mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-25 04:09:44 +03:00
[svn-r29226] HDFFV-9552: merge in java code.
This commit is contained in:
Allen Byrne
+159
-6
@@ -121,6 +121,9 @@ set (HDF5_F90_TEST_LIB_CORENAME "hdf5_test_fortran")
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set (HDF5_F90_C_TEST_LIB_CORENAME "hdf5_test_f90cstub")
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set (HDF5_HL_F90_LIB_CORENAME "hdf5_hl_fortran")
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set (HDF5_HL_F90_C_LIB_CORENAME "hdf5_hl_f90cstub")
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set (HDF5_JAVA_JNI_LIB_CORENAME "hdf5_java")
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set (HDF5_JAVA_HDF5_LIB_CORENAME "jarhdf5")
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set (HDF5_JAVA_TEST_LIB_CORENAME "jartest5")
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#-----------------------------------------------------------------------------
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# Set the true names of all the libraries if customized by external project
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@@ -137,6 +140,9 @@ set (HDF5_F90_TEST_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_F90_TEST_LIB_
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set (HDF5_F90_C_TEST_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_F90_C_TEST_LIB_CORENAME}")
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set (HDF5_HL_F90_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_HL_F90_LIB_CORENAME}")
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set (HDF5_HL_F90_C_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_HL_F90_C_LIB_CORENAME}")
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set (HDF5_JAVA_JNI_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_JAVA_JNI_LIB_CORENAME}")
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set (HDF5_JAVA_HDF5_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_JAVA_HDF5_LIB_CORENAME}")
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set (HDF5_JAVA_TEST_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_JAVA_TEST_LIB_CORENAME}")
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#-----------------------------------------------------------------------------
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# Set the target names of all the libraries
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@@ -153,6 +159,9 @@ set (HDF5_F90_TEST_LIB_TARGET "${HDF5_F90_TEST_LIB_CORENAME}-static")
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set (HDF5_F90_C_TEST_LIB_TARGET "${HDF5_F90_C_TEST_LIB_CORENAME}-static")
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set (HDF5_HL_F90_LIB_TARGET "${HDF5_HL_F90_LIB_CORENAME}-static")
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set (HDF5_HL_F90_C_LIB_TARGET "${HDF5_HL_F90_C_LIB_CORENAME}-static")
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set (HDF5_JAVA_JNI_LIB_TARGET "${HDF5_JAVA_JNI_LIB_CORENAME}")
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set (HDF5_JAVA_HDF5_LIB_TARGET "${HDF5_JAVA_HDF5_LIB_CORENAME}")
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set (HDF5_JAVA_TEST_LIB_TARGET "${HDF5_JAVA_TEST_LIB_CORENAME}")
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set (HDF5_LIBSH_TARGET "${HDF5_LIB_CORENAME}-shared")
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set (HDF5_TEST_LIBSH_TARGET "${HDF5_TEST_LIB_CORENAME}-shared")
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set (HDF5_CPP_LIBSH_TARGET "${HDF5_CPP_LIB_CORENAME}-shared")
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@@ -180,20 +189,37 @@ set (HDF5_HL_CPP_SRC_DIR ${HDF5_SOURCE_DIR}/hl/c++)
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set (HDF5_TOOLS_SRC_DIR ${HDF5_SOURCE_DIR}/tools)
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set (HDF5_PERFORM_SRC_DIR ${HDF5_SOURCE_DIR}/tools/perform)
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set (HDF5_F90_SRC_DIR ${HDF5_SOURCE_DIR}/fortran)
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set (HDF5_JAVA_JNI_SRC_DIR ${HDF5_SOURCE_DIR}/java/src/jni)
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set (HDF5_JAVA_HDF5_SRC_DIR ${HDF5_SOURCE_DIR}/java/src/hdf)
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set (HDF5_JAVA_TEST_SRC_DIR ${HDF5_SOURCE_DIR}/java/test)
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set (HDF5_JAVA_LIB_DIR ${HDF5_SOURCE_DIR}/java/lib)
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set (HDF5_JAVA_LOGGING_JAR ${HDF5_SOURCE_DIR}/java/lib/slf4j-api-1.7.5.jar)
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set (HDF5_JAVA_LOGGING_NOP_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-nop-1.7.5.jar)
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set (HDF5_JAVA_LOGGING_SIMPLE_JAR ${HDF5_SOURCE_DIR}/java/lib/ext/slf4j-simple-1.7.5.jar)
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if (APPLE)
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option (HDF5_BUILD_FRAMEWORKS "TRUE to build as frameworks libraries, FALSE to build according to BUILD_SHARED_LIBS" FALSE)
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endif (APPLE)
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if (NOT HDF5_INSTALL_BIN_DIR)
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set (HDF5_INSTALL_BIN_DIR bin)
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endif (NOT HDF5_INSTALL_BIN_DIR)
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if (NOT HDF5_INSTALL_LIB_DIR)
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if (APPLE)
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if (HDF5_BUILD_FRAMEWORKS)
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set (HDF5_INSTALL_JAR_DIR ../Java)
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else (HDF5_BUILD_FRAMEWORKS)
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set (HDF5_INSTALL_JAR_DIR lib)
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endif (HDF5_BUILD_FRAMEWORKS)
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set (HDF5_INSTALL_FMWK_DIR ${CMAKE_INSTALL_FRAMEWORK_PREFIX})
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else (APPLE)
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set (HDF5_INSTALL_JAR_DIR lib)
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endif (APPLE)
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set (HDF5_INSTALL_LIB_DIR lib)
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endif (NOT HDF5_INSTALL_LIB_DIR)
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if (NOT HDF5_INSTALL_INCLUDE_DIR)
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set (HDF5_INSTALL_INCLUDE_DIR include)
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endif (NOT HDF5_INSTALL_INCLUDE_DIR)
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option (HDF5_BUILD_FRAMEWORKS "TRUE to build as frameworks libraries, FALSE to build according to BUILD_SHARED_LIBS" FALSE)
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if (NOT HDF5_INSTALL_DATA_DIR)
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if (NOT WIN32)
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if (APPLE)
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@@ -242,6 +268,83 @@ string (REGEX REPLACE ".*LT_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_SOVERS_MAJOR ${H5_SOVERS_INTERFACE}-${H5_SOVERS_RELEASE})
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message (STATUS "SOVERSION: ${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
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string (REGEX MATCH ".*LT_TOOLS_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_TOOLS_SOVERS_EXISTS ${_lt_vers_am_contents})
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if(H5_TOOLS_SOVERS_EXISTS)
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string (REGEX REPLACE ".*LT_TOOLS_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_TOOLS_SOVERS_INTERFACE ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_TOOLS_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_TOOLS_SOVERS_MINOR ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_TOOLS_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_TOOLS_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_TOOLS_SOVERS_MAJOR ${H5_TOOLS_SOVERS_INTERFACE}-${H5_TOOLS_SOVERS_RELEASE})
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message (STATUS "SOVERSION_TOOLS: ${H5_TOOLS_SOVERS_MAJOR}.${H5_TOOLS_SOVERS_RELEASE}.${H5_TOOLS_SOVERS_MINOR}")
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endif()
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string (REGEX REPLACE ".*LT_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_CXX_SOVERS_EXISTS ${_lt_vers_am_contents})
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if(H5_CXX_SOVERS_EXISTS)
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string (REGEX REPLACE ".*LT_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_CXX_SOVERS_INTERFACE ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_CXX_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_CXX_SOVERS_MINOR ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_CXX_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_CXX_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_CXX_SOVERS_MAJOR ${H5_CXX_SOVERS_INTERFACE}-${H5_CXX_SOVERS_RELEASE})
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message (STATUS "SOVERSION_CXX: ${H5_CXX_SOVERS_MAJOR}.${H5_CXX_SOVERS_RELEASE}.${H5_CXX_SOVERS_MINOR}")
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endif()
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string (REGEX REPLACE ".*LT_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_F_SOVERS_EXISTS ${_lt_vers_am_contents})
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if(H5_F_SOVERS_EXISTS)
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string (REGEX REPLACE ".*LT_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_F_SOVERS_INTERFACE ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_F_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_F_SOVERS_MINOR ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_F_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_F_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_F_SOVERS_MAJOR ${H5_F_SOVERS_INTERFACE}-${H5_F_SOVERS_RELEASE})
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message (STATUS "SOVERSION_F: ${H5_F_SOVERS_MAJOR}.${H5_F_SOVERS_RELEASE}.${H5_F_SOVERS_MINOR}")
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endif()
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string (REGEX REPLACE ".*LT_HL_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_SOVERS_EXISTS ${_lt_vers_am_contents})
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if(H5_HL_SOVERS_EXISTS)
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string (REGEX REPLACE ".*LT_HL_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_SOVERS_INTERFACE ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_HL_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_SOVERS_MINOR ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_HL_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_HL_SOVERS_MAJOR ${H5_HL_SOVERS_INTERFACE}-${H5_HL_SOVERS_RELEASE})
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message (STATUS "SOVERSION_HL: ${H5_HL_SOVERS_MAJOR}.${H5_HL_SOVERS_RELEASE}.${H5_HL_SOVERS_MINOR}")
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endif()
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string (REGEX REPLACE ".*LT_HL_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_CXX_SOVERS_EXISTS ${_lt_vers_am_contents})
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if(H5_HL_CXX_SOVERS_EXISTS)
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string (REGEX REPLACE ".*LT_HL_CXX_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_CXX_SOVERS_INTERFACE ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_HL_CXX_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_CXX_SOVERS_MINOR ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_HL_CXX_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_CXX_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_HL_CXX_SOVERS_MAJOR ${H5_HL_CXX_SOVERS_INTERFACE}-${H5_HL_CXX_SOVERS_RELEASE})
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message (STATUS "SOVERSION_HL_CXX: ${H5_HL_CXX_SOVERS_MAJOR}.${H5_HL_CXX_SOVERS_RELEASE}.${H5_HL_CXX_SOVERS_MINOR}")
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endif()
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string (REGEX REPLACE ".*LT_HL_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_HL_F_SOVERS_EXISTS ${_lt_vers_am_contents})
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if(H5_HL_F_SOVERS_EXISTS)
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string (REGEX REPLACE ".*LT_HL_F_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_F_SOVERS_INTERFACE ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_HL_F_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_F_SOVERS_MINOR ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_HL_F_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_HL_F_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_HL_F_SOVERS_MAJOR ${H5_HL_F_SOVERS_INTERFACE}-${H5_HL_F_SOVERS_RELEASE})
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message (STATUS "SOVERSION_HL_F: ${H5_HL_F_SOVERS_MAJOR}.${H5_HL_F_SOVERS_RELEASE}.${H5_HL_F_SOVERS_MINOR}")
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endif()
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string (REGEX REPLACE ".*LT_JAVA_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$" H5_JAVA_SOVERS_EXISTS ${_lt_vers_am_contents})
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if(H5_JAVA_SOVERS_EXISTS)
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string (REGEX REPLACE ".*LT_JAVA_VERS_INTERFACE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_JAVA_SOVERS_INTERFACE ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_JAVA_VERS_REVISION[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_JAVA_SOVERS_MINOR ${_lt_vers_am_contents})
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string (REGEX REPLACE ".*LT_JAVA_VERS_AGE[ \t]+=[ \t]+([0-9]*).*$"
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"\\1" H5_JAVA_SOVERS_RELEASE ${_lt_vers_am_contents})
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MATH (EXPR H5_JAVA_SOVERS_MAJOR ${H5_JAVA_SOVERS_INTERFACE}-${H5_JAVA_SOVERS_RELEASE})
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message (STATUS "SOVERSION_JAVA: ${H5_JAVA_SOVERS_MAJOR}.${H5_JAVA_SOVERS_RELEASE}.${H5_JAVA_SOVERS_MINOR}")
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endif()
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#-----------------------------------------------------------------------------
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# Basic HDF5 stuff here
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@@ -257,6 +360,41 @@ else (NOT "${H5_VERS_SUBRELEASE}" STREQUAL "")
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set (HDF5_PACKAGE_VERSION_STRING "${HDF5_PACKAGE_VERSION}")
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endif (NOT "${H5_VERS_SUBRELEASE}" STREQUAL "")
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set (HDF5_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
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if(H5_TOOLS_SOVERS_EXISTS)
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set (HDF5_TOOLS_PACKAGE_SOVERSION "${H5_TOOLS_SOVERS_MAJOR}.${H5_TOOLS_SOVERS_RELEASE}.${H5_TOOLS_SOVERS_MINOR}")
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else()
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set (HDF5_TOOLS_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
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endif()
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if(H5_CXX_SOVERS_EXISTS)
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set (HDF5_CXX_PACKAGE_SOVERSION "${H5_CXX_SOVERS_MAJOR}.${H5_CXX_SOVERS_RELEASE}.${H5_CXX_SOVERS_MINOR}")
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else()
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set (HDF5_CXX_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
|
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endif()
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if(H5_F_SOVERS_EXISTS)
|
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set (HDF5_F_PACKAGE_SOVERSION "${H5_F_SOVERS_MAJOR}.${H5_F_SOVERS_RELEASE}.${H5_F_SOVERS_MINOR}")
|
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else()
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set (HDF5_F_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
|
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endif()
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if(H5_HL_SOVERS_EXISTS)
|
||||
set (HDF5_HL_PACKAGE_SOVERSION "${H5_HL_SOVERS_MAJOR}.${H5_HL_SOVERS_RELEASE}.${H5_HL_SOVERS_MINOR}")
|
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else()
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set (HDF5_HL_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
|
||||
endif()
|
||||
if(H5_HL_F_SOVERS_EXISTS)
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||||
set (HDF5_HL_CXX_PACKAGE_SOVERSION "${H5_HL_CXX_SOVERS_MAJOR}.${H5_HL_CXX_SOVERS_RELEASE}.${H5_HL_CXX_SOVERS_MINOR}")
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else()
|
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set (HDF5_HL_CXX_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
|
||||
endif()
|
||||
if(H5_HL_F_SOVERS_EXISTS)
|
||||
set (HDF5_HL_F_PACKAGE_SOVERSION "${H5_HL_F_SOVERS_MAJOR}.${H5_HL_F_SOVERS_RELEASE}.${H5_HL_F_SOVERS_MINOR}")
|
||||
else()
|
||||
set (HDF5_HL_F_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
|
||||
endif()
|
||||
if(H5_JAVA_SOVERS_EXISTS)
|
||||
set (HDF5_PACKAGE_SOVERSION "${H5_JAVA_SOVERS_MAJOR}.${H5_JAVA_SOVERS_RELEASE}.${H5_JAVA_SOVERS_MINOR}")
|
||||
else()
|
||||
set (HDF5_JAVA_PACKAGE_SOVERSION "${H5_SOVERS_MAJOR}.${H5_SOVERS_RELEASE}.${H5_SOVERS_MINOR}")
|
||||
endif()
|
||||
set (HDF5_PACKAGE_STRING "${HDF5_PACKAGE_NAME} ${HDF5_PACKAGE_VERSION_STRING}")
|
||||
set (HDF5_PACKAGE_TARNAME "${HDF5_PACKAGE}${HDF_PACKAGE_EXT}")
|
||||
set (HDF5_PACKAGE_URL "http://www.hdfgroup.org")
|
||||
@@ -285,6 +423,11 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED)
|
||||
set (CMAKE_Fortran_MODULE_DIRECTORY
|
||||
${PROJECT_BINARY_DIR}/bin CACHE PATH "Single Directory for all fortran modules."
|
||||
)
|
||||
if (WIN32)
|
||||
set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_BUILD_TYPE})
|
||||
else (WIN32)
|
||||
set (CMAKE_TEST_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
|
||||
endif (WIN32)
|
||||
else (NOT HDF5_EXTERNALLY_CONFIGURED)
|
||||
# if we are externally configured, but the project uses old cmake scripts
|
||||
# this may not be set and utilities like H5detect will fail
|
||||
@@ -773,11 +916,21 @@ endif (EXISTS "${HDF5_SOURCE_DIR}/c++" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/c++"
|
||||
# Check if Fortran's default real is double precision. If it is and HL is
|
||||
# being built then configure should fail due to bug HDFFV-889.
|
||||
#-----------------------------------------------------------------------------
|
||||
if (HDF5_BUILD_FORTRAN AND HDF5_BUILD_HL_LIB )
|
||||
if (NOT FORTRAN_DEFAULT_REAL_NOT_DOUBLE)
|
||||
message (FATAL_ERROR " **** Fortran high-level routines are not supported when the default REAL is DOUBLE PRECISION, use HDF5_BUILD_HL_LIB:BOOL=OFF **** ")
|
||||
endif (NOT FORTRAN_DEFAULT_REAL_NOT_DOUBLE)
|
||||
endif (HDF5_BUILD_FORTRAN AND HDF5_BUILD_HL_LIB )
|
||||
if (HDF5_BUILD_FORTRAN AND HDF5_BUILD_HL_LIB)
|
||||
if (NOT FORTRAN_DEFAULT_REAL_NOT_DOUBLE)
|
||||
message (FATAL_ERROR " **** Fortran high-level routines are not supported when the default REAL is DOUBLE PRECISION, use HDF5_BUILD_HL_LIB:BOOL=OFF **** ")
|
||||
endif (NOT FORTRAN_DEFAULT_REAL_NOT_DOUBLE)
|
||||
endif (HDF5_BUILD_FORTRAN AND HDF5_BUILD_HL_LIB)
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Option to build HDF5 Java Library
|
||||
#-----------------------------------------------------------------------------
|
||||
if (EXISTS "${HDF5_SOURCE_DIR}/java" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/java")
|
||||
option (HDF5_BUILD_JAVA "Build Java HDF5 Library" ON)
|
||||
if (HDF5_BUILD_JAVA)
|
||||
add_subdirectory (${HDF5_SOURCE_DIR}/java ${PROJECT_BINARY_DIR}/java)
|
||||
endif (HDF5_BUILD_JAVA)
|
||||
endif (EXISTS "${HDF5_SOURCE_DIR}/java" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/java")
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Generate the H5pubconf.h file containing user settings needed by compilation
|
||||
|
||||
@@ -27,14 +27,33 @@
|
||||
./MANIFEST
|
||||
./Makefile.dist
|
||||
./Makefile.am
|
||||
./m4/aclocal_fc.m4
|
||||
./m4/aclocal_cxx.m4
|
||||
./README.txt
|
||||
./BRANCH.txt
|
||||
./acsite.m4
|
||||
./autogen.sh
|
||||
./configure.ac
|
||||
|
||||
./m4/aclocal_cxx.m4
|
||||
./m4/aclocal_fc.m4
|
||||
./m4/ax_check_class.m4
|
||||
./m4/ax_check_classpath.m4
|
||||
./m4/ax_check_java_home.m4
|
||||
./m4/ax_check_junit.m4
|
||||
./m4/ax_check_rqrd_class.m4
|
||||
./m4/ax_java_check_class.m4
|
||||
./m4/ax_java_options.m4
|
||||
./m4/ax_jni_include_dir.m4
|
||||
./m4/ax_prog_jar.m4
|
||||
./m4/ax_prog_java_cc.m4
|
||||
./m4/ax_prog_java_works.m4
|
||||
./m4/ax_prog_java.m4
|
||||
./m4/ax_prog_javac_works.m4
|
||||
./m4/ax_prog_javac.m4
|
||||
./m4/ax_prog_javadoc.m4
|
||||
./m4/ax_prog_javah.m4
|
||||
./m4/ax_try_compile_java.m4
|
||||
./m4/ax_try_run_java.m4
|
||||
|
||||
./bin/COPYING
|
||||
./bin/bbrelease _DO_NOT_DISTRIBUTE_
|
||||
./bin/buildhdf5
|
||||
@@ -2416,13 +2435,306 @@
|
||||
./hl/c++/test/ptableTest.cpp
|
||||
./hl/c++/test/Makefile.am
|
||||
|
||||
# java
|
||||
./java/COPYING
|
||||
./java/Makefile.am
|
||||
./java/CMakeLists.txt
|
||||
|
||||
./java/src/Makefile.am
|
||||
./java/src/CMakeLists.txt
|
||||
./java/src/jni/Makefile.am
|
||||
./java/src/jni/CMakeLists.txt
|
||||
./java/src/jni/exceptionImp.c
|
||||
./java/src/jni/exceptionImp.h
|
||||
./java/src/jni/h5Constants.c
|
||||
./java/src/jni/nativeData.c
|
||||
./java/src/jni/nativeData.h
|
||||
./java/src/jni/h5jni.h
|
||||
./java/src/jni/h5util.c
|
||||
./java/src/jni/h5util.h
|
||||
./java/src/jni/h5Imp.c
|
||||
./java/src/jni/h5Imp.h
|
||||
./java/src/jni/h5aImp.c
|
||||
./java/src/jni/h5aImp.h
|
||||
./java/src/jni/h5dImp.c
|
||||
./java/src/jni/h5dImp.h
|
||||
./java/src/jni/h5eImp.c
|
||||
./java/src/jni/h5eImp.h
|
||||
./java/src/jni/h5fImp.c
|
||||
./java/src/jni/h5fImp.h
|
||||
./java/src/jni/h5gImp.c
|
||||
./java/src/jni/h5gImp.h
|
||||
./java/src/jni/h5iImp.c
|
||||
./java/src/jni/h5iImp.h
|
||||
./java/src/jni/h5lImp.c
|
||||
./java/src/jni/h5lImp.h
|
||||
./java/src/jni/h5oImp.c
|
||||
./java/src/jni/h5oImp.h
|
||||
./java/src/jni/h5pImp.c
|
||||
./java/src/jni/h5pImp.h
|
||||
./java/src/jni/h5plImp.c
|
||||
./java/src/jni/h5plImp.h
|
||||
./java/src/jni/h5rImp.c
|
||||
./java/src/jni/h5rImp.h
|
||||
./java/src/jni/h5sImp.c
|
||||
./java/src/jni/h5sImp.h
|
||||
./java/src/jni/h5tImp.c
|
||||
./java/src/jni/h5tImp.h
|
||||
./java/src/jni/h5zImp.c
|
||||
./java/src/jni/h5zImp.h
|
||||
|
||||
./java/src/hdf/CMakeLists.txt
|
||||
./java/src/hdf/hdf5lib/CMakeLists.txt
|
||||
|
||||
./java/src/hdf/hdf5lib/callbacks/Callbacks.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5A_iterate_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5A_iterate_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5D_iterate_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5D_iterate_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5E_walk_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5E_walk_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5L_iterate_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5L_iterate_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5O_iterate_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5O_iterate_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_cls_close_func_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_cls_create_func_t.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_iterate_cb.java
|
||||
./java/src/hdf/hdf5lib/callbacks/H5P_iterate_t.java
|
||||
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5AtomException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5AttributeException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5BtreeException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5DataFiltersException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5DataStorageException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5ExternalFileListException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5FileInterfaceException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5HeapException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5InternalErrorException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5JavaException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5LowLevelIOException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5ReferenceException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.java
|
||||
./java/src/hdf/hdf5lib/exceptions/HDF5SymbolTableException.java
|
||||
|
||||
./java/src/hdf/hdf5lib/structs/H5_ih_info_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5A_info_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5AC_cache_config_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5E_error2_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5F_info2_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5G_info_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5L_info_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5O_hdr_info_t.java
|
||||
./java/src/hdf/hdf5lib/structs/H5O_info_t.java
|
||||
|
||||
./java/src/hdf/hdf5lib/H5.java
|
||||
./java/src/hdf/hdf5lib/HDF5Constants.java
|
||||
./java/src/hdf/hdf5lib/HDF5GroupInfo.java
|
||||
./java/src/hdf/hdf5lib/HDFArray.java
|
||||
./java/src/hdf/hdf5lib/HDFNativeData.java
|
||||
|
||||
./java/examples/Makefile.am
|
||||
./java/examples/CMakeLists.txt
|
||||
|
||||
./java/examples/intro/Makefile.am
|
||||
./java/examples/intro/CMakeLists.txt
|
||||
./java/examples/intro/runExample.sh.in
|
||||
