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-rw-r--r--tools/h5repack/CMakeLists.txt35
-rw-r--r--tools/h5repack/CMakeTests.cmake116
-rw-r--r--tools/h5repack/Makefile.am18
-rw-r--r--tools/h5repack/Makefile.in155
-rw-r--r--tools/h5repack/h5repack.c1822
-rw-r--r--tools/h5repack/h5repack.sh.in48
-rw-r--r--tools/h5repack/h5repack_copy.c3239
-rw-r--r--tools/h5repack/h5repack_filters.c17
-rw-r--r--tools/h5repack/h5repack_main.c1088
-rw-r--r--tools/h5repack/h5repack_opttable.c530
-rw-r--r--tools/h5repack/h5repack_parse.c859
-rw-r--r--tools/h5repack/h5repack_plugin.sh.in238
-rw-r--r--tools/h5repack/h5repack_verify.c15
-rw-r--r--tools/h5repack/testfiles/deflate_limit.h5repack_layout.h5.ddl130
-rw-r--r--tools/h5repack/testfiles/h5repack-help.txt122
-rw-r--r--tools/h5repack/testfiles/h5repack_filters.h5.tst13
-rw-r--r--tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl158
-rw-r--r--tools/h5repack/testfiles/h5repack_layout.h5.ddl660
-rw-r--r--tools/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst14
19 files changed, 5337 insertions, 3940 deletions
diff --git a/tools/h5repack/CMakeLists.txt b/tools/h5repack/CMakeLists.txt
index f03ad69..176fc2b 100644
--- a/tools/h5repack/CMakeLists.txt
+++ b/tools/h5repack/CMakeLists.txt
@@ -44,6 +44,41 @@ IF (BUILD_TESTING)
TARGET_LINK_LIBRARIES (h5repacktest ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET})
SET_TARGET_PROPERTIES (h5repacktest PROPERTIES FOLDER tools)
+ #-----------------------------------------------------------------------------
+ # If plugin library tests can be tested
+ #-----------------------------------------------------------------------------
+ IF (BUILD_SHARED_LIBS)
+ SET (HDF5_TOOL_PLUGIN_LIB_CORENAME "dynlibadd")
+ SET (HDF5_TOOL_PLUGIN_LIB_NAME "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_TOOL_PLUGIN_LIB_CORENAME}")
+ SET (HDF5_TOOL_PLUGIN_LIB_TARGET ${HDF5_TOOL_PLUGIN_LIB_CORENAME})
+ ADD_DEFINITIONS (${HDF5_EXTRA_C_FLAGS})
+ INCLUDE_DIRECTORIES (${HDF5_SRC_DIR})
+
+ ADD_LIBRARY (${HDF5_TOOL_PLUGIN_LIB_TARGET} ${LIB_TYPE} ${HDF5_TEST_SRC_DIR}/dynlib1.c)
+ TARGET_C_PROPERTIES (${HDF5_TOOL_PLUGIN_LIB_TARGET} " " " ")
+ TARGET_LINK_LIBRARIES (${HDF5_TOOL_PLUGIN_LIB_TARGET} ${HDF5_TEST_LIB_TARGET})
+ H5_SET_LIB_OPTIONS (
+ ${HDF5_TOOL_PLUGIN_LIB_TARGET} ${HDF5_TOOL_PLUGIN_LIB_NAME}
+ ${LIB_TYPE}
+ HDF5_TOOL_PLUGIN_LIB_NAME_RELEASE
+ HDF5_TOOL_PLUGIN_LIB_NAME_DEBUG
+ )
+
+ # make plugins dir
+ FILE (MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/plugins")
+ #-----------------------------------------------------------------------------
+ # Copy plugin library to a plugins folder
+ #-----------------------------------------------------------------------------
+ ADD_CUSTOM_COMMAND (
+ TARGET ${HDF5_TOOL_PLUGIN_LIB_TARGET}
+ POST_BUILD
+ COMMAND ${CMAKE_COMMAND}
+ ARGS -E copy_if_different
+ "$<TARGET_FILE:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
+ "${CMAKE_BINARY_DIR}/plugins/$<TARGET_FILE_NAME:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
+ )
+ ENDIF (BUILD_SHARED_LIBS)
+
INCLUDE (CMakeTests.cmake)
ENDIF (BUILD_TESTING)
diff --git a/tools/h5repack/CMakeTests.cmake b/tools/h5repack/CMakeTests.cmake
index c27aaa0..7f8f71b 100644
--- a/tools/h5repack/CMakeTests.cmake
+++ b/tools/h5repack/CMakeTests.cmake
@@ -79,12 +79,15 @@
)
SET (LIST_OTHER_TEST_FILES
+ ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack-help.txt
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_ext.bin
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/ublock.bin
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack.info
+ ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/deflate_limit.h5repack_layout.h5.ddl
${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5.ddl
- # tools/testfiles
- ${HDF5_TOOLS_SRC_DIR}/testfiles/h5repack_filters.h5.ddl
+ ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_filters.h5.tst
+ ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5-plugin_test.ddl
+ ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/plugin_test.h5repack_layout.h5.tst
)
FOREACH (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
@@ -105,6 +108,37 @@
##############################################################################
##############################################################################
+ MACRO (ADD_HELP_TEST testname resultcode)
+ # If using memchecker add tests without using scripts
+ IF (HDF5_ENABLE_USING_MEMCHECKER)
+ ADD_TEST (NAME H5REPACK-${testname} COMMAND $<TARGET_FILE:h5repack> ${ARGN})
+ SET_TESTS_PROPERTIES (H5REPACK-${testname} PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
+ IF (NOT "${last_test}" STREQUAL "")
+ SET_TESTS_PROPERTIES (H5REPACK-${testname} PROPERTIES DEPENDS ${last_test})
+ ENDIF (NOT "${last_test}" STREQUAL "")
+ SET (last_test "H5REPACK-${testname}")
+ ELSE (HDF5_ENABLE_USING_MEMCHECKER)
+ ADD_TEST (
+ NAME H5REPACK-h5repack-${testname}-clear-objects
+ COMMAND ${CMAKE_COMMAND}
+ -E remove h5repack-${testname}.out h5repack-${testname}.out.err
+ )
+ SET_TESTS_PROPERTIES (H5REPACK-h5repack-${testname}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
+ ADD_TEST (
+ NAME H5REPACK-h5repack-${testname}
+ COMMAND "${CMAKE_COMMAND}"
+ -D "TEST_PROGRAM=$<TARGET_FILE:h5repack>"
+ -D "TEST_ARGS:STRING=${ARGN}"
+ -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
+ -D "TEST_OUTPUT=h5repack-${testname}.out"
+ -D "TEST_EXPECT=${resultcode}"
+ -D "TEST_REFERENCE=h5repack-${testname}.txt"
+ -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+ )
+ SET_TESTS_PROPERTIES (H5REPACK-h5repack-${testname} PROPERTIES DEPENDS "H5REPACK-h5repack-${testname}-clear-objects")
+ ENDIF (HDF5_ENABLE_USING_MEMCHECKER)
+ ENDMACRO (ADD_HELP_TEST)
+
MACRO (ADD_H5_TEST_OLD testname testtype testfile)
IF (${testtype} STREQUAL "SKIP")
IF (NOT HDF5_ENABLE_USING_MEMCHECKER)
@@ -177,7 +211,7 @@
-D "TEST_OUTPUT=./testfiles/${resultfile}-${testname}.out"
-D "TEST_EXPECT=${resultcode}"
-D "TEST_FILTER:STRING=${testfilter}"
- -D "TEST_REFERENCE=testfiles/${resultfile}.ddl"
+ -D "TEST_REFERENCE=testfiles/${resultfile}.tst"
-P "${HDF5_RESOURCES_DIR}/runTest.cmake"
)
ENDIF (HDF5_ENABLE_USING_MEMCHECKER)
@@ -212,7 +246,7 @@
-D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-D "TEST_OUTPUT=./testfiles/${resultfile}-${testname}.out"
-D "TEST_EXPECT=${resultcode}"
- -D "TEST_REFERENCE=testfiles/${resultfile}.ddl"
+ -D "TEST_REFERENCE=testfiles/${testname}.${resultfile}.ddl"
-P "${HDF5_RESOURCES_DIR}/runTest.cmake"
)
SET_TESTS_PROPERTIES (H5REPACK_DMP-h5dump-${testname} PROPERTIES DEPENDS "H5REPACK_DMP-${testname}")
@@ -303,6 +337,51 @@
SET_TESTS_PROPERTIES (H5REPACK_META-${testname} PROPERTIES DEPENDS H5REPACK_META-${testname}_M)
ENDMACRO (ADD_H5_TEST_META)
+ MACRO (ADD_H5_UD_TEST testname resultcode resultfile)
+ IF (HDF5_BUILD_TOOLS AND NOT HDF5_ENABLE_USING_MEMCHECKER)
+ # Remove any output file left over from previous test run
+ ADD_TEST (
+ NAME H5REPACK_UD-clearall-objects
+ COMMAND ${CMAKE_COMMAND}
+ -E remove
+ testfiles/out-${testname}.${resultfile}
+ testfiles/${testname}.${resultfile}.out
+ testfiles/${testname}.${resultfile}.out.err
+ testfiles/${resultfile}-${testname}.out
+ testfiles/${resultfile}-${testname}.out.err
+ )
+ ADD_TEST (
+ NAME H5REPACK_UD-${testname}
+ COMMAND "${CMAKE_COMMAND}"
+ -D "TEST_PROGRAM=$<TARGET_FILE:h5repack>"
+ -D "TEST_ARGS:STRING=${ARGN};${PROJECT_BINARY_DIR}/testfiles/${resultfile};${PROJECT_BINARY_DIR}/testfiles/out-${testname}.${resultfile}"
+ -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+ -D "TEST_EXPECT=${resultcode}"
+ -D "TEST_FILTER:STRING=O?...ing file[^\n]+\n"
+ -D "TEST_OUTPUT=./testfiles/${testname}.${resultfile}.out"
+ -D "TEST_REFERENCE=testfiles/${testname}.${resultfile}.tst"
+ -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH"
+ -D "TEST_ENV_VALUE=${CMAKE_BINARY_DIR}/plugins"
+ -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+ )
+ SET_TESTS_PROPERTIES (H5REPACK_UD-${testname} PROPERTIES DEPENDS H5REPACK_UD-clearall-objects)
+ ADD_TEST (
+ NAME H5REPACK_UD-h5dump-${testname}
+ COMMAND "${CMAKE_COMMAND}"
+ -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
+ -D "TEST_ARGS:STRING=-pH;testfiles/out-${testname}.${resultfile}"
+ -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+ -D "TEST_OUTPUT=./testfiles/${resultfile}-${testname}.out"
+ -D "TEST_EXPECT=${resultcode}"
+ -D "TEST_REFERENCE=testfiles/${resultfile}-${testname}.ddl"
+ -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH"
+ -D "TEST_ENV_VALUE=${CMAKE_BINARY_DIR}/plugins"
+ -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+ )
+ SET_TESTS_PROPERTIES (H5REPACK_UD-h5dump-${testname} PROPERTIES DEPENDS "H5REPACK_UD-${testname}")
+ ENDIF (HDF5_BUILD_TOOLS AND NOT HDF5_ENABLE_USING_MEMCHECKER)
+ ENDMACRO (ADD_H5_UD_TEST)
+
##############################################################################
##############################################################################
### T H E T E S T S ###
@@ -333,12 +412,13 @@
SET (FILE18 h5repack_layout2.h5)
SET (FILE_REF h5repack_refs.h5)
SET (FILE_ATTR_REF h5repack_attr_refs.h5)
-
+
# Remove any output file left over from previous test run
ADD_TEST (
