +++ /dev/null @@ -1,3 +0,0 @@ -Filter type is: H5Z_FILTER_SCALEOFFSET - -Maximum value in DS1 is: 1890 diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Szip.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Szip.txt deleted file mode 100644 index a1c0d19..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Szip.txt +++ /dev/null @@ -1,3 +0,0 @@ -Filter type is: H5Z_FILTER_SZIP - -Maximum value in DS1 is: 1890 diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_Transform.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_Transform.txt deleted file mode 100644 index 05257bc..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_Transform.txt +++ /dev/null @@ -1,15 +0,0 @@ -Original Data: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] -Data as written with transform 'x+1' - [ 1 0 -1 -2 -3 -4 -5 ] - [ 1 1 1 1 1 1 1 ] - [ 1 2 3 4 5 6 7 ] - [ 1 3 5 7 9 11 13 ] -Data as written with transform 'x+1' and read with transform 'x-1' - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedAdd.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedAdd.txt deleted file mode 100644 index d3a7281..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedAdd.txt +++ /dev/null @@ -1,14 +0,0 @@ -Dataset before extension: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] - -Dataset after extension: - [ 0 -1 -2 -3 -4 -5 -6 7 8 9 ] - [ 0 0 0 0 0 0 0 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 2 4 6 8 10 12 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedGzip.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedGzip.txt deleted file mode 100644 index 9e36281..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedGzip.txt +++ /dev/null @@ -1,16 +0,0 @@ -Dataset before extension: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] - -Filter type is: H5Z_FILTER_DEFLATE - -Dataset after extension: - [ 0 -1 -2 -3 -4 -5 -6 7 8 9 ] - [ 0 0 0 0 0 0 0 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 2 4 6 8 10 12 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - diff --git a/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedMod.txt b/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedMod.txt deleted file mode 100644 index 15eee16..0000000 --- a/java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedMod.txt +++ /dev/null @@ -1,14 +0,0 @@ -Dataset before extension: - [ 0 -1 -2 -3 -4 -5 -6 ] - [ 0 0 0 0 0 0 0 ] - [ 0 1 2 3 4 5 6 ] - [ 0 2 4 6 8 10 12 ] - -Dataset after extension: - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - [ 0 1 2 3 4 5 6 7 8 9 ] - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_Array.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_Array.txt deleted file mode 100644 index 7bcd8fa..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_Array.txt +++ /dev/null @@ -1,21 +0,0 @@ -DS1 [0]: - [0 0 0 0 0 ] - [0 -1 -2 -3 -4 ] - [0 -2 -4 -6 -8 ] - -DS1 [1]: - [0 1 2 3 4 ] - [1 1 1 1 1 ] - [2 1 0 -1 -2 ] - -DS1 [2]: - [0 2 4 6 8 ] - [2 3 4 5 6 ] - [4 4 4 4 4 ] - -DS1 [3]: - [0 3 6 9 12 ] - [3 5 7 9 11 ] - [6 7 8 9 10 ] - - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_ArrayAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_ArrayAttribute.txt deleted file mode 100644 index 7d27c0b..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_ArrayAttribute.txt +++ /dev/null @@ -1,21 +0,0 @@ -A1 [0]: - [0 0 0 0 0 ] - [0 -1 -2 -3 -4 ] - [0 -2 -4 -6 -8 ] - -A1 [1]: - [0 1 2 3 4 ] - [1 1 1 1 1 ] - [2 1 0 -1 -2 ] - -A1 [2]: - [0 2 4 6 8 ] - [2 3 4 5 6 ] - [4 4 4 4 4 ] - -A1 [3]: - [0 3 6 9 12 ] - [3 5 7 9 11 ] - [6 7 8 9 10 ] - - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_Bit.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_Bit.txt deleted file mode 100644 index 57769b2..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_Bit.txt +++ /dev/null @@ -1,6 +0,0 @@ -DS1: - [{0, 0, 0, 0}{3, 0, 1, 1}{2, 0, 2, 2}{1, 0, 3, 3}{0, 0, 0, 0}{3, 0, 1, 1}{2, 0, 2, 2}] - [{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}] - [{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}] - [{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}] - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_BitAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_BitAttribute.txt deleted file mode 100644 index 683bc7f..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_BitAttribute.txt +++ /dev/null @@ -1,6 +0,0 @@ -A1: - [{0, 0, 0, 0}{3, 0, 1, 1}{2, 0, 2, 2}{1, 0, 3, 3}{0, 0, 0, 0}{3, 0, 1, 1}{2, 0, 2, 2}] - [{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}] - [{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}] - [{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}{0, 0, 0, 0}] - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_Commit.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_Commit.txt deleted file mode 100644 index e6d0bef..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_Commit.txt +++ /dev/null @@ -1,6 +0,0 @@ -Named datatype: Sensor_Type: - Class: H5T_COMPOUND - Serial number - Location - Temperature (F) - Pressure (inHg) diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_Compound.