./java/examples/intro/H5_CreateAttribute.java
|
||||
./java/examples/intro/H5_CreateDataset.java
|
||||
./java/examples/intro/H5_CreateFile.java
|
||||
./java/examples/intro/H5_CreateGroup.java
|
||||
./java/examples/intro/H5_CreateGroupAbsoluteRelative.java
|
||||
./java/examples/intro/H5_CreateGroupDataset.java
|
||||
./java/examples/intro/H5_ReadWrite.java
|
||||
|
||||
./java/examples/groups/Makefile.am
|
||||
./java/examples/groups/CMakeLists.txt
|
||||
./java/examples/groups/runExample.sh.in
|
||||
./java/examples/groups/H5Ex_G_Create.java
|
||||
./java/examples/groups/H5Ex_G_Iterate.java
|
||||
./java/examples/groups/H5Ex_G_Compact.java
|
||||
./java/examples/groups/H5Ex_G_Corder.java
|
||||
./java/examples/groups/H5Ex_G_Intermediate.java
|
||||
./java/examples/groups/H5Ex_G_Phase.java
|
||||
./java/examples/groups/H5Ex_G_Traverse.java
|
||||
./java/examples/groups/H5Ex_G_Visit.java
|
||||
./java/examples/groups/h5ex_g_iterate.h5
|
||||
./java/examples/groups/h5ex_g_visit.h5
|
||||
|
||||
./java/examples/datasets/Makefile.am
|
||||
./java/examples/datasets/CMakeLists.txt
|
||||
./java/examples/datasets/runExample.sh.in
|
||||
./java/examples/datasets/H5Ex_D_Alloc.java
|
||||
./java/examples/datasets/H5Ex_D_Checksum.java
|
||||
./java/examples/datasets/H5Ex_D_Chunk.java
|
||||
./java/examples/datasets/H5Ex_D_Compact.java
|
||||
./java/examples/datasets/H5Ex_D_External.java
|
||||
./java/examples/datasets/H5Ex_D_FillValue.java
|
||||
./java/examples/datasets/H5Ex_D_Gzip.java
|
||||
./java/examples/datasets/H5Ex_D_Hyperslab.java
|
||||
./java/examples/datasets/H5Ex_D_ReadWrite.java
|
||||
./java/examples/datasets/H5Ex_D_Shuffle.java
|
||||
./java/examples/datasets/H5Ex_D_Szip.java
|
||||
./java/examples/datasets/H5Ex_D_UnlimitedAdd.java
|
||||
./java/examples/datasets/H5Ex_D_UnlimitedGzip.java
|
||||
./java/examples/datasets/H5Ex_D_UnlimitedMod.java
|
||||
./java/examples/datasets/H5Ex_D_Nbit.java
|
||||
./java/examples/datasets/H5Ex_D_Transform.java
|
||||
./java/examples/datasets/H5Ex_D_Sofloat.java
|
||||
./java/examples/datasets/H5Ex_D_Soint.java
|
||||
|
||||
./java/examples/datatypes/Makefile.am
|
||||
./java/examples/datatypes/CMakeLists.txt
|
||||
./java/examples/datatypes/runExample.sh.in
|
||||
./java/examples/datatypes/H5Ex_T_Array.java
|
||||
./java/examples/datatypes/H5Ex_T_ArrayAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_Bit.java
|
||||
./java/examples/datatypes/H5Ex_T_BitAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_Commit.java
|
||||
./java/examples/datatypes/H5Ex_T_Compound.java
|
||||
./java/examples/datatypes/H5Ex_T_CompoundAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_Float.java
|
||||
./java/examples/datatypes/H5Ex_T_FloatAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_Integer.java
|
||||
./java/examples/datatypes/H5Ex_T_IntegerAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_ObjectReference.java
|
||||
./java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_Opaque.java
|
||||
./java/examples/datatypes/H5Ex_T_OpaqueAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_String.java
|
||||
./java/examples/datatypes/H5Ex_T_StringAttribute.java
|
||||
./java/examples/datatypes/H5Ex_T_VLString.java
|
||||
|
||||
./java/examples/testfiles/examples.intro.H5_CreateAttribute.txt
|
||||
./java/examples/testfiles/examples.intro.H5_CreateDataset.txt
|
||||
./java/examples/testfiles/examples.intro.H5_CreateFile.txt
|
||||
./java/examples/testfiles/examples.intro.H5_CreateGroup.txt
|
||||
./java/examples/testfiles/examples.intro.H5_CreateGroupAbsoluteRelative.txt
|
||||
./java/examples/testfiles/examples.intro.H5_CreateGroupDataset.txt
|
||||
./java/examples/testfiles/examples.intro.H5_ReadWrite.txt
|
||||
./java/examples/testfiles/examples.groups.H5Ex_G_Create.txt
|
||||
./java/examples/testfiles/examples.groups.H5Ex_G_Iterate.txt
|
||||
./java/examples/testfiles/examples.groups.H5Ex_G_Compact.txt
|
||||
./java/examples/testfiles/examples.groups.H5Ex_G_Corder.txt
|
||||
./java/examples/testfiles/examples.groups.H5Ex_G_Intermediate.txt
|
||||
./java/examples/testfiles/examples.groups.H5Ex_G_Phase.txt
|
||||
./java/examples/testfiles/examples.groups.H5Ex_G_Visit.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Alloc.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Checksum.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Chunk.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Compact.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_External.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_FillValue.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Gzip.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Hyperslab.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_ReadWrite.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Shuffle.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Szip.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedAdd.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedGzip.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_UnlimitedMod.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Nbit.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Transform.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Sofloat.txt
|
||||
./java/examples/testfiles/examples.datasets.H5Ex_D_Soint.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_Array.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_ArrayAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_Bit.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_BitAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_Commit.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_Compound.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_CompoundAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_Float.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_FloatAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_Integer.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_IntegerAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReference.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_ObjectReferenceAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_Opaque.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_OpaqueAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_String.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_StringAttribute.txt
|
||||
./java/examples/testfiles/examples.datatypes.H5Ex_T_VLString.txt
|
||||
|
||||
./java/test/Makefile.am
|
||||
./java/test/CMakeLists.txt
|
||||
./java/test/junit.sh.in
|
||||
./java/test/JUnit-interface.txt
|
||||
./java/test/h5ex_g_iterate.hdf
|
||||
./java/test/TestH5.java
|
||||
./java/test/TestH5A.java
|
||||
./java/test/TestH5Dparams.java
|
||||
./java/test/TestH5D.java
|
||||
./java/test/TestH5Dplist.java
|
||||
./java/test/TestH5E.java
|
||||
./java/test/TestH5Edefault.java
|
||||
./java/test/TestH5Eregister.java
|
||||
./java/test/TestH5Fparams.java
|
||||
./java/test/TestH5Fbasic.java
|
||||
./java/test/TestH5F.java
|
||||
./java/test/TestH5Gbasic.java
|
||||
./java/test/TestH5G.java
|
||||
./java/test/TestH5Giterate.java
|
||||
./java/test/TestH5Lparams.java
|
||||
./java/test/TestH5Lbasic.java
|
||||
./java/test/TestH5Lcreate.java
|
||||
./java/test/TestH5Oparams.java
|
||||
./java/test/TestH5Obasic.java
|
||||
./java/test/TestH5Ocreate.java
|
||||
./java/test/TestH5Ocopy.java
|
||||
./java/test/TestH5P.java
|
||||
./java/test/TestH5PData.java
|
||||
./java/test/TestH5Pfapl.java
|
||||
./java/test/TestH5Plist.java
|
||||
./java/test/TestH5Pvirtual.java
|
||||
./java/test/TestH5PL.java
|
||||
./java/test/TestH5R.java
|
||||
./java/test/TestH5Sbasic.java
|
||||
./java/test/TestH5S.java
|
||||
./java/test/TestH5Tparams.java
|
||||
./java/test/TestH5Tbasic.java
|
||||
./java/test/TestH5T.java
|
||||
./java/test/TestH5Z.java
|
||||
./java/test/TestAll.java
|
||||
|
||||
./java/lib/hamcrest-core.jar
|
||||
./java/lib/junit.jar
|
||||
./java/lib/simplelogger.properties
|
||||
./java/lib/slf4j-api-1.7.5.jar
|
||||
./java/lib/ext/slf4j-nop-1.7.5.jar
|
||||
./java/lib/ext/slf4j-simple-1.7.5.jar
|
||||
|
||||
# CMake-specific Files
|
||||
./config/cmake/cacheinit.cmake
|
||||
./config/cmake/CMakeFindJavaCommon.cmake
|
||||
./config/cmake/ConversionTests.c
|
||||
./config/cmake/ConfigureChecks.cmake
|
||||
./config/cmake/CPack.Info.plist.in
|
||||
./config/cmake/CTestCustom.cmake
|
||||
./config/cmake/FindHDF5.cmake.in
|
||||
./config/cmake/FindHDFJAVA.cmake.in
|
||||
./config/cmake/FindJNI.cmake
|
||||
./config/cmake/H5cxx_config.h.in
|
||||
./config/cmake/H5pubconf.h.in
|
||||
./config/cmake/hdf5-config.cmake.in
|
||||
@@ -2431,11 +2743,15 @@
|
||||
./config/cmake/HDF5_Process_Flex_Files.cmake
|
||||
./config/cmake/HDF5Macros.cmake
|
||||
./config/cmake/HDF5UseFortran.cmake
|
||||
./config/cmake/jrunTest.cmake
|
||||
./config/cmake/libhdf5.settings.cmake.in
|
||||
./config/cmake/mccacheinit.cmake
|
||||
./config/cmake/patch.xml
|
||||
./config/cmake/PkgInfo.in
|
||||
./config/cmake/README.txt.cmake.in
|
||||
./config/cmake/UseJava.cmake
|
||||
./config/cmake/UseJavaClassFilelist.cmake
|
||||
./config/cmake/UseJavaSymlinks.cmake
|
||||
./config/cmake/userblockTest.cmake
|
||||
./config/cmake/vfdTest.cmake
|
||||
|
||||
|
||||
+7
-2
@@ -66,6 +66,11 @@ if BUILD_FORTRAN_CONDITIONAL
|
||||
else
|
||||
FORTRAN_DIR=
|
||||
endif
|
||||
if BUILD_JAVA_CONDITIONAL
|
||||
JAVA_DIR=java
|
||||
else
|
||||
JAVA_DIR=
|
||||
endif
|
||||
if BUILD_HDF5_HL_CONDITIONAL
|
||||
HDF5_HL_DIR =hl
|
||||
else
|
||||
@@ -73,8 +78,8 @@ else
|
||||
endif
|
||||
|
||||
SUBDIRS = src test $(TESTPARALLEL_DIR) tools . $(CXX_DIR) $(FORTRAN_DIR) \
|
||||
$(HDF5_HL_DIR)
|
||||
DIST_SUBDIRS = src test testpar tools . c++ fortran hl examples
|
||||
$(JAVA_DIR) $(HDF5_HL_DIR)
|
||||
DIST_SUBDIRS = src test testpar tools . c++ fortran hl examples java
|
||||
|
||||
# Some files generated during configure that should be cleaned
|
||||
DISTCLEANFILES=config/stamp1 config/stamp2
|
||||
|
||||
@@ -94,7 +94,7 @@ if (BUILD_SHARED_LIBS)
|
||||
TARGET_C_PROPERTIES (${HDF5_CPP_LIBSH_TARGET} SHARED " " " ")
|
||||
target_link_libraries (${HDF5_CPP_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
|
||||
set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_CPP_LIBSH_TARGET}")
|
||||
H5_SET_LIB_OPTIONS (${HDF5_CPP_LIBSH_TARGET} ${HDF5_CPP_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_CPP_LIBSH_TARGET} ${HDF5_CPP_LIB_NAME} SHARED ${HDF5_CXX_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_CPP_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/cpp
|
||||
COMPILE_DEFINITIONS "H5_BUILT_AS_DYNAMIC_LIB"
|
||||
|
||||
@@ -0,0 +1,41 @@
|
||||
|
||||
#=============================================================================
|
||||
# Copyright 2013-2014 Kitware, Inc.
|
||||
#
|
||||
# Distributed under the OSI-approved BSD License (the "License");
|
||||
# see accompanying file Copyright.txt for details.
|
||||
#
|
||||
# This software is distributed WITHOUT ANY WARRANTY; without even the
|
||||
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
|
||||
# See the License for more information.
|
||||
#=============================================================================
|
||||
# (To distribute this file outside of CMake, substitute the full
|
||||
# License text for the above reference.)
|
||||
|
||||
# Do not include this module directly from code outside CMake!
|
||||
set(_JAVA_HOME "")
|
||||
if(JAVA_HOME AND IS_DIRECTORY "${JAVA_HOME}")
|
||||
set(_JAVA_HOME "${JAVA_HOME}")
|
||||
set(_JAVA_HOME_EXPLICIT 1)
|
||||
else()
|
||||
set(_ENV_JAVA_HOME "")
|
||||
if(DEFINED ENV{JAVA_HOME})
|
||||
file(TO_CMAKE_PATH "$ENV{JAVA_HOME}" _ENV_JAVA_HOME)
|
||||
endif()
|
||||
if(_ENV_JAVA_HOME AND IS_DIRECTORY "${_ENV_JAVA_HOME}")
|
||||
set(_JAVA_HOME "${_ENV_JAVA_HOME}")
|
||||
set(_JAVA_HOME_EXPLICIT 1)
|
||||
else()
|
||||
set(_CMD_JAVA_HOME "")
|
||||
if(APPLE AND EXISTS /usr/libexec/java_home)
|
||||
execute_process(COMMAND /usr/libexec/java_home
|
||||
OUTPUT_VARIABLE _CMD_JAVA_HOME OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
endif()
|
||||
if(_CMD_JAVA_HOME AND IS_DIRECTORY "${_CMD_JAVA_HOME}")
|
||||
set(_JAVA_HOME "${_CMD_JAVA_HOME}")
|
||||
set(_JAVA_HOME_EXPLICIT 0)
|
||||
endif()
|
||||
unset(_CMD_JAVA_HOME)
|
||||
endif()
|
||||
unset(_ENV_JAVA_HOME)
|
||||
endif()
|
||||
@@ -0,0 +1,68 @@
|
||||
#
|
||||
# To be used by projects that make use of CMakeified hdf-java
|
||||
#
|
||||
|
||||
#
|
||||
# Find the HDFJAVA includes and get all installed hdf-java library settings from
|
||||
# HDFJAVA-config.cmake file : Requires a CMake compatible hdf-java-@HDFJAVA_PACKAGE_VERSION@ or later
|
||||
# for this feature to work. The following vars are set if hdf-java is found.
|
||||
#
|
||||
# HDFJAVA_FOUND - True if found, otherwise all other vars are undefined
|
||||
# HDFJAVA_VERSION_STRING - full version (e.g. @HDFJAVA_PACKAGE_VERSION@)
|
||||
# HDFJAVA_VERSION_MAJOR - major part of version (e.g. @HDFJAVA_PACKAGE_VERSION_MAJOR@)
|
||||
# HDFJAVA_VERSION_MINOR - minor part (e.g. @HDFJAVA_PACKAGE_VERSION_MINOR@)
|
||||
#
|
||||
# Target names that are valid (depending on enabled options)
|
||||
# will be the following
|
||||
#
|
||||
#
|
||||
# To aid in finding HDFJAVA as part of a subproject set
|
||||
# HDFJAVA_ROOT_DIR_HINT to the location where @HDFJAVA_PACKAGE@@HDF_PACKAGE_EXT@-config.cmake lies
|
||||
|
||||
INCLUDE (SelectLibraryConfigurations)
|
||||
INCLUDE (FindPackageHandleStandardArgs)
|
||||
|
||||
# The HINTS option should only be used for values computed from the system.
|
||||
set (_HDFJAVA_HINTS
|
||||
$ENV{HOME}/.local
|
||||
$ENV{HDFJAVA_ROOT}
|
||||
$ENV{HDFJAVA_ROOT_DIR_HINT}
|
||||
)
|
||||
# Hard-coded guesses should still go in PATHS. This ensures that the user
|
||||
# environment can always override hard guesses.
|
||||
set (_HDFJAVA_PATHS
|
||||
$ENV{HOME}/.local
|
||||
$ENV{HDFJAVA_ROOT}
|
||||
$ENV{HDFJAVA_ROOT_DIR_HINT}
|
||||
/usr/lib/@HDFJAVA_PACKAGE@
|
||||
/usr/share/@HDFJAVA_PACKAGE@
|
||||
/usr/local/@HDFJAVA_PACKAGE@
|
||||
/usr/local/@HDFJAVA_PACKAGE@/share
|
||||
)
|
||||
|
||||
FIND_PATH (HDFJAVA_ROOT_DIR "@HDFJAVA_PACKAGE@@HDF_PACKAGE_EXT@-config.cmake"
|
||||
HINTS ${_HDFJAVA_HINTS}
|
||||
PATHS ${_HDFJAVA_PATHS}
|
||||
PATH_SUFFIXES
|
||||
cmake/@HDFJAVA_PACKAGE@
|
||||
lib/cmake/@HDFJAVA_PACKAGE@
|
||||
share/cmake/@HDFJAVA_PACKAGE@
|
||||
)
|
||||
|
||||
FIND_PATH (HDFJAVA_LIBRARY "jarhdf5-@HDFJAVA_PACKAGE_VERSION@.jar"
|
||||
HINTS ${_HDFJAVA_HINTS}
|
||||
PATHS ${_HDFJAVA_PATHS}
|
||||
PATH_SUFFIXES
|
||||
lib
|
||||
)
|
||||
|
||||
if (HDFJAVA_ROOT_DIR)
|
||||
set (HDFJAVA_FOUND "YES")
|
||||
INCLUDE (${HDFJAVA_ROOT_DIR}/@HDFJAVA_PACKAGE@@HDF_PACKAGE_EXT@-config.cmake)
|
||||
set (HDFJAVA_LIBRARIES "${HDFJAVA_LIBRARY}")
|
||||
set (HDFJAVA_INCLUDE_DIRS
|
||||
${HDFJAVA_LIBRARY}/jarhdf-@HDFJAVA_PACKAGE_VERSION@.jar
|
||||
${HDFJAVA_LIBRARY}/jarhdf5-@HDFJAVA_PACKAGE_VERSION@.jar
|
||||
)
|
||||
|
||||
endif (HDFJAVA_ROOT_DIR)
|
||||
@@ -0,0 +1,342 @@
|
||||
#.rst:
|
||||
# FindJNI
|
||||
# -------
|
||||
#
|
||||
# Find JNI java libraries.
|
||||
#
|
||||
# This module finds if Java is installed and determines where the
|
||||
# include files and libraries are. It also determines what the name of
|
||||
# the library is. The caller may set variable JAVA_HOME to specify a
|
||||
# Java installation prefix explicitly.
|
||||
#
|
||||
# This module sets the following result variables:
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# JNI_INCLUDE_DIRS = the include dirs to use
|
||||
# JNI_LIBRARIES = the libraries to use
|
||||
# JNI_FOUND = TRUE if JNI headers and libraries were found.
|
||||
# JAVA_AWT_LIBRARY = the path to the jawt library
|
||||
# JAVA_JVM_LIBRARY = the path to the jvm library
|
||||
# JAVA_INCLUDE_PATH = the include path to jni.h
|
||||
# JAVA_INCLUDE_PATH2 = the include path to jni_md.h
|
||||
# JAVA_AWT_INCLUDE_PATH = the include path to jawt.h
|
||||
|
||||
#=============================================================================
|
||||
# Copyright 2001-2009 Kitware, Inc.
|
||||
#
|
||||
# Distributed under the OSI-approved BSD License (the "License");
|
||||
# see accompanying file Copyright.txt for details.
|
||||
#
|
||||
# This software is distributed WITHOUT ANY WARRANTY; without even the
|
||||
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
|
||||
# See the License for more information.
|
||||
#=============================================================================
|
||||
# (To distribute this file outside of CMake, substitute the full
|
||||
# License text for the above reference.)
|
||||
|
||||
# Expand {libarch} occurences to java_libarch subdirectory(-ies) and set ${_var}
|
||||
macro(java_append_library_directories _var)
|
||||
# Determine java arch-specific library subdir
|
||||
# Mostly based on openjdk/jdk/make/common/shared/Platform.gmk as of openjdk
|
||||
# 1.6.0_18 + icedtea patches. However, it would be much better to base the
|
||||
# guess on the first part of the GNU config.guess platform triplet.
|
||||
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
|
||||
if(CMAKE_LIBRARY_ARCHITECTURE STREQUAL "x86_64-linux-gnux32")
|
||||
set(_java_libarch "x32" "amd64" "i386")
|
||||
else()
|
||||
set(_java_libarch "amd64" "i386")
|
||||
endif()
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^i.86$")
|
||||
set(_java_libarch "i386")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^alpha")
|
||||
set(_java_libarch "alpha")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm")
|
||||
# Subdir is "arm" for both big-endian (arm) and little-endian (armel).
|
||||
set(_java_libarch "arm")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^mips")
|
||||
# mips* machines are bi-endian mostly so processor does not tell
|
||||
# endianess of the underlying system.
|
||||
set(_java_libarch "${CMAKE_SYSTEM_PROCESSOR}" "mips" "mipsel" "mipseb" "mips64" "mips64el" "mipsn32" "mipsn32el")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(powerpc|ppc)64le")
|
||||
set(_java_libarch "ppc64" "ppc64le")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(powerpc|ppc)64")
|
||||
set(_java_libarch "ppc64" "ppc")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(powerpc|ppc)")
|
||||
set(_java_libarch "ppc")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^sparc")
|
||||
# Both flavours can run on the same processor
|
||||
set(_java_libarch "${CMAKE_SYSTEM_PROCESSOR}" "sparc" "sparcv9")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(parisc|hppa)")
|
||||
set(_java_libarch "parisc" "parisc64")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^s390")
|
||||
# s390 binaries can run on s390x machines
|
||||
set(_java_libarch "${CMAKE_SYSTEM_PROCESSOR}" "s390" "s390x")
|
||||
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^sh")
|
||||
set(_java_libarch "sh")
|
||||
else()
|
||||
set(_java_libarch "${CMAKE_SYSTEM_PROCESSOR}")
|
||||
endif()
|
||||
|
||||
# Append default list architectures if CMAKE_SYSTEM_PROCESSOR was empty or
|
||||
# system is non-Linux (where the code above has not been well tested)
|
||||
if(NOT _java_libarch OR NOT (CMAKE_SYSTEM_NAME MATCHES "Linux"))
|
||||
list(APPEND _java_libarch "i386" "amd64" "ppc")
|
||||
endif()
|
||||
|
||||
# Sometimes ${CMAKE_SYSTEM_PROCESSOR} is added to the list to prefer
|
||||
# current value to a hardcoded list. Remove possible duplicates.
|
||||
list(REMOVE_DUPLICATES _java_libarch)
|
||||
|
||||
foreach(_path ${ARGN})
|
||||
if(_path MATCHES "{libarch}")
|
||||
foreach(_libarch ${_java_libarch})
|
||||
string(REPLACE "{libarch}" "${_libarch}" _newpath "${_path}")
|
||||
list(APPEND ${_var} "${_newpath}")
|
||||
endforeach()
|
||||
else()
|
||||
list(APPEND ${_var} "${_path}")
|
||||
endif()
|
||||
endforeach()
|
||||
endmacro()
|
||||
|
||||
#include(${CMAKE_CURRENT_LIST_DIR}/CMakeFindJavaCommon.cmake)
|
||||
INCLUDE (CMakeFindJavaCommon)
|
||||
|
||||
# Save CMAKE_FIND_FRAMEWORK
|
||||
if(DEFINED CMAKE_FIND_FRAMEWORK)
|
||||
set(_JNI_CMAKE_FIND_FRAMEWORK ${CMAKE_FIND_FRAMEWORK})
|
||||
else()
|
||||
unset(_JNI_CMAKE_FIND_FRAMEWORK)
|
||||
endif()
|
||||
|
||||
if(_JAVA_HOME_EXPLICIT)
|
||||
set(CMAKE_FIND_FRAMEWORK NEVER)
|
||||
endif()
|
||||
|
||||
set(JAVA_AWT_LIBRARY_DIRECTORIES)
|
||||
if(_JAVA_HOME)
|
||||
JAVA_APPEND_LIBRARY_DIRECTORIES(JAVA_AWT_LIBRARY_DIRECTORIES
|
||||
${_JAVA_HOME}/jre/lib/{libarch}
|
||||
${_JAVA_HOME}/jre/lib
|
||||
${_JAVA_HOME}/lib/{libarch}
|
||||
${_JAVA_HOME}/lib
|
||||
${_JAVA_HOME}
|
||||
)
|
||||
endif()
|
||||
get_filename_component(java_install_version
|
||||
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit;CurrentVersion]" NAME)
|
||||
|
||||
list(APPEND JAVA_AWT_LIBRARY_DIRECTORIES
|
||||
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/lib"
|
||||
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/lib"
|
||||
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\${java_install_version};JavaHome]/lib"
|
||||
)
|
||||
JAVA_APPEND_LIBRARY_DIRECTORIES(JAVA_AWT_LIBRARY_DIRECTORIES
|
||||
/usr/java/lib
|
||||
/usr/java/jre/lib
|
||||
/usr/lib
|
||||
/usr/lib64
|
||||
/usr/local/lib
|
||||
/usr/local/lib64
|
||||
/usr/lib/jvm/java/lib
|
||||
/usr/lib64/jvm/java/lib
|
||||
/usr/lib/java/jre/lib/{libarch}
|
||||
/usr/lib64/java/jre/lib/{libarch}
|
||||
/usr/lib/jvm/jre/lib/{libarch}
|
||||
/usr/lib64/jvm/jre/lib/{libarch}
|
||||
/usr/local/lib/java/jre/lib/{libarch}
|
||||
/usr/local/share/java/jre/lib/{libarch}
|
||||
/usr/lib/j2sdk1.4-sun/jre/lib/{libarch}
|
||||
/usr/lib/j2sdk1.5-sun/jre/lib/{libarch}
|
||||
/opt/sun-jdk-1.5.0.04/jre/lib/{libarch}
|
||||
/usr/lib/jvm/java-6-sun/jre/lib/{libarch}
|
||||
/usr/lib/jvm/java-1.5.0-sun/jre/lib/{libarch}
|
||||
/usr/lib/jvm/java-6-sun-1.6.0.00/jre/lib/{libarch} # can this one be removed according to #8821 ? Alex
|
||||
/usr/lib/jvm/java-6-openjdk/jre/lib/{libarch}
|
||||
/usr/lib/jvm/java-7-openjdk/jre/lib/{libarch}
|
||||
/usr/lib/jvm/java-7-openjdk-{libarch}/jre/lib/{libarch}
|
||||
/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/{libarch} # fedora
|
||||
# Debian specific paths for default JVM
|
||||
/usr/lib/jvm/default-java/jre/lib/{libarch}
|
||||
/usr/lib/jvm/default-java/jre/lib
|
||||
/usr/lib/jvm/default-java/lib
|
||||
# OpenBSD specific paths for default JVM
|
||||
/usr/local/jdk-1.7.0/jre/lib/{libarch}
|
||||
/usr/local/jre-1.7.0/lib/{libarch}
|
||||
/usr/local/jdk-1.6.0/jre/lib/{libarch}
|
||||
/usr/local/jre-1.6.0/lib/{libarch}
|
||||
# SuSE specific paths for default JVM
|
||||
/usr/lib64/jvm/java/jre/lib/{libarch}
|
||||
/usr/lib64/jvm/jre/lib/{libarch}
|
||||
)
|
||||
|
||||
set(JAVA_JVM_LIBRARY_DIRECTORIES)
|
||||
foreach(dir ${JAVA_AWT_LIBRARY_DIRECTORIES})
|
||||
list(APPEND JAVA_JVM_LIBRARY_DIRECTORIES
|
||||
"${dir}"
|
||||
"${dir}/client"
|
||||
"${dir}/server"
|
||||
# IBM SDK, Java Technology Edition, specific paths
|
||||
"${dir}/j9vm"
|
||||
"${dir}/default"
|
||||
)
|
||||
endforeach()
|
||||
|
||||
set(JAVA_AWT_INCLUDE_DIRECTORIES)
|
||||
if(_JAVA_HOME)
|
||||
list(APPEND JAVA_AWT_INCLUDE_DIRECTORIES ${_JAVA_HOME}/include)
|
||||
endif()
|
||||
list(APPEND JAVA_AWT_INCLUDE_DIRECTORIES
|
||||
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/include"
|
||||
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/include"
|
||||
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\${java_install_version};JavaHome]/include"
|
||||
${_JAVA_HOME}/include
|
||||
/usr/include
|
||||
/usr/java/include
|
||||
/usr/local/include
|
||||
/usr/lib/java/include
|
||||
/usr/lib64/java/include
|
||||
/usr/local/lib/java/include
|
||||
/usr/lib/jvm/java/include
|
||||
/usr/lib64/jvm/java/include
|
||||
/usr/lib/jvm/java-6-sun/include
|
||||
/usr/lib/jvm/java-1.5.0-sun/include
|
||||
/usr/lib/jvm/java-6-sun-1.6.0.00/include # can this one be removed according to #8821 ? Alex
|
||||
/usr/lib/jvm/java-6-openjdk/include
|
||||
/usr/lib/jvm/java-7-openjdk/include
|
||||
/usr/lib/jvm/java-7-openjdk-i386/include
|
||||
/usr/lib/jvm/java-7-openjdk-amd64/include
|
||||
/usr/lib64/jvm/java-7-openjdk/include
|
||||
/usr/lib64/jvm/java-7-openjdk-amd64/include
|
||||
/usr/local/share/java/include
|
||||
/usr/lib/j2sdk1.4-sun/include
|
||||
/usr/lib/j2sdk1.5-sun/include
|
||||
/opt/sun-jdk-1.5.0.04/include
|
||||
# Debian specific path for default JVM
|
||||
/usr/lib/jvm/default-java/include
|
||||
# OpenBSD specific path for default JVM
|
||||
/usr/local/jdk-1.7.0/include
|
||||
/usr/local/jdk-1.6.0/include
|
||||
# SuSE specific paths for default JVM
|
||||
/usr/lib64/jvm/java/include
|
||||
)
|
||||
|
||||
foreach(JAVA_PROG "${JAVA_RUNTIME}" "${JAVA_COMPILE}" "${JAVA_ARCHIVE}")
|
||||
get_filename_component(jpath "${JAVA_PROG}" PATH)
|
||||
foreach(JAVA_INC_PATH ../include ../java/include ../share/java/include)
|
||||
if(EXISTS ${jpath}/${JAVA_INC_PATH})
|
||||
list(APPEND JAVA_AWT_INCLUDE_DIRECTORIES "${jpath}/${JAVA_INC_PATH}")
|
||||
endif()
|
||||
endforeach()
|
||||
foreach(JAVA_LIB_PATH
|
||||
../lib ../jre/lib ../jre/lib/i386
|
||||
../java/lib ../java/jre/lib ../java/jre/lib/i386
|
||||
../share/java/lib ../share/java/jre/lib ../share/java/jre/lib/i386)
|
||||
if(EXISTS ${jpath}/${JAVA_LIB_PATH})
|
||||
list(APPEND JAVA_AWT_LIBRARY_DIRECTORIES "${jpath}/${JAVA_LIB_PATH}")
|
||||
endif()
|
||||
endforeach()
|
||||
endforeach()
|
||||
|
||||
if(APPLE)
|
||||
if(CMAKE_FIND_FRAMEWORK STREQUAL "ONLY")
|
||||
set(_JNI_SEARCHES FRAMEWORK)
|
||||
elseif(CMAKE_FIND_FRAMEWORK STREQUAL "NEVER")
|
||||
set(_JNI_SEARCHES NORMAL)
|
||||
elseif(CMAKE_FIND_FRAMEWORK STREQUAL "LAST")
|
||||
set(_JNI_SEARCHES NORMAL FRAMEWORK)
|
||||
else()
|
||||
set(_JNI_SEARCHES FRAMEWORK NORMAL)
|
||||
endif()
|
||||
set(_JNI_FRAMEWORK_JVM NAMES JavaVM)
|
||||
set(_JNI_FRAMEWORK_JAWT "${_JNI_FRAMEWORK_JVM}")
|
||||
else()
|
||||
set(_JNI_SEARCHES NORMAL)
|
||||
endif()
|
||||
|
||||
set(_JNI_NORMAL_JVM
|
||||
NAMES jvm
|
||||
PATHS ${JAVA_JVM_LIBRARY_DIRECTORIES}
|
||||
)
|
||||
|
||||
set(_JNI_NORMAL_JAWT
|
||||
NAMES jawt
|
||||
PATHS ${JAVA_AWT_LIBRARY_DIRECTORIES}
|
||||
)
|
||||
|
||||
foreach(search ${_JNI_SEARCHES})
|
||||
find_library(JAVA_JVM_LIBRARY ${_JNI_${search}_JVM})
|
||||
find_library(JAVA_AWT_LIBRARY ${_JNI_${search}_JAWT})
|
||||
if(JAVA_JVM_LIBRARY)
|
||||
break()
|
||||
endif()
|
||||
endforeach()
|
||||
unset(_JNI_SEARCHES)
|
||||
unset(_JNI_FRAMEWORK_JVM)
|
||||
unset(_JNI_FRAMEWORK_JAWT)
|
||||
unset(_JNI_NORMAL_JVM)
|
||||
unset(_JNI_NORMAL_JAWT)