NAME H5REPACK-clearall-objects
COMMAND ${CMAKE_COMMAND}
-E remove
+ ./testfiles/h5dump-help.out
./testfiles/h5repack_filters.h5-gzip_verbose_filters.out
./testfiles/h5repack_filters.h5-gzip_verbose_filters.out.err
./testfiles/h5repack_layout.h5-chunk_18x13-v.out
@@ -353,6 +433,8 @@
./testfiles/h5repack_layout.h5-compa-v.out.err
./testfiles/h5repack_layout.h5-conti-v.out
./testfiles/h5repack_layout.h5-conti-v.out.err
+ ./testfiles/h5repack_layout.h5-deflate_limit.out
+ ./testfiles/h5repack_layout.h5-deflate_limit.out.err
./testfiles/h5repack_layout.h5-dset2_chunk_20x10-v.out
./testfiles/h5repack_layout.h5-dset2_chunk_20x10-v.out.err
./testfiles/h5repack_layout.h5-dset2_compa-v.out
@@ -375,10 +457,16 @@
./testfiles/h5repack_layout.h5-layout_long_switches-v.out.err
./testfiles/h5repack_layout.h5-layout_short_switches-v.out
./testfiles/h5repack_layout.h5-layout_short_switches-v.out.err
+ ./testfiles/h5repack_layout.h5-plugin_test.out
+ ./testfiles/h5repack_layout.h5-plugin_test.out.err
./testfiles/h5repack_layout2.h5-contig_small_compa-v.out
./testfiles/h5repack_layout2.h5-contig_small_compa-v.out.err
./testfiles/h5repack_layout2.h5-contig_small_fixed_compa-v.out
./testfiles/h5repack_layout2.h5-contig_small_fixed_compa-v.out.err
+ ./testfiles/h5repack_layout3.h5-ckdim_biger-v.out
+ ./testfiles/h5repack_layout3.h5-ckdim_biger-v.out.err
+ ./testfiles/h5repack_layout3.h5-ckdim_smaller-v.out
+ ./testfiles/h5repack_layout3.h5-ckdim_smaller-v.out.err
./testfiles/h5repack_layout3.h5-chunk2chunk-v.out
./testfiles/h5repack_layout3.h5-chunk2chunk-v.out.err
./testfiles/h5repack_layout3.h5-chunk2compa-v.out
@@ -431,11 +519,14 @@
./testfiles/out-layout_long_switches.h5repack_layout.h5
./testfiles/out-layout_short_switches.h5repack_layout.h5
./testfiles/out-old_style_layout_short_switches.h5repack_layout.h5
+ ./testfiles/out-plugin_test.h5repack_layout.h5
./testfiles/out-shuffle_all.h5repack_layout.h5
./testfiles/out-shuffle_individual.h5repack_layout.h5
./testfiles/out-upgrade_layout.h5repack_layouto.h5
./testfiles/out-contig_small_compa.h5repack_layout2.h5
./testfiles/out-contig_small_fixed_compa.h5repack_layout2.h5
+ ./testfiles/out-ckdim_biger.h5repack_layout3.h5
+ ./testfiles/out-ckdim_smaller.h5repack_layout3.h5
./testfiles/out-chunk2chunk.h5repack_layout3.h5
./testfiles/out-chunk2compa.h5repack_layout3.h5
./testfiles/out-chunk2conti.h5repack_layout3.h5
@@ -507,6 +598,8 @@
SET_TESTS_PROPERTIES (H5REPACK-clearall-objects PROPERTIES DEPENDS ${last_test})
ENDIF (NOT "${last_test}" STREQUAL "")
+ ADD_HELP_TEST(help 0 -h)
+
ADD_TEST (NAME H5REPACK-testh5repack_detect_szip COMMAND $<TARGET_FILE:testh5repack_detect_szip>)
IF (HDF5_ENABLE_SZIP_SUPPORT)
IF (HDF5_ENABLE_SZIP_ENCODING)
@@ -965,6 +1058,19 @@ ADD_H5_VERIFY_TEST (ckdim_smaller "TEST" 0 h5repack_layout3.h5 chunk_unlimit3 CO
ADD_H5_TEST_META (meta_short h5repack_layout.h5 -M 8192)
ADD_H5_TEST_META (meta_long h5repack_layout.h5 --metadata_block_size=8192)
+##############################################################################
+### P L U G I N T E S T S
+##############################################################################
+IF (BUILD_SHARED_LIBS)
+ ADD_H5_UD_TEST (plugin_test 0 h5repack_layout.h5 -v -f UD=257,1,9)
+ELSE (BUILD_SHARED_LIBS)
+ MESSAGE (STATUS " **** Plugins libraries must be built as shared libraries **** ")
+ ADD_TEST (
+ NAME H5REPACK-plugin
+ COMMAND ${CMAKE_COMMAND} -E echo "SKIP H5PLUGIN TESTING"
+ )
+ENDIF (BUILD_SHARED_LIBS)
+
IF (HDF5_TEST_VFD)
# Run test with different Virtual File Driver
FOREACH (vfd ${VFD_LIST})
diff --git a/tools/h5repack/Makefile.am b/tools/h5repack/Makefile.am
index 96f0082..c52112b 100644
--- a/tools/h5repack/Makefile.am
+++ b/tools/h5repack/Makefile.am
@@ -28,11 +28,14 @@ TEST_SCRIPT=h5repack.sh
TEST_PROG=h5repacktst
noinst_PROGRAMS=testh5repack_detect_szip
+SCRIPT_DEPEND=h5repack$(EXEEXT)
+if HAVE_SHARED_CONDITIONAL
+ TEST_SCRIPT += h5repack_plugin.sh
+endif
+
check_SCRIPTS=$(TEST_SCRIPT)
check_PROGRAMS=$(TEST_PROG)
-SCRIPT_DEPEND=h5repack$(EXEEXT)
-
# Our main target, h5repack tool
bin_PROGRAMS=h5repack
@@ -56,9 +59,18 @@ testh5repack_detect_szip_SOURCES=testh5repack_detect_szip.c
# The h5repack.sh script needs h5repacktst to run first.
h5repack.sh.chkexe_: h5repacktst.chkexe_
+if HAVE_SHARED_CONDITIONAL
+ # Build it as shared library if configure is enabled for shared library.
+ lib_LTLIBRARIES=libdynlibadd.la
+ libdynlibadd_la_SOURCES=$(top_srcdir)/test/dynlib1.c
+
+install-exec-hook:
+ $(RM) $(DESTDIR)$(libdir)/*dynlib*
+endif
+
# Temporary files. *.h5 are generated by h5repack. They should
# copied to the testfiles/ directory if update is required.
CHECK_CLEANFILES+=*.h5 *.bin
-DISTCLEANFILES=h5repack.sh
+DISTCLEANFILES=h5repack.sh h5repack_plugin.sh
include $(top_srcdir)/config/conclude.am
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index fe3a11c..addb530 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -31,6 +31,7 @@
# HDF5 Library Makefile(.in)
#
+
VPATH = @srcdir@
am__make_dryrun = \
{ \
@@ -68,11 +69,12 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
- $(srcdir)/h5repack.sh.in $(top_srcdir)/bin/depcomp \
- $(top_srcdir)/bin/mkinstalldirs \
+ $(srcdir)/h5repack.sh.in $(srcdir)/h5repack_plugin.sh.in \
+ $(top_srcdir)/bin/depcomp $(top_srcdir)/bin/mkinstalldirs \
$(top_srcdir)/config/commence.am \
$(top_srcdir)/config/conclude.am
noinst_PROGRAMS = testh5repack_detect_szip$(EXEEXT)
+@HAVE_SHARED_CONDITIONAL_TRUE@am__append_1 = h5repack_plugin.sh
check_PROGRAMS = $(am__EXEEXT_1)
bin_PROGRAMS = h5repack$(EXEEXT)
TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
@@ -83,9 +85,47 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
CONFIG_HEADER = $(top_builddir)/src/H5config.h
-CONFIG_CLEAN_FILES = h5repack.sh
+CONFIG_CLEAN_FILES = h5repack.sh h5repack_plugin.sh
CONFIG_CLEAN_VPATH_FILES =
-am__installdirs = "$(DESTDIR)$(bindir)"
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+ *) f=$$p;; \
+ esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+ for p in $$list; do echo "$$p $$p"; done | \
+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+ if (++n[$$2] == $(am__install_max)) \
+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+ END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__uninstall_files_from_dir = { \
+ test -z "$$files" \
+ || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
+ || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
+ $(am__cd) "$$dir" && rm -f $$files; }; \
+ }
+am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"
+LTLIBRARIES = $(lib_LTLIBRARIES)
+libdynlibadd_la_LIBADD =
+am__libdynlibadd_la_SOURCES_DIST = $(top_srcdir)/test/dynlib1.c
+@HAVE_SHARED_CONDITIONAL_TRUE@am_libdynlibadd_la_OBJECTS = dynlib1.lo
+libdynlibadd_la_OBJECTS = $(am_libdynlibadd_la_OBJECTS)
+AM_V_lt = $(am__v_lt_@AM_V@)
+am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 =
+@HAVE_SHARED_CONDITIONAL_TRUE@am_libdynlibadd_la_rpath = -rpath \
+@HAVE_SHARED_CONDITIONAL_TRUE@ $(libdir)
am__EXEEXT_1 = h5repacktst$(EXEEXT)
PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
am__objects_1 = h5repack.$(OBJEXT) h5repack_copy.$(OBJEXT) \
@@ -96,10 +136,6 @@ am_h5repack_OBJECTS = $(am__objects_1) h5repack_main.$(OBJEXT)
h5repack_OBJECTS = $(am_h5repack_OBJECTS)
h5repack_LDADD = $(LDADD)
h5repack_DEPENDENCIES = $(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
-AM_V_lt = $(am__v_lt_@AM_V@)
-am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
-am__v_lt_0 = --silent
-am__v_lt_1 =
h5repack_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(h5repack_LDFLAGS) $(LDFLAGS) -o $@
@@ -148,10 +184,10 @@ AM_V_CCLD = $(am__v_CCLD_@AM_V@)
am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
-SOURCES = $(h5repack_SOURCES) $(h5repacktst_SOURCES) \
- $(testh5repack_detect_szip_SOURCES)
-DIST_SOURCES = $(h5repack_SOURCES) $(h5repacktst_SOURCES) \
- $(testh5repack_detect_szip_SOURCES)
+SOURCES = $(libdynlibadd_la_SOURCES) $(h5repack_SOURCES) \
+ $(h5repacktst_SOURCES) $(testh5repack_detect_szip_SOURCES)
+DIST_SOURCES = $(am__libdynlibadd_la_SOURCES_DIST) $(h5repack_SOURCES) \
+ $(h5repacktst_SOURCES) $(testh5repack_detect_szip_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -450,10 +486,10 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5 *.bin
INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
# Test programs and scripts
-TEST_SCRIPT = h5repack.sh
+TEST_SCRIPT = h5repack.sh $(am__append_1)
TEST_PROG = h5repacktst
-check_SCRIPTS = $(TEST_SCRIPT)
SCRIPT_DEPEND = h5repack$(EXEEXT)
+check_SCRIPTS = $(TEST_SCRIPT)
# Add h5repack specific linker flags here
h5repack_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
@@ -469,7 +505,9 @@ COMMON_SOURCES = h5repack.c h5repack_copy.c h5repack_filters.c \
h5repack_SOURCES = $(COMMON_SOURCES) h5repack_main.c
h5repacktst_SOURCES = $(COMMON_SOURCES) h5repacktst.c
testh5repack_detect_szip_SOURCES = testh5repack_detect_szip.c
-DISTCLEANFILES = h5repack.sh
+@HAVE_SHARED_CONDITIONAL_TRUE@lib_LTLIBRARIES = libdynlibadd.la
+@HAVE_SHARED_CONDITIONAL_TRUE@libdynlibadd_la_SOURCES = $(top_srcdir)/test/dynlib1.c