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_Compound.txt deleted file mode 100644 index 0505c78..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_Compound.txt +++ /dev/null @@ -1,25 +0,0 @@ -DS1 [0]: -Serial number : 1153 -Location : Exterior (static) -Temperature (F) : 53.23 -Pressure (inHg) : 24.57 - -DS1 [1]: -Serial number : 1184 -Location : Intake -Temperature (F) : 55.12 -Pressure (inHg) : 22.95 - -DS1 [2]: -Serial number : 1027 -Location : Intake manifold -Temperature (F) : 103.55 -Pressure (inHg) : 31.23 - -DS1 [3]: -Serial number : 1313 -Location : Exhaust manifold -Temperature (F) : 1252.89 -Pressure (inHg) : 84.11 - - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_CompoundAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_CompoundAttribute.txt deleted file mode 100644 index dd77f8d..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_CompoundAttribute.txt +++ /dev/null @@ -1,25 +0,0 @@ -A1 [0]: -Serial number : 1153 -Location : Exterior (static) -Temperature (F) : 53.23 -Pressure (inHg) : 24.57 - -A1 [1]: -Serial number : 1184 -Location : Intake -Temperature (F) : 55.12 -Pressure (inHg) : 22.95 - -A1 [2]: -Serial number : 1027 -Location : Intake manifold -Temperature (F) : 103.55 -Pressure (inHg) : 31.23 - -A1 [3]: -Serial number : 1313 -Location : Exhaust manifold -Temperature (F) : 1252.89 -Pressure (inHg) : 84.11 - - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_Float.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_Float.txt deleted file mode 100644 index 85d8ced..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_Float.txt +++ /dev/null @@ -1,6 +0,0 @@ -DS1: - [ 0.0000 1.0000 2.0000 3.0000 4.0000 5.0000 6.0000] - [ 2.0000 1.6667 2.4000 3.2857 4.2222 5.1818 6.1538] - [ 4.0000 2.3333 2.8000 3.5714 4.4444 5.3636 6.3077] - [ 6.0000 3.0000 3.2000 3.8571 4.6667 5.5455 6.4615] - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_FloatAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_FloatAttribute.txt deleted file mode 100644 index cfa1f92..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_FloatAttribute.txt +++ /dev/null @@ -1,6 +0,0 @@ -A1: - [ 0.0000 1.0000 2.0000 3.0000 4.0000 5.0000 6.0000] - [ 2.0000 1.6667 2.4000 3.2857 4.2222 5.1818 6.1538] - [ 4.0000 2.3333 2.8000 3.5714 4.4444 5.3636 6.3077] - [ 6.0000 3.0000 3.2000 3.8571 4.6667 5.5455 6.4615] - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_Integer.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_Integer.txt deleted file mode 100644 index f686bd1..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_Integer.txt +++ /dev/null @@ -1,6 +0,0 @@ -DS1: - [ 0 -1 -2 -3 -4 -5 -6] - [ 0 0 0 0 0 0 0] - [ 0 1 2 3 4 5 6] - [ 0 2 4 6 8 10 12] - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_IntegerAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_IntegerAttribute.txt deleted file mode 100644 index dccd4a6..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_IntegerAttribute.txt +++ /dev/null @@ -1,6 +0,0 @@ -A1: - [ 0 -1 -2 -3 -4 -5 -6] - [ 0 0 0 0 0 0 0] - [ 0 1 2 3 4 5 6] - [ 0 2 4 6 8 10 12] - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReference.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReference.txt deleted file mode 100644 index d8afa56..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReference.txt +++ /dev/null @@ -1,4 +0,0 @@ -DS1[0]: - ->H5G_GROUP: /G1 -DS1[1]: - ->H5G_DATASET: /DS2 diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReferenceAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReferenceAttribute.txt deleted file mode 100644 index 3fabd66..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReferenceAttribute.txt +++ /dev/null @@ -1,4 +0,0 @@ -A1[0]: - ->H5G_GROUP: /G1 -A1[1]: - ->H5G_DATASET: /DS2 diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_Opaque.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_Opaque.txt deleted file mode 100644 index fb74236..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_Opaque.txt +++ /dev/null @@ -1,6 +0,0 @@ -Datatype tag for DS1 is: "Character array" -DS1[0]: OPAQUE0 -DS1[1]: OPAQUE1 -DS1[2]: OPAQUE2 -DS1[3]: OPAQUE3 - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_OpaqueAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_OpaqueAttribute.txt deleted file mode 100644 index bc9a730..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_OpaqueAttribute.txt +++ /dev/null @@ -1,6 +0,0 @@ -Datatype tag for A1 is: "Character array" -A1[0]: OPAQUE0 -A1[1]: OPAQUE1 -A1[2]: OPAQUE2 -A1[3]: OPAQUE3 - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_String.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_String.txt deleted file mode 100644 index 4df6a41..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_String.txt +++ /dev/null @@ -1,5 +0,0 @@ -DS1 [0]: Parting -DS1 [1]: is such -DS1 [2]: sweet -DS1 [3]: sorrow. - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_StringAttribute.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_StringAttribute.txt deleted file mode 100644 index 4df6a41..