|
||||
|
||||
# Find headers matching the library.
|
||||
if("${JAVA_JVM_LIBRARY};${JAVA_AWT_LIBRARY};" MATCHES "(/JavaVM.framework|-framework JavaVM);")
|
||||
set(CMAKE_FIND_FRAMEWORK ONLY)
|
||||
else()
|
||||
set(CMAKE_FIND_FRAMEWORK NEVER)
|
||||
endif()
|
||||
|
||||
# add in the include path
|
||||
find_path(JAVA_INCLUDE_PATH jni.h
|
||||
${JAVA_AWT_INCLUDE_DIRECTORIES}
|
||||
)
|
||||
|
||||
find_path(JAVA_INCLUDE_PATH2 jni_md.h
|
||||
${JAVA_INCLUDE_PATH}
|
||||
${JAVA_INCLUDE_PATH}/darwin
|
||||
${JAVA_INCLUDE_PATH}/win32
|
||||
${JAVA_INCLUDE_PATH}/linux
|
||||
${JAVA_INCLUDE_PATH}/freebsd
|
||||
${JAVA_INCLUDE_PATH}/openbsd
|
||||
${JAVA_INCLUDE_PATH}/solaris
|
||||
${JAVA_INCLUDE_PATH}/hp-ux
|
||||
${JAVA_INCLUDE_PATH}/alpha
|
||||
)
|
||||
|
||||
find_path(JAVA_AWT_INCLUDE_PATH jawt.h
|
||||
${JAVA_INCLUDE_PATH}
|
||||
)
|
||||
|
||||
# Restore CMAKE_FIND_FRAMEWORK
|
||||
if(DEFINED _JNI_CMAKE_FIND_FRAMEWORK)
|
||||
set(CMAKE_FIND_FRAMEWORK ${_JNI_CMAKE_FIND_FRAMEWORK})
|
||||
unset(_JNI_CMAKE_FIND_FRAMEWORK)
|
||||
else()
|
||||
unset(CMAKE_FIND_FRAMEWORK)
|
||||
endif()
|
||||
|
||||
#include(${CMAKE_CURRENT_LIST_DIR}/FindPackageHandleStandardArgs.cmake)
|
||||
INCLUDE (FindPackageHandleStandardArgs)
|
||||
FIND_PACKAGE_HANDLE_STANDARD_ARGS(JNI DEFAULT_MSG JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
|
||||
JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
|
||||
|
||||
mark_as_advanced(
|
||||
JAVA_AWT_LIBRARY
|
||||
JAVA_JVM_LIBRARY
|
||||
JAVA_AWT_INCLUDE_PATH
|
||||
JAVA_INCLUDE_PATH
|
||||
JAVA_INCLUDE_PATH2
|
||||
)
|
||||
|
||||
set(JNI_LIBRARIES
|
||||
${JAVA_AWT_LIBRARY}
|
||||
${JAVA_JVM_LIBRARY}
|
||||
)
|
||||
|
||||
set(JNI_INCLUDE_DIRS
|
||||
${JAVA_INCLUDE_PATH}
|
||||
${JAVA_INCLUDE_PATH2}
|
||||
${JAVA_AWT_INCLUDE_PATH}
|
||||
)
|
||||
|
||||
message ("JNI_LIBRARIES=${JNI_LIBRARIES}")
|
||||
message ("JNI_INCLUDE_DIRS=${JNI_INCLUDE_DIRS}")
|
||||
@@ -9,6 +9,7 @@ It was built with the following options:
|
||||
-- @LIB_TYPE@ C/C++/Fortran libraries
|
||||
-- SZIP (encoder enabled) and ZLIB
|
||||
-- @LIB_TYPE@ HDF5 tools
|
||||
-- Java
|
||||
|
||||
The contents of this directory are:
|
||||
|
||||
|
||||
@@ -0,0 +1,1290 @@
|
||||
#.rst:
|
||||
# UseJava
|
||||
# -------
|
||||
#
|
||||
# Use Module for Java
|
||||
#
|
||||
# This file provides functions for Java. It is assumed that
|
||||
# FindJava.cmake has already been loaded. See FindJava.cmake for
|
||||
# information on how to load Java into your CMake project.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# add_jar(target_name
|
||||
# [SOURCES] source1 [source2 ...] [resource1 ...]
|
||||
# [INCLUDE_JARS jar1 [jar2 ...]]
|
||||
# [ENTRY_POINT entry]
|
||||
# [VERSION version]
|
||||
# [OUTPUT_NAME name]
|
||||
# [OUTPUT_DIR dir]
|
||||
# )
|
||||
#
|
||||
# This command creates a <target_name>.jar. It compiles the given
|
||||
# source files (source) and adds the given resource files (resource) to
|
||||
# the jar file. Source files can be java files or listing files
|
||||
# (prefixed by '@'). If only resource files are given then just a jar file
|
||||
# is created. The list of include jars are added to the classpath when
|
||||
# compiling the java sources and also to the dependencies of the target.
|
||||
# INCLUDE_JARS also accepts other target names created by add_jar. For
|
||||
# backwards compatibility, jar files listed as sources are ignored (as
|
||||
# they have been since the first version of this module).
|
||||
#
|
||||
# The default OUTPUT_DIR can also be changed by setting the variable
|
||||
# CMAKE_JAVA_TARGET_OUTPUT_DIR.
|
||||
#
|
||||
# Additional instructions:
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# To add compile flags to the target you can set these flags with
|
||||
# the following variable:
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# set(CMAKE_JAVA_COMPILE_FLAGS -nowarn)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# To add a path or a jar file to the class path you can do this
|
||||
# with the CMAKE_JAVA_INCLUDE_PATH variable.
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# set(CMAKE_JAVA_INCLUDE_PATH /usr/share/java/shibboleet.jar)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# To use a different output name for the target you can set it with:
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# add_jar(foobar foobar.java OUTPUT_NAME shibboleet.jar)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# To use a different output directory than CMAKE_CURRENT_BINARY_DIR
|
||||
# you can set it with:
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# add_jar(foobar foobar.java OUTPUT_DIR ${PROJECT_BINARY_DIR}/bin)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# To define an entry point in your jar you can set it with the ENTRY_POINT
|
||||
# named argument:
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# add_jar(example ENTRY_POINT com/examples/MyProject/Main)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# To define a custom manifest for the jar, you can set it with the manifest
|
||||
# named argument:
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# add_jar(example MANIFEST /path/to/manifest)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# To add a VERSION to the target output name you can set it using
|
||||
# the VERSION named argument to add_jar. This will create a jar file with the
|
||||
# name shibboleet-1.0.0.jar and will create a symlink shibboleet.jar
|
||||
# pointing to the jar with the version information.
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# add_jar(shibboleet shibbotleet.java VERSION 1.2.0)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# If the target is a JNI library, utilize the following commands to
|
||||
# create a JNI symbolic link:
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# set(CMAKE_JNI_TARGET TRUE)
|
||||
# add_jar(shibboleet shibbotleet.java VERSION 1.2.0)
|
||||
# install_jar(shibboleet ${LIB_INSTALL_DIR}/shibboleet)
|
||||
# install_jni_symlink(shibboleet ${JAVA_LIB_INSTALL_DIR})
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# If a single target needs to produce more than one jar from its
|
||||
# java source code, to prevent the accumulation of duplicate class
|
||||
# files in subsequent jars, set/reset CMAKE_JAR_CLASSES_PREFIX prior
|
||||
# to calling the add_jar() function:
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# set(CMAKE_JAR_CLASSES_PREFIX com/redhat/foo)
|
||||
# add_jar(foo foo.java)
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# set(CMAKE_JAR_CLASSES_PREFIX com/redhat/bar)
|
||||
# add_jar(bar bar.java)
|
||||
#
|
||||
#
|
||||
#
|
||||
# Target Properties:
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# The add_jar() functions sets some target properties. You can get these
|
||||
# properties with the
|
||||
# get_property(TARGET <target_name> PROPERTY <propery_name>)
|
||||
# command.
|
||||
#
|
||||
#
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# INSTALL_FILES The files which should be installed. This is used by
|
||||
# install_jar().
|
||||
# JNI_SYMLINK The JNI symlink which should be installed.
|
||||
# This is used by install_jni_symlink().
|
||||
# JAR_FILE The location of the jar file so that you can include
|
||||
# it.
|
||||
# CLASS_DIR The directory where the class files can be found. For
|
||||
# example to use them with javah.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# find_jar(<VAR>
|
||||
# name | NAMES name1 [name2 ...]
|
||||
# [PATHS path1 [path2 ... ENV var]]
|
||||
# [VERSIONS version1 [version2]]
|
||||
# [DOC "cache documentation string"]
|
||||
# )
|
||||
#
|
||||
# This command is used to find a full path to the named jar. A cache
|
||||
# entry named by <VAR> is created to stor the result of this command.
|
||||
# If the full path to a jar is found the result is stored in the
|
||||
# variable and the search will not repeated unless the variable is
|
||||
# cleared. If nothing is found, the result will be <VAR>-NOTFOUND, and
|
||||
# the search will be attempted again next time find_jar is invoked with
|
||||
# the same variable. The name of the full path to a file that is
|
||||
# searched for is specified by the names listed after NAMES argument.
|
||||
# Additional search locations can be specified after the PATHS argument.
|
||||
# If you require special a version of a jar file you can specify it with
|
||||
# the VERSIONS argument. The argument after DOC will be used for the
|
||||
# documentation string in the cache.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# install_jar(target_name destination)
|
||||
# install_jar(target_name DESTINATION destination [COMPONENT component])
|
||||
#
|
||||
# This command installs the TARGET_NAME files to the given DESTINATION.
|
||||
# It should be called in the same scope as add_jar() or it will fail.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# install_jni_symlink(target_name destination)
|
||||
# install_jni_symlink(target_name DESTINATION destination [COMPONENT component])
|
||||
#
|
||||
# This command installs the TARGET_NAME JNI symlinks to the given
|
||||
# DESTINATION. It should be called in the same scope as add_jar() or it
|
||||
# will fail.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# create_javadoc(<VAR>
|
||||
# PACKAGES pkg1 [pkg2 ...]
|
||||
# [SOURCEPATH <sourcepath>]
|
||||
# [CLASSPATH <classpath>]
|
||||
# [INSTALLPATH <install path>]
|
||||
# [DOCTITLE "the documentation title"]
|
||||
# [WINDOWTITLE "the title of the document"]
|
||||
# [AUTHOR TRUE|FALSE]
|
||||
# [USE TRUE|FALSE]
|
||||
# [VERSION TRUE|FALSE]
|
||||
# )
|
||||
#
|
||||
# Create java documentation based on files or packages. For more
|
||||
# details please read the javadoc manpage.
|
||||
#
|
||||
# There are two main signatures for create_javadoc. The first signature
|
||||
# works with package names on a path with source files:
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# Example:
|
||||
# create_javadoc(my_example_doc
|
||||
# PACKAGES com.exmaple.foo com.example.bar
|
||||
# SOURCEPATH "${CMAKE_CURRENT_SOURCE_DIR}"
|
||||
# CLASSPATH ${CMAKE_JAVA_INCLUDE_PATH}
|
||||
# WINDOWTITLE "My example"
|
||||
# DOCTITLE "<h1>My example</h1>"
|
||||
# AUTHOR TRUE
|
||||
# USE TRUE
|
||||
# VERSION TRUE
|
||||
# )
|
||||
#
|
||||
#
|
||||
#
|
||||
# The second signature for create_javadoc works on a given list of
|
||||
# files.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# create_javadoc(<VAR>
|
||||
# FILES file1 [file2 ...]
|
||||
# [CLASSPATH <classpath>]
|
||||
# [INSTALLPATH <install path>]
|
||||
# [DOCTITLE "the documentation title"]
|
||||
# [WINDOWTITLE "the title of the document"]
|
||||
# [AUTHOR TRUE|FALSE]
|
||||
# [USE TRUE|FALSE]
|
||||
# [VERSION TRUE|FALSE]
|
||||
# )
|
||||
#
|
||||
#
|
||||
#
|
||||
# Example:
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# create_javadoc(my_example_doc
|
||||
# FILES ${example_SRCS}
|
||||
# CLASSPATH ${CMAKE_JAVA_INCLUDE_PATH}
|
||||
# WINDOWTITLE "My example"
|
||||
# DOCTITLE "<h1>My example</h1>"
|
||||
# AUTHOR TRUE
|
||||
# USE TRUE
|
||||
# VERSION TRUE
|
||||
# )
|
||||
#
|
||||
#
|
||||
#
|
||||
# Both signatures share most of the options. These options are the same
|
||||
# as what you can find in the javadoc manpage. Please look at the
|
||||
# manpage for CLASSPATH, DOCTITLE, WINDOWTITLE, AUTHOR, USE and VERSION.
|
||||
#
|
||||
# The documentation will be by default installed to
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# ${CMAKE_INSTALL_PREFIX}/share/javadoc/<VAR>
|
||||
#
|
||||
#
|
||||
#
|
||||
# if you don't set the INSTALLPATH.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# create_javah(TARGET <target>
|
||||
# GENERATED_FILES <VAR>
|
||||
# CLASSES <class>...
|
||||
# [CLASSPATH <classpath>...]
|
||||
# [DEPENDS <depend>...]
|
||||
# [OUTPUT_NAME <path>|OUTPUT_DIR <path>]
|
||||
# )
|
||||
#
|
||||
# Create C header files from java classes. These files provide the connective glue
|
||||
# that allow your Java and C code to interact.
|
||||
#
|
||||
# There are two main signatures for create_javah. The first signature
|
||||
# returns generated files throught variable specified by GENERATED_FILES option:
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# Example:
|
||||
# Create_javah(GENERATED_FILES files_headers
|
||||
# CLASSES org.cmake.HelloWorld
|
||||
# CLASSPATH hello.jar
|
||||
# )
|
||||
#
|
||||
#
|
||||
#
|
||||
# The second signature for create_javah creates a target which encapsulates
|
||||
# header files generation.
|
||||
#
|
||||
# ::
|
||||
#
|
||||
# Example:
|
||||
# Create_javah(TARGET target_headers
|
||||
# CLASSES org.cmake.HelloWorld
|
||||
# CLASSPATH hello.jar
|
||||
# )
|
||||
#
|
||||
#
|
||||
#
|
||||
# Both signatures share same options.
|
||||
#
|
||||
# ``CLASSES <class>...``
|
||||
# Specifies Java classes used to generate headers.
|
||||
#
|
||||
# ``CLASSPATH <classpath>...``
|
||||
# Specifies various paths to look up classes. Here .class files, jar files or targets
|
||||
# created by command add_jar can be used.
|
||||
#
|
||||
# ``DEPENDS <depend>...``
|
||||
# Targets on which the javah target depends
|
||||
#
|
||||
# ``OUTPUT_NAME <path>``
|
||||
# Concatenates the resulting header files for all the classes listed by option CLASSES
|
||||
# into <path>. Same behavior as option '-o' of javah tool.
|
||||
#
|
||||
# ``OUTPUT_DIR <path>``
|
||||
# Sets the directory where the header files will be generated. Same behavior as option
|
||||
# '-d' of javah tool. If not specified, ${CMAKE_CURRENT_BINARY_DIR} is used as output directory.
|
||||
|
||||
#=============================================================================
|
||||
# Copyright 2013 OpenGamma Ltd. <graham@opengamma.com>
|
||||
# Copyright 2010-2011 Andreas schneider <asn@redhat.com>
|
||||
# Copyright 2010-2013 Kitware, Inc.
|
||||
#
|
||||
# Distributed under the OSI-approved BSD License (the "License");
|
||||
# see accompanying file Copyright.txt for details.
|
||||
#
|
||||
# This software is distributed WITHOUT ANY WARRANTY; without even the
|
||||
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
|
||||
# See the License for more information.
|
||||
#=============================================================================
|
||||
# (To distribute this file outside of CMake, substitute the full
|
||||
# License text for the above reference.)
|
||||
|
||||
include(CMakeParseArguments)
|
||||
|
||||
function (__java_copy_file src dest comment)
|
||||
add_custom_command(
|
||||
OUTPUT ${dest}
|
||||
COMMAND cmake -E copy_if_different
|
||||
ARGS ${src}
|
||||
${dest}
|
||||
DEPENDS ${src}
|
||||
COMMENT ${comment})
|
||||
endfunction ()
|
||||
|
||||
# define helper scripts
|
||||
set(_JAVA_CLASS_FILELIST_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/UseJavaClassFilelist.cmake)
|
||||
set(_JAVA_SYMLINK_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/UseJavaSymlinks.cmake)
|
||||
|
||||
function(add_jar _TARGET_NAME)
|
||||
|
||||
cmake_parse_arguments(_add_jar
|
||||
""
|
||||
"VERSION;OUTPUT_DIR;OUTPUT_NAME;ENTRY_POINT;MANIFEST"
|
||||
"SOURCES;INCLUDE_JARS"
|
||||
${ARGN}
|
||||
)