+DISTCLEANFILES = h5repack.sh h5repack_plugin.sh
# Automake needs to be taught how to build lib, progs, and tests targets.
# These will be filled in automatically for the most part (e.g.,
@@ -527,6 +565,44 @@ $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
h5repack.sh: $(top_builddir)/config.status $(srcdir)/h5repack.sh.in
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+h5repack_plugin.sh: $(top_builddir)/config.status $(srcdir)/h5repack_plugin.sh.in
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+install-libLTLIBRARIES: $(lib_LTLIBRARIES)
+ @$(NORMAL_INSTALL)
+ @list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+ list2=; for p in $$list; do \
+ if test -f $$p; then \
+ list2="$$list2 $$p"; \
+ else :; fi; \
+ done; \
+ test -z "$$list2" || { \
+ echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
+ $(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
+ echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
+ $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
+ }
+
+uninstall-libLTLIBRARIES:
+ @$(NORMAL_UNINSTALL)
+ @list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+ for p in $$list; do \
+ $(am__strip_dir) \
+ echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$f'"; \
+ $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
+ done
+
+clean-libLTLIBRARIES:
+ -test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
+ @list='$(lib_LTLIBRARIES)'; \
+ locs=`for p in $$list; do echo $$p; done | \
+ sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
+ sort -u`; \
+ test -z "$$locs" || { \
+ echo rm -f $${locs}; \
+ rm -f $${locs}; \
+ }
+libdynlibadd.la: $(libdynlibadd_la_OBJECTS) $(libdynlibadd_la_DEPENDENCIES) $(EXTRA_libdynlibadd_la_DEPENDENCIES)
+ $(AM_V_CCLD)$(LINK) $(am_libdynlibadd_la_rpath) $(libdynlibadd_la_OBJECTS) $(libdynlibadd_la_LIBADD) $(LIBS)
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -607,6 +683,7 @@ mostlyclean-compile:
distclean-compile:
-rm -f *.tab.c
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dynlib1.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_copy.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_filters.Po@am__quote@
@@ -639,6 +716,13 @@ distclean-compile:
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(LTCOMPILE) -c -o $@ $<
+dynlib1.lo: $(top_srcdir)/test/dynlib1.c
+@am__fastdepCC_TRUE@ $(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT dynlib1.lo -MD -MP -MF $(DEPDIR)/dynlib1.Tpo -c -o dynlib1.lo `test -f '$(top_srcdir)/test/dynlib1.c' || echo '$(srcdir)/'`$(top_srcdir)/test/dynlib1.c
+@am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/dynlib1.Tpo $(DEPDIR)/dynlib1.Plo
+@AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='$(top_srcdir)/test/dynlib1.c' object='dynlib1.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -c -o dynlib1.lo `test -f '$(top_srcdir)/test/dynlib1.c' || echo '$(srcdir)/'`$(top_srcdir)/test/dynlib1.c
+
mostlyclean-libtool:
-rm -f *.lo
@@ -745,9 +829,11 @@ check-am: all-am
$(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS) $(check_SCRIPTS)
$(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: check-am
-all-am: Makefile $(PROGRAMS) all-local
+all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) all-local
+install-binPROGRAMS: install-libLTLIBRARIES
+
installdirs:
- for dir in "$(DESTDIR)$(bindir)"; do \
+ for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
done
install: install-am
@@ -781,10 +867,12 @@ distclean-generic:
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@echo "it deletes files that may require special tools to rebuild."
+@HAVE_SHARED_CONDITIONAL_FALSE@install-exec-hook:
clean: clean-am
clean-am: clean-binPROGRAMS clean-checkPROGRAMS clean-generic \
- clean-libtool clean-noinstPROGRAMS mostlyclean-am
+ clean-libLTLIBRARIES clean-libtool clean-noinstPROGRAMS \
+ mostlyclean-am
distclean: distclean-am
-rm -rf ./$(DEPDIR)
@@ -810,8 +898,9 @@ install-dvi: install-dvi-am
install-dvi-am:
-install-exec-am: install-binPROGRAMS
-
+install-exec-am: install-binPROGRAMS install-libLTLIBRARIES
+ @$(NORMAL_INSTALL)
+ $(MAKE) $(AM_MAKEFLAGS) install-exec-hook
install-html: install-html-am
install-html-am:
@@ -850,25 +939,26 @@ ps: ps-am
ps-am:
-uninstall-am: uninstall-binPROGRAMS
+uninstall-am: uninstall-binPROGRAMS uninstall-libLTLIBRARIES
-.MAKE: check-am install-am install-strip
+.MAKE: check-am install-am install-exec-am install-strip
.PHONY: CTAGS GTAGS all all-am all-local check check-TESTS check-am \
clean clean-binPROGRAMS clean-checkPROGRAMS clean-generic \
- clean-libtool clean-noinstPROGRAMS cscopelist ctags distclean \
- distclean-compile distclean-generic distclean-libtool \
- distclean-tags distdir dvi dvi-am html html-am info info-am \
- install install-am install-binPROGRAMS install-data \
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
+ clean-libLTLIBRARIES clean-libtool clean-noinstPROGRAMS \
+ cscopelist ctags distclean distclean-compile distclean-generic \
+ distclean-libtool distclean-tags distdir dvi dvi-am html \
+ html-am info info-am install install-am install-binPROGRAMS \
+ install-data install-data-am install-dvi install-dvi-am \
+ install-exec install-exec-am install-exec-hook install-html \
+ install-html-am install-info install-info-am \
+ install-libLTLIBRARIES install-man install-pdf install-pdf-am \
install-ps install-ps-am install-strip installcheck \
installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-compile \
mostlyclean-generic mostlyclean-libtool mostlyclean-local pdf \
pdf-am ps ps-am tags uninstall uninstall-am \
- uninstall-binPROGRAMS
+ uninstall-binPROGRAMS uninstall-libLTLIBRARIES
# List all build rules defined by HDF5 Makefiles as "PHONY" targets here.
@@ -885,6 +975,11 @@ help:
# The h5repack.sh script needs h5repacktst to run first.
h5repack.sh.chkexe_: h5repacktst.chkexe_
+@HAVE_SHARED_CONDITIONAL_TRUE@ # Build it as shared library if configure is enabled for shared library.
+
+@HAVE_SHARED_CONDITIONAL_TRUE@install-exec-hook:
+@HAVE_SHARED_CONDITIONAL_TRUE@ $(RM) $(DESTDIR)$(libdir)/*dynlib*
+
# lib/progs/tests targets recurse into subdirectories. build-* targets
# build files in this directory.
build-lib: $(LIB)
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 5d30bf2..c79fea7 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -1,17 +1,17 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* 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. *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdlib.h>
#include <string.h>
@@ -23,224 +23,198 @@
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
-* File: h5repack.c
-* Purpose: Public API functions
-*-------------------------------------------------------------------------
-*/
+ * File: h5repack.c
+ * Purpose: Public API functions
+ *-------------------------------------------------------------------------
+ */
static int check_options(pack_opt_t *options);
static int check_objects(const char* fname, pack_opt_t *options);
-static const char* get_sfilter (H5Z_filter_t filtn);
+static const char* get_sfilter(H5Z_filter_t filtn);
static int have_request(pack_opt_t *options);
-
-
/*-------------------------------------------------------------------------
-* Function: h5repack
-*
-* Purpose: locate all high-level HDF5 objects in the file
-* and compress/chunk them using options
-*
-* Algorithm: 2 traversals are made to the file; the 1st builds a list of
-* the objects, the 2nd makes a copy of them, using the options;
-* the reason for the 1st traversal is to check for invalid
-* object name requests
-*
-* Return: 0, ok, -1, fail
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack(const char* infile,
- const char* outfile,
- pack_opt_t *options)
-{
- /* check input */
- if (check_options(options)<0)
- return -1;
-
- /* check for objects in input that are in the file */
- if (check_objects(infile,options) < 0)
- return -1;
-
- /* copy the objects */
- if (copy_objects(infile,outfile,options) < 0)
- return -1;
-
-
- return 0;
-}
+ * Function: h5repack
+ *
+ * Purpose: locate all high-level HDF5 objects in the file
+ * and compress/chunk them using options
+ *
+ * Algorithm: 2 traversals are made to the file; the 1st builds a list of
+ * the objects, the 2nd makes a copy of them, using the options;
+ * the reason for the 1st traversal is to check for invalid
+ * object name requests
+ *
+ * Return: 0, ok, -1, fail
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
+ /* check input */
+ if (check_options(options) < 0)
+ return -1;
+ /* check for objects in input that are in the file */
+ if (check_objects(infile, options) < 0)
+ return -1;
+ /* copy the objects */
+ if (copy_objects(infile, outfile, options) < 0)
+ return -1;
-/*-------------------------------------------------------------------------
-* Function: h5repack_init
-*
-* Purpose: initialize options
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-
-int
-h5repack_init(pack_opt_t *options, int verbose, hbool_t latest,
- H5F_file_space_type_t strategy, hsize_t threshold)
-{
- int k, n;
-
- HDmemset(options, 0, sizeof(pack_opt_t));
- options->min_comp = 0;
- options->verbose = verbose;
- options->latest = latest;
- options->layout_g = H5D_LAYOUT_ERROR;
-
- for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++)
- {
- options->filter_g[n].filtn = -1;
- options->filter_g[n].cd_nelmts = 0;
- for ( k = 0; k < CD_VALUES; k++)
- options->filter_g[n].cd_values[k] = 0;
- }
-
- options->fs_strategy = strategy;
- options->fs_threshold = threshold;
-
- return (options_table_init(&(options->op_tbl)));
+ return 0;
}
-
/*-------------------------------------------------------------------------
-* Function: h5repack_end
-*
-* Purpose: free options table
-*
-*-------------------------------------------------------------------------
-*/
-
-int h5repack_end (pack_opt_t *options)
-{
- return options_table_free(options->op_tbl);
+ * Function: h5repack_init
+ *
+ * Purpose: initialize options
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest,
+ H5F_file_space_type_t strategy, hsize_t threshold) {
+ int k, n;
+
+ HDmemset(options, 0, sizeof(pack_opt_t));
+ options->min_comp = 0;
+ options->verbose = verbose;
+ options->latest = latest;
+ options->layout_g = H5D_LAYOUT_ERROR;
+
+ for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) {
+ options->filter_g[n].filtn = -1;
+ options->filter_g[n].cd_nelmts = 0;
+ for (k = 0; k < CD_VALUES; k++)
+ options->filter_g[n].cd_values[k] = 0;
+ }
+
+ options->fs_strategy = strategy;
+ options->fs_threshold = threshold;
+
+ return (options_table_init(&(options->op_tbl)));
}
-
/*-------------------------------------------------------------------------
-* Function: h5repack_addfilter
-*
-* Purpose: add a compression -f option to table
-* Example: -f dset:GZIP=6
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack_addfilter(const char* str,
- pack_opt_t *options)
-{
- obj_list_t *obj_list=NULL; /* one object list for the -f and -l option entry */
- filter_info_t filter; /* filter info for the current -f option entry */
- int n_objs; /* number of objects in the current -f or -l option entry */
- int is_glb; /* is the filter global */
-
-
-
- /* parse the -f option */
- if(NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
- return -1;
-
- /* if it applies to all objects */
- if(is_glb)
- {
- int n;
-
- n = options->n_filter_g++; /* increase # of global filters */
-
- if(options->n_filter_g > H5_REPACK_MAX_NFILTERS)
- {
- error_msg("maximum number of filters exceeded for <%s>\n", str);
- HDfree(obj_list);
- return -1;
- }
-
- options->filter_g[n] = filter;
- }
- else
- options_add_filter(obj_list, n_objs, filter, options->op_tbl);
-
- HDfree(obj_list);
- return 0;
+ * Function: h5repack_end
+ *
+ * Purpose: free options table
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_end(pack_opt_t *options) {
+ return options_table_free(options->op_tbl);
}
+/*-------------------------------------------------------------------------
+ * Function: h5repack_addfilter
+ *
+ * Purpose: add a compression -f option to table
+ * Example: -f dset:GZIP=6
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack_addfilter(const char* str, pack_opt_t *options) {
+ obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */
+ filter_info_t filter; /* filter info for the current -f option entry */
+ int n_objs; /* number of objects in the current -f or -l option entry */
+ int is_glb; /* is the filter global */
+
+ /* parse the -f option */
+ if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
+ return -1;
+
+ /* if it applies to all objects */
+ if (is_glb) {