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_StringAttribute.txt +++ /dev/null @@ -1,5 +0,0 @@ -DS1 [0]: Parting -DS1 [1]: is such -DS1 [2]: sweet -DS1 [3]: sorrow. - diff --git a/java/examples/testfiles/examples.datatypes.H5Ex_T_VLString.txt b/java/examples/testfiles/examples.datatypes.H5Ex_T_VLString.txt deleted file mode 100644 index 0322953..0000000 --- a/java/examples/testfiles/examples.datatypes.H5Ex_T_VLString.txt +++ /dev/null @@ -1,4 +0,0 @@ -DS1 [0]: Parting -DS1 [1]: is such -DS1 [2]: sweet -DS1 [3]: sorrow. diff --git a/java/examples/testfiles/examples.groups.H5Ex_G_Compact.txt b/java/examples/testfiles/examples.groups.H5Ex_G_Compact.txt deleted file mode 100644 index 0a88d3f..0000000 --- a/java/examples/testfiles/examples.groups.H5Ex_G_Compact.txt +++ /dev/null @@ -1,5 +0,0 @@ -Group storage type for H5Ex_G_Compact1.h5 is: H5G_STORAGE_TYPE_SYMBOL_TABLE -File size for H5Ex_G_Compact1.h5 is: 1832 bytes - -Group storage type for H5Ex_G_Compact2.h5 is: H5G_STORAGE_TYPE_COMPACT -File size for H5Ex_G_Compact2.h5 is: 342 bytes diff --git a/java/examples/testfiles/examples.groups.H5Ex_G_Corder.txt b/java/examples/testfiles/examples.groups.H5Ex_G_Corder.txt deleted file mode 100644 index 2d959fc..0000000 --- a/java/examples/testfiles/examples.groups.H5Ex_G_Corder.txt +++ /dev/null @@ -1,10 +0,0 @@ -Traversing group using alphabetical indices: -Index 0: 5 -Index 1: D -Index 2: F -Index 3: H -Traversing group using creation order indices: -Index 0: H -Index 1: D -Index 2: F -Index 3: 5 diff --git a/java/examples/testfiles/examples.groups.H5Ex_G_Create.txt b/java/examples/testfiles/examples.groups.H5Ex_G_Create.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.groups.H5Ex_G_Create.txt +++ /dev/null diff --git a/java/examples/testfiles/examples.groups.H5Ex_G_Intermediate.txt b/java/examples/testfiles/examples.groups.H5Ex_G_Intermediate.txt deleted file mode 100644 index 65a0fc2..0000000 --- a/java/examples/testfiles/examples.groups.H5Ex_G_Intermediate.txt +++ /dev/null @@ -1,5 +0,0 @@ -Objects in the file_id: -/ (Group) -/G1 (Group) -/G1/G2 (Group) -/G1/G2/G3 (Group) diff --git a/java/examples/testfiles/examples.groups.H5Ex_G_Iterate.txt b/java/examples/testfiles/examples.groups.H5Ex_G_Iterate.txt deleted file mode 100644 index 66a4ae9..0000000 --- a/java/examples/testfiles/examples.groups.H5Ex_G_Iterate.txt +++ /dev/null @@ -1,5 +0,0 @@ -Objects in root group: - Dataset: DS1 - Datatype: DT1 - Group: G1 - Dataset: L1 diff --git a/java/examples/testfiles/examples.groups.H5Ex_G_Phase.txt b/java/examples/testfiles/examples.groups.H5Ex_G_Phase.txt deleted file mode 100644 index 9e666d4..0000000 --- a/java/examples/testfiles/examples.groups.H5Ex_G_Phase.txt +++ /dev/null @@ -1,15 +0,0 @@ -1 Group : Storage type is H5G_STORAGE_TYPE_COMPACT -2 Groups: Storage type is H5G_STORAGE_TYPE_COMPACT -3 Groups: Storage type is H5G_STORAGE_TYPE_COMPACT -4 Groups: Storage type is H5G_STORAGE_TYPE_COMPACT -5 Groups: Storage type is H5G_STORAGE_TYPE_COMPACT -6 Groups: Storage type is H5G_STORAGE_TYPE_DENSE -7 Groups: Storage type is H5G_STORAGE_TYPE_DENSE - -6 Groups: Storage type is H5G_STORAGE_TYPE_DENSE -5 Groups: Storage type is H5G_STORAGE_TYPE_DENSE -4 Groups: Storage type is H5G_STORAGE_TYPE_DENSE -3 Groups: Storage type is H5G_STORAGE_TYPE_DENSE -2 Groups: Storage type is H5G_STORAGE_TYPE_COMPACT -1 Group : Storage type is H5G_STORAGE_TYPE_COMPACT -0 Groups: Storage type is H5G_STORAGE_TYPE_COMPACT diff --git a/java/examples/testfiles/examples.groups.H5Ex_G_Visit.txt b/java/examples/testfiles/examples.groups.H5Ex_G_Visit.txt deleted file mode 100644 index 126a588..0000000 --- a/java/examples/testfiles/examples.groups.H5Ex_G_Visit.txt +++ /dev/null @@ -1,19 +0,0 @@ -Objects in the file: -/ (Group) -/group1 (Group) -/group1/dset1 (Dataset) -/group1/group3 (Group) -/group1/group3/group4 (Group) -/group1/group3/group4/group1 (Group) -/group1/group3/group4/group2 (Group) - -Links in the file: -/group1 (Group) -/group1/dset1 (Dataset) -/group1/group3 (Group) -/group1/group3/dset2 (Dataset) -/group1/group3/group4 (Group) -/group1/group3/group4/group1 (Group) -/group1/group3/group4/group1/group5 (Group) -/group1/group3/group4/group2 (Group) -/group2 (Group) diff --git a/java/examples/testfiles/examples.intro.H5_CreateAttribute.txt b/java/examples/testfiles/examples.intro.H5_CreateAttribute.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.intro.H5_CreateAttribute.txt +++ /dev/null diff --git a/java/examples/testfiles/examples.intro.H5_CreateDataset.txt b/java/examples/testfiles/examples.intro.H5_CreateDataset.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.intro.H5_CreateDataset.txt +++ /dev/null diff --git a/java/examples/testfiles/examples.intro.H5_CreateFile.txt b/java/examples/testfiles/examples.intro.H5_CreateFile.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.intro.H5_CreateFile.txt +++ /dev/null diff --git a/java/examples/testfiles/examples.intro.H5_CreateGroup.txt b/java/examples/testfiles/examples.intro.H5_CreateGroup.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.intro.H5_CreateGroup.txt +++ /dev/null diff --git a/java/examples/testfiles/examples.intro.H5_CreateGroupAbsoluteRelative.txt b/java/examples/testfiles/examples.intro.H5_CreateGroupAbsoluteRelative.