|
||||
|
||||
# In CMake < 2.8.12, add_jar used variables which were set prior to calling
|
||||
# add_jar for customizing the behavior of add_jar. In order to be backwards
|
||||
# compatible, check if any of those variables are set, and use them to
|
||||
# initialize values of the named arguments. (Giving the corresponding named
|
||||
# argument will override the value set here.)
|
||||
#
|
||||
# New features should use named arguments only.
|
||||
if(NOT DEFINED _add_jar_VERSION AND DEFINED CMAKE_JAVA_TARGET_VERSION)
|
||||
set(_add_jar_VERSION "${CMAKE_JAVA_TARGET_VERSION}")
|
||||
endif()
|
||||
if(NOT DEFINED _add_jar_OUTPUT_DIR AND DEFINED CMAKE_JAVA_TARGET_OUTPUT_DIR)
|
||||
set(_add_jar_OUTPUT_DIR "${CMAKE_JAVA_TARGET_OUTPUT_DIR}")
|
||||
endif()
|
||||
if(NOT DEFINED _add_jar_OUTPUT_NAME AND DEFINED CMAKE_JAVA_TARGET_OUTPUT_NAME)
|
||||
set(_add_jar_OUTPUT_NAME "${CMAKE_JAVA_TARGET_OUTPUT_NAME}")
|
||||
# reset
|
||||
set(CMAKE_JAVA_TARGET_OUTPUT_NAME)
|
||||
endif()
|
||||
if(NOT DEFINED _add_jar_ENTRY_POINT AND DEFINED CMAKE_JAVA_JAR_ENTRY_POINT)
|
||||
set(_add_jar_ENTRY_POINT "${CMAKE_JAVA_JAR_ENTRY_POINT}")
|
||||
endif()
|
||||
|
||||
set(_JAVA_SOURCE_FILES ${_add_jar_SOURCES} ${_add_jar_UNPARSED_ARGUMENTS})
|
||||
|
||||
if (NOT DEFINED _add_jar_OUTPUT_DIR)
|
||||
set(_add_jar_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR})
|
||||
endif()
|
||||
|
||||
if (_add_jar_ENTRY_POINT)
|
||||
set(_ENTRY_POINT_OPTION e)
|
||||
set(_ENTRY_POINT_VALUE ${_add_jar_ENTRY_POINT})
|
||||
endif ()
|
||||
|
||||
if (_add_jar_MANIFEST)
|
||||
set(_MANIFEST_OPTION m)
|
||||
set(_MANIFEST_VALUE ${_add_jar_MANIFEST})
|
||||
endif ()
|
||||
|
||||
if (LIBRARY_OUTPUT_PATH)
|
||||
set(CMAKE_JAVA_LIBRARY_OUTPUT_PATH ${LIBRARY_OUTPUT_PATH})
|
||||
else ()
|
||||
set(CMAKE_JAVA_LIBRARY_OUTPUT_PATH ${_add_jar_OUTPUT_DIR})
|
||||
endif ()
|
||||
|
||||
set(CMAKE_JAVA_INCLUDE_PATH
|
||||
${CMAKE_JAVA_INCLUDE_PATH}
|
||||
${CMAKE_CURRENT_SOURCE_DIR}
|
||||
${CMAKE_JAVA_OBJECT_OUTPUT_PATH}
|
||||
${CMAKE_JAVA_LIBRARY_OUTPUT_PATH}
|
||||
)
|
||||
|
||||
if (CMAKE_HOST_WIN32 AND NOT CYGWIN AND CMAKE_HOST_SYSTEM_NAME MATCHES "Windows")
|
||||
set(CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
|
||||
else ()
|
||||
set(CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
|
||||
endif()
|
||||
|
||||
foreach (JAVA_INCLUDE_DIR ${CMAKE_JAVA_INCLUDE_PATH})
|
||||
set(CMAKE_JAVA_INCLUDE_PATH_FINAL "${CMAKE_JAVA_INCLUDE_PATH_FINAL}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${JAVA_INCLUDE_DIR}")
|
||||
endforeach()
|
||||
|
||||
set(CMAKE_JAVA_CLASS_OUTPUT_PATH "${_add_jar_OUTPUT_DIR}${CMAKE_FILES_DIRECTORY}/${_TARGET_NAME}.dir")
|
||||
|
||||
set(_JAVA_TARGET_OUTPUT_NAME "${_TARGET_NAME}.jar")
|
||||
if (_add_jar_OUTPUT_NAME AND _add_jar_VERSION)
|
||||
set(_JAVA_TARGET_OUTPUT_NAME "${_add_jar_OUTPUT_NAME}-${_add_jar_VERSION}.jar")
|
||||
set(_JAVA_TARGET_OUTPUT_LINK "${_add_jar_OUTPUT_NAME}.jar")
|
||||
elseif (_add_jar_VERSION)
|
||||
set(_JAVA_TARGET_OUTPUT_NAME "${_TARGET_NAME}-${_add_jar_VERSION}.jar")
|
||||
set(_JAVA_TARGET_OUTPUT_LINK "${_TARGET_NAME}.jar")
|
||||
elseif (_add_jar_OUTPUT_NAME)
|
||||
set(_JAVA_TARGET_OUTPUT_NAME "${_add_jar_OUTPUT_NAME}.jar")
|
||||
endif ()
|
||||
|
||||
set(_JAVA_CLASS_FILES)
|
||||
set(_JAVA_COMPILE_FILES)
|
||||
set(_JAVA_COMPILE_FILELISTS)
|
||||
set(_JAVA_DEPENDS)
|
||||
set(_JAVA_COMPILE_DEPENDS)
|
||||
set(_JAVA_RESOURCE_FILES)
|
||||
set(_JAVA_RESOURCE_FILES_RELATIVE)
|
||||
foreach(_JAVA_SOURCE_FILE ${_JAVA_SOURCE_FILES})
|
||||
get_filename_component(_JAVA_EXT ${_JAVA_SOURCE_FILE} EXT)
|
||||
get_filename_component(_JAVA_FILE ${_JAVA_SOURCE_FILE} NAME_WE)
|
||||
get_filename_component(_JAVA_PATH ${_JAVA_SOURCE_FILE} PATH)
|
||||
get_filename_component(_JAVA_FULL ${_JAVA_SOURCE_FILE} ABSOLUTE)
|
||||
|
||||
if (_JAVA_SOURCE_FILE MATCHES "^@(.+)$")
|
||||
get_filename_component(_JAVA_FULL ${CMAKE_MATCH_1} ABSOLUTE)
|
||||
list(APPEND _JAVA_COMPILE_FILELISTS ${_JAVA_FULL})
|
||||
|
||||
elseif (_JAVA_EXT MATCHES ".java")
|
||||
file(RELATIVE_PATH _JAVA_REL_BINARY_PATH ${_add_jar_OUTPUT_DIR} ${_JAVA_FULL})
|
||||
file(RELATIVE_PATH _JAVA_REL_SOURCE_PATH ${CMAKE_CURRENT_SOURCE_DIR} ${_JAVA_FULL})
|
||||
string(LENGTH ${_JAVA_REL_BINARY_PATH} _BIN_LEN)
|
||||
string(LENGTH ${_JAVA_REL_SOURCE_PATH} _SRC_LEN)
|
||||
if (${_BIN_LEN} LESS ${_SRC_LEN})
|
||||
set(_JAVA_REL_PATH ${_JAVA_REL_BINARY_PATH})
|
||||
else ()
|
||||
set(_JAVA_REL_PATH ${_JAVA_REL_SOURCE_PATH})
|
||||
endif ()
|
||||
get_filename_component(_JAVA_REL_PATH ${_JAVA_REL_PATH} PATH)
|
||||
|
||||
list(APPEND _JAVA_COMPILE_FILES ${_JAVA_SOURCE_FILE})
|
||||
set(_JAVA_CLASS_FILE "${CMAKE_JAVA_CLASS_OUTPUT_PATH}/${_JAVA_REL_PATH}/${_JAVA_FILE}.class")
|
||||
set(_JAVA_CLASS_FILES ${_JAVA_CLASS_FILES} ${_JAVA_CLASS_FILE})
|
||||
|
||||
elseif (_JAVA_EXT MATCHES ".jar"
|
||||
OR _JAVA_EXT MATCHES ".war"
|
||||
OR _JAVA_EXT MATCHES ".ear"
|
||||
OR _JAVA_EXT MATCHES ".sar")
|
||||
# Ignored for backward compatibility
|
||||
|
||||
elseif (_JAVA_EXT STREQUAL "")
|
||||
list(APPEND CMAKE_JAVA_INCLUDE_PATH ${JAVA_JAR_TARGET_${_JAVA_SOURCE_FILE}} ${JAVA_JAR_TARGET_${_JAVA_SOURCE_FILE}_CLASSPATH})
|
||||
list(APPEND _JAVA_DEPENDS ${JAVA_JAR_TARGET_${_JAVA_SOURCE_FILE}})
|
||||
|
||||
else ()
|
||||
__java_copy_file(${CMAKE_CURRENT_SOURCE_DIR}/${_JAVA_SOURCE_FILE}
|
||||
${CMAKE_JAVA_CLASS_OUTPUT_PATH}/${_JAVA_SOURCE_FILE}
|
||||
"Copying ${_JAVA_SOURCE_FILE} to the build directory")
|
||||
list(APPEND _JAVA_RESOURCE_FILES ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/${_JAVA_SOURCE_FILE})
|
||||
list(APPEND _JAVA_RESOURCE_FILES_RELATIVE ${_JAVA_SOURCE_FILE})
|
||||
endif ()
|
||||
endforeach()
|
||||
|
||||
foreach(_JAVA_INCLUDE_JAR ${_add_jar_INCLUDE_JARS})
|
||||
if (TARGET ${_JAVA_INCLUDE_JAR})
|
||||
get_target_property(_JAVA_JAR_PATH ${_JAVA_INCLUDE_JAR} JAR_FILE)
|
||||
if (_JAVA_JAR_PATH)
|
||||
set(CMAKE_JAVA_INCLUDE_PATH_FINAL "${CMAKE_JAVA_INCLUDE_PATH_FINAL}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${_JAVA_JAR_PATH}")
|
||||
list(APPEND CMAKE_JAVA_INCLUDE_PATH ${_JAVA_JAR_PATH})
|
||||
list(APPEND _JAVA_DEPENDS ${_JAVA_INCLUDE_JAR})
|
||||
list(APPEND _JAVA_COMPILE_DEPENDS ${_JAVA_INCLUDE_JAR})
|
||||
else ()
|
||||
message(SEND_ERROR "add_jar: INCLUDE_JARS target ${_JAVA_INCLUDE_JAR} is not a jar")
|
||||
endif ()
|
||||
else ()
|
||||
set(CMAKE_JAVA_INCLUDE_PATH_FINAL "${CMAKE_JAVA_INCLUDE_PATH_FINAL}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${_JAVA_INCLUDE_JAR}")
|
||||
list(APPEND CMAKE_JAVA_INCLUDE_PATH "${_JAVA_INCLUDE_JAR}")
|
||||
list(APPEND _JAVA_DEPENDS "${_JAVA_INCLUDE_JAR}")
|
||||
list(APPEND _JAVA_COMPILE_DEPENDS "${_JAVA_INCLUDE_JAR}")
|
||||
endif ()
|
||||
endforeach()
|
||||
|
||||
# create an empty java_class_filelist
|
||||
if (NOT EXISTS ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist)
|
||||
file(WRITE ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist "")
|
||||
endif()
|
||||
|
||||
if (_JAVA_COMPILE_FILES OR _JAVA_COMPILE_FILELISTS)
|
||||
set (_JAVA_SOURCES_FILELISTS)
|
||||
|
||||
if (_JAVA_COMPILE_FILES)
|
||||
# Create the list of files to compile.
|
||||
set(_JAVA_SOURCES_FILE ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_sources)
|
||||
string(REPLACE ";" "\"\n\"" _JAVA_COMPILE_STRING "\"${_JAVA_COMPILE_FILES}\"")
|
||||
file(WRITE ${_JAVA_SOURCES_FILE} ${_JAVA_COMPILE_STRING})
|
||||
list (APPEND _JAVA_SOURCES_FILELISTS "@${_JAVA_SOURCES_FILE}")
|
||||
endif()
|
||||
if (_JAVA_COMPILE_FILELISTS)
|
||||
foreach (_JAVA_FILELIST IN LISTS _JAVA_COMPILE_FILELISTS)
|
||||
list (APPEND _JAVA_SOURCES_FILELISTS "@${_JAVA_FILELIST}")
|
||||
endforeach()
|
||||
endif()
|
||||
|
||||
# Compile the java files and create a list of class files
|
||||
add_custom_command(
|
||||
# NOTE: this command generates an artificial dependency file
|
||||
OUTPUT ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_compiled_${_TARGET_NAME}
|
||||
COMMAND ${Java_JAVAC_EXECUTABLE}
|
||||
${CMAKE_JAVA_COMPILE_FLAGS}
|
||||
-classpath "${CMAKE_JAVA_INCLUDE_PATH_FINAL}"
|
||||
-d ${CMAKE_JAVA_CLASS_OUTPUT_PATH}
|
||||
${_JAVA_SOURCES_FILELISTS}
|
||||
COMMAND ${CMAKE_COMMAND} -E touch ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_compiled_${_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"
|
||||
)
|
||||
add_custom_command(
|
||||
OUTPUT ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-DCMAKE_JAVA_CLASS_OUTPUT_PATH=${CMAKE_JAVA_CLASS_OUTPUT_PATH}
|
||||
-DCMAKE_JAR_CLASSES_PREFIX="${CMAKE_JAR_CLASSES_PREFIX}"
|
||||
-P ${_JAVA_CLASS_FILELIST_SCRIPT}
|
||||
DEPENDS ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_compiled_${_TARGET_NAME}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
|
||||
)
|
||||
endif ()
|
||||
|
||||
# create the jar file
|
||||
set(_JAVA_JAR_OUTPUT_PATH
|
||||
${_add_jar_OUTPUT_DIR}/${_JAVA_TARGET_OUTPUT_NAME})
|
||||
if (CMAKE_JNI_TARGET)
|
||||
add_custom_command(
|
||||
OUTPUT ${_JAVA_JAR_OUTPUT_PATH}
|
||||
COMMAND ${Java_JAR_EXECUTABLE}
|
||||
-cf${_ENTRY_POINT_OPTION}${_MANIFEST_OPTION} ${_JAVA_JAR_OUTPUT_PATH} ${_ENTRY_POINT_VALUE} ${_MANIFEST_VALUE}
|
||||
${_JAVA_RESOURCE_FILES_RELATIVE} @java_class_filelist
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-D_JAVA_TARGET_DIR=${_add_jar_OUTPUT_DIR}
|
||||
-D_JAVA_TARGET_OUTPUT_NAME=${_JAVA_TARGET_OUTPUT_NAME}
|
||||
-D_JAVA_TARGET_OUTPUT_LINK=${_JAVA_TARGET_OUTPUT_LINK}
|
||||
-P ${_JAVA_SYMLINK_SCRIPT}
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-D_JAVA_TARGET_DIR=${_add_jar_OUTPUT_DIR}
|
||||
-D_JAVA_TARGET_OUTPUT_NAME=${_JAVA_JAR_OUTPUT_PATH}
|
||||
-D_JAVA_TARGET_OUTPUT_LINK=${_JAVA_TARGET_OUTPUT_LINK}
|
||||
-P ${_JAVA_SYMLINK_SCRIPT}
|
||||
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}"
|
||||
)
|
||||
else ()
|
||||
add_custom_command(
|
||||
OUTPUT ${_JAVA_JAR_OUTPUT_PATH}
|
||||
COMMAND ${Java_JAR_EXECUTABLE}
|
||||
-cf${_ENTRY_POINT_OPTION}${_MANIFEST_OPTION} ${_JAVA_JAR_OUTPUT_PATH} ${_ENTRY_POINT_VALUE} ${_MANIFEST_VALUE}
|
||||
${_JAVA_RESOURCE_FILES_RELATIVE} @java_class_filelist
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-D_JAVA_TARGET_DIR=${_add_jar_OUTPUT_DIR}
|
||||
-D_JAVA_TARGET_OUTPUT_NAME=${_JAVA_TARGET_OUTPUT_NAME}
|
||||
-D_JAVA_TARGET_OUTPUT_LINK=${_JAVA_TARGET_OUTPUT_LINK}
|
||||
-P ${_JAVA_SYMLINK_SCRIPT}
|
||||
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 ${_JAVA_TARGET_OUTPUT_NAME}"
|
||||
)
|
||||
endif ()
|
||||
|
||||
# Add the target and make sure we have the latest resource files.
|
||||
add_custom_target(${_TARGET_NAME} ALL DEPENDS ${_JAVA_JAR_OUTPUT_PATH})
|
||||
|
||||
set_property(
|
||||
TARGET
|
||||
${_TARGET_NAME}
|
||||
PROPERTY
|
||||
INSTALL_FILES
|
||||
${_JAVA_JAR_OUTPUT_PATH}
|
||||
)
|
||||
|
||||
if (_JAVA_TARGET_OUTPUT_LINK)
|
||||
set_property(
|
||||
TARGET
|
||||
${_TARGET_NAME}
|
||||
PROPERTY
|
||||
INSTALL_FILES
|
||||
${_JAVA_JAR_OUTPUT_PATH}
|
||||
${_add_jar_OUTPUT_DIR}/${_JAVA_TARGET_OUTPUT_LINK}
|
||||
)
|
||||
|
||||
if (CMAKE_JNI_TARGET)
|
||||
set_property(
|
||||
TARGET
|
||||
${_TARGET_NAME}
|
||||
PROPERTY
|
||||
JNI_SYMLINK
|
||||
${_add_jar_OUTPUT_DIR}/${_JAVA_TARGET_OUTPUT_LINK}
|
||||
)
|
||||
endif ()
|
||||
endif ()
|
||||
|
||||
set_property(
|
||||
TARGET
|
||||
${_TARGET_NAME}
|
||||
PROPERTY
|
||||
JAR_FILE
|
||||
${_JAVA_JAR_OUTPUT_PATH}
|
||||
)
|
||||
|
||||
set_property(
|
||||
TARGET
|
||||
${_TARGET_NAME}
|
||||
PROPERTY
|
||||
CLASSDIR
|
||||
${CMAKE_JAVA_CLASS_OUTPUT_PATH}
|
||||
)
|
||||
|
||||
endfunction()
|
||||
|
||||
function(INSTALL_JAR _TARGET_NAME)
|
||||
if (ARGC EQUAL 2)
|
||||
set (_DESTINATION ${ARGV1})
|
||||
else()
|
||||
cmake_parse_arguments(_install_jar
|
||||
""
|
||||
"DESTINATION;COMPONENT"
|
||||
""
|
||||
${ARGN})
|
||||
if (_install_jar_DESTINATION)
|
||||
set (_DESTINATION ${_install_jar_DESTINATION})
|
||||
else()
|
||||
message(SEND_ERROR "install_jar: ${_TARGET_NAME}: DESTINATION must be specified.")
|
||||
endif()
|
||||
|
||||
if (_install_jar_COMPONENT)
|
||||
set (_COMPONENT COMPONENT ${_install_jar_COMPONENT})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
get_property(__FILES
|
||||
TARGET
|
||||
${_TARGET_NAME}
|
||||
PROPERTY
|
||||
INSTALL_FILES
|
||||
)
|
||||
|
||||
if (__FILES)
|
||||
install(
|
||||
FILES
|
||||
${__FILES}
|
||||
DESTINATION
|
||||
${_DESTINATION}
|
||||
${_COMPONENT}
|
||||
)
|
||||
else ()
|
||||
message(SEND_ERROR "install_jar: The target ${_TARGET_NAME} is not known in this scope.")
|
||||
endif ()
|
||||
endfunction()
|
||||
|
||||
function(INSTALL_JNI_SYMLINK _TARGET_NAME)
|
||||
if (ARGC EQUAL 2)
|
||||
set (_DESTINATION ${ARGV1})
|
||||
else()
|
||||
cmake_parse_arguments(_install_jni_symlink
|
||||
""
|
||||
"DESTINATION;COMPONENT"
|
||||
""
|
||||
${ARGN})
|
||||
if (_install_jni_symlink_DESTINATION)
|
||||
set (_DESTINATION ${_install_jni_symlink_DESTINATION})
|
||||
else()
|
||||
message(SEND_ERROR "install_jni_symlink: ${_TARGET_NAME}: DESTINATION must be specified.")
|
||||
endif()
|
||||
|
||||
if (_install_jni_symlink_COMPONENT)
|
||||
set (_COMPONENT COMPONENT ${_install_jni_symlink_COMPONENT})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
get_property(__SYMLINK
|
||||
TARGET
|
||||
${_TARGET_NAME}
|
||||
PROPERTY
|
||||
JNI_SYMLINK
|
||||
)
|
||||
|
||||
if (__SYMLINK)
|
||||
install(
|
||||
FILES
|
||||
${__SYMLINK}
|
||||
DESTINATION
|
||||
${_DESTINATION}
|
||||
${_COMPONENT}
|
||||
)
|
||||
else ()
|
||||
message(SEND_ERROR "install_jni_symlink: The target ${_TARGET_NAME} is not known in this scope.")
|
||||
endif ()
|
||||
endfunction()
|
||||
|
||||
function (find_jar VARIABLE)
|
||||
set(_jar_names)
|
||||
set(_jar_files)
|
||||
set(_jar_versions)
|
||||
set(_jar_paths
|
||||
/usr/share/java/
|
||||
/usr/local/share/java/
|
||||
${Java_JAR_PATHS})
|
||||
set(_jar_doc "NOTSET")
|
||||
|
||||
set(_state "name")
|
||||
|
||||
foreach (arg ${ARGN})
|
||||
if (${_state} STREQUAL "name")
|
||||
if (${arg} STREQUAL "VERSIONS")
|
||||
set(_state "versions")
|
||||
elseif (${arg} STREQUAL "NAMES")
|
||||
set(_state "names")
|
||||
elseif (${arg} STREQUAL "PATHS")
|
||||
set(_state "paths")
|
||||
elseif (${arg} STREQUAL "DOC")
|
||||
set(_state "doc")
|
||||
else ()
|
||||
set(_jar_names ${arg})
|
||||
if (_jar_doc STREQUAL "NOTSET")
|
||||
set(_jar_doc "Finding ${arg} jar")
|
||||
endif ()
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "versions")
|
||||
if (${arg} STREQUAL "NAMES")
|
||||
set(_state "names")
|
||||
elseif (${arg} STREQUAL "PATHS")
|
||||
set(_state "paths")
|
||||
elseif (${arg} STREQUAL "DOC")
|
||||
set(_state "doc")
|
||||
else ()
|
||||
set(_jar_versions ${_jar_versions} ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "names")
|
||||
if (${arg} STREQUAL "VERSIONS")
|
||||
set(_state "versions")
|
||||
elseif (${arg} STREQUAL "PATHS")
|
||||
set(_state "paths")
|
||||
elseif (${arg} STREQUAL "DOC")
|
||||
set(_state "doc")
|
||||
else ()
|
||||
set(_jar_names ${_jar_names} ${arg})
|
||||
if (_jar_doc STREQUAL "NOTSET")
|
||||
set(_jar_doc "Finding ${arg} jar")
|
||||
endif ()
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "paths")
|
||||
if (${arg} STREQUAL "VERSIONS")
|
||||
set(_state "versions")
|
||||
elseif (${arg} STREQUAL "NAMES")
|
||||
set(_state "names")
|
||||
elseif (${arg} STREQUAL "DOC")
|
||||
set(_state "doc")
|
||||
else ()
|
||||
set(_jar_paths ${_jar_paths} ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "doc")
|
||||
if (${arg} STREQUAL "VERSIONS")
|
||||
set(_state "versions")
|
||||
elseif (${arg} STREQUAL "NAMES")
|
||||
set(_state "names")
|
||||
elseif (${arg} STREQUAL "PATHS")
|
||||
set(_state "paths")
|
||||
else ()
|
||||
set(_jar_doc ${arg})
|
||||
endif ()
|
||||
endif ()
|
||||
endforeach ()
|
||||
|
||||
if (NOT _jar_names)
|
||||
message(FATAL_ERROR "find_jar: No name to search for given")
|
||||
endif ()
|
||||
|
||||
foreach (jar_name ${_jar_names})
|
||||
foreach (version ${_jar_versions})
|
||||
set(_jar_files ${_jar_files} ${jar_name}-${version}.jar)
|
||||
endforeach ()
|
||||
set(_jar_files ${_jar_files} ${jar_name}.jar)
|
||||
endforeach ()
|
||||
|
||||
find_file(${VARIABLE}
|
||||
NAMES ${_jar_files}
|
||||
PATHS ${_jar_paths}
|
||||
DOC ${_jar_doc}
|
||||
NO_DEFAULT_PATH)
|
||||
endfunction ()
|
||||
|
||||
function(create_javadoc _target)
|
||||
set(_javadoc_packages)
|
||||
set(_javadoc_files)
|
||||
set(_javadoc_sourcepath)
|
||||
set(_javadoc_classpath)
|
||||
set(_javadoc_installpath "${CMAKE_INSTALL_PREFIX}/share/javadoc")
|
||||
set(_javadoc_doctitle)
|
||||
set(_javadoc_windowtitle)
|
||||
set(_javadoc_author FALSE)
|
||||
set(_javadoc_version FALSE)
|
||||
set(_javadoc_use FALSE)
|
||||
|
||||
set(_state "package")
|
||||
|
||||
foreach (arg ${ARGN})
|
||||
if (${_state} STREQUAL "package")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
set(_javadoc_packages ${arg})
|
||||
set(_state "packages")
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "packages")
|
||||
if (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
list(APPEND _javadoc_packages ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "files")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
list(APPEND _javadoc_files ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "sourcepath")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
list(APPEND _javadoc_sourcepath ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "classpath")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
list(APPEND _javadoc_classpath ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "installpath")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
set(_javadoc_installpath ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "doctitle")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
set(_javadoc_doctitle ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "windowtitle")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
set(_javadoc_windowtitle ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "author")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
set(_javadoc_author ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "use")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
set(_javadoc_use ${arg})
|
||||
endif ()
|
||||
elseif (${_state} STREQUAL "version")
|
||||
if (${arg} STREQUAL "PACKAGES")
|
||||
set(_state "packages")
|
||||
elseif (${arg} STREQUAL "FILES")
|
||||
set(_state "files")
|
||||
elseif (${arg} STREQUAL "SOURCEPATH")
|
||||
set(_state "sourcepath")
|
||||
elseif (${arg} STREQUAL "CLASSPATH")
|
||||
set(_state "classpath")
|
||||
elseif (${arg} STREQUAL "INSTALLPATH")
|
||||
set(_state "installpath")
|
||||
elseif (${arg} STREQUAL "DOCTITLE")
|
||||
set(_state "doctitle")
|
||||
elseif (${arg} STREQUAL "WINDOWTITLE")
|
||||
set(_state "windowtitle")
|
||||
elseif (${arg} STREQUAL "AUTHOR")
|
||||
set(_state "author")
|
||||
elseif (${arg} STREQUAL "USE")
|
||||
set(_state "use")
|
||||
elseif (${arg} STREQUAL "VERSION")
|
||||
set(_state "version")
|
||||
else ()
|
||||
set(_javadoc_version ${arg})
|
||||
endif ()
|
||||
endif ()
|
||||
endforeach ()
|
||||
|
||||
set(_javadoc_builddir ${CMAKE_CURRENT_BINARY_DIR}/javadoc/${_target})
|
||||
set(_javadoc_options -d ${_javadoc_builddir})
|
||||
|
||||
if (_javadoc_sourcepath)
|
||||
set(_start TRUE)
|
||||
foreach(_path ${_javadoc_sourcepath})
|
||||
if (_start)
|
||||
set(_sourcepath ${_path})
|
||||
set(_start FALSE)
|
||||
else ()
|
||||
set(_sourcepath ${_sourcepath}:${_path})
|
||||
endif ()
|
||||
endforeach()
|
||||
set(_javadoc_options ${_javadoc_options} -sourcepath ${_sourcepath})
|
||||
endif ()
|
||||
|
||||
if (_javadoc_classpath)
|
||||
set(_start TRUE)
|
||||
foreach(_path ${_javadoc_classpath})
|
||||
if (_start)
|
||||
set(_classpath ${_path})
|
||||
set(_start FALSE)
|
||||
else ()
|
||||
set(_classpath ${_classpath}:${_path})
|
||||
endif ()
|
||||
endforeach()
|
||||
set(_javadoc_options ${_javadoc_options} -classpath "${_classpath}")
|
||||
endif ()
|
||||
|
||||
if (_javadoc_doctitle)
|
||||
set(_javadoc_options ${_javadoc_options} -doctitle '${_javadoc_doctitle}')
|
||||
endif ()
|
||||
|
||||
if (_javadoc_windowtitle)
|
||||
set(_javadoc_options ${_javadoc_options} -windowtitle '${_javadoc_windowtitle}')
|
||||
endif ()
|
||||
|
||||
if (_javadoc_author)
|
||||
set(_javadoc_options ${_javadoc_options} -author)
|
||||
endif ()
|
||||
|
||||
if (_javadoc_use)
|
||||
set(_javadoc_options ${_javadoc_options} -use)
|
||||
endif ()
|
||||
|
||||
if (_javadoc_version)
|
||||
set(_javadoc_options ${_javadoc_options} -version)
|
||||
endif ()
|
||||
|
||||
add_custom_target(${_target}_javadoc ALL
|
||||
COMMAND ${Java_JAVADOC_EXECUTABLE} ${_javadoc_options}
|
||||
${_javadoc_files}
|
||||
${_javadoc_packages}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
|
||||
)
|
||||
|
||||
install(
|
||||
DIRECTORY ${_javadoc_builddir}
|
||||
DESTINATION ${_javadoc_installpath}
|
||||
)
|
||||
endfunction()
|
||||
|
||||
function (create_javah)
|
||||
cmake_parse_arguments(_create_javah
|
||||
""
|
||||
"TARGET;GENERATED_FILES;OUTPUT_NAME;OUTPUT_DIR"
|
||||
"CLASSES;CLASSPATH;DEPENDS"
|
||||
${ARGN})
|
||||
|
||||
# ckeck parameters
|
||||
if (NOT _create_javah_TARGET AND NOT _create_javah_GENERATED_FILES)
|
||||
message (FATAL_ERROR "create_javah: TARGET or GENERATED_FILES must be specified.")