+ int n;
+
+ n = options->n_filter_g++; /* increase # of global filters */
+
+ if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) {
+ error_msg("maximum number of filters exceeded for <%s>\n", str);
+ HDfree(obj_list);
+ return -1;
+ }
+
+ options->filter_g[n] = filter;
+ }
+ else
+ options_add_filter(obj_list, n_objs, filter, options->op_tbl);
+
+ HDfree(obj_list);
+ return 0;
+}
/*-------------------------------------------------------------------------
-* Function: h5repack_addlayout
-*
-* Purpose: add a layout option
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-
-
-int h5repack_addlayout(const char* str,
- pack_opt_t *options)
-{
-
- obj_list_t *obj_list=NULL; /*one object list for the -t and -c option entry */
- int n_objs; /*number of objects in the current -t or -c option entry */
- pack_info_t pack; /*info about layout to extract from parse */
- int j;
-
- init_packobject(&pack);
-
- if (options->all_layout==1){
- error_msg("invalid layout input: 'all' option \
- is present with other objects <%s>\n",str);
- return -1;
- }
-
- /* parse the layout option */
- obj_list=parse_layout(str,&n_objs,&pack,options);
- if (obj_list==NULL)
- return -1;
-
- /* set layout option */
- options->layout_g = pack.layout;
-
- /* no individual dataset specified */
- if (options->all_layout==1 )
- {
- if (pack.layout==H5D_CHUNKED)
- {
- /* -2 means the NONE option, remove chunking
- and set the global layout to contiguous */
- if (pack.chunk.rank==-2)
- {
- options->layout_g = H5D_CONTIGUOUS;
- }
- /* otherwise set the global chunking type */
- else
- {
- options->chunk_g.rank=pack.chunk.rank;
- for (j = 0; j < pack.chunk.rank; j++)
- options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
- }
- }
- }
-
- /* individual dataset specified */
- if (options->all_layout==0)
- options_add_layout(obj_list,
- n_objs,
- &pack,
- options->op_tbl);
-
- HDfree(obj_list);
- return 0;
+ * Function: h5repack_addlayout
+ *
+ * Purpose: add a layout option
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_addlayout(const char* str, pack_opt_t *options) {
+
+ obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */
+ int n_objs; /*number of objects in the current -t or -c option entry */
+ pack_info_t pack; /*info about layout to extract from parse */
+ int j;
+ int ret_value = -1;
+
+ init_packobject(&pack);
+
+ if (options->all_layout == 1) {
+ error_msg(
+ "invalid layout input: 'all' option \
+ is present with other objects <%s>\n",
+ str);
+ return ret_value;
+ }
+
+ /* parse the layout option */
+ obj_list = parse_layout(str, &n_objs, &pack, options);
+ if (obj_list) {
+
+ /* set layout option */
+ options->layout_g = pack.layout;
+
+ /* no individual dataset specified */
+ if (options->all_layout == 1) {
+ if (pack.layout == H5D_CHUNKED) {
+ /* -2 means the NONE option, remove chunking
+ and set the global layout to contiguous */
+ if (pack.chunk.rank == -2) {
+ options->layout_g = H5D_CONTIGUOUS;
+ }
+ /* otherwise set the global chunking type */
+ else {
+ options->chunk_g.rank = pack.chunk.rank;
+ for (j = 0; j < pack.chunk.rank; j++)
+ options->chunk_g.chunk_lengths[j] =
+ pack.chunk.chunk_lengths[j];
+ }
+ }
+ }
+
+ /* individual dataset specified */
+ if (options->all_layout == 0)
+ ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl);
+
+ HDfree(obj_list);
+ ret_value = 0;
+ }
+
+ return ret_value;
}
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
@@ -250,766 +224,720 @@ int h5repack_addlayout(const char* str,
* others to static in h5repack_copy.c.
*/
/*-------------------------------------------------------------------------
-* Function: copy_named_datatype
-*
-* Purpose: Copies the specified datatype anonymously, and returns an open
-* id for that datatype in the output file. The first time this
-* is called it scans every named datatype in travt into a
-* private stack, afterwards it simply scans that stack. The id
-* returned must be closed after it is no longer needed.
-* named_datatype_free must be called before the program exits
-* to free the stack.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
-{
- named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
- named_dt_t *dt_ret = NULL; /* Datatype to return */
- H5O_info_t oinfo; /* Object info of input dtype */
- hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
-
- if(H5Oget_info(type_in, &oinfo) < 0)
- goto error;
-
- if(*named_dt_head_p)
- {
- /* Stack already exists, search for the datatype */
- while(dt && dt->addr_in != oinfo.addr)
- dt = dt->next;
-
- dt_ret = dt;
- }
- else
- {
- /* Create the stack */
- size_t i;
-
- for(i=0; i<travt->nobjs; i++)
- if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
- {
- /* Push onto the stack */
- if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
- goto error;
- dt->next = *named_dt_head_p;
- *named_dt_head_p = dt;
-
- /* Update the address and id */
- dt->addr_in = travt->objs[i].objno;
- dt->id_out = -1;
-
- /* Check if this type is the one requested */
- if(oinfo.addr == dt->addr_in)
- {
- HDassert(!dt_ret);
- dt_ret = dt;
- } /* end if */
- } /* end if */
- } /* end else */
-
- /* Handle the case that the requested datatype was not found. This is
- * possible if the datatype was committed anonymously in the input file. */
- if(!dt_ret)
- {
- /* Push the new datatype onto the stack */
- if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
- goto error;
- dt_ret->next = *named_dt_head_p;
- *named_dt_head_p = dt_ret;
-
- /* Update the address and id */
- dt_ret->addr_in = oinfo.addr;
- dt_ret->id_out = -1;
- } /* end if */
-
- /* If the requested datatype does not yet exist in the output file, copy it
- * anonymously */
- if(dt_ret->id_out < 0)
- {
- if (options->use_native==1)
- dt_ret->id_out = h5tools_get_native_type(type_in);
- else
- dt_ret->id_out = H5Tcopy(type_in);
- if(dt_ret->id_out < 0)
- goto error;
- if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
- goto error;
- } /* end if */
-
- /* Set return value */
- ret_value = dt_ret->id_out;
-
- /* Increment the ref count on id_out, because the calling function will try
- * to close it */
- if(H5Iinc_ref(ret_value) < 0)
- goto error;
-
- return(ret_value);
-
-error:
- return(-1);
+ * Function: copy_named_datatype
+ *
+ * Purpose: Copies the specified datatype anonymously, and returns an open
+ * id for that datatype in the output file. The first time this
+ * is called it scans every named datatype in travt into a
+ * private stack, afterwards it simply scans that stack. The id
+ * returned must be closed after it is no longer needed.
+ * named_datatype_free must be called before the program exits
+ * to free the stack.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
+ named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+ named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
+ named_dt_t *dt_ret = NULL; /* Datatype to return */
+ H5O_info_t oinfo; /* Object info of input dtype */
+ hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
+
+ if (H5Oget_info(type_in, &oinfo) < 0)
+ goto done;
+
+ if (*named_dt_head_p) {
+ /* Stack already exists, search for the datatype */
+ while (dt && dt->addr_in != oinfo.addr)
+ dt = dt->next;
+
+ dt_ret = dt;
+ }
+ else {
+ /* Create the stack */
+ size_t i;
+
+ for (i = 0; i < travt->nobjs; i++) {
+ if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
+ /* Push onto the stack */
+ if (NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+ goto done;
+ }
+ dt->next = *named_dt_head_p;
+ *named_dt_head_p = dt;
+
+ /* Update the address and id */
+ dt->addr_in = travt->objs[i].objno;
+ dt->id_out = -1;
+
+ /* Check if this type is the one requested */
+ if (oinfo.addr == dt->addr_in) {
+ HDassert(!dt_ret);
+ dt_ret = dt;
+ } /* end if */
+ } /* end if */
+ } /* end for */
+ } /* end else */
+
+ /* Handle the case that the requested datatype was not found. This is
+ * possible if the datatype was committed anonymously in the input file. */
+ if (!dt_ret) {
+ /* Push the new datatype onto the stack */
+ if (NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+ goto done;
+ }
+ dt_ret->next = *named_dt_head_p;
+ *named_dt_head_p = dt_ret;
+
+ /* Update the address and id */
+ dt_ret->addr_in = oinfo.addr;
+ dt_ret->id_out = -1;
+ } /* end if */
+
+ /* If the requested datatype does not yet exist in the output file, copy it
+ * anonymously */
+ if (dt_ret->id_out < 0) {
+ if (options->use_native == 1)
+ dt_ret->id_out = h5tools_get_native_type(type_in);
+ else
+ dt_ret->id_out = H5Tcopy(type_in);
+ if (dt_ret->id_out < 0)
+ goto done;
+ if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto done;
+ } /* end if */
+
+ /* Set return value */
+ ret_value = dt_ret->id_out;
+
+ /* Increment the ref count on id_out, because the calling function will try
+ * to close it */
+ if(H5Iinc_ref(ret_value) < 0) {
+ ret_value = -1;
+ }
+
+done:
+ return (ret_value);
} /* end copy_named_datatype */
-
/*-------------------------------------------------------------------------
-* Function: named_datatype_free
-*
-* Purpose: Frees the stack of named datatypes.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
-{
- named_dt_t *dt = *named_dt_head_p;
-
- while(dt)
- {
- /* Pop the datatype off the stack and free it */
- if(H5Tclose(dt->id_out) < 0 && !ignore_err)
- goto error;
- dt = dt->next;
- HDfree(*named_dt_head_p);
- *named_dt_head_p = dt;
- } /* end while */
-
- return 0;
-
-error:
- return -1;
+ * Function: named_datatype_free
+ *
+ * Purpose: Frees the stack of named datatypes.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
+ named_dt_t *dt = *named_dt_head_p;
+ hid_t ret_value = -1;
+
+ while (dt) {
+ /* Pop the datatype off the stack and free it */
+ if (H5Tclose(dt->id_out) < 0 && !ignore_err)
+ goto done;
+ dt = dt->next;
+ HDfree(*named_dt_head_p);
+ *named_dt_head_p = dt;
+ } /* end while */
+
+ ret_value = 0;
+
+done:
+ return (ret_value);
} /* end named_datatype_free */
/*-------------------------------------------------------------------------
-* Function: copy_attr
-*
-* Purpose: copy attributes located in LOC_IN, which is obtained either from
-* loc_id = H5Gopen2( fid, name);
-* loc_id = H5Dopen2( fid, name);
-* loc_id = H5Topen2( fid, name);
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 28, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int copy_attr(hid_t loc_in,
- hid_t loc_out,
- named_dt_t **named_dt_head_p,
- trav_table_t *travt,
- pack_opt_t *options)
-{
- hid_t attr_id=-1; /* attr ID */
- hid_t attr_out=-1; /* attr ID */
- hid_t space_id=-1; /* space ID */
- hid_t ftype_id=-1; /* file type ID */
- hid_t wtype_id=-1; /* read/write type ID */
- size_t msize; /* size of type */
- void *buf = NULL; /* data buffer */
- hsize_t nelmts; /* number of elements in dataset */
- int rank; /* rank of dataset */
- htri_t is_named; /* Whether the datatype is named */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- char name[255];
- H5O_info_t oinfo; /* object info */
- int j;
- unsigned u;
- hbool_t is_ref=0;
- H5T_class_t type_class = -1;
-
- if(H5Oget_info(loc_in, &oinfo) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * copy all attributes
- *-------------------------------------------------------------------------
- */
- for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
- /* open attribute */
- if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
- goto error;
-
- /* get name */
- if(H5Aget_name(attr_id, (size_t)255, name) < 0)
- goto error;
-
- /* get the file datatype */
- if((ftype_id = H5Aget_type(attr_id)) < 0 )
- goto error;
-
- /* Check if the datatype is committed */
- if((is_named = H5Tcommitted(ftype_id)) < 0)
- goto error;
- if(is_named && travt) {
- hid_t fidout;
-
- /* Create out file id */
- if((fidout = H5Iget_file_id(loc_out)) < 0)
- goto error;
-
- /* Copy named dt */
- if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
- travt, options)) < 0)
- {
- H5Fclose(fidout);
- goto error;
- } /* end if */
-
- if(H5Fclose(fidout) < 0)
- goto error;
- } /* end if */
- else {
- if(options->use_native == 1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
- } /* end else */
-
-
- /* get the dataspace handle */
- if((space_id = H5Aget_space(attr_id)) < 0)
- goto error;
-
- /* get dimensions */
- if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
- goto error;
-
- nelmts = 1;
- for(j = 0; j < rank; j++)
- nelmts *= dims[j];
-
- if((msize = H5Tget_size(wtype_id)) == 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * object references are a special case. We cannot just copy the buffers,
- * but instead we recreate the reference.