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.intro.H5_CreateGroupAbsoluteRelative.txt +++ /dev/null diff --git a/java/examples/testfiles/examples.intro.H5_CreateGroupDataset.txt b/java/examples/testfiles/examples.intro.H5_CreateGroupDataset.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.intro.H5_CreateGroupDataset.txt +++ /dev/null diff --git a/java/examples/testfiles/examples.intro.H5_ReadWrite.txt b/java/examples/testfiles/examples.intro.H5_ReadWrite.txt deleted file mode 100644 index e69de29..0000000 --- a/java/examples/testfiles/examples.intro.H5_ReadWrite.txt +++ /dev/null diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 824905b..fb2769d 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -47,6 +47,20 @@ New Features Configuration: ------------- + - Incorporated HDF5 examples repository into HDF5 library. + + The HDF5Examples folder is equivalent to the repository hdf5-examples. + As such it can build and test the examples during library build or after + the library is installed. Previously, the hdf5-repository archives were + downloaded for packaging with the library. Now the examples can be built + and tested without a packaged install of the library. + + However to maintain the ability to use the HDF5Examples with an installed + library, it is necessary to translate or synch the option names from those + used by the library to those used by the examples. The typical pattern is: + <example option> = <library option> + HDF_BUILD_FORTRAN = ${HDF5_BUILD_FORTRAN} + - Added new option for CMake to mark tests as SKIPPED. HDF5_DISABLE_TESTS_REGEX is a REGEX string that will be checked with diff --git a/release_docs/USING_HDF5_VS.txt b/release_docs/USING_HDF5_VS.txt index f0edcbb..39c66ea 100644 --- a/release_docs/USING_HDF5_VS.txt +++ b/release_docs/USING_HDF5_VS.txt @@ -11,6 +11,9 @@ be found in the USING_HDF5_CMake.txt file found in this folder. NOTE: Building applications with the dynamic/shared hdf5 libraries requires that the "H5_BUILT_AS_DYNAMIC_LIB" compile definition be used. + Go to "Project" and select "Properties", find "Configuration Properties", + and then "C/C+±"and then "Preprocessor". + Add H5_BUILT_AS_DYNAMIC_LIB to Preprocessor definitions. The following two sections are helpful if you do not use CMake to build your applications. diff --git a/tools/libtest/CMakeLists.txt b/tools/libtest/CMakeLists.txt index f6d8912..3578560 100644 --- a/tools/libtest/CMakeLists.txt +++ b/tools/libtest/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_LIBTEST C) #----------------------------------------------------------------------------- add_executable (h5tools_test_utils ${HDF5_TOOLS_LIBTEST_SOURCE_DIR}/h5tools_test_utils.c) target_compile_options(h5tools_test_utils PRIVATE "${HDF5_CMAKE_C_FLAGS}") -target_include_directories(h5tools_test_utils PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") +target_include_directories(h5tools_test_utils PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") if (BUILD_STATIC_LIBS) TARGET_C_PROPERTIES (h5tools_test_utils STATIC) target_link_libraries (h5tools_test_utils PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET}) diff --git a/tools/src/h5copy/CMakeLists.txt b/tools/src/h5copy/CMakeLists.txt index efd38cd..5b79a85 100644 --- a/tools/src/h5copy/CMakeLists.txt +++ b/tools/src/h5copy/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5COPY C) # -------------------------------------------------------------------- if (BUILD_STATIC_LIBS) add_executable (h5copy ${HDF5_TOOLS_SRC_H5COPY_SOURCE_DIR}/h5copy.c) - target_include_directories (h5copy PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5copy PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5copy PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5copy STATIC) target_link_libraries (h5copy PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -18,7 +18,7 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5copy-shared ${HDF5_TOOLS_SRC_H5COPY_SOURCE_DIR}/h5copy.c) - target_include_directories (h5copy-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5copy-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5copy-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5copy-shared SHARED) target_link_libraries (h5copy-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) diff --git a/tools/src/h5diff/CMakeLists.txt b/tools/src/h5diff/CMakeLists.txt index f01d1aa..8de7c61 100644 --- a/tools/src/h5diff/CMakeLists.txt +++ b/tools/src/h5diff/CMakeLists.txt @@ -10,7 +10,7 @@ if (BUILD_STATIC_LIBS) ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.h ) - target_include_directories (h5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5diff PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5diff PRIVATE "${HDF5_CMAKE_C_FLAGS}") #target_compile_definitions (h5diff PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5diff STATIC) @@ -26,7 +26,7 @@ if (BUILD_SHARED_LIBS) ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.h ) - target_include_directories (h5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5diff-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5diff-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") #target_compile_definitions (h5diff-shared PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5diff-shared SHARED) @@ -54,7 +54,7 @@ if (H5_HAVE_PARALLEL) ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c ) - target_include_directories (ph5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (ph5diff PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(ph5diff PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (ph5diff STATIC) target_link_libraries (ph5diff PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>") @@ -67,7 +67,7 @@ if (H5_HAVE_PARALLEL) ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c ) - target_include_directories (ph5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (ph5diff-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(ph5diff-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (ph5diff-shared SHARED) target_link_libraries (ph5diff-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>") diff --git a/tools/src/h5dump/CMakeLists.txt b/tools/src/h5dump/CMakeLists.txt index f382020..3284949 100644 --- a/tools/src/h5dump/CMakeLists.txt +++ b/tools/src/h5dump/CMakeLists.txt @@ -15,7 +15,7 @@ if (BUILD_STATIC_LIBS) ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.h ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.h ) - target_include_directories (h5dump PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5dump PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5dump PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5dump STATIC) target_link_libraries (h5dump PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -36,7 +36,7 @@ if (BUILD_SHARED_LIBS) ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.h ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.h ) - target_include_directories (h5dump-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5dump-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5dump-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5dump-shared SHARED) target_link_libraries (h5dump-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) diff --git a/tools/src/h5format_convert/CMakeLists.txt b/tools/src/h5format_convert/CMakeLists.txt index d1e2158..2a7e3cb 100644 --- a/tools/src/h5format_convert/CMakeLists.txt +++ b/tools/src/h5format_convert/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5FC C) # -------------------------------------------------------------------- if (BUILD_STATIC_LIBS) add_executable (h5format_convert ${HDF5_TOOLS_SRC_H5FC_SOURCE_DIR}/h5format_convert.c) - target_include_directories (h5format_convert PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5format_convert PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5format_convert PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5format_convert STATIC) target_link_libraries (h5format_convert PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -17,7 +17,7 @@ if (BUILD_STATIC_LIBS) endif () if (BUILD_SHARED_LIBS) add_executable (h5format_convert-shared ${HDF5_TOOLS_SRC_H5FC_SOURCE_DIR}/h5format_convert.c) - target_include_directories (h5format_convert-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5format_convert-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5format_convert-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5format_convert-shared SHARED) target_link_libraries (h5format_convert-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) diff --git a/tools/src/h5import/CMakeLists.txt b/tools/src/h5import/CMakeLists.txt index b2337cd..f8268a1 100644 --- a/tools/src/h5import/CMakeLists.txt +++ b/tools/src/h5import/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5IMPORT C) # -------------------------------------------------------------------- if (BUILD_STATIC_LIBS) add_executable (h5import ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.h) - target_include_directories (h5import PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5import PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5import STATIC) target_link_libraries (h5import PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) #set_target_properties (h5import PROPERTIES COMPILE_DEFINITIONS H5DEBUGIMPORT) @@ -18,7 +18,7 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5import-shared ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.h) - target_include_directories (h5import-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5import-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5import-shared SHARED) target_link_libraries (h5import-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) #set_target_properties (h5import-shared PROPERTIES COMPILE_DEFINITIONS H5DEBUGIMPORT) diff --git a/tools/src/h5jam/CMakeLists.txt b/tools/src/h5jam/CMakeLists.txt index 8642d6f..7efd0d8 100644 --- a/tools/src/h5jam/CMakeLists.txt +++ b/tools/src/h5jam/CMakeLists.txt @@ -6,14 +6,14 @@ project (HDF5_TOOLS_SRC_H5JAM C) # -------------------------------------------------------------------- if (BUILD_STATIC_LIBS) add_executable (h5jam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c) - target_include_directories (h5jam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5jam PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5jam STATIC) target_link_libraries (h5jam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5jam PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam") add_executable (h5unjam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c) - target_include_directories (h5unjam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5unjam PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5unjam STATIC) target_link_libraries (h5unjam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) set_target_properties (h5unjam PROPERTIES FOLDER tools) @@ -27,14 +27,14 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5jam-shared ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c) - target_include_directories (h5jam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5jam-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5jam-shared SHARED) target_link_libraries (h5jam-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5jam-shared PROPERTIES FOLDER tools) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam-shared") add_executable (h5unjam-shared ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c) - target_include_directories (h5unjam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5unjam-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5unjam-shared SHARED) target_link_libraries (h5unjam-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) set_target_properties (h5unjam-shared PROPERTIES FOLDER tools) diff --git a/tools/src/h5ls/CMakeLists.txt b/tools/src/h5ls/CMakeLists.txt index 9499253..67122a1 100644 --- a/tools/src/h5ls/CMakeLists.txt +++ b/tools/src/h5ls/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5LS C) #----------------------------------------------------------------------------- if (BUILD_STATIC_LIBS) add_executable (h5ls ${HDF5_TOOLS_SRC_H5LS_SOURCE_DIR}/h5ls.c) - target_include_directories (h5ls PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5ls PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5ls PRIVATE "${HDF5_CMAKE_C_FLAGS}") #target_compile_definitions(h5ls PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5ls STATIC) @@ -19,7 +19,7 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5ls-shared ${HDF5_TOOLS_SRC_H5LS_SOURCE_DIR}/h5ls.c) - target_include_directories (h5ls-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5ls-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5ls-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") #target_compile_definitions(h5ls-shared PRIVATE H5_TOOLS_DEBUG) TARGET_C_PROPERTIES (h5ls-shared SHARED) diff --git a/tools/src/h5repack/CMakeLists.txt b/tools/src/h5repack/CMakeLists.txt index 360fb0f..ea1ee80 100644 --- a/tools/src/h5repack/CMakeLists.txt +++ b/tools/src/h5repack/CMakeLists.txt @@ -17,7 +17,7 @@ set (REPACK_COMMON_SOURCES if (BUILD_STATIC_LIBS) add_executable (h5repack ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c) - target_include_directories (h5repack PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repack PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5repack PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repack STATIC) target_link_libraries (h5repack PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -29,7 +29,7 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5repack-shared ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c) - target_include_directories (h5repack-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repack-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5repack-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repack-shared SHARED) target_link_libraries (h5repack-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) diff --git a/tools/src/h5stat/CMakeLists.txt b/tools/src/h5stat/CMakeLists.txt index c0c0b32..c3aef5f 100644 --- a/tools/src/h5stat/CMakeLists.txt +++ b/tools/src/h5stat/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5STAT C) # -------------------------------------------------------------------- if (BUILD_STATIC_LIBS) add_executable (h5stat ${HDF5_TOOLS_SRC_H5STAT_SOURCE_DIR}/h5stat.c) - target_include_directories (h5stat PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5stat PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5stat PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5stat STATIC) target_link_libraries (h5stat PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -18,7 +18,7 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5stat-shared ${HDF5_TOOLS_SRC_H5STAT_SOURCE_DIR}/h5stat.c) - target_include_directories (h5stat-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5stat-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5stat-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5stat-shared SHARED) target_link_libraries (h5stat-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) diff --git a/tools/src/misc/CMakeLists.txt b/tools/src/misc/CMakeLists.txt index d2b1f51..62bd443 