|
||||
endif()
|
||||
if (_create_javah_OUTPUT_NAME AND _create_javah_OUTPUT_DIR)
|
||||
message (FATAL_ERROR "create_javah: OUTPUT_NAME and OUTPUT_DIR are mutually exclusive.")
|
||||
endif()
|
||||
|
||||
if (NOT _create_javah_CLASSES)
|
||||
message (FATAL_ERROR "create_javah: CLASSES is a required parameter.")
|
||||
endif()
|
||||
|
||||
set (_output_files)
|
||||
if (WIN32 AND NOT CYGWIN AND CMAKE_HOST_SYSTEM_NAME MATCHES "Windows")
|
||||
set(_classpath_sep ";")
|
||||
else ()
|
||||
set(_classpath_sep ":")
|
||||
endif()
|
||||
|
||||
# handle javah options
|
||||
set (_javah_options)
|
||||
|
||||
if (_create_javah_CLASSPATH)
|
||||
# CLASSPATH can specify directories, jar files or targets created with add_jar command
|
||||
set (_classpath)
|
||||
foreach (_path IN LISTS _create_javah_CLASSPATH)
|
||||
if (TARGET ${_path})
|
||||
get_target_property (_jar_path ${_path} JAR_FILE)
|
||||
if (_jar_path)
|
||||
list (APPEND _classpath "${_jar_path}")
|
||||
list (APPEND _create_javah_DEPENDS "${_path}")
|
||||
else()
|
||||
message(SEND_ERROR "create_javah: CLASSPATH target ${_path} is not a jar.")
|
||||
endif()
|
||||
elseif (EXISTS "${_path}")
|
||||
list (APPEND _classpath "${_path}")
|
||||
if (NOT IS_DIRECTORY "${_path}")
|
||||
list (APPEND _create_javah_DEPENDS "${_path}")
|
||||
endif()
|
||||
else()
|
||||
message(SEND_ERROR "create_javah: CLASSPATH entry ${_path} does not exist.")
|
||||
endif()
|
||||
endforeach()
|
||||
string (REPLACE ";" "${_classpath_sep}" _classpath "${_classpath}")
|
||||
list (APPEND _javah_options -classpath ${_classpath})
|
||||
endif()
|
||||
|
||||
if (_create_javah_OUTPUT_DIR)
|
||||
list (APPEND _javah_options -d "${_create_javah_OUTPUT_DIR}")
|
||||
endif()
|
||||
|
||||
if (_create_javah_OUTPUT_NAME)
|
||||
list (APPEND _javah_options -o "${_create_javah_OUTPUT_NAME}")
|
||||
set (_output_files "${_create_javah_OUTPUT_NAME}")
|
||||
|
||||
get_filename_component (_create_javah_OUTPUT_DIR "${_create_javah_OUTPUT_NAME}" DIRECTORY)
|
||||
get_filename_component (_create_javah_OUTPUT_DIR "${_create_javah_OUTPUT_DIR}" ABSOLUTE)
|
||||
endif()
|
||||
|
||||
if (NOT _create_javah_OUTPUT_DIR)
|
||||
set (_create_javah_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}")
|
||||
endif()
|
||||
|
||||
if (NOT _create_javah_OUTPUT_NAME)
|
||||
# compute output names
|
||||
foreach (_class IN LISTS _create_javah_CLASSES)
|
||||
string (REPLACE "." "_" _c_header "${_class}")
|
||||
set (_c_header "${_create_javah_OUTPUT_DIR}/${_c_header}.h")
|
||||
list (APPEND _output_files "${_c_header}")
|
||||
endforeach()
|
||||
endif()
|
||||
|
||||
# finalize custom command arguments
|
||||
if (_create_javah_DEPENDS)
|
||||
list (INSERT _create_javah_DEPENDS 0 DEPENDS)
|
||||
endif()
|
||||
|
||||
add_custom_command (OUTPUT ${_output_files}
|
||||
COMMAND "${Java_JAVAH_EXECUTABLE}" ${_javah_options} -jni ${_create_javah_CLASSES}
|
||||
${_create_javah_DEPENDS}
|
||||
WORKING_DIRECTORY ${_create_javah_OUTPUT_DIR}
|
||||
COMMENT "Building C header files from classes...")
|
||||
|
||||
if (_create_javah_TARGET)
|
||||
add_custom_target (${_create_javah_TARGET} ALL DEPENDS ${_output_files})
|
||||
endif()
|
||||
if (_create_javah_GENERATED_FILES)
|
||||
set (${_create_javah_GENERATED_FILES} ${_output_files} PARENT_SCOPE)
|
||||
endif()
|
||||
endfunction()
|
||||
@@ -0,0 +1,58 @@
|
||||
#.rst:
|
||||
# UseJavaClassFilelist
|
||||
# --------------------
|
||||
#
|
||||
#
|
||||
#
|
||||
#
|
||||
#
|
||||
# This script create a list of compiled Java class files to be added to
|
||||
# a jar file. This avoids including cmake files which get created in
|
||||
# the binary directory.
|
||||
|
||||
#=============================================================================
|
||||
# Copyright 2010-2011 Andreas schneider <asn@redhat.com>
|
||||
#
|
||||
# Distributed under the OSI-approved BSD License (the "License");
|
||||
# see accompanying file Copyright.txt for details.
|
||||
#
|
||||
# This software is distributed WITHOUT ANY WARRANTY; without even the
|
||||
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
|
||||
# See the License for more information.
|
||||
#=============================================================================
|
||||
# (To distribute this file outside of CMake, substitute the full
|
||||
# License text for the above reference.)
|
||||
|
||||
if (CMAKE_JAVA_CLASS_OUTPUT_PATH)
|
||||
if (EXISTS "${CMAKE_JAVA_CLASS_OUTPUT_PATH}")
|
||||
|
||||
set(_JAVA_GLOBBED_FILES)
|
||||
if (CMAKE_JAR_CLASSES_PREFIX)
|
||||
foreach(JAR_CLASS_PREFIX ${CMAKE_JAR_CLASSES_PREFIX})
|
||||
message(STATUS "JAR_CLASS_PREFIX: ${JAR_CLASS_PREFIX}")
|
||||
|
||||
file(GLOB_RECURSE _JAVA_GLOBBED_TMP_FILES "${CMAKE_JAVA_CLASS_OUTPUT_PATH}/${JAR_CLASS_PREFIX}/*.class")
|
||||
if (_JAVA_GLOBBED_TMP_FILES)
|
||||
list(APPEND _JAVA_GLOBBED_FILES ${_JAVA_GLOBBED_TMP_FILES})
|
||||
endif ()
|
||||
endforeach()
|
||||
else()
|
||||
file(GLOB_RECURSE _JAVA_GLOBBED_FILES "${CMAKE_JAVA_CLASS_OUTPUT_PATH}/*.class")
|
||||
endif ()
|
||||
|
||||
set(_JAVA_CLASS_FILES)
|
||||
# file(GLOB_RECURSE foo RELATIVE) is broken so we need this.
|
||||
foreach(_JAVA_GLOBBED_FILE ${_JAVA_GLOBBED_FILES})
|
||||
file(RELATIVE_PATH _JAVA_CLASS_FILE ${CMAKE_JAVA_CLASS_OUTPUT_PATH} ${_JAVA_GLOBBED_FILE})
|
||||
set(_JAVA_CLASS_FILES ${_JAVA_CLASS_FILES}${_JAVA_CLASS_FILE}\n)
|
||||
endforeach()
|
||||
|
||||
# write to file
|
||||
file(WRITE ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist ${_JAVA_CLASS_FILES})
|
||||
|
||||
else ()
|
||||
message(SEND_ERROR "FATAL: Java class output path doesn't exist")
|
||||
endif ()
|
||||
else ()
|
||||
message(SEND_ERROR "FATAL: Can't find CMAKE_JAVA_CLASS_OUTPUT_PATH")
|
||||
endif ()
|
||||
@@ -0,0 +1,38 @@
|
||||
#.rst:
|
||||
# UseJavaSymlinks
|
||||
# ---------------
|
||||
#
|
||||
#
|
||||
#
|
||||
#
|
||||
#
|
||||
# Helper script for UseJava.cmake
|
||||
|
||||
#=============================================================================
|
||||
# Copyright 2010-2011 Andreas schneider <asn@redhat.com>
|
||||
#
|
||||
# Distributed under the OSI-approved BSD License (the "License");
|
||||
# see accompanying file Copyright.txt for details.
|
||||
#
|
||||
# This software is distributed WITHOUT ANY WARRANTY; without even the
|
||||
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
|
||||
# See the License for more information.
|
||||
#=============================================================================
|
||||
# (To distribute this file outside of CMake, substitute the full
|
||||
# License text for the above reference.)
|
||||
|
||||
if (UNIX AND _JAVA_TARGET_OUTPUT_LINK)
|
||||
if (_JAVA_TARGET_OUTPUT_NAME)
|
||||
find_program(LN_EXECUTABLE
|
||||
NAMES
|
||||
ln
|
||||
)
|
||||
|
||||
execute_process(
|
||||
COMMAND ${LN_EXECUTABLE} -sf "${_JAVA_TARGET_OUTPUT_NAME}" "${_JAVA_TARGET_OUTPUT_LINK}"
|
||||
WORKING_DIRECTORY ${_JAVA_TARGET_DIR}
|
||||
)
|
||||
else ()
|
||||
message(SEND_ERROR "FATAL: Can't find _JAVA_TARGET_OUTPUT_NAME")
|
||||
endif ()
|
||||
endif ()
|
||||
@@ -14,6 +14,7 @@ set (${HDF5_PACKAGE_NAME}_VALID_COMPONENTS
|
||||
HL
|
||||
CXX_HL
|
||||
Fortran_HL
|
||||
Java
|
||||
Tools
|
||||
)
|
||||
|
||||
@@ -23,6 +24,7 @@ set (${HDF5_PACKAGE_NAME}_VALID_COMPONENTS
|
||||
set (${HDF5_PACKAGE_NAME}_ENABLE_PARALLEL @HDF5_ENABLE_PARALLEL@)
|
||||
set (${HDF5_PACKAGE_NAME}_BUILD_FORTRAN @HDF5_BUILD_FORTRAN@)
|
||||
set (${HDF5_PACKAGE_NAME}_BUILD_CPP_LIB @HDF5_BUILD_CPP_LIB@)
|
||||
set (${HDF5_PACKAGE_NAME}_BUILD_JAVA @HDF5_BUILD_JAVA@)
|
||||
set (${HDF5_PACKAGE_NAME}_BUILD_TOOLS @HDF5_BUILD_TOOLS@)
|
||||
set (${HDF5_PACKAGE_NAME}_BUILD_HL_LIB @HDF5_BUILD_HL_LIB@)
|
||||
set (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT @HDF5_ENABLE_Z_LIB_SUPPORT@)
|
||||
@@ -40,6 +42,16 @@ if (${HDF5_PACKAGE_NAME}_ENABLE_PARALLEL)
|
||||
set (${HDF5_PACKAGE_NAME}_MPI_C_LIBRARIES "@MPI_C_LIBRARIES@")
|
||||
endif ()
|
||||
|
||||
if (${HDF5_PACKAGE_NAME}_BUILD_JAVA)
|
||||
set (${HDF5_PACKAGE_NAME}_JAVA_INCLUDE_DIRS
|
||||
@PACKAGE_CURRENT_BUILD_DIR@/lib/jarhdf5-@HDF5_VERSION_STRING@.jar
|
||||
@PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-api-1.7.5.jar
|
||||
@PACKAGE_CURRENT_BUILD_DIR@/lib/slf4j-nop-1.7.5.jar
|
||||
)
|
||||
set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARY "@PACKAGE_CURRENT_BUILD_DIR@/lib")
|
||||
set (${HDF5_PACKAGE_NAME}_JAVA_LIBRARIES "${${HDF5_PACKAGE_NAME}_JAVA_LIBRARY}")
|
||||
endif()
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Directories
|
||||
#-----------------------------------------------------------------------------
|
||||
@@ -123,6 +135,8 @@ foreach (libtype IN LISTS ${HDF5_PACKAGE_NAME}_LIB_TYPE)
|
||||
set (hdf5_comp "hdf5_hl")
|
||||
elseif (${comp} STREQUAL "CXX_HL")
|
||||
set (hdf5_comp "hdf5_hl_cpp")
|
||||
elseif (${comp} STREQUAL "Java")
|
||||
set (hdf5_comp "hdf5_java")
|
||||
elseif (${comp} STREQUAL "Tools")
|
||||
set (hdf5_comp "hdf5_tools")
|
||||
elseif (${comp} STREQUAL "Fortran")
|
||||
|
||||
@@ -0,0 +1,212 @@
|
||||
# runTest.cmake executes a command and captures the output in a file. File is then compared
|
||||
# against a reference file. Exit status of command can also be compared.
|
||||
cmake_policy(SET CMP0007 NEW)
|
||||
|
||||
# arguments checking
|
||||
if (NOT TEST_TESTER)
|
||||
message (FATAL_ERROR "Require TEST_TESTER to be defined")
|
||||
endif (NOT TEST_TESTER)
|
||||
if (NOT TEST_PROGRAM)
|
||||
message (FATAL_ERROR "Require TEST_PROGRAM to be defined")
|
||||
endif (NOT TEST_PROGRAM)
|
||||
if (NOT TEST_LIBRARY_DIRECTORY)
|
||||
message (STATUS "Require TEST_LIBRARY_DIRECTORY to be defined")
|
||||
endif (NOT TEST_LIBRARY_DIRECTORY)
|
||||
if (NOT TEST_FOLDER)
|
||||
message ( FATAL_ERROR "Require TEST_FOLDER to be defined")
|
||||
endif (NOT TEST_FOLDER)
|
||||
if (NOT TEST_OUTPUT)
|
||||
message (FATAL_ERROR "Require TEST_OUTPUT to be defined")
|
||||
endif (NOT TEST_OUTPUT)
|
||||
if (NOT TEST_CLASSPATH)
|
||||
message (STATUS "Require TEST_CLASSPATH to be defined")
|
||||
endif (NOT TEST_CLASSPATH)
|
||||
if (NOT TEST_REFERENCE)
|
||||
message (FATAL_ERROR "Require TEST_REFERENCE to be defined")
|
||||
endif (NOT TEST_REFERENCE)
|
||||
|
||||
if (NOT TEST_ERRREF)
|
||||
set (ERROR_APPEND 1)
|
||||
endif (NOT TEST_ERRREF)
|
||||
|
||||
if (NOT TEST_LOG_LEVEL)
|
||||
set (LOG_LEVEL "info")
|
||||
else (NOT TEST_LOG_LEVEL)
|
||||
set (LOG_LEVEL "${TEST_LOG_LEVEL}")
|
||||
endif (NOT TEST_LOG_LEVEL)
|
||||
|
||||
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} ${ARGN}")
|
||||
|
||||
if (WIN32 AND NOT MINGW)
|
||||
set (ENV{PATH} "$ENV{PATH}\\;${TEST_LIBRARY_DIRECTORY}")
|
||||
endif (WIN32 AND NOT MINGW)
|
||||
|
||||
# run the test program, capture the stdout/stderr and the result var
|
||||
execute_process (
|
||||
COMMAND ${TEST_TESTER} -Xmx1024M
|
||||
-Dorg.slf4j.simpleLogger.defaultLogLevel=${LOG_LEVEL}
|
||||
-Djava.library.path=${TEST_LIBRARY_DIRECTORY}
|
||||
-cp "${TEST_CLASSPATH}" ${TEST_ARGS} ${TEST_PROGRAM}
|
||||
${ARGN}
|
||||
WORKING_DIRECTORY ${TEST_FOLDER}
|
||||
RESULT_VARIABLE TEST_RESULT
|
||||
OUTPUT_FILE ${TEST_OUTPUT}
|
||||
ERROR_FILE ${TEST_OUTPUT}.err
|
||||
ERROR_VARIABLE TEST_ERROR
|
||||
)
|
||||
|
||||
message (STATUS "COMMAND Result: ${TEST_RESULT}")
|
||||
|
||||
if (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}.err)
|
||||
file (READ ${TEST_FOLDER}/${TEST_OUTPUT}.err TEST_STREAM)
|
||||
if (TEST_MASK_FILE)
|
||||
STRING(REGEX REPLACE "CurrentDir is [^\n]+\n" "CurrentDir is (dir name)\n" TEST_STREAM "${TEST_STREAM}")
|
||||
endif (TEST_MASK_FILE)
|
||||
|
||||
if (ERROR_APPEND)
|
||||
file (APPEND ${TEST_FOLDER}/${TEST_OUTPUT} "${TEST_STREAM}")
|
||||
else (ERROR_APPEND)
|
||||
file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT}.err "${TEST_STREAM}")
|
||||
endif (ERROR_APPEND)
|
||||
endif (EXISTS ${TEST_FOLDER}/${TEST_OUTPUT}.err)
|
||||
|
||||
if (TEST_MASK_ERROR)
|
||||
if (NOT TEST_ERRREF)
|
||||
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
|
||||
else (NOT TEST_ERRREF)
|
||||
file (READ ${TEST_FOLDER}/${TEST_OUTPUT}.err TEST_STREAM)
|
||||
endif (NOT TEST_ERRREF)
|
||||
string (REGEX REPLACE "Time:[^\n]+\n" "Time: XXXX\n" TEST_STREAM "${TEST_STREAM}")
|
||||
string (REGEX REPLACE "thread [0-9]*:" "thread (IDs):" TEST_STREAM "${TEST_STREAM}")
|
||||
string (REGEX REPLACE ": ([^\n]*)[.]c " ": (file name) " TEST_STREAM "${TEST_STREAM}")
|
||||
string (REGEX REPLACE " line [0-9]*" " line (number)" TEST_STREAM "${TEST_STREAM}")
|
||||
#string (REGEX REPLACE "v[1-9]*[.][0-9]*[.]" "version (number)." TEST_STREAM "${TEST_STREAM}")
|
||||
string (REGEX REPLACE "HDF5 .[1-9]*[.][0-9]*[.][0-9]*[^)]*" "HDF5 (version (number)" TEST_STREAM "${TEST_STREAM}")
|
||||
string (REGEX REPLACE "H5Eget_auto[1-2]*" "H5Eget_auto(1 or 2)" TEST_STREAM "${TEST_STREAM}")
|
||||
string (REGEX REPLACE "H5Eset_auto[1-2]*" "H5Eset_auto(1 or 2)" TEST_STREAM "${TEST_STREAM}")
|
||||
if (NOT TEST_ERRREF)
|
||||
file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT} "${TEST_STREAM}")
|
||||
else (NOT TEST_ERRREF)
|
||||
file (WRITE ${TEST_FOLDER}/${TEST_OUTPUT}.err "${TEST_STREAM}")
|
||||
endif (NOT TEST_ERRREF)
|
||||
endif (TEST_MASK_ERROR)
|
||||
|
||||
# if the return value is !=0 bail out
|
||||
if (NOT ${TEST_RESULT} STREQUAL ${TEST_EXPECT})
|
||||
message (STATUS "ERROR OUTPUT: ${TEST_STREAM}")
|
||||
message (FATAL_ERROR "Failed: Test program ${TEST_PROGRAM} exited != 0.\n${TEST_ERROR}")
|
||||
endif (NOT ${TEST_RESULT} STREQUAL ${TEST_EXPECT})
|
||||
|
||||
message (STATUS "COMMAND Error: ${TEST_ERROR}")
|
||||
|
||||
if (NOT TEST_SKIP_COMPARE)
|
||||
if (WIN32 AND NOT MINGW)
|
||||
file (READ ${TEST_FOLDER}/${TEST_REFERENCE} TEST_STREAM)
|
||||
file (WRITE ${TEST_FOLDER}/${TEST_REFERENCE} "${TEST_STREAM}")
|
||||
endif (WIN32 AND NOT MINGW)
|
||||
|
||||
# now compare the output with the reference
|
||||
execute_process (
|
||||
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_FOLDER}/${TEST_REFERENCE}
|
||||
RESULT_VARIABLE TEST_RESULT
|
||||
)
|
||||
if (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
set (TEST_RESULT 0)
|
||||
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT} test_act)
|
||||
list (LENGTH test_act len_act)
|
||||
file (STRINGS ${TEST_FOLDER}/${TEST_REFERENCE} test_ref)
|
||||
list (LENGTH test_ref len_ref)
|
||||
if (NOT ${len_act} STREQUAL "0")
|
||||
MATH (EXPR _FP_LEN "${len_ref} - 1")
|
||||
foreach (line RANGE 0 ${_FP_LEN})
|
||||
list (GET test_act ${line} str_act)
|
||||
list (GET test_ref ${line} str_ref)
|
||||
if (NOT "${str_act}" STREQUAL "${str_ref}")
|
||||
if (NOT "${str_act}" STREQUAL "")
|
||||
set (TEST_RESULT 1)
|
||||
message ("line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
|
||||
endif (NOT "${str_act}" STREQUAL "")
|
||||
endif (NOT "${str_act}" STREQUAL "${str_ref}")
|
||||
endforeach (line RANGE 0 ${_FP_LEN})
|
||||
endif (NOT ${len_act} STREQUAL "0")
|
||||
if (NOT ${len_act} STREQUAL ${len_ref})
|
||||
set (TEST_RESULT 1)
|
||||
endif (NOT ${len_act} STREQUAL ${len_ref})
|
||||
endif (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
|
||||
message (STATUS "COMPARE Result: ${TEST_RESULT}")
|
||||
|
||||
# again, if return value is !=0 scream and shout
|
||||
if (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
message (FATAL_ERROR "Failed: The output of ${TEST_OUTPUT} did not match ${TEST_REFERENCE}")
|
||||
endif (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
|
||||
if (TEST_ERRREF)
|
||||
if (WIN32 AND NOT MINGW)
|
||||
file (READ ${TEST_FOLDER}/${TEST_ERRREF} TEST_STREAM)
|
||||
file (WRITE ${TEST_FOLDER}/${TEST_ERRREF} "${TEST_STREAM}")
|
||||
endif (WIN32 AND NOT MINGW)
|
||||
|
||||
# now compare the error output with the error reference
|
||||
execute_process (
|
||||
COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT}.err ${TEST_FOLDER}/${TEST_ERRREF}
|
||||
RESULT_VARIABLE TEST_RESULT
|
||||
)
|
||||
if (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
set (TEST_RESULT 0)
|
||||
file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT}.err test_act)
|
||||
list (LENGTH test_act len_act)
|
||||
file (STRINGS ${TEST_FOLDER}/${TEST_ERRREF} test_ref)
|
||||
list (LENGTH test_ref len_ref)
|
||||
MATH (EXPR _FP_LEN "${len_ref} - 1")
|
||||
if (NOT ${len_act} STREQUAL "0")
|
||||
MATH (EXPR _FP_LEN "${len_ref} - 1")
|
||||
foreach (line RANGE 0 ${_FP_LEN})
|
||||
list (GET test_act ${line} str_act)
|
||||
list (GET test_ref ${line} str_ref)
|
||||
if (NOT "${str_act}" STREQUAL "${str_ref}")
|
||||
if (NOT "${str_act}" STREQUAL "")
|
||||
set (TEST_RESULT 1)
|
||||
message ("line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
|
||||
endif (NOT "${str_act}" STREQUAL "")
|
||||
endif (NOT "${str_act}" STREQUAL "${str_ref}")
|
||||
endforeach (line RANGE 0 ${_FP_LEN})
|
||||
endif (NOT ${len_act} STREQUAL "0")
|
||||
if (NOT ${len_act} STREQUAL ${len_ref})
|
||||
set (TEST_RESULT 1)
|
||||
endif (NOT ${len_act} STREQUAL ${len_ref})
|
||||
endif (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
|
||||
message (STATUS "COMPARE Result: ${TEST_RESULT}")
|
||||
|
||||
# again, if return value is !=0 scream and shout
|
||||
if (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
message (FATAL_ERROR "Failed: The error output of ${TEST_OUTPUT}.err did not match ${TEST_ERRREF}")
|
||||
endif (NOT ${TEST_RESULT} STREQUAL 0)
|
||||
endif (TEST_ERRREF)
|
||||
endif (NOT TEST_SKIP_COMPARE)
|
||||
|
||||
if (TEST_GREP_COMPARE)
|
||||
# now grep the output with the reference
|
||||
file (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
|
||||
|
||||
# TEST_REFERENCE should always be matched
|
||||
string (REGEX MATCH "${TEST_REFERENCE}" TEST_MATCH ${TEST_STREAM})
|
||||
string (COMPARE EQUAL "${TEST_REFERENCE}" "${TEST_MATCH}" TEST_RESULT)
|
||||
if (${TEST_RESULT} STREQUAL "0")
|
||||
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_REFERENCE}")
|
||||
endif (${TEST_RESULT} STREQUAL "0")
|
||||
|
||||
string (REGEX MATCH "${TEST_FILTER}" TEST_MATCH ${TEST_STREAM})
|
||||
if (${TEST_EXPECT} STREQUAL "1")
|
||||
# TEST_EXPECT (1) interperts TEST_FILTER as NOT to match
|
||||
string (LENGTH "${TEST_MATCH}" TEST_RESULT)
|
||||
if (NOT ${TEST_RESULT} STREQUAL "0")
|
||||
message (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did contain ${TEST_FILTER}")
|
||||
endif (NOT ${TEST_RESULT} STREQUAL "0")
|
||||
endif (${TEST_EXPECT} STREQUAL "0")
|
||||
endif (TEST_GREP_COMPARE)