- * This is done on a second sweep of the file that just copies the referenced
- * objects at copy_refs_attr()
- *-------------------------------------------------------------------------
- */
- type_class = H5Tget_class(wtype_id);
- is_ref = (type_class == H5T_REFERENCE);
- if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
- hid_t base_type = -1;
- base_type = H5Tget_super(ftype_id);
- is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
- H5Tclose(base_type);
- }
-
- if (type_class == H5T_COMPOUND) {
- int nmembers = H5Tget_nmembers(wtype_id) ;
- for (j=0; j<nmembers; j++) {
- hid_t mtid = H5Tget_member_type( wtype_id, (unsigned) j );
- H5T_class_t mtclass = H5Tget_class(mtid);
- H5Tclose(mtid);
-
- if (mtclass==H5T_REFERENCE) {
- is_ref = 1;
- break;
- }
- } /* for (j=0; i<nmembers; j++) */
- } /* if (type_class == H5T_COMPOUND) */
-
- if(is_ref) {
- ; /* handled by copy_refs_attr() */
- }
- else {
- /*-------------------------------------------------------------------------
- * read to memory
- *-------------------------------------------------------------------------
- */
-
- buf = (void *)HDmalloc((size_t)(nelmts * msize));
- if(buf == NULL) {
- error_msg("h5repack", "cannot read into memory\n" );
- goto error;
- } /* end if */
- if(H5Aread(attr_id, wtype_id, buf) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * copy
- *-------------------------------------------------------------------------
- */
-
- if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
- goto error;
- if(H5Awrite(attr_out, wtype_id, buf) < 0)
- goto error;
-
- /*close*/
- if(H5Aclose(attr_out) < 0)
- goto error;
-
- /* Check if we have VL data and string in the attribute's datatype that must
- * be reclaimed */
- if (TRUE == h5tools_detect_vlen(wtype_id))
- H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
- HDfree(buf);
- buf = NULL;
- } /*H5T_REFERENCE*/
-
-
- if(options->verbose)
- printf(FORMAT_OBJ_ATTR, "attr", name);
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if(H5Tclose(ftype_id) < 0)
- goto error;
- if(H5Tclose(wtype_id) < 0)
- goto error;
- if(H5Sclose(space_id) < 0)
- goto error;
- if(H5Aclose(attr_id) < 0)
- goto error;
- } /* u */
-
- return 0;
+ * Function: copy_attr
+ *
+ * Purpose: copy attributes located in LOC_IN, which is obtained either from
+ * loc_id = H5Gopen2( fid, name);
+ * loc_id = H5Dopen2( fid, name);
+ * loc_id = H5Topen2( fid, name);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
+ trav_table_t *travt, pack_opt_t *options) {
+ hid_t attr_id = -1; /* attr ID */
+ hid_t attr_out = -1; /* attr ID */
+ hid_t space_id = -1; /* space ID */
+ hid_t ftype_id = -1; /* file type ID */
+ hid_t wtype_id = -1; /* read/write type ID */
+ size_t msize; /* size of type */
+ void *buf = NULL; /* data buffer */
+ hsize_t nelmts; /* number of elements in dataset */
+ int rank; /* rank of dataset */
+ htri_t is_named; /* Whether the datatype is named */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ char name[255];
+ H5O_info_t oinfo; /* object info */
+ int j;
+ unsigned u;
+ hbool_t is_ref = 0;
+ H5T_class_t type_class = -1;
+
+ if (H5Oget_info(loc_in, &oinfo) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy all attributes
+ *-------------------------------------------------------------------------
+ */
+ for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
+ /* open attribute */
+ if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER,
+ H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /* get name */
+ if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
+ goto error;
+
+ /* get the file datatype */
+ if ((ftype_id = H5Aget_type(attr_id)) < 0)
+ goto error;
+
+ /* Check if the datatype is committed */
+ if ((is_named = H5Tcommitted(ftype_id)) < 0)
+ goto error;
+ if (is_named && travt) {
+ hid_t fidout;
+
+ /* Create out file id */
+ if ((fidout = H5Iget_file_id(loc_out)) < 0)
+ goto error;
+
+ /* Copy named dt */
+ if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+ named_dt_head_p, travt, options)) < 0) {
+ H5Fclose(fidout);
+ goto error;
+ } /* end if */
+
+ if (H5Fclose(fidout) < 0)
+ goto error;
+ } /* end if */
+ else {
+ if (options->use_native == 1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
+ } /* end else */
+
+ /* get the dataspace handle */
+ if ((space_id = H5Aget_space(attr_id)) < 0)
+ goto error;
+
+ /* get dimensions */
+ if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
+ goto error;
+
+ nelmts = 1;
+ for (j = 0; j < rank; j++)
+ nelmts *= dims[j];
+
+ if ((msize = H5Tget_size(wtype_id)) == 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * object references are a special case. We cannot just copy the buffers,
+ * but instead we recreate the reference.
+ * This is done on a second sweep of the file that just copies the referenced
+ * objects at copy_refs_attr()
+ *-------------------------------------------------------------------------
+ */
+ type_class = H5Tget_class(wtype_id);
+ is_ref = (type_class == H5T_REFERENCE);
+ if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
+ hid_t base_type = -1;
+ base_type = H5Tget_super(ftype_id);
+ is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
+ H5Tclose(base_type);
+ }
+
+ if (type_class == H5T_COMPOUND) {
+ int nmembers = H5Tget_nmembers(wtype_id);
+ for (j = 0; j < nmembers; j++) {
+ hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j);
+ H5T_class_t mtclass = H5Tget_class(mtid);
+ H5Tclose(mtid);
+
+ if (mtclass == H5T_REFERENCE) {
+ is_ref = 1;
+ break;
+ }
+ } /* for (j=0; i<nmembers; j++) */
+ } /* if (type_class == H5T_COMPOUND) */
+
+ if (is_ref) {
+ ; /* handled by copy_refs_attr() */
+ }
+ else {
+ /*-------------------------------------------------------------------------
+ * read to memory
+ *-------------------------------------------------------------------------
+ */
+
+ buf = (void *) HDmalloc((size_t)(nelmts * msize));
+ if (buf == NULL) {
+ error_msg("h5repack", "cannot read into memory\n");
+ goto error;
+ } /* end if */
+ if (H5Aread(attr_id, wtype_id, buf) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy
+ *-------------------------------------------------------------------------
+ */
+
+ if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id,
+ H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+ if (H5Awrite(attr_out, wtype_id, buf) < 0)
+ goto error;
+
+ /*close*/
+ if (H5Aclose(attr_out) < 0)
+ goto error;
+
+ /* Check if we have VL data and string in the attribute's datatype that must
+ * be reclaimed */
+ if (TRUE == h5tools_detect_vlen(wtype_id))
+ H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+ HDfree(buf);
+ buf = NULL;
+ } /*H5T_REFERENCE*/
+
+ if (options->verbose)
+ printf(FORMAT_OBJ_ATTR, "attr", name);
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Tclose(ftype_id) < 0)
+ goto error;
+ if (H5Tclose(wtype_id) < 0)
+ goto error;
+ if (H5Sclose(space_id) < 0)
+ goto error;
+ if (H5Aclose(attr_id) < 0)
+ goto error;
+ } /* u */
+
+ return 0;
error:
- H5E_BEGIN_TRY {
- if(buf) {
- /* Check if we have VL data and string in the attribute's datatype that must
- * be reclaimed */
- if (TRUE == h5tools_detect_vlen(wtype_id))
- H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-
- /* Free buf */
- HDfree(buf);
- } /* end if */
-
- H5Tclose(ftype_id);
- H5Tclose(wtype_id);
- H5Sclose(space_id);
- H5Aclose(attr_id);
- H5Aclose(attr_out);
- } H5E_END_TRY;
-
- return -1;
+ H5E_BEGIN_TRY
+ {
+ if (buf) {
+ /* Check if we have VL data and string in the attribute's datatype that must
+ * be reclaimed */
+ if (TRUE == h5tools_detect_vlen(wtype_id))
+ H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+
+ /* Free buf */
+ HDfree(buf);
+ } /* end if */
+
+ H5Tclose(ftype_id);
+ H5Tclose(wtype_id);
+ H5Sclose(space_id);
+ H5Aclose(attr_id);
+ H5Aclose(attr_out);
+ } H5E_END_TRY;
+
+ return -1;
} /* end copy_attr() */
/*-------------------------------------------------------------------------
-* Function: check_options
-*
-* Purpose: print options, checks for invalid options
-*
-* Return: void, return -1 on error
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-* Modification:
-* Peter Cao, July 9, 2007
-* Add "-L, --latest" and other options to pack a file with the latest file format
-*
-*-------------------------------------------------------------------------
-*/
-static int check_options(pack_opt_t *options)
-{
- unsigned int i;
- int k, j, has_cp=0, has_ck=0;
- char slayout[30];
-
- /*-------------------------------------------------------------------------
- * objects to layout
- *-------------------------------------------------------------------------
- */
- if (options->verbose && have_request(options) /* only print if requested */)
- {
- printf("Objects to modify layout are...\n");
- if (options->all_layout==1)
- {
- switch (options->layout_g)
- {
- case H5D_COMPACT:
- strcpy(slayout,"compact");
- break;
- case H5D_CONTIGUOUS:
- strcpy(slayout,"contiguous");
- break;
- case H5D_CHUNKED:
- strcpy(slayout,"chunked");
- break;
- case H5D_LAYOUT_ERROR:
- case H5D_NLAYOUTS:
- error_msg("invalid layout\n");
- return -1;
- default:
- strcpy(slayout,"invalid layout\n");
- return -1;
- }
- printf(" Apply %s layout to all\n", slayout);
- if (H5D_CHUNKED==options->layout_g)
- {
- printf("with dimension [");
- for ( j = 0; j < options->chunk_g.rank; j++)
- printf("%d ",(int)options->chunk_g.chunk_lengths[j]);
- printf("]\n");
- }
- }
- }/* verbose */
-
- for ( i = 0; i < options->op_tbl->nelems; i++)
- {
- char* name=options->op_tbl->objs[i].path;
-
- if (options->op_tbl->objs[i].chunk.rank>0)
- {
- if (options->verbose){
- printf(" <%s> with chunk size ",name);
- for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
- printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
- printf("\n");
- }
- has_ck=1;
- }
- else if (options->op_tbl->objs[i].chunk.rank==-2)
- {
- if (options->verbose)
- printf(" <%s> %s\n",name,"NONE (contigous)");
- has_ck=1;
- }
- }
-
- if (options->all_layout==1 && has_ck)
- {
- error_msg("invalid chunking input: 'all' option\
+ * Function: check_options
+ *
+ * Purpose: print options, checks for invalid options
+ *
+ * Return: void, return -1 on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ * Modification:
+ * Peter Cao, July 9, 2007
+ * Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_options(pack_opt_t *options) {
+ unsigned int i;
+ int k, j, has_cp = 0, has_ck = 0;
+ char slayout[30];
+
+ /*-------------------------------------------------------------------------
+ * objects to layout
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose && have_request(options) /* only print if requested */) {
+ printf("Objects to modify layout are...\n");
+ if (options->all_layout == 1) {
+ switch (options->layout_g) {
+ case H5D_COMPACT:
+ strcpy(slayout, "compact");
+ break;
+ case H5D_CONTIGUOUS:
+ strcpy(slayout, "contiguous");
+ break;
+ case H5D_CHUNKED:
+ strcpy(slayout, "chunked");
+ break;
+ case H5D_LAYOUT_ERROR:
+ case H5D_NLAYOUTS:
+ error_msg("invalid layout\n");
+ return -1;
+ default:
+ strcpy(slayout, "invalid layout\n");
+ return -1;
+ }
+ printf(" Apply %s layout to all\n", slayout);
+ if (H5D_CHUNKED == options->layout_g) {
+ printf("with dimension [");
+ for (j = 0; j < options->chunk_g.rank; j++)
+ printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+ printf("]\n");
+ }
+ }
+ }/* verbose */
+
+ for (i = 0; i < options->op_tbl->nelems; i++) {
+ char* name = options->op_tbl->objs[i].path;
+
+ if (options->op_tbl->objs[i].chunk.rank > 0) {
+ if (options->verbose) {
+ printf(" <%s> with chunk size ", name);
+ for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
+ printf("%d ",
+ (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+ printf("\n");
+ }
+ has_ck = 1;
+ }
+ else if (options->op_tbl->objs[i].chunk.rank == -2) {
+ if (options->verbose)
+ printf(" <%s> %s\n", name, "NONE (contigous)");
+ has_ck = 1;
+ }
+ }
+
+ if (options->all_layout == 1 && has_ck) {
+ error_msg(
+ "invalid chunking input: 'all' option\
is present with other objects\n");
- return -1;
- }
-
- /*-------------------------------------------------------------------------
- * objects to filter
- *-------------------------------------------------------------------------
- */
-
- if (options->verbose && have_request(options) /* only print if requested */)
- {
- printf("Objects to apply filter are...\n");
- if (options->all_filter==1)
- {
-
- for (k = 0; k < options->n_filter_g; k++ )
- {
- H5Z_filter_t filtn=options->filter_g[k].filtn;
- switch (filtn)