100644 --- a/tools/src/misc/CMakeLists.txt +++ b/tools/src/misc/CMakeLists.txt @@ -7,7 +7,7 @@ project (HDF5_TOOLS_SRC_MISC C) #-- Misc Executables if (BUILD_STATIC_LIBS) add_executable (h5debug ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5debug.c) - target_include_directories (h5debug PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5debug PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5debug PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5debug STATIC) target_link_libraries (h5debug PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -15,7 +15,7 @@ if (BUILD_STATIC_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5debug") add_executable (h5repart ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5repart.c) - target_include_directories (h5repart PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repart PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5repart PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repart STATIC) target_link_libraries (h5repart PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -23,7 +23,7 @@ if (BUILD_STATIC_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repart") add_executable (h5mkgrp ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5mkgrp.c) - target_include_directories (h5mkgrp PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5mkgrp PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5mkgrp PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5mkgrp STATIC) target_link_libraries (h5mkgrp PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -31,7 +31,7 @@ if (BUILD_STATIC_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp") add_executable (h5clear ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5clear.c) - target_include_directories (h5clear PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5clear PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5clear PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5clear STATIC) target_link_libraries (h5clear PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -39,7 +39,7 @@ if (BUILD_STATIC_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5clear") add_executable (h5delete ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5delete.c) - target_include_directories (h5delete PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5delete PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5delete PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5delete STATIC) target_link_libraries (h5delete PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -56,7 +56,7 @@ if (BUILD_STATIC_LIBS) endif () if (BUILD_SHARED_LIBS) add_executable (h5debug-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5debug.c) - target_include_directories (h5debug-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5debug-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5debug-shared SHARED) target_compile_options(h5debug-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") target_link_libraries (h5debug-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) @@ -64,7 +64,7 @@ if (BUILD_SHARED_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5debug-shared") add_executable (h5repart-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5repart.c) - target_include_directories (h5repart-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5repart-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5repart-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5repart-shared SHARED) target_link_libraries (h5repart-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) @@ -72,7 +72,7 @@ if (BUILD_SHARED_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repart-shared") add_executable (h5mkgrp-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5mkgrp.c) - target_include_directories (h5mkgrp-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5mkgrp-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5mkgrp-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5mkgrp-shared SHARED) target_link_libraries (h5mkgrp-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) @@ -80,7 +80,7 @@ if (BUILD_SHARED_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp-shared") add_executable (h5clear-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5clear.c) - target_include_directories (h5clear-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5clear-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5clear-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5clear-shared SHARED) target_link_libraries (h5clear-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) @@ -88,7 +88,7 @@ if (BUILD_SHARED_LIBS) set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5clear-shared") add_executable (h5delete-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5delete.c) - target_include_directories (h5delete-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5delete-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5delete-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5delete-shared SHARED) target_link_libraries (h5delete-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET}) diff --git a/tools/test/h5jam/CMakeLists.txt b/tools/test/h5jam/CMakeLists.txt index 160ecdf..e6017fd 100644 --- a/tools/test/h5jam/CMakeLists.txt +++ b/tools/test/h5jam/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_TEST_H5JAM C) # -------------------------------------------------------------------- if (HDF5_BUILD_GENERATORS AND BUILD_STATIC_LIBS) add_executable (h5jamgentest ${HDF5_TOOLS_TEST_H5JAM_SOURCE_DIR}/h5jamgentest.c) - target_include_directories (h5jamgentest PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5jamgentest PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") TARGET_C_PROPERTIES (h5jamgentest STATIC) target_link_libraries (h5jamgentest PRIVATE ${HDF5_LIB_TARGET}) set_target_properties (h5jamgentest PROPERTIES FOLDER generator/tools) @@ -22,7 +22,7 @@ if (HDF5_BUILD_GENERATORS AND BUILD_STATIC_LIBS) endif () add_executable (getub ${HDF5_TOOLS_TEST_H5JAM_SOURCE_DIR}/getub.c) -target_include_directories (getub PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") +target_include_directories (getub PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") if (BUILD_STATIC_LIBS) TARGET_C_PROPERTIES (getub STATIC) target_link_libraries (getub PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) @@ -33,7 +33,7 @@ endif () set_target_properties (getub PROPERTIES FOLDER tools) add_executable (tellub ${HDF5_TOOLS_TEST_H5JAM_SOURCE_DIR}/tellub.c) -target_include_directories (tellub PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") +target_include_directories (tellub PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") if (BUILD_STATIC_LIBS) TARGET_C_PROPERTIES (tellub STATIC) target_link_libraries (tellub PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET}) diff --git a/tools/test/h5repack/CMakeLists.txt b/tools/test/h5repack/CMakeLists.txt index 3e7c6c2..5c0075c 100644 --- a/tools/test/h5repack/CMakeLists.txt +++ b/tools/test/h5repack/CMakeLists.txt @@ -6,7 +6,7 @@ project (HDF5_TOOLS_TEST_H5REPACK C) # -------------------------------------------------------------------- add_executable (testh5repack_detect_szip ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testh5repack_detect_szip.c) target_include_directories (testh5repack_detect_szip - PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>" + PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>" ) if (BUILD_STATIC_LIBS) TARGET_C_PROPERTIES (testh5repack_detect_szip STATIC) @@ -29,7 +29,7 @@ set (REPACK_COMMON_SOURCES ) add_executable (h5repacktest ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/h5repacktst.c) target_include_directories (h5repacktest - PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_TEST_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>" + PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_TEST_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>" ) if (BUILD_STATIC_LIBS) TARGET_C_PROPERTIES (h5repacktest STATIC) diff --git a/utils/tools/h5dwalk/CMakeLists.txt b/utils/tools/h5dwalk/CMakeLists.txt index 9e4eb6d..f0611e0 100644 --- a/utils/tools/h5dwalk/CMakeLists.txt +++ b/utils/tools/h5dwalk/CMakeLists.txt @@ -7,9 +7,9 @@ project (HDF5_UTILS_TOOLS_H5DWALK C) if (BUILD_STATIC_LIBS) add_executable (h5dwalk ${HDF5_UTILS_TOOLS_H5DWALK_SOURCE_DIR}/h5dwalk.c) # add_custom_target(generate_demo ALL -# DEPENDS "${HDF5_TOOLS_DIR}/test/demo_destfiles.test" +# DEPENDS "${HDF5_TOOLS_ROOT_DIR}/test/demo_destfiles.test" # ) - target_include_directories (h5dwalk PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5dwalk PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5dwalk PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5dwalk STATIC) target_link_libraries (h5dwalk PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} ${MFU_LIBRARY} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>") @@ -21,7 +21,7 @@ endif () if (BUILD_SHARED_LIBS) add_executable (h5dwalk-shared ${HDF5_UTILS_TOOLS_H5DWALK_SOURCE_DIR}/h5dwalk.c) - target_include_directories (h5dwalk-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") + target_include_directories (h5dwalk-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") target_compile_options(h5dwalk-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}") TARGET_C_PROPERTIES (h5dwalk-shared SHARED) target_link_libraries (h5dwalk-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${MFU_LIBRARY} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>") diff --git a/utils/tools/test/h5dwalk/CMakeLists.txt b/utils/tools/test/h5dwalk/CMakeLists.txt index 530bed8..a27190c 100644 --- a/utils/tools/test/h5dwalk/CMakeLists.txt +++ b/utils/tools/test/h5dwalk/CMakeLists.txt @@ -3,9 +3,9 @@ project (HDF5_TOOLS_TEST_H5DWALK) if (HDF5_BUILD_PARALLEL_TOOLS) add_custom_command( - OUTPUT ${HDF5_TOOLS_DIR}/test/demo_destfiles.test + OUTPUT ${HDF5_TOOLS_ROOT_DIR}/test/demo_destfiles.test COMMAND bash -c ${HDF5_TOOLS_SRC_H5DWALK_SOURCE_DIR}/copy_demo_files.sh - ARGS ${HDF5_TOOLS_DIR}/test ${CMAKE_BINARY_DIR}/bin + ARGS ${HDF5_TOOLS_ROOT_DIR}/test ${CMAKE_BINARY_DIR}/bin DEPENDS ${HDF5_TOOLS_SRC_H5DWALK_SOURCE_DIR}/copy_demo_files.sh ) endif () |