|
||||
|
||||
# everything went fine...
|
||||
message ("${TEST_PROGRAM} Passed")
|
||||
|
||||
@@ -1,43 +1,50 @@
|
||||
SUMMARY OF THE HDF5 CONFIGURATION
|
||||
=================================
|
||||
SUMMARY OF THE HDF5 CONFIGURATION
|
||||
=================================
|
||||
|
||||
General Information:
|
||||
-------------------
|
||||
HDF5 Version: @HDF5_PACKAGE_VERSION_STRING@
|
||||
Configured on: @CONFIG_DATE@
|
||||
Configured by: @CMAKE_GENERATOR@
|
||||
Configure mode: CMAKE @CMAKE_VERSION@
|
||||
Host system: @CMAKE_HOST_SYSTEM@
|
||||
Uname information: @CMAKE_SYSTEM_NAME@
|
||||
Byte sex: @BYTESEX@
|
||||
Libraries: @BUILD_NAME_EXT@
|
||||
Installation point: @CMAKE_INSTALL_PREFIX@
|
||||
|
||||
Compiling Options:
|
||||
------------------
|
||||
Compilation Mode: @CMAKE_BUILD_TYPE@
|
||||
C Compiler: @CMAKE_C_COMPILER@
|
||||
CFLAGS: @CMAKE_C_FLAGS@
|
||||
H5_CFLAGS: @H5_CFLAGS@
|
||||
AM_CFLAGS: @AM_CFLAGS@
|
||||
CPPFLAGS: @CPPFLAGS@
|
||||
H5_CPPFLAGS: @H5_CPPFLAGS@
|
||||
AM_CPPFLAGS: @AM_CPPFLAGS@
|
||||
Shared C Library: @H5_ENABLE_SHARED_LIB@
|
||||
Static C Library: @H5_ENABLE_STATIC_LIB@
|
||||
Build Mode: @CMAKE_BUILD_TYPE@
|
||||
Debugging Symbols: @SYMBOLS@
|
||||
Asserts: @ASSERTS@
|
||||
Profiling: @PROFILING@
|
||||
Optimization Level: @OPTIMIZATION@
|
||||
|
||||
Linking Options:
|
||||
----------------
|
||||
Libraries: @BUILD_NAME_EXT@
|
||||
Statically Linked Executables: @BUILD_STATIC_EXECS@
|
||||
LDFLAGS: @CMAKE_SHARED_LINKER_FLAGS@
|
||||
H5_LDFLAGS: @H5_LDFLAGS@
|
||||
AM_LDFLAGS: @AM_LDFLAGS@
|
||||
Extra libraries: @LINK_LIBS@
|
||||
Archiver: @CMAKE_AR@
|
||||
Ranlib: @CMAKE_RANLIB@
|
||||
Debugged Packages: @DEBUG_PKG@
|
||||
API Tracing: @HDF5_ENABLE_TRACE@
|
||||
|
||||
Languages:
|
||||
----------
|
||||
C: yes
|
||||
C Compiler: @CMAKE_C_COMPILER@ @CMAKE_C_COMPILER_VERSION@
|
||||
CPPFLAGS: @CPPFLAGS@
|
||||
H5_CPPFLAGS: @H5_CPPFLAGS@
|
||||
AM_CPPFLAGS: @AM_CPPFLAGS@
|
||||
CFLAGS: @CMAKE_C_FLAGS@
|
||||
H5_CFLAGS: @H5_CFLAGS@
|
||||
AM_CFLAGS: @AM_CFLAGS@
|
||||
Shared C Library: @H5_ENABLE_SHARED_LIB@
|
||||
Static C Library: YES
|
||||
|
||||
Fortran: @HDF5_BUILD_FORTRAN@
|
||||
@BUILD_FORTRAN_CONDITIONAL_TRUE@ Fortran Compiler: @CMAKE_Fortran_COMPILER@
|
||||
@BUILD_FORTRAN_CONDITIONAL_TRUE@ Fortran Compiler: @CMAKE_Fortran_COMPILER@ @CMAKE_Fortran_COMPILER_VERSION@
|
||||
@BUILD_FORTRAN_CONDITIONAL_TRUE@ Fortran Flags: @CMAKE_Fortran_FLAGS@
|
||||
@BUILD_FORTRAN_CONDITIONAL_TRUE@ H5 Fortran Flags: @H5_FCFLAGS@
|
||||
@BUILD_FORTRAN_CONDITIONAL_TRUE@ AM Fortran Flags: @AM_FCFLAGS@
|
||||
@@ -45,27 +52,32 @@ Languages:
|
||||
@BUILD_FORTRAN_CONDITIONAL_TRUE@ Static Fortran Library: YES
|
||||
|
||||
C++: @HDF5_BUILD_CPP_LIB@
|
||||
@BUILD_CXX_CONDITIONAL_TRUE@ C++ Compiler: @CMAKE_CXX_COMPILER@
|
||||
@BUILD_CXX_CONDITIONAL_TRUE@ C++ Compiler: @CMAKE_CXX_COMPILER@ @CMAKE_CXX_COMPILER_VERSION@
|
||||
@BUILD_CXX_CONDITIONAL_TRUE@ C++ Flags: @CMAKE_CXX_FLAGS@
|
||||
@BUILD_CXX_CONDITIONAL_TRUE@ H5 C++ Flags: @H5_CXXFLAGS@
|
||||
@BUILD_CXX_CONDITIONAL_TRUE@ AM C++ Flags: @AM_CXXFLAGS@
|
||||
@BUILD_CXX_CONDITIONAL_TRUE@ Shared C++ Library: @H5_ENABLE_SHARED_LIB@
|
||||
@BUILD_CXX_CONDITIONAL_TRUE@ Static C++ Library: YES
|
||||
|
||||
JAVA: @HDF5_BUILD_JAVA@
|
||||
@BUILD_JAVA_CONDITIONAL_TRUE@ JAVA Compiler: @CMAKE_Java_COMPILER@ @Java_VERSION@
|
||||
|
||||
Features:
|
||||
---------
|
||||
Parallel HDF5: @HDF5_ENABLE_PARALLEL@
|
||||
High Level library: @HDF5_BUILD_HL_LIB@
|
||||
High-level library: @HDF5_BUILD_HL_LIB@
|
||||
Threadsafety: @HDF5_ENABLE_THREADSAFE@
|
||||
Default API Mapping: @DEFAULT_API_VERSION@
|
||||
With Deprecated Public Symbols: @HDF5_ENABLE_DEPRECATED_SYMBOLS@
|
||||
Default API mapping: @DEFAULT_API_VERSION@
|
||||
With deprecated public symbols: @HDF5_ENABLE_DEPRECATED_SYMBOLS@
|
||||
I/O filters (external): @EXTERNAL_FILTERS@
|
||||
MPE: @H5_HAVE_LIBLMPE@
|
||||
Direct VFD: @H5_HAVE_DIRECT@
|
||||
dmalloc: @H5_HAVE_LIBDMALLOC@
|
||||
Clear file buffers before write: @HDF5_Enable_Clear_File_Buffers@
|
||||
Packages w/ extra debug output: @INTERNAL_DEBUG_OUTPUT@
|
||||
API Tracing: @HDF5_ENABLE_TRACE@
|
||||
Using memory checker: @HDF5_ENABLE_USING_MEMCHECKER@
|
||||
Memory allocation sanity checks: @HDF5_MEMORY_ALLOC_SANITY_CHECK@
|
||||
Metadata trace file: @METADATATRACEFILE@
|
||||
Function Stack Tracing: @HDF5_ENABLE_CODESTACK@
|
||||
Strict File Format Checks: @HDF5_STRICT_FORMAT_CHECKS@
|
||||
Optimization Instrumentation: @HDF5_Enable_Instrument@
|
||||
|
||||
@@ -37,6 +37,7 @@ LIBH5TEST=$(top_builddir)/test/libh5test.la
|
||||
LIBH5F=$(top_builddir)/fortran/src/libhdf5_fortran.la
|
||||
LIBH5FTEST=$(top_builddir)/fortran/test/libh5test_fortran.la
|
||||
LIBH5CPP=$(top_builddir)/c++/src/libhdf5_cpp.la
|
||||
LIBH5JNI=$(top_builddir)/java/src/jni/libhdf5_java.la
|
||||
LIBH5TOOLS=$(top_builddir)/tools/lib/libh5tools.la
|
||||
LIBH5_HL=$(top_builddir)/hl/src/libhdf5_hl.la
|
||||
LIBH5F_HL=$(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la
|
||||
|
||||
+105
-1
@@ -100,6 +100,7 @@ AC_CONFIG_COMMANDS([pubconf], [
|
||||
|
||||
AC_CANONICAL_HOST
|
||||
AC_SUBST([CPPFLAGS])
|
||||
AC_SUBST([JNIFLAGS])
|
||||
|
||||
## H5_CFLAGS (and company) are for CFLAGS that should be used on HDF5, but
|
||||
## not exported to h5cc (or h5fc, etc.)
|
||||
@@ -107,6 +108,9 @@ AC_SUBST([H5_CFLAGS])
|
||||
AC_SUBST([H5_CPPFLAGS])
|
||||
AC_SUBST([H5_FCFLAGS])
|
||||
AC_SUBST([H5_CXXFLAGS])
|
||||
AC_SUBST([H5_JNIFLAGS])
|
||||
AC_SUBST([H5_JAVACFLAGS])
|
||||
AC_SUBST([H5_JAVAFLAGS])
|
||||
AC_SUBST([H5_LDFLAGS])
|
||||
|
||||
## AM_CFLAGS (and company) are for CFLAGS that should be used on HDF5,
|
||||
@@ -115,6 +119,9 @@ AC_SUBST([AM_CFLAGS])
|
||||
AC_SUBST([AM_FCFLAGS])
|
||||
AC_SUBST([AM_CXXFLAGS])
|
||||
AC_SUBST([AM_CPPFLAGS])
|
||||
AC_SUBST([AM_JNIFLAGS])
|
||||
AC_SUBST([AM_JAVACFLAGS])
|
||||
AC_SUBST([AM_JAVAFLAGS])
|
||||
AC_SUBST([AM_LDFLAGS])
|
||||
|
||||
## Make sure flags are initialized.
|
||||
@@ -122,11 +129,17 @@ AM_CFLAGS="${AM_CFLAGS}"
|
||||
AM_CXXFLAGS="${AM_CXXFLAGS}"
|
||||
AM_FCFLAGS="${AM_FCFLAGS}"
|
||||
AM_CPPFLAGS="${AM_CPPFLAGS}"
|
||||
AM_JNIFLAGS="${AM_JNIFLAGS}"
|
||||
AM_JAVACFLAGS="${AM_JAVACFLAGS}"
|
||||
AM_JAVAFLAGS="${AM_JAVAFLAGS}"
|
||||
AM_LDFLAGS="${AM_LDFLAGS}"
|
||||
CFLAGS="${CFLAGS}"
|
||||
CXXFLAGS="${CXXFLAGS}"
|
||||
FCFLAGS="${FCFLAGS}"
|
||||
CPPFLAGS="${CPPFLAGS}"
|
||||
JNIFLAGS="${JNIFLAGS}"
|
||||
JAVACFLAGS="${JAVACFLAGS}"
|
||||
JAVAFLAGS="${JAVAFLAGS}"
|
||||
LDFLAGS="${LDFLAGS}"
|
||||
|
||||
## Configure may need to alter any of the *FLAGS variables in order for
|
||||
@@ -135,6 +148,8 @@ LDFLAGS="${LDFLAGS}"
|
||||
saved_user_CFLAGS="$CFLAGS"
|
||||
saved_user_CXXFLAGS="$CXXFLAGS"
|
||||
saved_user_FCFLAGS="$FCFLAGS"
|
||||
saved_user_JAVACFLAGS="$JAVACFLAGS"
|
||||
saved_user_JAVAFLAGS="$JAVAFLAGS"
|
||||
saved_user_LDFLAGS="$LDFLAGS"
|
||||
saved_user_CPPFLAGS="$CPPFLAGS"
|
||||
|
||||
@@ -326,6 +341,8 @@ esac
|
||||
## reset this value at the end of configure, to preserve the user's settings.
|
||||
CFLAGS="${AM_CFLAGS} ${CFLAGS}"
|
||||
FCFLAGS="${AM_FCFLAGS} ${FCFLAGS}"
|
||||
JAVACFLAGS="${AM_JAVACFLAGS} ${JAVACFLAGS}"
|
||||
JAVAFLAGS="${AM_JAVAFLAGS} ${JAVAFLAGS}"
|
||||
CXXFLAGS="${AM_CXXFLAGS} ${CXXFLAGS}"
|
||||
CPPFLAGS="${AM_CPPFLAGS} ${CPPFLAGS}"
|
||||
LDFLAGS="${AM_LDFLAGS} ${LDFLAGS}"
|
||||
@@ -834,6 +851,55 @@ case "`uname`" in
|
||||
;;
|
||||
esac
|
||||
|
||||
## ----------------------------------------------------------------------
|
||||
## Check if they would like the Java native interface (JNI) compiled
|
||||
##
|
||||
|
||||
AC_SUBST([H5_CLASSPATH]) H5_CLASSPATH=""
|
||||
AC_MSG_CHECKING([if Java JNI interface enabled])
|
||||
|
||||
AC_ARG_ENABLE([java],
|
||||
[AS_HELP_STRING([--enable-java],
|
||||
[Compile the Java JNI interface [default=no]])],
|
||||
[HDF_JAVA=$enableval],
|
||||
[HDF_JAVA=no])
|
||||
|
||||
if test "X$HDF_JAVA" = "Xyes" && test "X${enable_shared}" != "Xno"; then
|
||||
echo "yes"
|
||||
if test "X$CLASSPATH" = "X"; then
|
||||
H5_CLASSPATH=".:$srcdir/java/lib"
|
||||
else
|
||||
H5_CLASSPATH=".:$CLASSPATH:$srcdir/java/lib"
|
||||
fi
|
||||
## Checks for programs.
|
||||
AX_JAVA_OPTIONS
|
||||
H5_JAVACFLAGS=$JAVACFLAGS
|
||||
H5_JAVAFLAGS=$JAVAFLAGS
|
||||
AX_PROG_JAVAC
|
||||
AX_PROG_JAVA
|
||||
AX_PROG_JAR
|
||||
AX_PROG_JAVADOC
|
||||
## Find the include directories needed for building JNI code
|
||||
AX_JNI_INCLUDE_DIR()
|
||||
for JNI_INCLUDE_DIR in $JNI_INCLUDE_DIRS
|
||||
do
|
||||
JNIFLAGS="$JNIFLAGS -I$JNI_INCLUDE_DIR"
|
||||
done
|
||||
## Find junit for testing the JNI code
|
||||
AX_CHECK_CLASSPATH()
|
||||
CLASSPATH_ENV=$H5_CLASSPATH
|
||||
AX_CHECK_JUNIT()
|
||||
AX_CHECK_JAVA_HOME
|
||||
|
||||
AC_MSG_RESULT([yes])
|
||||
else
|
||||
if test "X${enable_shared}" = "Xno"; then
|
||||
AC_MSG_ERROR([Java requires shared libraries to be built])
|
||||
fi
|
||||
HDF_JAVA="no"
|
||||
AC_MSG_RESULT([no])
|
||||
fi
|
||||
|
||||
## ----------------------------------------------------------------------
|
||||
## Fortran libraries are not currently supported on Mac. Disable them.
|
||||
## (this is overridable with --enable-unsupported).
|
||||
@@ -3071,7 +3137,7 @@ CXX_NOFLAGS=`echo $CXX | sed 's/ -.*//'`
|
||||
if `echo $CXX_NOFLAGS | grep ^/ >/dev/null 2>&1`; then
|
||||
CXX_VERSION="$CXX"
|
||||
else
|
||||
CXX_VERSION="$FC";
|
||||
CXX_VERSION="$CXX";
|
||||
for x in `echo $PATH | sed -e 's/:/ /g'`; do
|
||||
if test -x $x/$CXX_NOFLAGS; then
|
||||
CXX_VERSION="$x/$CXX"
|
||||
@@ -3083,6 +3149,27 @@ if test -n "$cxx_version_info"; then
|
||||
CXX_VERSION="$CXX_VERSION ( $cxx_version_info)"
|
||||
fi
|
||||
|
||||
AC_SUBST([JAVA_VERSION])
|
||||
## Strip anything that looks like a flag off of $JAVA
|
||||
JAVA_NOFLAGS=`echo $JAVA | sed 's/ -.*//'`
|
||||
|
||||
if `echo $JAVA_NOFLAGS | grep ^/ >/dev/null 2>&1`; then
|
||||
JAVA_VERSION="$JAVA"
|
||||
else
|
||||
JAVA_VERSION="$JAVA";
|
||||
for x in `echo $PATH | sed -e 's/:/ /g'`; do
|
||||
if test -x $x/$JAVA_NOFLAGS; then
|
||||
JAVA_VERSION="$x/$JAVA"
|
||||
break
|
||||
fi
|
||||
done
|
||||
fi
|
||||
java_version_info=`$JAVA -version 2>&1 |\
|
||||
grep 'version' | sed -e 's/version "//' | sed -e 's/"//'`
|
||||
if test -n "$java_version_info"; then
|
||||
JAVA_VERSION="$JAVA_VERSION ( $java_version_info)"
|
||||
fi
|
||||
|
||||
## ----------------------------------------------------------------------
|
||||
## Where is the root of the source tree. Give an absolute address so
|
||||
## we can find it no matter which directory of the distribution is our
|
||||
@@ -3296,6 +3383,8 @@ CFLAGS="$saved_user_CFLAGS"
|
||||
FCFLAGS="$saved_user_FCFLAGS"
|
||||
CXXFLAGS="$saved_user_CXXFLAGS"
|
||||
CPPFLAGS="$saved_user_CPPFLAGS"
|
||||
JAVACFLAGS="$saved_user_JAVACFLAGS"
|
||||
JAVAFLAGS="$saved_user_JAVAFLAGS"
|
||||
LDFLAGS="$saved_user_LDFLAGS"
|
||||
|
||||
|
||||
@@ -3306,6 +3395,7 @@ LDFLAGS="$saved_user_LDFLAGS"
|
||||
AM_CONDITIONAL([BUILD_CXX_CONDITIONAL], [test "X$HDF_CXX" = "Xyes"])
|
||||
AM_CONDITIONAL([BUILD_PARALLEL_CONDITIONAL], [test -n "$TESTPARALLEL"])
|
||||
AM_CONDITIONAL([BUILD_FORTRAN_CONDITIONAL], [test "X$HDF_FORTRAN" = "Xyes"])
|
||||
AM_CONDITIONAL([BUILD_JAVA_CONDITIONAL], [test "X$HDF_JAVA" = "Xyes"])
|
||||
AM_CONDITIONAL([BUILD_HDF5_HL_CONDITIONAL], [test "X$HDF5_HL" = "Xyes"])
|
||||
|
||||
|
||||
@@ -3451,6 +3541,20 @@ AC_CONFIG_FILES([src/libhdf5.settings
|
||||
fortran/examples/Makefile
|
||||
fortran/examples/run-fortran-ex.sh
|
||||
fortran/examples/testh5fc.sh
|
||||
java/Makefile
|
||||
java/src/Makefile
|
||||
java/src/jni/Makefile
|
||||
java/test/Makefile
|
||||
java/test/junit.sh
|
||||
java/examples/Makefile
|
||||
java/examples/intro/Makefile
|
||||
java/examples/intro/runExample.sh
|
||||
java/examples/datasets/Makefile
|
||||
java/examples/datasets/runExample.sh
|
||||
java/examples/datatypes/Makefile
|
||||
java/examples/datatypes/runExample.sh
|
||||
java/examples/groups/Makefile
|
||||
java/examples/groups/runExample.sh
|
||||
hl/Makefile
|
||||
hl/src/Makefile
|
||||
hl/test/Makefile
|
||||
|
||||
@@ -139,7 +139,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
|
||||
TARGET_C_PROPERTIES (${HDF5_F90_C_LIBSH_TARGET} SHARED " " " ")
|
||||
target_link_libraries (${HDF5_F90_C_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${LINK_SHARED_LIBS})
|
||||
set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_F90_C_LIBSH_TARGET}")
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_C_LIBSH_TARGET} ${HDF5_F90_C_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_C_LIBSH_TARGET} ${HDF5_F90_C_LIB_NAME} SHARED ${HDF5_F_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_F90_C_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/fortran
|
||||
LINKER_LANGUAGE C
|
||||
@@ -235,7 +235,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
|
||||
target_link_libraries (${HDF5_F90_LIBSH_TARGET} ${MPI_Fortran_LIBRARIES})
|
||||
endif (H5_HAVE_PARALLEL AND MPI_Fortran_FOUND)
|
||||
set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_F90_LIBSH_TARGET}")
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_LIBSH_TARGET} ${HDF5_F90_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_LIBSH_TARGET} ${HDF5_F90_LIB_NAME} SHARED ${HDF5_F_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_F90_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/fortran
|
||||
LINKER_LANGUAGE Fortran
|
||||
|
||||
@@ -65,7 +65,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
|
||||
${HDF5_F90_C_LIBSH_TARGET}
|
||||
${HDF5_TEST_LIBSH_TARGET}
|
||||
)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_C_TEST_LIBSH_TARGET} ${HDF5_F90_C_TEST_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_C_TEST_LIBSH_TARGET} ${HDF5_F90_C_TEST_LIB_NAME} SHARED ${HDF5_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_F90_C_TEST_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/test/fortran
|
||||
LINKER_LANGUAGE C
|
||||
@@ -128,7 +128,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
|
||||
${HDF5_F90_LIBSH_TARGET}
|
||||
${HDF5_LIBSH_TARGET}
|
||||
)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_TEST_LIBSH_TARGET} ${HDF5_F90_TEST_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_F90_TEST_LIBSH_TARGET} ${HDF5_F90_TEST_LIB_NAME} SHARED ${HDF5_PACKAGE_SOVERSION})
|
||||
target_include_directories (${HDF5_F90_TEST_LIBSH_TARGET} PRIVATE ${CMAKE_Fortran_MODULE_DIRECTORY}/shared)
|
||||
set_target_properties (${HDF5_F90_TEST_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/test/fortran
|
||||
|
||||
@@ -34,7 +34,7 @@ if (BUILD_SHARED_LIBS)
|
||||
${HDF5_LIBSH_TARGET}
|
||||
)
|
||||
set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_CPP_LIBSH_TARGET}")
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_CPP_LIBSH_TARGET} ${HDF5_HL_CPP_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_CPP_LIBSH_TARGET} ${HDF5_HL_CPP_LIB_NAME} SHARED ${HDF5_HL_CXX_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_HL_CPP_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/hl
|
||||
COMPILE_DEFINITIONS "H5_BUILT_AS_DYNAMIC_LIB"
|
||||
|
||||
@@ -91,7 +91,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
|
||||
TARGET_C_PROPERTIES (${HDF5_HL_F90_C_LIBSH_TARGET} SHARED " " " ")
|
||||
target_link_libraries (${HDF5_HL_F90_C_LIBSH_TARGET} ${HDF5_F90_C_LIBSH_TARGET} ${HDF5_HL_LIBSH_TARGET})
|
||||
set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_F90_C_LIBSH_TARGET}")
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_F90_C_LIBSH_TARGET} ${HDF5_HL_F90_C_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_F90_C_LIBSH_TARGET} ${HDF5_HL_F90_C_LIB_NAME} SHARED ${HDF5_HL_F_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_HL_F90_C_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/hl/fortran
|
||||
LINKER_LANGUAGE C
|
||||
@@ -163,7 +163,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
|
||||
TARGET_FORTRAN_PROPERTIES (${HDF5_HL_F90_LIBSH_TARGET} SHARED " " ${SHARED_LINK_FLAGS})
|
||||
target_link_libraries (${HDF5_HL_F90_LIBSH_TARGET} ${HDF5_HL_F90_C_LIBSH_TARGET} ${HDF5_F90_LIBSH_TARGET})
|
||||
set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_F90_LIBSH_TARGET}")
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_F90_LIBSH_TARGET} ${HDF5_HL_F90_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_F90_LIBSH_TARGET} ${HDF5_HL_F90_LIB_NAME} SHARED ${HDF5_HL_F_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_HL_F90_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/hl/fortran
|
||||
LINKER_LANGUAGE Fortran
|
||||
|
||||
@@ -42,7 +42,7 @@ if (BUILD_SHARED_LIBS)
|
||||
add_library (${HDF5_HL_LIBSH_TARGET} SHARED ${HL_SRCS} ${HL_HEADERS})
|
||||
TARGET_C_PROPERTIES (${HDF5_HL_LIBSH_TARGET} SHARED " " " ")
|
||||
target_link_libraries (${HDF5_HL_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_LIBSH_TARGET} ${HDF5_HL_LIB_NAME} SHARED)
|
||||
H5_SET_LIB_OPTIONS (${HDF5_HL_LIBSH_TARGET} ${HDF5_HL_LIB_NAME} SHARED ${HDF5_HL_PACKAGE_SOVERSION})
|
||||
set_target_properties (${HDF5_HL_LIBSH_TARGET} PROPERTIES
|
||||
FOLDER libraries/hl
|
||||
COMPILE_DEFINITIONS "H5_BUILT_AS_DYNAMIC_LIB"
|
||||
|
||||
@@ -0,0 +1,77 @@
|
||||
cmake_minimum_required(VERSION 3.1.0)
|
||||
PROJECT ( HDF5_JAVA C Java )
|
||||
|
||||
set (CMAKE_MODULE_PATH "${HDF_RESOURCES_DIR};${HDF_RESOURCES_EXT_DIR}")
|
||||
find_package (Java)
|
||||
#-----------------------------------------------------------------------------
|
||||
# Include some macros for reusable code
|
||||
#-----------------------------------------------------------------------------
|
||||
include (${HDF_RESOURCES_DIR}/UseJava.cmake)
|
||||
|
||||
message (STATUS "JAVA: JAVA_HOME=$ENV{JAVA_HOME} JAVA_ROOT=$ENV{JAVA_ROOT}")
|
||||
find_package (JNI)
|
||||
|
||||
INCLUDE_DIRECTORIES ( ${JNI_INCLUDE_DIRS} )
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Include the main src and config directories
|
||||
#-----------------------------------------------------------------------------
|
||||
set (HDF5_JAVA_INCLUDE_DIRECTORIES
|
||||
${HDF5_JAVA_JNI_SRC_DIR}
|
||||
${JAVA_INCLUDE_PATH}
|
||||
${JAVA_INCLUDE_PATH2}
|
||||
)
|
||||
INCLUDE_DIRECTORIES (${HDF5_JAVA_INCLUDE_DIRECTORIES})
|
||||
set (CMAKE_JAVA_INCLUDE_PATH "")
|
||||
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Traverse source subdirectory
|
||||
#-----------------------------------------------------------------------------
|
||||
add_subdirectory (${HDF5_JAVA_SOURCE_DIR}/src ${HDF5_JAVA_BINARY_DIR}/src)
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Build the Java Examples
|
||||
#-----------------------------------------------------------------------------
|
||||
if (HDF5_BUILD_EXAMPLES)
|
||||
add_subdirectory (${HDF5_JAVA_SOURCE_DIR}/examples ${HDF5_JAVA_BINARY_DIR}/examples)
|
||||
endif (HDF5_BUILD_EXAMPLES)
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Testing
|
||||
#-----------------------------------------------------------------------------
|
||||
if (BUILD_TESTING)
|
||||
add_subdirectory (${HDF5_JAVA_SOURCE_DIR}/test ${HDF5_JAVA_BINARY_DIR}/test)
|
||||
endif (BUILD_TESTING)
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Add Required Jar(s)
|
||||
#-----------------------------------------------------------------------------
|
||||
install (
|
||||
FILES
|
||||
${HDF5_JAVA_LOGGING_JAR}
|
||||
${HDF5_JAVA_LOGGING_NOP_JAR}
|
||||
${HDF5_JAVA_LOGGING_SIMPLE_JAR}
|
||||
DESTINATION ${HDF5_INSTALL_JAR_DIR}
|
||||
COMPONENT libraries
|
||||
)
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# Option to include jre
|
||||
#-----------------------------------------------------------------------------
|
||||
option (HDF5_JAVA_PACK_JRE "Package a JRE installer directory" OFF)
|
||||
if (HDF5_JAVA_PACK_JRE)
|
||||
if (WIN32)
|
||||
install (
|
||||
DIRECTORY "C:/Program Files/Java/jre8"
|
||||
DESTINATION ${HDF5_INSTALL_BIN_DIR}
|
||||
USE_SOURCE_PERMISSIONS
|
||||
)
|
||||
else (WIN32)
|
||||
install (
|
||||
DIRECTORY "/usr/lib/jvm/jre"
|
||||
DESTINATION ${HDF5_INSTALL_BIN_DIR}
|
||||
USE_SOURCE_PERMISSIONS
|
||||
)
|
||||
endif (WIN32)
|
||||
endif (HDF5_JAVA_PACK_JRE)
|
||||
@@ -0,0 +1,16 @@
|
||||
|
||||
Copyright by The HDF Group and
|
||||
The Board of Trustees of the University of Illinois.