- {
- case H5Z_FILTER_NONE:
- printf(" Uncompress all\n");
- break;
- case H5Z_FILTER_SHUFFLE:
- case H5Z_FILTER_FLETCHER32:
- printf(" All with %s\n",get_sfilter(filtn));
- break;
- case H5Z_FILTER_SZIP:
- case H5Z_FILTER_DEFLATE:
- printf(" All with %s, parameter %d\n",
- get_sfilter(filtn),
- options->filter_g[k].cd_values[0]);
- break;
- default:
- break;
- } /* k */
- };
- }
- } /* verbose */
-
- for ( i = 0; i < options->op_tbl->nelems; i++)
- {
- pack_info_t pack = options->op_tbl->objs[i];
- char* name = pack.path;
-
- for ( j=0; j<pack.nfilters; j++)
- {
- if (options->verbose)
- {
- printf(" <%s> with %s filter\n",
- name,
- get_sfilter(pack.filter[j].filtn));
- }
-
- has_cp=1;
-
- } /* j */
- } /* i */
-
- if (options->all_filter==1 && has_cp)
- {
- error_msg("invalid compression input: 'all' option\
+ return -1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * objects to filter
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->verbose && have_request(options) /* only print if requested */) {
+ printf("Objects to apply filter are...\n");
+ if (options->all_filter == 1) {
+ for (k = 0; k < options->n_filter_g; k++) {
+ H5Z_filter_t filtn = options->filter_g[k].filtn;
+ switch (filtn) {
+ case H5Z_FILTER_NONE:
+ printf(" Uncompress all\n");
+ break;
+ case H5Z_FILTER_SHUFFLE:
+ case H5Z_FILTER_FLETCHER32:
+ printf(" All with %s\n", get_sfilter(filtn));
+ break;
+ case H5Z_FILTER_SZIP:
+ case H5Z_FILTER_DEFLATE:
+ printf(" All with %s, parameter %d\n", get_sfilter(filtn),
+ options->filter_g[k].cd_values[0]);
+ break;
+ default:
+ printf(" User Defined %d\n", filtn);
+ break;
+ } /* k */
+ };
+ }
+ } /* verbose */
+
+ for (i = 0; i < options->op_tbl->nelems; i++) {
+ pack_info_t pack = options->op_tbl->objs[i];
+ char* name = pack.path;
+
+ for (j = 0; j < pack.nfilters; j++) {
+ if (options->verbose) {
+ printf(" <%s> with %s filter\n", name,
+ get_sfilter(pack.filter[j].filtn));
+ }
+
+ has_cp = 1;
+
+ } /* j */
+ } /* i */
+
+ if (options->all_filter == 1 && has_cp) {
+ error_msg(
+ "invalid compression input: 'all' option\
is present with other objects\n");
- return -1;
- }
-
- /*-------------------------------------------------------------------------
- * check options for the latest format
- *-------------------------------------------------------------------------
- */
-
- if (options->grp_compact < 0)
- {
- error_msg("invalid maximum number of links to store as header messages\n");
- return -1;
- }
- if (options->grp_indexed < 0)
- {
- error_msg("invalid minimum number of links to store in the indexed format\n");
- return -1;
- }
- if (options->grp_indexed > options->grp_compact)
- {
- error_msg("minimum indexed size is greater than the maximum compact size\n");
- return -1;
- }
- for (i=0; i<8; i++)
- {
- if (options->msg_size[i]<0)
- {
- error_msg("invalid shared message size\n");
- return -1;
- }
- }
-
-
- /*--------------------------------------------------------------------------------
- * verify new user userblock options; file name must be present
- *---------------------------------------------------------------------------------
- */
- if ( options->ublock_filename != NULL && options->ublock_size == 0 )
- {
- if ( options->verbose )
- {
- printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
- options->ublock_filename);
- options->ublock_size = 1024;
- }
- }
-
- if ( options->ublock_filename == NULL && options->ublock_size != 0 )
- {
- error_msg("file name missing for user block\n",
- options->ublock_filename);
- return -1;
- }
-
-
- /*--------------------------------------------------------------------------------
- * verify alignment options; threshold is zero default but alignment not
- *---------------------------------------------------------------------------------
- */
-
- if ( options->alignment == 0 && options->threshold != 0 )
- {
- error_msg("alignment for H5Pset_alignment missing\n");
- return -1;
- }
-
- return 0;
+ return -1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * check options for the latest format
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->grp_compact < 0) {
+ error_msg(
+ "invalid maximum number of links to store as header messages\n");
+ return -1;
+ }
+ if (options->grp_indexed < 0) {
+ error_msg(
+ "invalid minimum number of links to store in the indexed format\n");
+ return -1;
+ }
+ if (options->grp_indexed > options->grp_compact) {
+ error_msg(
+ "minimum indexed size is greater than the maximum compact size\n");
+ return -1;
+ }
+ for (i = 0; i < 8; i++) {
+ if (options->msg_size[i] < 0) {
+ error_msg("invalid shared message size\n");
+ return -1;
+ }
+ }
+
+ /*--------------------------------------------------------------------------------
+ * verify new user userblock options; file name must be present
+ *---------------------------------------------------------------------------------
+ */
+ if (options->ublock_filename != NULL && options->ublock_size == 0) {
+ if (options->verbose) {
+ printf(
+ "Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
+ options->ublock_filename);
+ options->ublock_size = 1024;
+ }
+ }
+
+ if (options->ublock_filename == NULL && options->ublock_size != 0) {
+ error_msg("file name missing for user block\n",
+ options->ublock_filename);
+ return -1;
+ }
+
+ /*--------------------------------------------------------------------------------
+ * verify alignment options; threshold is zero default but alignment not
+ *---------------------------------------------------------------------------------
+ */
+
+ if (options->alignment == 0 && options->threshold != 0) {
+ error_msg("alignment for H5Pset_alignment missing\n");
+ return -1;
+ }
+
+ return 0;
}
-
/*-------------------------------------------------------------------------
-* Function: check_objects
-*
-* Purpose: locate all HDF5 objects in the file and compare with user
-* supplied list
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: September, 23, 2003
-*
-*-------------------------------------------------------------------------
-*/
-static int check_objects(const char* fname,
- pack_opt_t *options)
-{
- hid_t fid;
- unsigned int i;
- trav_table_t *travt = NULL;
-
- /* nothing to do */
- if(options->op_tbl->nelems == 0)
- return 0;
-
- /*-------------------------------------------------------------------------
- * open the file
- *-------------------------------------------------------------------------
- */
- if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
- {
- printf("<%s>: %s\n", fname, H5FOPENERROR );
- return -1;
- }
-
- /*-------------------------------------------------------------------------
- * get the list of objects in the file
- *-------------------------------------------------------------------------
- */
-
- /* init table */
- trav_table_init(&travt);
-
- /* get the list of objects in the file */
- if(h5trav_gettable(fid, travt) < 0)
- goto out;
-
- /*-------------------------------------------------------------------------
- * compare with user supplied list
- *-------------------------------------------------------------------------
- */
-
- if(options->verbose)
- printf("Opening file <%s>. Searching for objects to modify...\n", fname);
-
- for(i = 0; i < options->op_tbl->nelems; i++)
- {
- char* name=options->op_tbl->objs[i].path;
- if(options->verbose)
- printf(" <%s>",name);
-
- /* the input object names are present in the file and are valid */
- if(h5trav_getindext(name, travt) < 0)
- {
- error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
- (options->verbose?"\n":""),name,fname);
- goto out;
- }
- if(options->verbose)
- printf("...Found\n");
-
- /* check for extra filter conditions */
- switch(options->op_tbl->objs[i].filter->filtn)
- {
- /* chunk size must be smaller than pixels per block */
- case H5Z_FILTER_SZIP:
- {
- int j;
- hsize_t csize = 1;
- unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
- hsize_t dims[H5S_MAX_RANK];
- int rank;
- hid_t did;
- hid_t sid;
-
- if(options->op_tbl->objs[i].chunk.rank > 0) {
- rank = options->op_tbl->objs[i].chunk.rank;
- for(j = 0; j < rank; j++)
- csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
- }
- else {
- if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
- goto out;
- if((sid = H5Dget_space(did)) < 0)
- goto out;
- if((rank = H5Sget_simple_extent_ndims(sid)) < 0)
- goto out;
- HDmemset(dims, 0, sizeof dims);
- if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
- goto out;
- for(j = 0; j < rank; j++)
- csize *= dims[j];
- if(H5Sclose(sid) < 0)
- goto out;
- if(H5Dclose(did) < 0)
- goto out;
- }
-
- if (csize < ppb ) {
- printf(" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
- goto out;
- }
- }
- break;
- default:
- break;
- }
- } /* i */
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
- H5Fclose(fid);
- trav_table_free(travt);
- return 0;
+ * Function: check_objects
+ *
+ * Purpose: locate all HDF5 objects in the file and compare with user
+ * supplied list
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_objects(const char* fname, pack_opt_t *options) {
+ hid_t fid;
+ unsigned int i;
+ trav_table_t *travt = NULL;
+
+ /* nothing to do */
+ if (options->op_tbl->nelems == 0)
+ return 0;
+
+ /*-------------------------------------------------------------------------
+ * open the file
+ *-------------------------------------------------------------------------
+ */
+ if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
+ < 0) {
+ printf("<%s>: %s\n", fname, H5FOPENERROR);
+ return -1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * get the list of objects in the file
+ *-------------------------------------------------------------------------
+ */
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fid, travt) < 0)
+ goto out;
+
+ /*-------------------------------------------------------------------------
+ * compare with user supplied list
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->verbose)
+ printf("Opening file <%s>. Searching for objects to modify...\n",
+ fname);
+
+ for (i = 0; i < options->op_tbl->nelems; i++) {
+ char* name = options->op_tbl->objs[i].path;
+ if (options->verbose)
+ printf(" <%s>", name);
+
+ /* the input object names are present in the file and are valid */
+ if (h5trav_getindext(name, travt) < 0) {
+ error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
+ (options->verbose ? "\n" : ""), name, fname);
+ goto out;
+ }
+ if (options->verbose)
+ printf("...Found\n");
+
+ /* check for extra filter conditions */
+ switch (options->op_tbl->objs[i].filter->filtn) {
+ /* chunk size must be smaller than pixels per block */
+ case H5Z_FILTER_SZIP:
+ {
+ int j;
+ hsize_t csize = 1;
+ unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
+ hsize_t dims[H5S_MAX_RANK];
+ int rank;
+ hid_t did;
+ hid_t sid;
+
+ if (options->op_tbl->objs[i].chunk.rank > 0) {
+ rank = options->op_tbl->objs[i].chunk.rank;
+ for (j = 0; j < rank; j++)
+ csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+ }
+ else {
+ if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+ goto out;
+ if ((sid = H5Dget_space(did)) < 0)
+ goto out;
+ if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
+ goto out;
+ HDmemset(dims, 0, sizeof dims);
+ if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
+ goto out;
+ for (j = 0; j < rank; j++)
+ csize *= dims[j];
+ if (H5Sclose(sid) < 0)
+ goto out;
+ if (H5Dclose(did) < 0)
+ goto out;
+ }
+
+ if (csize < ppb) {
+ printf(
+ " <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
+ goto out;
+ }
+ }
+ break;
+ default:
+ break;
+ }
+ } /* i */
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ H5Fclose(fid);
+ trav_table_free(travt);
+ return 0;
out:
- H5Fclose(fid);
- trav_table_free(travt);
- return -1;
+ H5Fclose(fid);
+ trav_table_free(travt);
+ return -1;
}
+/*-------------------------------------------------------------------------
+ * Function: have_request
+ *
+ * Purpose: check if a filter or layout was requested
+ *
+ * Return: 1 yes, 0 no
+ *
+ * Date: May, 24, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int have_request(pack_opt_t *options) {
+ if (options->all_filter || options->all_layout || options->op_tbl->nelems)
+ return 1;
-
-
-/*-------------------------------------------------------------------------
-* Function: have_request
-*
-* Purpose: check if a filter or layout was requested
-*
-* Return: 1 yes, 0 no
-*
-* Date: May, 24, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int have_request(pack_opt_t *options)
-{
-
- if (options->all_filter || options->all_layout || options->op_tbl->nelems)
- return 1;
-
- return 0;
+ return 0;
}
-
/*-------------------------------------------------------------------------
-* Function: get_sfilter
-*
-* Purpose: return the filter as a string name
-*
-* Return: name of filter, exit on error
-*
-*-------------------------------------------------------------------------
-*/
-
-static const char* get_sfilter(H5Z_filter_t filtn)
-{
- if (filtn==H5Z_FILTER_NONE)
- return "NONE";
- else if (filtn==H5Z_FILTER_DEFLATE)
- return "GZIP";
- else if (filtn==H5Z_FILTER_SZIP)
- return "SZIP";
- else if (filtn==H5Z_FILTER_SHUFFLE)
- return "SHUFFLE";
- else if (filtn==H5Z_FILTER_FLETCHER32)
- return "FLETCHER32";
- else if (filtn==H5Z_FILTER_NBIT)
- return "NBIT";
- else if (filtn==H5Z_FILTER_SCALEOFFSET)
- return "SOFF";
- else {
- error_msg("input error in filter type\n");
- HDexit(EXIT_FAILURE);
- }
+ * Function: get_sfilter
+ *
+ * Purpose: return the filter as a string name
+ *
+ * Return: name of filter, exit on error
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static const char* get_sfilter(H5Z_filter_t filtn) {
+ if (filtn == H5Z_FILTER_NONE)
+ return "NONE";
+ else if (filtn == H5Z_FILTER_DEFLATE)
+ return "GZIP";
+ else if (filtn == H5Z_FILTER_SZIP)
+ return "SZIP";
+ else if (filtn == H5Z_FILTER_SHUFFLE)
+ return "SHUFFLE";
+ else if (filtn == H5Z_FILTER_FLETCHER32)
+ return "FLETCHER32";
+ else if (filtn == H5Z_FILTER_NBIT)
+ return "NBIT";
+ else if (filtn == H5Z_FILTER_SCALEOFFSET)
+ return "SOFF";
+ else
+ return "UD";
}
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 42b8ecb..583b6ef 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -117,11 +117,15 @@ $SRC_TOOLS_TESTFILES/tfamily00010.h5
"
LIST_OTHER_TEST_FILES="
+$SRC_H5REPACK_TESTFILES/h5repack-help.txt
$SRC_H5REPACK_TESTFILES/h5repack_ext.bin
$SRC_H5REPACK_TESTFILES/ublock.bin
$SRC_H5REPACK_TESTFILES/h5repack.info
+$SRC_H5REPACK_TESTFILES/deflate_limit.h5repack_layout.h5.ddl
$SRC_H5REPACK_TESTFILES/h5repack_layout.h5.ddl
-$SRC_TOOLS_TESTFILES/h5repack_filters.h5.ddl
+$SRC_H5REPACK_TESTFILES/h5repack_filters.h5.tst
+$SRC_H5REPACK_TESTFILES/h5repack_layout.h5-plugin_test.ddl
+$SRC_H5REPACK_TESTFILES/plugin_test.h5repack_layout.h5.tst
"
#
@@ -436,7 +440,7 @@ TOOLTEST1()
#
TOOLTESTV()
{
- expect="$TESTDIR/$2.ddl"
+ expect="$TESTDIR/$2.tst"
actual="$TESTDIR/`basename $2 .ddl`.out"
actual_err="$TESTDIR/`basename $2 .ddl`.err"
@@ -468,7 +472,7 @@ TOOLTESTV()
echo " PASSED"
else
echo "*FAILED*"
- echo " Expected result (*.ddl) differs from actual result (*.out)"
+ echo " Expected result (*.tst) differs from actual result (*.out)"
nerrors="`expr $nerrors + 1`"
test yes = "$verbose" && diff -c $expect $actual |sed 's/^/ /'
fi
@@ -484,7 +488,7 @@ TOOLTEST_DUMP()
{
infile=$TESTDIR/$2
outfile=$TESTDIR/out-$1.$2
- expect="$TESTDIR/$2.ddl"
+ expect="$TESTDIR/$1.$2.ddl"
actual="$TESTDIR/out-$1.$2.out"
actual_err="$TESTDIR/out-$1.$2.err"
@@ -592,6 +596,40 @@ TOOLTEST_META()
rm -f $outfile
}
+# ADD_HELP_TEST
+TOOLTEST_HELP() {
+
+ expect="$TESTDIR/$1"
+ actual="$TESTDIR/`basename $1 .txt`.out"
+ actual_err="$TESTDIR/`basename $1 .txt`.err"
+ shift
+
+ # Run test.
+ TESTING $H5REPACK $@
+ (
+ cd $TESTDIR
+ $RUNSERIAL $H5REPACK_BIN "$@"
+ ) >$actual 2>$actual_err
+ cat $actual_err >> $actual
+
+ if [ ! -f $expect ]; then
+ # Create the expect data file if it doesn't yet exist.
+ echo " CREATED"
+ cp $actual $expect-CREATED
+ elif cmp -s $expect $actual; then
+ echo " PASSED"
+ else
+ echo "*FAILED*"
+ echo " Expected output (*.txt) differs from actual output (*.out)"
+ nerrors="`expr $nerrors + 1`"
+ fi
+
+ # Clean up output file
+ if test -z "$HDF5_NOCLEANUP"; then
+ rm -f $actual $actual_err
+ fi
+
+}
# This is different from $srcdir/../../bin/output_filter.sh
STDOUT_FILTER() {
@@ -630,6 +668,8 @@ fi
# prepare for test
COPY_TESTFILES_TO_TESTDIR
+TOOLTEST_HELP h5repack-help.txt -h
+
# copy files (these files have no filters)
TOOLTEST fill h5repack_fill.h5
TOOLTEST objs h5repack_objs.h5
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 02337fd..521b9bd 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -1,36 +1,36 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* 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. *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
-* typedefs
-*-------------------------------------------------------------------------
-*/
+ * typedefs
+ *-------------------------------------------------------------------------
+ */
/*-------------------------------------------------------------------------
-* globals
-*-------------------------------------------------------------------------
-*/
+ * globals
+ *-------------------------------------------------------------------------
+ */
/*-------------------------------------------------------------------------
-* macros
-*-------------------------------------------------------------------------
-*/
+ * macros
+ *-------------------------------------------------------------------------
+ */
/* size of buffer/# of bytes to xfer at a time when copying userblock */
#define USERBLOCK_XFER_SIZE 512
@@ -48,1701 +48,1630 @@
} \
} H5E_END_TRY; \
}
-
+
/*-------------------------------------------------------------------------
-* local functions
-*-------------------------------------------------------------------------
-*/
-static int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
-static void print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
-static int do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
-static int copy_user_block(const char *infile, const char *outfile, hsize_t size);
+ * local functions
+ *-------------------------------------------------------------------------
+ */
+static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+ size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
+static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
+static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+ pack_opt_t *options);
+static int copy_user_block(const char *infile, const char *outfile,
+ hsize_t size);
#if defined (H5REPACK_DEBUG_USER_BLOCK)
-static void print_user_block(const char *filename, hid_t fid);
+static void print_user_block(const char *filename, hid_t fid);
#endif
static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
/* get the major number from the error stack. */
-static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata)
-{
- if (err_desc)
- *((int *)udata) = err_desc->maj_num;
-
- return 0;
+static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
+ if (err_desc)
+ *((int *) udata) = err_desc->maj_num;
+
+ return 0;
}
/*-------------------------------------------------------------------------
-* Function: copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modification:
-* Peter Cao, June 13, 2007
-* Add "-L, --latest" and other options to pack a file with the latest file format
-*
-* Peter Cao, September 25, 2007
-* Copy user block when repacking a file
-*
-* Pedro Vicente, August 20, 2008
-* Add a user block to file if requested
-*
-*-------------------------------------------------------------------------
-*/
-
-int copy_objects(const char* fnamein,
- const char* fnameout,
- pack_opt_t *options)
-{
- hid_t fidin;
- hid_t fidout = -1;
- trav_table_t *travt = NULL;
- hsize_t ub_size = 0; /* size of user block */
- hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
- hid_t fapl = H5P_DEFAULT; /* file access property list ID */
-
- /*-------------------------------------------------------------------------
- * open input file
- *-------------------------------------------------------------------------
- */
- if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0)
- {
- error_msg("<%s>: %s\n", fnamein, H5FOPENERROR );
- goto out;
- }
-
- /* get user block size and file space strategy/threshold */
- {
- hid_t fcpl_in; /* file creation property list ID for input file */
-
- if((fcpl_in = H5Fget_create_plist(fidin)) < 0)
- {
- error_msg("failed to retrieve file creation property list\n");
- goto out;
- }
-
- if(H5Pget_userblock(fcpl_in, &ub_size) < 0)
- {
- error_msg("failed to retrieve userblock size\n");
- goto out;
- }
-
- if(!options->fs_strategy)
- {
- if(H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0)
- {
- error_msg("failed to retrieve file space strategy\n");
- goto out;
- }
- }
-
- if(!options->fs_threshold)
- {
- if(H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0)
- {
- error_msg("failed to retrieve file space threshold\n");
- goto out;
- }
- }
-
- if(H5Pclose(fcpl_in) < 0)
- {
- error_msg("failed to close property list\n");
- goto out;
- }
- }
-
- /* Check if we need to create a non-default file creation property list */
- if(options->latest || ub_size > 0)
- {
- /* Create file creation property list */
- if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
- {
- error_msg("fail to create a file creation property list\n");
- goto out;
- }
-
- if(ub_size > 0)
- {
- if(H5Pset_userblock(fcpl, ub_size) < 0)
- {
- error_msg("failed to set non-default userblock size\n");
- goto out;
- }
- }
-
- if(options->latest)
- {
- unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
-
- /* Adjust group creation parameters for root group */
- /* (So that it is created in "dense storage" form) */
- if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
- {
- error_msg("fail to adjust group creation parameters for root group\n");
- goto out;
- }
-
- for(i = 0; i < 5; i++)
- {
- if(options->msg_size[i] > 0)
- {
- switch(i)
- {
- case 0:
- mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
- break;
-
- case 1:
- mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
- break;
-
- case 2:
- mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
- break;
-
- case 3:
- mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
- break;
-
- case 4:
- mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
- break;
- default:
- break;
- } /* end switch */
- min_mesg_sizes[nindex] = (unsigned)options->msg_size[i];
-
- nindex++;
- } /* end if */
- } /* end for */
-
- if(nindex > 0)
- {
- if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0)
- {
- error_msg("fail to set the number of shared object header message indexes\n");
- goto out;
- }
-
- /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
- for(i = 0; i < (nindex - 1); i++)
- {
- if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
- error_msg("fail to configure the specified shared object header message index\n");
- goto out;
- } /* end if */
- } /* end for */
- } /* if (nindex>0) */
-
- /* Create file access property list */
- if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
- {
- error_msg("Could not create file access property list\n");
- goto out;
- } /* end if */
-
- if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
- {
- error_msg("Could not set property for using latest version of the format\n");
- goto out;
- } /* end if */
- } /* end if */
- } /* end if */
+ * Function: copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modification:
+ * Peter Cao, June 13, 2007
+ * Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ * Peter Cao, September 25, 2007
+ * Copy user block when repacking a file
+ *
+ * Pedro Vicente, August 20, 2008
+ * Add a user block to file if requested
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) {
+ hid_t fidin;
+ hid_t fidout = -1;
+ trav_table_t *travt = NULL;
+ hsize_t ub_size = 0; /* size of user block */
+ hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
+ hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+
+ /*-------------------------------------------------------------------------
+ * open input file
+ *-------------------------------------------------------------------------
+ */
+ if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL,
+ (size_t) 0)) < 0) {
+ error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
+ goto out;
+ }
+
+ /* get user block size and file space strategy/threshold */
+ {
+ hid_t fcpl_in; /* file creation property list ID for input file */
+
+ if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
+ goto out;
+ }
+
+ if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
+ goto out;
+ }
+
+ if (!options->fs_strategy) {
+ if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
+ error_msg("failed to retrieve file space strategy\n");
+ goto out;
+ }
+ }
+
+ if (!options->fs_threshold) {
+ if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
+ error_msg("failed to retrieve file space threshold\n");
+ goto out;
+ }
+ }