|
||||
All rights reserved.
|
||||
|
||||
The files and subdirectories in this directory are part of HDF5.
|
||||
The full HDF5 copyright notice, including terms governing use,
|
||||
modification, and redistribution, is contained in the files COPYING
|
||||
and Copyright.html. COPYING can be found at the root of the source
|
||||
code distribution tree; Copyright.html can be found at the root
|
||||
level of an installed copy of the electronic HDF5 document set and
|
||||
is linked from the top-level documents page. It can also be found
|
||||
at http://www.hdfgroup.org/HDF5/doc/Copyright.html. If you do not
|
||||
have access to either file, you may request a copy from
|
||||
help@hdfgroup.org.
|
||||
|
||||
@@ -0,0 +1,38 @@
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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 native interface (JNI) Library Makefile(.in)
|
||||
|
||||
include $(top_srcdir)/config/commence.am
|
||||
|
||||
## Only recurse into subdirectories if the Java (JNI) interface is enabled.
|
||||
if BUILD_JAVA_CONDITIONAL
|
||||
|
||||
# Mark this directory as part of the JNI API
|
||||
JAVA_API=yes
|
||||
|
||||
SUBDIRS=src test examples
|
||||
|
||||
endif
|
||||
|
||||
include $(top_srcdir)/config/conclude.am
|
||||
@@ -0,0 +1,7 @@
|
||||
cmake_minimum_required (VERSION 3.1.0)
|
||||
PROJECT (HDFJAVA_EXAMPLES)
|
||||
|
||||
add_subdirectory (${HDFJAVA_EXAMPLES_SOURCE_DIR}/datasets datasets)
|
||||
add_subdirectory (${HDFJAVA_EXAMPLES_SOURCE_DIR}/datatypes datatypes)
|
||||
add_subdirectory (${HDFJAVA_EXAMPLES_SOURCE_DIR}/groups groups)
|
||||
add_subdirectory (${HDFJAVA_EXAMPLES_SOURCE_DIR}/intro intro)
|
||||
@@ -0,0 +1,31 @@
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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
|
||||
@@ -0,0 +1,121 @@
|
||||
cmake_minimum_required (VERSION 3.1.0)
|
||||
PROJECT (HDFJAVA_EXAMPLES_DATASETS Java)
|
||||
|
||||
set (CMAKE_VERBOSE_MAKEFILE 1)
|
||||
|
||||
INCLUDE_DIRECTORIES (
|
||||
${HDF5_JAVA_JNI_BINARY_DIR}
|
||||
${HDF5_JAVA_HDF5_LIB_DIR}
|
||||
)
|
||||
|
||||
set (HDF_JAVA_EXAMPLES
|
||||
H5Ex_D_Alloc
|
||||
H5Ex_D_Checksum
|
||||
H5Ex_D_Chunk
|
||||
H5Ex_D_Compact
|
||||
H5Ex_D_External
|
||||
H5Ex_D_FillValue
|
||||
H5Ex_D_Gzip
|
||||
H5Ex_D_Hyperslab
|
||||
H5Ex_D_ReadWrite
|
||||
H5Ex_D_Shuffle
|
||||
H5Ex_D_Szip
|
||||
H5Ex_D_UnlimitedAdd
|
||||
H5Ex_D_UnlimitedGzip
|
||||
H5Ex_D_UnlimitedMod
|
||||
H5Ex_D_Nbit
|
||||
H5Ex_D_Transform
|
||||
H5Ex_D_Sofloat
|
||||
H5Ex_D_Soint
|
||||
)
|
||||
|
||||
if (WIN32)
|
||||
set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
|
||||
else (WIN32)
|
||||
set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
|
||||
endif (WIN32)
|
||||
|
||||
set (CMAKE_JAVA_INCLUDE_PATH "${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 (CMAKE_INCLUDE_PATH)
|
||||
|
||||
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})
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
|
||||
set (CMAKE_JAVA_INCLUDE_PATH "${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 (HDFJAVA_JAR)
|
||||
|
||||
MACRO (ADD_H5_TEST resultfile resultcode)
|
||||
add_test (
|
||||
NAME JAVA_datasets-${resultfile}
|
||||
COMMAND "${CMAKE_COMMAND}"
|
||||
-D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}"
|
||||
-D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${resultfile}_JAR_FILE}"
|
||||
-D "TEST_ARGS:STRING=${ARGN}"
|
||||
-D "TEST_PROGRAM=examples.datasets.${resultfile}"
|
||||
-D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}"
|
||||
-D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}"
|
||||
-D "TEST_OUTPUT=datasets/${resultfile}.out"
|
||||
-D "TEST_EXPECT=${resultcode}"
|
||||
-D "TEST_REFERENCE=datasets/${resultfile}.txt"
|
||||
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_datasets-${resultfile} PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
set (last_test "JAVA_datasets-${resultfile}")
|
||||
ENDMACRO (ADD_H5_TEST file)
|
||||
|
||||
if (BUILD_TESTING)
|
||||
foreach (example ${HDF_JAVA_EXAMPLES})
|
||||
if (${example} STREQUAL "H5Ex_D_External")
|
||||
add_test (
|
||||
NAME JAVA_datasets-${example}-clearall-objects
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-E remove
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.data
|
||||
${example}.out
|
||||
${example}.out.err
|
||||
)
|
||||
else (${example} STREQUAL "H5Ex_D_External")
|
||||
add_test (
|
||||
NAME JAVA_datasets-${example}-clearall-objects
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-E remove
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
|
||||
${example}.out
|
||||
${example}.out.err
|
||||
)
|
||||
endif (${example} STREQUAL "H5Ex_D_External")
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_datasets-${example}-clearall-objects PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
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}-clearall-objects)
|
||||
set (last_test "JAVA_datasets-${example}-copy-objects")
|
||||
ADD_H5_TEST (${example} 0)
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
endif (BUILD_TESTING)
|
||||
@@ -0,0 +1,301 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id1 = -1;
|
||||
long dataset_id2 = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,347 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,366 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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_NLAYOUTS(3);
|
||||
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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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_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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,289 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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_NLAYOUTS(3);
|
||||
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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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_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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,238 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dcpl_id = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dcpl_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,246 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dcpl_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,336 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,269 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,305 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dtype_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,179 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,373 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,356 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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.util.EnumSet;
|
||||
import java.util.HashMap;
|
||||
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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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.
|
||||
System.out.println("Maximum value in write buffer is: " + max);
|
||||
System.out.println("Minimum value in write buffer is: " + 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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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.
|
||||
System.out.println("Maximum value in " + DATASETNAME + " is: " + max);
|
||||
System.out.println("Minimum value in " + DATASETNAME + " is: " + 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();
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,335 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,337 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,250 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filespace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dxpl_id = -1;
|
||||
|
||||
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 = -1;
|
||||
long dataset_id = -1;
|
||||
long dxpl_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,393 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dcpl_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,504 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dcpl_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,379 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 utputs 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 = -1;
|
||||
long dcpl_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,78 @@
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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:
|
||||
$(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-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.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 = runExample.sh
|
||||
TEST_SCRIPT = $(check_SCRIPTS)
|
||||
|
||||
CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class runExample.sh
|
||||
|
||||
clean:
|
||||
rm -rf $(JAVAROOT)
|
||||
rm -f $(jarfile)
|
||||
rm -f classnoinst.stamp
|
||||
|
||||
include $(top_srcdir)/config/conclude.am
|
||||
@@ -0,0 +1,413 @@
|
||||
#! /bin/sh
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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@
|
||||
|
||||
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'
|
||||
LS='ls'
|
||||
AWK='awk'
|
||||
|
||||
nerrors=0
|
||||
|
||||
# where the libs exist
|
||||
HDFLIB_HOME="$top_srcdir/java/lib"
|
||||
BLDLIBDIR="./lib"
|
||||
BLDDIR="."
|
||||
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="
|
||||
$HDFLIB_HOME/slf4j-api-1.7.5.jar
|
||||
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
|
||||
$top_builddir/src/.libs/libhdf5.*
|
||||
$top_builddir/java/src/jni/.libs/libhdf5_java.*
|
||||
$top_builddir/java/src/$JARFILE
|
||||
"
|
||||
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_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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$CP -f $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=`$DIRNAME $tstfile`
|
||||
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
|
||||
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $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 $TESTDIR | $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()
|
||||
{
|
||||
# skip rm 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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $BLDDIR/*.txt
|
||||
$RM $BLDDIR/*.out
|
||||
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
|
||||
|
||||
CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.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
|
||||
Darwin)
|
||||
DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
|
||||
export DYLD_LIBRARY_PATH
|
||||
LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
|
||||
;;
|
||||
*)
|
||||
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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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
|
||||
|
||||
echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Gzip"
|
||||
($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
|
||||
|
||||
echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Hyperslab"
|
||||
($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"
|
||||
($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
|
||||
|
||||
echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.datasets.H5Ex_D_Shuffle"
|
||||
($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
|
||||
|
||||
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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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
|
||||
@@ -0,0 +1,109 @@
|
||||
cmake_minimum_required (VERSION 3.1.0)
|
||||
PROJECT (HDFJAVA_EXAMPLES_DATATYPES Java)
|
||||
|
||||
set (CMAKE_VERBOSE_MAKEFILE 1)
|
||||
|
||||
INCLUDE_DIRECTORIES (
|
||||
${HDF5_JAVA_JNI_BINARY_DIR}
|
||||
${HDF5_JAVA_HDF5_LIB_DIR}
|
||||
)
|
||||
|
||||
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 (WIN32)
|
||||
set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
|
||||
endif (WIN32)
|
||||
|
||||
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 (CMAKE_INCLUDE_PATH)
|
||||
|
||||
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})
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
|
||||
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 (HDFJAVA_JAR)
|
||||
|
||||
MACRO (ADD_H5_TEST resultfile resultcode)
|
||||
add_test (
|
||||
NAME JAVA_datatypes-${resultfile}
|
||||
COMMAND "${CMAKE_COMMAND}"
|
||||
-D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}"
|
||||
-D "TEST_PROGRAM=examples.datatypes.${resultfile}"
|
||||
-D "TEST_ARGS:STRING=${ARGN}"
|
||||
-D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${resultfile}_JAR_FILE}"
|
||||
-D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}"
|
||||
-D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}"
|
||||
-D "TEST_OUTPUT=datatypes/${resultfile}.out"
|
||||
-D "TEST_EXPECT=${resultcode}"
|
||||
-D "TEST_REFERENCE=datatypes/${resultfile}.txt"
|
||||
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_datatypes-${resultfile} PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
set (last_test "JAVA_datatypes-${resultfile}")
|
||||
ENDMACRO (ADD_H5_TEST file)
|
||||
|
||||
if (BUILD_TESTING)
|
||||
foreach (example ${HDF_JAVA_EXAMPLES})
|
||||
add_test (
|
||||
NAME JAVA_datatypes-${example}-clearall-objects
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-E remove
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
|
||||
${example}.out
|
||||
${example}.out.err
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_datatypes-${example}-clearall-objects PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
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}-clearall-objects)
|
||||
set (last_test "JAVA_datatypes-${example}-copy-objects")
|
||||
ADD_H5_TEST (${example} 0)
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
endif (BUILD_TESTING)
|
||||
@@ -0,0 +1,282 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filetype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long filetype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,322 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long filetype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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 = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
long filetype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,227 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,267 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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 = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,265 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
|
||||
import java.util.EnumSet;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
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 = -1;
|
||||
long strtype_id = -1;
|
||||
long filetype_id = -1;
|
||||
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 = -1;
|
||||
long typeclass_id = -1;
|
||||
long filetype_id = -1;
|
||||
|
||||
// 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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,443 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
|
||||
import java.nio.ByteBuffer;
|
||||
import java.nio.ByteOrder;
|
||||
import java.nio.charset.Charset;
|
||||
|
||||
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(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));
|
||||
}
|
||||
|
||||
@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 = -1;
|
||||
long strtype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long filetype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
Sensor[] object_data = new Sensor[DIM0];
|
||||
byte[] dset_data = null;
|
||||
|
||||
// Initialize data.
|
||||
object_data[0] = new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57);
|
||||
object_data[1] = new Sensor(1184, new String("Intake"), 55.12, 22.95);
|
||||
object_data[2] = new Sensor(1027, new String("Intake manifold"), 103.55, 31.23);
|
||||
object_data[3] = new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11);
|
||||
|
||||
// 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.
|
||||
// allocate memory for read buffer.
|
||||
dset_data = new byte[(int)dims[0] * (int)Sensor_Datatype.getDataSize()];
|
||||
ByteBuffer outBuf = ByteBuffer.wrap(dset_data);
|
||||
outBuf.order(ByteOrder.nativeOrder());
|
||||
for (int indx = 0; indx < (int) dims[0]; indx++) {
|
||||
object_data[indx].writeBuffer(outBuf, indx * (int)Sensor_Datatype.getDataSize());
|
||||
}
|
||||
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();
|
||||
}
|
||||
|
||||
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 = -1;
|
||||
long strtype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
Sensor[] object_data2;
|
||||
byte[] 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();
|
||||
}
|
||||
|
||||
// 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();
|
||||
}
|
||||
|
||||
// allocate memory for read buffer.
|
||||
dset_data = new byte[(int) dims[0] * (int)Sensor_Datatype.getDataSize()];
|
||||
|
||||
object_data2 = new Sensor[(int) dims[0]];
|
||||
|
||||
// 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);
|
||||
|
||||
ByteBuffer inBuf = ByteBuffer.wrap(dset_data);
|
||||
inBuf.order(ByteOrder.nativeOrder());
|
||||
for (int indx = 0; indx < (int) dims[0]; indx++) {
|
||||
object_data2[indx] = new Sensor(inBuf, indx * (int)Sensor_Datatype.getDataSize());
|
||||
}
|
||||
}
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,486 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
|
||||
import java.nio.ByteBuffer;
|
||||
import java.nio.ByteOrder;
|
||||
import java.nio.charset.Charset;
|
||||
|
||||
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;
|
||||
|
||||
// Using Java Externalization will add a two-byte object header in
|
||||
// the stream, which needs to be called out in the datatypes.
|
||||
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(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));
|
||||
}
|
||||
|
||||
@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 = -1;
|
||||
long strtype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long filetype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
Sensor[] object_data = new Sensor[DIM0];
|
||||
byte[] dset_data = null;
|
||||
|
||||
// Initialize data.
|
||||
object_data[0] = new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57);
|
||||
object_data[1] = new Sensor(1184, new String("Intake"), 55.12, 22.95);
|
||||
object_data[2] = new Sensor(1027, new String("Intake manifold"), 103.55, 31.23);
|
||||
object_data[3] = new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11);
|
||||
|
||||
// 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 = -1;
|
||||
}
|
||||
}
|
||||
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.
|
||||
dset_data = new byte[(int) dims[0] * (int)Sensor_Datatype.getDataSize()];
|
||||
ByteBuffer outBuf = ByteBuffer.wrap(dset_data);
|
||||
outBuf.order(ByteOrder.nativeOrder());
|
||||
for (int indx = 0; indx < (int) dims[0]; indx++) {
|
||||
object_data[indx].writeBuffer(outBuf, indx * (int)Sensor_Datatype.getDataSize());
|
||||
}
|
||||
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();
|
||||
}
|
||||
|
||||
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 = -1;
|
||||
long strtype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
Sensor[] object_data2;
|
||||
byte[] 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. 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();
|
||||
}
|
||||
|
||||
// allocate memory for read buffer.
|
||||
dset_data = new byte[(int) dims[0] * (int)Sensor_Datatype.getDataSize()];
|
||||
|
||||
object_data2 = new Sensor[(int) dims[0]];
|
||||
|
||||
// Read data.
|
||||
try {
|
||||
if ((attribute_id >= 0) && (memtype_id >= 0))
|
||||
H5.H5Aread(attribute_id, memtype_id, dset_data);
|
||||
|
||||
ByteBuffer inBuf = ByteBuffer.wrap(dset_data);
|
||||
inBuf.order(ByteOrder.nativeOrder());
|
||||
for (int indx = 0; indx < (int) dims[0]; indx++) {
|
||||
object_data2[indx] = new Sensor(inBuf, indx * (int)Sensor_Datatype.getDataSize());
|
||||
}
|
||||
}
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,227 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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_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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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");
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,263 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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 = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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");
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,226 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,263 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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 = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,347 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long filespace_id = -1;
|
||||
long group_id = -1;
|
||||
long dataset_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
byte[][] dset_data = new byte[DIM0][8];
|
||||
|
||||
// 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 = -1;
|
||||
H5.H5Sclose(dataspace_id);
|
||||
dataspace_id = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
// Create references to the previously created objects. Passing -1
|
||||
// as space_id causes this parameter to be ignored. Other values
|
||||
// besides valid dataspaces result in an error.
|
||||
try {
|
||||
if (file_id >= 0) {
|
||||
byte rbuf0[] = H5.H5Rcreate(file_id, GROUPNAME, HDF5Constants.H5R_OBJECT, -1);
|
||||
byte rbuf1[] = H5.H5Rcreate(file_id, DATASETNAME2, HDF5Constants.H5R_OBJECT, -1);
|
||||
for (int indx = 0; indx < 8; indx++) {
|
||||
dset_data[0][indx] = rbuf0[indx];
|
||||
dset_data[1][indx] = rbuf1[indx];
|
||||
}
|
||||
}
|
||||
}
|
||||
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.
|
||||
try {
|
||||
if ((file_id >= 0) && (filespace_id >= 0))
|
||||
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_REF_OBJ, 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_OBJ, 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 readObjRef() {
|
||||
long file_id = -1;
|
||||
long dataset_id = -1;
|
||||
long dataspace_id = -1;
|
||||
int object_type = -1;
|
||||
long object_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
byte[][] 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 byte[(int)dims[0]][8];
|
||||
|
||||
// Read the data using the default properties.
|
||||
try {
|
||||
if (dataset_id >= 0) {
|
||||
H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, 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 + "]:");
|
||||
System.out.print(" ->");
|
||||
// Open the referenced object, get its name and type.
|
||||
try {
|
||||
if (dataset_id >= 0) {
|
||||
object_id = H5.H5Rdereference(dataset_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, dset_data[indx]);
|
||||
object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]);
|
||||
}
|
||||
String[] obj_name = new String[1];
|
||||
long name_size = 1;
|
||||
if (object_type >= 0) {
|
||||
// Get the length of the name and retrieve the name.
|
||||
name_size = 1 + H5.H5Iget_name(object_id, obj_name, name_size);
|
||||
}
|
||||
if ((object_id >= 0) && (object_type >= -1)) {
|
||||
switch (H5G_obj.get(object_type)) {
|
||||
case H5G_GROUP:
|
||||
System.out.print("H5G_GROUP");
|
||||
try {
|
||||
if (object_id >= 0)
|
||||
H5.H5Gclose(object_id);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
break;
|
||||
case H5G_DATASET:
|
||||
System.out.print("H5G_DATASET");
|
||||
try {
|
||||
if (object_id >= 0)
|
||||
H5.H5Dclose(object_id);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
break;
|
||||
case H5G_TYPE:
|
||||
System.out.print("H5G_TYPE");
|
||||
try {
|
||||
if (object_id >= 0)
|
||||
H5.H5Tclose(object_id);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
break;
|
||||
default:
|
||||
System.out.print("UNHANDLED");
|
||||
}
|
||||
}
|
||||
// Print the name.
|
||||
if (name_size > 1)
|
||||
System.out.println(": " + obj_name[0]);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
|
||||
// End access to the dataset and release resources used by it.
|
||||
try {
|
||||
if (dataspace_id >= 0)
|
||||
H5.H5Sclose(dataspace_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.
|
||||
H5Ex_T_ObjectReference.writeObjRef();
|
||||
H5Ex_T_ObjectReference.readObjRef();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,389 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long group_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
byte[][] dset_data = new byte[DIM0][8];
|
||||
|
||||
// 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, 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 = -1;
|
||||
H5.H5Sclose(dataspace_id);
|
||||
dataspace_id = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
// Create references to the previously created objects. Passing -1
|
||||
// as space_id causes this parameter to be ignored. Other values
|
||||
// besides valid dataspaces result in an error.
|
||||
try {
|
||||
if (file_id >= 0) {
|
||||
byte rbuf0[] = H5.H5Rcreate(file_id, GROUPNAME, HDF5Constants.H5R_OBJECT, -1);
|
||||
byte rbuf1[] = H5.H5Rcreate(file_id, DATASETNAME2, HDF5Constants.H5R_OBJECT, -1);
|
||||
for (int indx = 0; indx < 8; indx++) {
|
||||
dset_data[0][indx] = rbuf0[indx];
|
||||
dset_data[1][indx] = rbuf1[indx];
|
||||
}
|
||||
}
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.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 = -1;
|
||||
}
|
||||
}
|
||||
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_OBJ, 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_OBJ, 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
int object_type = -1;
|
||||
long object_id = -1;
|
||||
long[] dims = { DIM0 };
|
||||
byte[][] 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 byte[(int) dims[0]][8];
|
||||
|
||||
// Read data.
|
||||
try {
|
||||
if (attribute_id >= 0)
|
||||
H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, 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 + "]:");
|
||||
System.out.print(" ->");
|
||||
// Open the referenced object, get its name and type.
|
||||
try {
|
||||
if (dataset_id >= 0) {
|
||||
object_id = H5.H5Rdereference(dataset_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, dset_data[indx]);
|
||||
object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]);
|
||||
}
|
||||
String[] obj_name = new String[1];
|
||||
long name_size = 1;
|
||||
if (object_type >= 0) {
|
||||
// Get the length of the name and retrieve the name.
|
||||
name_size = 1 + H5.H5Iget_name(object_id, obj_name, name_size);
|
||||
}
|
||||
if ((object_id >= 0) && (object_type >= -1)) {
|
||||
switch (H5G_obj.get(object_type)) {
|
||||
case H5G_GROUP:
|
||||
System.out.print("H5G_GROUP");
|
||||
try {
|
||||
if (object_id >= 0)
|
||||
H5.H5Gclose(object_id);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
break;
|
||||
case H5G_DATASET:
|
||||
System.out.print("H5G_DATASET");
|
||||
try {
|
||||
if (object_id >= 0)
|
||||
H5.H5Dclose(object_id);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
break;
|
||||
case H5G_TYPE:
|
||||
System.out.print("H5G_TYPE");
|
||||
try {
|
||||
if (object_id >= 0)
|
||||
H5.H5Tclose(object_id);
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
break;
|
||||
default:
|
||||
System.out.print("UNHANDLED");
|
||||
}
|
||||
}
|
||||
// Print the name.
|
||||
if (name_size > 1)
|
||||
System.out.println(": " + obj_name[0]);
|
||||
}
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,270 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long datatype_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long datatype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
// 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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,307 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long datatype_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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 = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
long datatype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,311 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long memtype_id = -1;
|
||||
long filetype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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 = -1;
|
||||
long filetype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,351 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long memtype_id = -1;
|
||||
long filetype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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 = -1;
|
||||
}
|
||||
}
|
||||
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 = -1;
|
||||
long filetype_id = -1;
|
||||
long memtype_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,138 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long type_id = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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.H5Dwrite_VLStrings(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 = -1;
|
||||
long type_id = -1;
|
||||
long dataset_id = -1;
|
||||
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.H5Dread_VLStrings(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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,78 @@
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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:
|
||||
$(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-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.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 = runExample.sh
|
||||
TEST_SCRIPT = $(check_SCRIPTS)
|
||||
|
||||
CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class runExample.sh
|
||||
|
||||
clean:
|
||||
rm -rf $(JAVAROOT)
|
||||
rm -f $(jarfile)
|
||||
rm -f classnoinst.stamp
|
||||
|
||||
include $(top_srcdir)/config/conclude.am
|
||||
@@ -0,0 +1,408 @@
|
||||
#! /bin/sh
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# All rights reserved.
|
||||
#
|
||||
# This file is part of HDF5. The full HDF5 copyright notice, including
|
||||
# terms governing use, modification, and redistribution, is contained in
|
||||
# the files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
|
||||
# access to either file, you may request a copy from help@hdfgroup.org.
|
||||
#
|
||||
|
||||
top_builddir=@top_builddir@
|
||||
top_srcdir=@top_srcdir@
|
||||
srcdir=@srcdir@
|
||||
|
||||
TESTNAME=EX_Datatypes
|
||||
EXIT_SUCCESS=0
|
||||
EXIT_FAILURE=1
|
||||
|
||||
# Set up default variable values if not supplied by the user.
|
||||
RM='rm -rf'
|
||||
CMP='cmp'
|
||||
DIFF='diff -c'
|
||||
CP='cp'
|
||||
DIRNAME='dirname'
|
||||
LS='ls'
|
||||
AWK='awk'
|
||||
|
||||
nerrors=0
|
||||
|
||||
# where the libs exist
|
||||
HDFLIB_HOME="$top_srcdir/java/lib"
|
||||
BLDLIBDIR="./lib"
|
||||
BLDDIR="."
|
||||
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="
|
||||
$HDFLIB_HOME/slf4j-api-1.7.5.jar
|
||||
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
|
||||
$top_builddir/src/.libs/libhdf5.*
|
||||
$top_builddir/java/src/jni/.libs/libhdf5_java.*
|
||||
$top_builddir/java/src/$JARFILE
|
||||
"
|
||||
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_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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$CP -f $tstfile $BLDLIBDIR
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Error: FAILED to copy $tstfile ."
|
||||
|
||||
# Comment out this to CREATE expected file
|
||||
exit $EXIT_FAILURE
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
}
|
||||
|
||||
CLEAN_LIBFILES_AND_BLDLIBDIR()
|
||||
{
|
||||
# skip rm if srcdir is same as destdir
|
||||
# this occurs when build/test performed in source dir and
|
||||
# make cp fail
|
||||
SDIR=`$DIRNAME $tstfile`
|
||||
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
|
||||
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $BLDLIBDIR
|
||||
fi
|
||||
}
|
||||
|
||||
COPY_DATAFILES="$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 $TESTDIR | $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 $EXIT_FAILURE
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
}
|
||||
|
||||
CLEAN_DATAFILES_AND_BLDDIR()
|
||||
{
|
||||
# skip rm if srcdir is same as destdir
|
||||
# this occurs when build/test performed in source dir and
|
||||
# make cp fail
|
||||
SDIR=`$DIRNAME $tstfile`
|
||||
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
|
||||
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $BLDDIR/*.txt
|
||||
$RM $BLDDIR/*.out
|
||||
fi
|
||||
}
|
||||
|
||||
# Print a line-line message left justified in a field of 70 characters
|
||||
# beginning with the word "Testing".
|
||||
#
|
||||
TESTING() {
|
||||
SPACES=" "
|
||||
echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012'
|
||||
}
|
||||
|
||||
# where Java is installed (requires jdk1.7.x)
|
||||
JAVAEXE=@JAVA@
|
||||
JAVAEXEFLAGS=@H5_JAVAFLAGS@
|
||||
|
||||
###############################################################################
|
||||
# DO NOT MODIFY BELOW THIS LINE
|
||||
###############################################################################
|
||||
|
||||
# prepare for test
|
||||
COPY_LIBFILES_TO_BLDLIBDIR
|
||||
COPY_DATAFILES_TO_BLDDIR
|
||||
|
||||
CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.jar:"$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 $os_name in
|
||||
Darwin)
|
||||
DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
|
||||
export DYLD_LIBRARY_PATH
|
||||
LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
|
||||
;;
|
||||
*)
|
||||
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 $CLASSPATH examples.datatypes.H5Ex_T_Array"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_ArrayAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_Bit"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_BitAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_Commit"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_Compound"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_CompoundAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_Float"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_FloatAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_Integer"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_IntegerAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_ObjectReference"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_ObjectReferenceAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_Opaque"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_OpaqueAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_String"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_StringAttribute"
|
||||
($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 $CLASSPATH examples.datatypes.H5Ex_T_VLString"
|
||||
($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
|
||||
@@ -0,0 +1,138 @@
|
||||
cmake_minimum_required (VERSION 3.1.0)
|
||||
PROJECT (HDFJAVA_EXAMPLES_GROUPS Java)
|
||||
|
||||
set (CMAKE_VERBOSE_MAKEFILE 1)
|
||||
|
||||
INCLUDE_DIRECTORIES (
|
||||
${HDF5_JAVA_JNI_BINARY_DIR}
|
||||
${HDF5_JAVA_HDF5_LIB_DIR}
|
||||
)
|
||||
|
||||
set (HDF_JAVA_EXAMPLES
|
||||
H5Ex_G_Create
|
||||
H5Ex_G_Iterate
|
||||
H5Ex_G_Compact
|
||||
H5Ex_G_Corder
|
||||
H5Ex_G_Intermediate
|
||||
H5Ex_G_Phase
|
||||
H5Ex_G_Visit
|
||||
)
|
||||
|
||||
if (WIN32)
|
||||
set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
|
||||
else (WIN32)
|
||||
set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
|
||||
endif (WIN32)
|
||||
|
||||
set (CMAKE_JAVA_INCLUDE_PATH "${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 (CMAKE_INCLUDE_PATH)
|
||||
|
||||
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})
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
|
||||
set (CMAKE_JAVA_INCLUDE_PATH "${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 (HDFJAVA_JAR)
|
||||
|
||||
set (HDF_JAVA_TEST_FILES
|
||||
h5ex_g_iterate.h5
|
||||
h5ex_g_visit.h5
|
||||
)
|
||||
|
||||
foreach (h5_file ${HDF_JAVA_TEST_FILES})
|
||||
set (dest "${PROJECT_BINARY_DIR}/${h5_file}")
|
||||
#message (STATUS " Copying ${h5_file}")
|
||||
add_custom_command (
|
||||
TARGET H5Ex_G_Visit
|
||||
POST_BUILD
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
ARGS -E copy_if_different ${PROJECT_SOURCE_DIR}/${h5_file} ${dest}
|
||||
)
|
||||
endforeach (h5_file ${HDF_JAVA_TEST_FILES})
|
||||
|
||||
MACRO (ADD_H5_TEST resultfile resultcode)
|
||||
add_test (
|
||||
NAME JAVA_groups-${resultfile}
|
||||
COMMAND "${CMAKE_COMMAND}"
|
||||
-D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}"
|
||||
-D "TEST_PROGRAM=examples.groups.${resultfile}"
|
||||
-D "TEST_ARGS:STRING=${ARGN}"
|
||||
-D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${resultfile}_JAR_FILE}"
|
||||
-D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}"
|
||||
-D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}"
|
||||
-D "TEST_OUTPUT=groups/${resultfile}.out"
|
||||
-D "TEST_EXPECT=${resultcode}"
|
||||
-D "TEST_REFERENCE=groups/${resultfile}.txt"
|
||||
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_groups-${resultfile} PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
set (last_test "JAVA_groups-${resultfile}")
|
||||
ENDMACRO (ADD_H5_TEST file)
|
||||
|
||||
if (BUILD_TESTING)
|
||||
foreach (example ${HDF_JAVA_EXAMPLES})
|
||||
add_test (
|
||||
NAME JAVA_groups-${example}-clearall-objects
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-E remove
|
||||
${example}.out
|
||||
${example}.out.err
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_groups-${example}-clearall-objects PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
set (last_test "JAVA_groups-${example}-clearall-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}-clearall-h5s
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-E remove
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}1.h5
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}2.h5
|
||||
)
|
||||
else (${example} STREQUAL "H5Ex_G_Compact")
|
||||
add_test (
|
||||
NAME JAVA_groups-${example}-clearall-h5s
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-E remove
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
|
||||
)
|
||||
endif (${example} STREQUAL "H5Ex_G_Compact")
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_groups-${example}-clearall-h5s PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
set (last_test "JAVA_groups-${example}-clearall-h5s")
|
||||
endif (NOT ${example} STREQUAL "H5Ex_G_Iterate" AND NOT ${example} STREQUAL "H5Ex_G_Visit")
|
||||
add_test (
|
||||
NAME JAVA_groups-${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
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_groups-${example}-copy-objects PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
set (last_test "JAVA_groups-${example}-copy-objects")
|
||||
ADD_H5_TEST (${example} 0)
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
endif (BUILD_TESTING)
|
||||
@@ -0,0 +1,266 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
import hdf.hdf5lib.structs.H5G_info_t;
|
||||
|
||||
import java.util.EnumSet;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
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 = -1;
|
||||
long group_id = -1;
|
||||
long fapl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,121 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 alpabetical 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 = -1;
|
||||
long group_id = -1;
|
||||
long subgroup_id = -1;
|
||||
long gcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,94 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long group_id = -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 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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,125 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
import hdf.hdf5lib.callbacks.H5O_iterate_cb;
|
||||
import hdf.hdf5lib.callbacks.H5O_iterate_t;
|
||||
import hdf.hdf5lib.structs.H5O_info_t;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
||||
public class H5Ex_G_Intermediate {
|
||||
|
||||
private static String FILE = "H5Ex_G_Intermediate.h5";
|
||||
|
||||
private void CreateGroup() throws Exception {
|
||||
|
||||
long file_id = -1;
|
||||
long group_id = -1;
|
||||
long gcpl_id = -1;
|
||||
|
||||
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_t iter_data = null;
|
||||
H5O_iterate_t iter_data = new H5O_iter_data();
|
||||
H5O_iterate_cb 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_t {
|
||||
public ArrayList<idata> iterdata = new ArrayList<idata>();
|
||||
}
|
||||
|
||||
private class H5O_iter_callback implements H5O_iterate_cb {
|
||||
public int callback(long group, String name, H5O_info_t info, H5O_iterate_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;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,119 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
|
||||
import java.util.EnumSet;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
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 = -1;
|
||||
|
||||
// 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];
|
||||
long[] orefs = new long[count];
|
||||
H5.H5Gget_obj_info_all(file_id, DATASETNAME, oname, otype, ltype, orefs, 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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,241 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
import hdf.hdf5lib.structs.H5G_info_t;
|
||||
|
||||
import java.util.EnumSet;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
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 = -1;
|
||||
long group_id = -1;
|
||||
long subgroup_id = -1;
|
||||
long fapl_id = -1;
|
||||
long gcpl_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,167 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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_cb;
|
||||
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_t {
|
||||
int recurs;
|
||||
opdata prev;
|
||||
long addr;
|
||||
}
|
||||
|
||||
public class H5Ex_G_Traverse {
|
||||
|
||||
private static String FILE = "h5ex_g_traverse.h5";
|
||||
public static H5L_iterate_cb iter_cb = new H5L_iter_callbackT();
|
||||
|
||||
private static void OpenGroup() {
|
||||
long file_id = -1;
|
||||
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.addr = infobuf.addr;
|
||||
}
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
// Print the root group and formatting, begin iteration.
|
||||
try {
|
||||
System.out.println("/ {");
|
||||
// H5L_iterate_cb 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_cb {
|
||||
public int callback(long group, String name, H5L_info_t info, H5L_iterate_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 address 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.addr)) {
|
||||
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.addr = infobuf.addr;
|
||||
H5L_iterate_cb 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, long target_addr) {
|
||||
if (od.addr == target_addr)
|
||||
return true; // Addresses match
|
||||
else if (od.recurs == 0)
|
||||
return false; // Root group reached with no matches
|
||||
else
|
||||
return group_check(od.prev, target_addr); // Recursively examine the next node
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,152 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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's
|
||||
Guide, chapter 4, figure 26.
|
||||
************************************************************/
|
||||
package examples.groups;
|
||||
|
||||
import hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
import hdf.hdf5lib.callbacks.H5L_iterate_cb;
|
||||
import hdf.hdf5lib.callbacks.H5L_iterate_t;
|
||||
import hdf.hdf5lib.callbacks.H5O_iterate_cb;
|
||||
import hdf.hdf5lib.callbacks.H5O_iterate_t;
|
||||
import hdf.hdf5lib.structs.H5L_info_t;
|
||||
import hdf.hdf5lib.structs.H5O_info_t;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
||||
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 = -1;
|
||||
|
||||
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_t iter_data = new H5O_iter_data();
|
||||
H5O_iterate_cb 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_t iter_data2 = new H5L_iter_data();
|
||||
H5L_iterate_cb 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_t {
|
||||
public ArrayList<idata> iterdata = new ArrayList<idata>();
|
||||
}
|
||||
|
||||
private class H5L_iter_callback implements H5L_iterate_cb {
|
||||
public int callback(long group, String name, H5L_info_t info, H5L_iterate_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_cb iter_cbO = new H5O_iter_callback();
|
||||
H5O_iterate_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_t {
|
||||
public ArrayList<idata> iterdata = new ArrayList<idata>();
|
||||
}
|
||||
|
||||
private class H5O_iter_callback implements H5O_iterate_cb {
|
||||
public int callback(long group, String name, H5O_info_t info, H5O_iterate_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;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,68 @@
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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:
|
||||
$(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-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.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 = runExample.sh
|
||||
TEST_SCRIPT = $(check_SCRIPTS)
|
||||
|
||||
CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class runExample.sh
|
||||
|
||||
clean:
|
||||
rm -rf $(JAVAROOT)
|
||||
rm -f $(jarfile)
|
||||
rm -f classnoinst.stamp
|
||||
|
||||
include $(top_srcdir)/config/conclude.am
|
||||
Binary file not shown.
Binary file not shown.
@@ -0,0 +1,349 @@
|
||||
#! /bin/sh
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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@
|
||||
|
||||
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'
|
||||
LS='ls'
|
||||
AWK='awk'
|
||||
|
||||
nerrors=0
|
||||
|
||||
# where the libs exist
|
||||
HDFLIB_HOME="$top_srcdir/java/lib"
|
||||
BLDLIBDIR="./lib"
|
||||
BLDREFDIR="./groups"
|
||||
BLDDIR="."
|
||||
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 $BLDREFDIR || mkdir -p $BLDREFDIR
|
||||
|
||||
######################################################################
|
||||
# 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="
|
||||
$HDFLIB_HOME/slf4j-api-1.7.5.jar
|
||||
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
|
||||
$top_builddir/src/.libs/libhdf5.*
|
||||
$top_builddir/java/src/jni/.libs/libhdf5_java.*
|
||||
$top_builddir/java/src/$JARFILE
|
||||
"
|
||||
LIST_REF_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_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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$CP -f $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=`$DIRNAME $tstfile`
|
||||
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
|
||||
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $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 $TESTDIR | $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()
|
||||
{
|
||||
# skip rm 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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $BLDDIR/*.txt
|
||||
$RM $BLDDIR/*.out
|
||||
fi
|
||||
}
|
||||
|
||||
COPY_REFFILES="$LIST_REF_FILES"
|
||||
|
||||
COPY_REFFILES_TO_BLDREFDIR()
|
||||
{
|
||||
# copy test files. Used -f to make sure get a new copy
|
||||
for tstfile in $COPY_REFFILES
|
||||
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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$CP -f $tstfile $BLDREFDIR
|
||||
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_REFFILES_AND_BLDREFDIR()
|
||||
{
|
||||
# skip rm 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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $BLDREFDIR
|
||||
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_REFFILES_TO_BLDREFDIR
|
||||
|
||||
CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.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
|
||||
Darwin)
|
||||
DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
|
||||
export DYLD_LIBRARY_PATH
|
||||
LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
|
||||
;;
|
||||
*)
|
||||
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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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"
|
||||
($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_LIBFILES_AND_BLDLIBDIR
|
||||
CLEAN_DATAFILES_AND_BLDDIR
|
||||
CLEAN_REFFILES_AND_BLDREFDIR
|
||||
|
||||
# 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
|
||||
@@ -0,0 +1,112 @@
|
||||
cmake_minimum_required (VERSION 3.1.0)
|
||||
PROJECT (HDFJAVA_EXAMPLES_INTRO Java)
|
||||
|
||||
set (CMAKE_VERBOSE_MAKEFILE 1)
|
||||
|
||||
INCLUDE_DIRECTORIES (
|
||||
${HDF5_JAVA_JNI_BINARY_DIR}
|
||||
${HDF5_JAVA_HDF5_LIB_DIR}
|
||||
)
|
||||
|
||||
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 (WIN32)
|
||||
set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
|
||||
endif (WIN32)
|
||||
|
||||
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 (CMAKE_INCLUDE_PATH)
|
||||
|
||||
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})
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
|
||||
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 (HDFJAVA_JAR)
|
||||
|
||||
foreach (example ${HDF_JAVA_OBJECT_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} ${HDFJAVA_H5_LIB_TARGET})
|
||||
endforeach (example ${HDF_JAVA_OBJECT_EXAMPLES})
|
||||
|
||||
MACRO (ADD_H5_TEST resultfile resultcode)
|
||||
add_test (
|
||||
NAME JAVA_intro-${resultfile}
|
||||
COMMAND "${CMAKE_COMMAND}"
|
||||
-D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}"
|
||||
-D "TEST_PROGRAM=examples.intro.${resultfile}"
|
||||
-D "TEST_ARGS:STRING=${ARGN}"
|
||||
-D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${resultfile}_JAR_FILE}"
|
||||
-D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}"
|
||||
-D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}"
|
||||
-D "TEST_OUTPUT=intro/${resultfile}.out"
|
||||
-D "TEST_EXPECT=${resultcode}"
|
||||
-D "TEST_REFERENCE=intro/${resultfile}.txt"
|
||||
-P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_intro-${resultfile} PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
set (last_test "JAVA_intro-${resultfile}")
|
||||
ENDMACRO (ADD_H5_TEST file)
|
||||
|
||||
if (BUILD_TESTING)
|
||||
|
||||
foreach (example ${HDF_JAVA_EXAMPLES})
|
||||
add_test (
|
||||
NAME JAVA_intro-${example}-clearall-objects
|
||||
COMMAND ${CMAKE_COMMAND}
|
||||
-E remove
|
||||
${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
|
||||
${example}.out
|
||||
${example}.out.err
|
||||
)
|
||||
if (NOT "${last_test}" STREQUAL "")
|
||||
set_tests_properties (JAVA_intro-${example}-clearall-objects PROPERTIES DEPENDS ${last_test})
|
||||
endif (NOT "${last_test}" STREQUAL "")
|
||||
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}-clearall-objects)
|
||||
set (last_test "JAVA_intro-${example}-copy-objects")
|
||||
ADD_H5_TEST (${example} 0)
|
||||
endforeach (example ${HDF_JAVA_EXAMPLES})
|
||||
|
||||
endif (BUILD_TESTING)
|
||||
@@ -0,0 +1,145 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long attribute_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,97 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,55 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -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();
|
||||
}
|
||||
|
||||
// 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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,76 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long group_id = -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 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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,118 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long group1_id = -1;
|
||||
long group2_id = -1;
|
||||
long group3_id = -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 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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,207 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
long group_id = -1;
|
||||
long group1_id = -1;
|
||||
long group2_id = -1;
|
||||
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 = -1;
|
||||
}
|
||||
catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
// Close the first dataset.
|
||||
try {
|
||||
if (dataset_id >= 0)
|
||||
H5.H5Dclose(dataset_id);
|
||||
dataset_id = -1;
|
||||
}
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,112 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
|
||||
* of the source code distribution tree; Copyright.html can be found at the *
|
||||
* root level of an installed copy of the electronic HDF5 document set and *
|
||||
* is linked from the top-level documents page. It can also be found at *
|
||||
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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 = -1;
|
||||
long dataspace_id = -1;
|
||||
long dataset_id = -1;
|
||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,67 @@
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# 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 files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. 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:
|
||||
$(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-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.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 = runExample.sh
|
||||
TEST_SCRIPT = $(check_SCRIPTS)
|
||||
|
||||
CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class runExample.sh
|
||||
|
||||
clean:
|
||||
rm -rf $(JAVAROOT)
|
||||
rm -f $(jarfile)
|
||||
rm -f classnoinst.stamp
|
||||
|
||||
include $(top_srcdir)/config/conclude.am
|
||||
@@ -0,0 +1,298 @@
|
||||
#! /bin/sh
|
||||
#
|
||||
# Copyright by The HDF Group.
|
||||
# Copyright by the Board of Trustees of the University of Illinois.
|
||||
# All rights reserved.
|
||||
#
|
||||
# This file is part of HDF5. The full HDF5 copyright notice, including
|
||||
# terms governing use, modification, and redistribution, is contained in
|
||||
# the files COPYING and Copyright.html. COPYING can be found at the root
|
||||
# of the source code distribution tree; Copyright.html can be found at the
|
||||
# root level of an installed copy of the electronic HDF5 document set and
|
||||
# is linked from the top-level documents page. It can also be found at
|
||||
# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
|
||||
# access to either file, you may request a copy from help@hdfgroup.org.
|
||||
#
|
||||
|
||||
top_builddir=@top_builddir@
|
||||
top_srcdir=@top_srcdir@
|
||||
srcdir=@srcdir@
|
||||
|
||||
TESTNAME=EX_Intro
|
||||
EXIT_SUCCESS=0
|
||||
EXIT_FAILURE=1
|
||||
|
||||
# Set up default variable values if not supplied by the user.
|
||||
RM='rm -rf'
|
||||
CMP='cmp'
|
||||
DIFF='diff -c'
|
||||
CP='cp'
|
||||
DIRNAME='dirname'
|
||||
LS='ls'
|
||||
AWK='awk'
|
||||
|
||||
nerrors=0
|
||||
|
||||
# where the libs exist
|
||||
HDFLIB_HOME="$top_srcdir/java/lib"
|
||||
BLDLIBDIR="./lib"
|
||||
BLDDIR="."
|
||||
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="
|
||||
$HDFLIB_HOME/slf4j-api-1.7.5.jar
|
||||
$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
|
||||
$top_builddir/src/.libs/libhdf5.*
|
||||
$top_builddir/java/src/jni/.libs/libhdf5_java.*
|
||||
$top_builddir/java/src/$JARFILE
|
||||
"
|
||||
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_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 $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$CP -f $tstfile $BLDLIBDIR
|
||||
if [ $? -ne 0 ]; then
|
||||
echo "Error: FAILED to copy $tstfile ."
|
||||
|
||||
# Comment out this to CREATE expected file
|
||||
exit $EXIT_FAILURE
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
}
|
||||
|
||||
CLEAN_LIBFILES_AND_BLDLIBDIR()
|
||||
{
|
||||
# skip rm if srcdir is same as destdir
|
||||
# this occurs when build/test performed in source dir and
|
||||
# make cp fail
|
||||
SDIR=`$DIRNAME $tstfile`
|
||||
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
|
||||
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $BLDLIBDIR
|
||||
fi
|
||||
}
|
||||
|
||||
COPY_DATAFILES="$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 $TESTDIR | $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 $EXIT_FAILURE
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
done
|
||||
}
|
||||
|
||||
CLEAN_DATAFILES_AND_BLDDIR()
|
||||
{
|
||||
# skip rm if srcdir is same as destdir
|
||||
# this occurs when build/test performed in source dir and
|
||||
# make cp fail
|
||||
SDIR=`$DIRNAME $tstfile`
|
||||
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
|
||||
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
|
||||
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
|
||||
$RM $BLDDIR/*.txt
|
||||
$RM $BLDDIR/*.out
|
||||
fi
|
||||
}
|
||||
|
||||
# Print a line-line message left justified in a field of 70 characters
|
||||
# beginning with the word "Testing".
|
||||
#
|
||||
TESTING() {
|
||||
SPACES=" "
|
||||
echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012'
|
||||
}
|
||||
|
||||
# where Java is installed (requires jdk1.7.x)
|
||||
JAVAEXE=@JAVA@
|
||||
JAVAEXEFLAGS=@H5_JAVAFLAGS@
|
||||
|
||||
###############################################################################
|
||||
# DO NOT MODIFY BELOW THIS LINE
|
||||
###############################################################################
|
||||
|
||||
# prepare for test
|
||||
COPY_LIBFILES_TO_BLDLIBDIR
|
||||
COPY_DATAFILES_TO_BLDDIR
|
||||
|
||||
CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.jar:"$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 $os_name in
|
||||
Darwin)
|
||||
DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
|
||||
export DYLD_LIBRARY_PATH
|
||||
LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
|
||||
;;
|
||||
*)
|
||||
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 $CLASSPATH examples.intro.H5_CreateDataset"
|
||||
($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 $CLASSPATH examples.intro.H5_CreateAttribute"
|
||||
($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 $CLASSPATH examples.intro.H5_CreateFile"
|
||||
($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 $CLASSPATH examples.intro.H5_CreateGroup"
|
||||
($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 $CLASSPATH examples.intro.H5_CreateGroupAbsoluteRelative"
|
||||
($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 $CLASSPATH examples.intro.H5_CreateGroupDataset"
|
||||
($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 $CLASSPATH examples.intro.H5_ReadWrite"
|
||||
($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
|
||||
@@ -0,0 +1,16 @@
|
||||
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.
|
||||
|
||||
@@ -0,0 +1,3 @@
|
||||
Filter type is: H5Z_FILTER_FLETCHER32
|
||||
|
||||
Maximum value in DS1 is: 1890
|
||||
@@ -0,0 +1,26 @@
|
||||
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 ]
|
||||
|
||||
@@ -0,0 +1,8 @@
|
||||
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 ]
|
||||
|
||||
@@ -0,0 +1,7 @@
|
||||
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 ]
|
||||
|
||||
@@ -0,0 +1,20 @@
|
||||
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 ]
|
||||
|
||||
@@ -0,0 +1,3 @@
|
||||
Filter type is: H5Z_FILTER_DEFLATE
|
||||
|
||||
Maximum value in DS1 is: 1890
|
||||
@@ -0,0 +1,24 @@
|
||||
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 ]
|
||||
|
||||
@@ -0,0 +1,3 @@
|
||||
Filter type is: H5Z_FILTER_NBIT
|
||||
|
||||
Maximum value in DS1 is: 1890
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user