+
+ if (H5Pclose(fcpl_in) < 0) {
+ error_msg("failed to close property list\n");
+ goto out;
+ }
+ }
+
+ /* Check if we need to create a non-default file creation property list */
+ if (options->latest || ub_size > 0) {
+ /* Create file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ goto out;
+ }
+
+ if (ub_size > 0) {
+ if (H5Pset_userblock(fcpl, ub_size) < 0) {
+ error_msg("failed to set non-default userblock size\n");
+ goto out;
+ }
+ }
+
+ if (options->latest) {
+ unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
+
+ /* Adjust group creation parameters for root group */
+ /* (So that it is created in "dense storage" form) */
+ if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
+ (unsigned) options->grp_indexed) < 0) {
+ error_msg(
+ "fail to adjust group creation parameters for root group\n");
+ goto out;
+ }
+
+ for (i = 0; i < 5; i++) {
+ if (options->msg_size[i] > 0) {
+ switch (i) {
+ case 0:
+ mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
+ break;
+
+ case 1:
+ mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
+ break;
+
+ case 2:
+ mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
+ break;
+
+ case 3:
+ mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
+ break;
+
+ case 4:
+ mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
+ break;
+ default:
+ break;
+ } /* end switch */
+ min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];
+
+ nindex++;
+ } /* end if */
+ } /* end for */
+
+ if (nindex > 0) {
+ if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
+ error_msg(
+ "fail to set the number of shared object header message indexes\n");
+ goto out;
+ }
+
+ /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
+ for (i = 0; i < (nindex - 1); i++) {
+ if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i],
+ min_mesg_sizes[i]) < 0) {
+ error_msg(
+ "fail to configure the specified shared object header message index\n");
+ goto out;
+ } /* end if */
+ } /* end for */
+ } /* if (nindex>0) */
+
+ /* Create file access property list */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ error_msg("Could not create file access property list\n");
+ goto out;
+ } /* end if */
+
+ if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+ error_msg(
+ "Could not set property for using latest version of the format\n");
+ goto out;
+ } /* end if */
+ } /* end if */
+ } /* end if */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
- print_user_block(fnamein, fidin);
+ print_user_block(fnamein, fidin);
#endif
- /*-------------------------------------------------------------------------
- * set the new user userblock options in the FCPL (before H5Fcreate )
- *-------------------------------------------------------------------------
- */
- if ( options->ublock_size > 0 )
- {
- /* either use the FCPL already created or create a new one */
- if(fcpl == H5P_DEFAULT)
- {
- /* create a file creation property list */
- if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
- {
- error_msg("fail to create a file creation property list\n");
- goto out;
- }
- }
-
- /* set user block size */
- if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
- {
- error_msg("failed to set userblock size\n");
- goto out;
- }
- }
-
- /*-------------------------------------------------------------------------
- * set alignment options
- *-------------------------------------------------------------------------
- */
- if ( options->alignment > 0 )
- {
- /* either use the FAPL already created or create a new one */
- if (fapl == H5P_DEFAULT)
- {
- /* create a file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
- {
- error_msg("Could not create file access property list\n");
- goto out;
- }
- }
-
- if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
- {
- error_msg("failed to set alignment\n");
- goto out;
- }
- }
-
- /*-------------------------------------------------------------------------
- * set metadata block size option
- *-------------------------------------------------------------------------
- */
- if ( options->meta_block_size > 0 )
- {
- /* either use the FAPL already created or create a new one */
- if (fapl == H5P_DEFAULT)
- {
- /* create a file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
- {
- error_msg("Could not create file access property list\n");
- goto out;
- }
- }
-
- if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
- {
- error_msg("failed to set metadata block size\n");
- goto out;
- }
- }
-
- /*-------------------------------------------------------------------------
- * set free-space strategy options
- *-------------------------------------------------------------------------
- */
-
- /* either use the FCPL already created or create a new one */
- if(fcpl == H5P_DEFAULT)
- {
- /* create a file creation property list */
- if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
- {
- error_msg("fail to create a file creation property list\n");
- goto out;
- }
- }
-
- /* set file space strategy and free space threshold */
- if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0)
- {
- error_msg("failed to set file space strategy & threshold \n");
- goto out;
- }
-
- /*-------------------------------------------------------------------------
- * create the output file
- *-------------------------------------------------------------------------
- */
- if(options->verbose)
- printf("Making file <%s>...\n",fnameout);
-
- if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0)
- {
- error_msg("<%s>: Could not create file\n", fnameout );
- goto out;
- }
-
-
- /*-------------------------------------------------------------------------
- * write a new user block if requested
- *-------------------------------------------------------------------------
- */
- if ( options->ublock_size > 0 )
- {
- if ( copy_user_block( options->ublock_filename, fnameout, options->ublock_size) < 0 )
- {
- error_msg("Could not copy user block. Exiting...\n");
- goto out;
-
- }
- }
-
- /*-------------------------------------------------------------------------
- * get list of objects
- *-------------------------------------------------------------------------
- */
-
- /* init table */
- trav_table_init(&travt);
-
- /* get the list of objects in the file */
- if(h5trav_gettable(fidin, travt) < 0)
- goto out;
-
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
- if(do_copy_objects(fidin, fidout, travt, options) < 0)
- {
- error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
- goto out;
- } /* end if */
-
- /*-------------------------------------------------------------------------
- * do the copy of referenced objects
- * and create hard links
- *-------------------------------------------------------------------------
- */
- if ( do_copy_refobjs(fidin, fidout, travt, options) < 0 )
- {
- printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
- goto out;
- }
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if(fapl > 0)
- H5Pclose(fapl);
-
- if(fcpl > 0)
- H5Pclose(fcpl);
-
- H5Fclose(fidin);
- H5Fclose(fidout);
-
- /* free table */
- trav_table_free(travt);
- travt = NULL;
-
- /*-------------------------------------------------------------------------
- * write only the input file user block if there is no user block file input
- *-------------------------------------------------------------------------
- */
-
- if( ub_size > 0 && options->ublock_size == 0 )
- {
- if ( copy_user_block(fnamein, fnameout, ub_size) < 0 )
- {
- error_msg("Could not copy user block. Exiting...\n");
- goto out;
-
- }
- }
-
- return 0;
-
- /*-------------------------------------------------------------------------
- * out
- *-------------------------------------------------------------------------
- */
+ /*-------------------------------------------------------------------------
+ * set the new user userblock options in the FCPL (before H5Fcreate )
+ *-------------------------------------------------------------------------
+ */
+ if (options->ublock_size > 0) {
+ /* either use the FCPL already created or create a new one */
+ if (fcpl == H5P_DEFAULT) {
+ /* create a file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ goto out;
+ }
+ }
+
+ /* set user block size */
+ if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
+ error_msg("failed to set userblock size\n");
+ goto out;
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * set alignment options
+ *-------------------------------------------------------------------------
+ */
+ if (options->alignment > 0) {
+ /* either use the FAPL already created or create a new one */
+ if (fapl == H5P_DEFAULT) {
+ /* create a file access property list */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ error_msg("Could not create file access property list\n");
+ goto out;
+ }
+ }
+
+ if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
+ error_msg("failed to set alignment\n");
+ goto out;
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * set metadata block size option
+ *-------------------------------------------------------------------------
+ */
+ if (options->meta_block_size > 0) {
+ /* either use the FAPL already created or create a new one */
+ if (fapl == H5P_DEFAULT) {
+ /* create a file access property list */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ error_msg("Could not create file access property list\n");
+ goto out;
+ }
+ }
+
+ if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
+ error_msg("failed to set metadata block size\n");
+ goto out;
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * set free-space strategy options
+ *-------------------------------------------------------------------------
+ */
+
+ /* either use the FCPL already created or create a new one */
+ if (fcpl == H5P_DEFAULT) {
+ /* create a file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ goto out;
+ }
+ }
+
+ /* set file space strategy and free space threshold */
+ if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) {
+ error_msg("failed to set file space strategy & threshold \n");
+ goto out;
+ }
+
+ /*-------------------------------------------------------------------------
+ * create the output file
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose)
+ printf("Making file <%s>...\n", fnameout);
+
+ if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
+ error_msg("<%s>: Could not create file\n", fnameout);
+ goto out;
+ }
+
+ /*-------------------------------------------------------------------------
+ * write a new user block if requested
+ *-------------------------------------------------------------------------
+ */
+ if (options->ublock_size > 0) {
+ if (copy_user_block(options->ublock_filename, fnameout,
+ options->ublock_size) < 0) {
+ error_msg("Could not copy user block. Exiting...\n");
+ goto out;
+
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * get list of objects
+ *-------------------------------------------------------------------------
+ */
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fidin, travt) < 0)
+ goto out;
+
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_objects(fidin, fidout, travt, options) < 0) {
+ error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
+ goto out;
+ } /* end if */
+
+ /*-------------------------------------------------------------------------
+ * do the copy of referenced objects
+ * and create hard links
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
+ printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein,
+ fnameout);
+ goto out;
+ }
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ if (fapl > 0)
+ H5Pclose(fapl);
+
+ if (fcpl > 0)
+ H5Pclose(fcpl);
+
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+
+ /* free table */
+ trav_table_free(travt);
+ travt = NULL;
+
+ /*-------------------------------------------------------------------------
+ * write only the input file user block if there is no user block file input
+ *-------------------------------------------------------------------------
+ */
+
+ if (ub_size > 0 && options->ublock_size == 0) {
+ if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
+ error_msg("Could not copy user block. Exiting...\n");
+ goto out;
+
+ }
+ }
+
+ return 0;
+
+ /*-------------------------------------------------------------------------
+ * out
+ *-------------------------------------------------------------------------
+ */
out:
- H5E_BEGIN_TRY
- {
- H5Pclose(fapl);
- H5Pclose(fcpl);
- H5Fclose(fidin);
- H5Fclose(fidout);
- } H5E_END_TRY;
- if(travt)
- trav_table_free(travt);
-
- return -1;
+ H5E_BEGIN_TRY
+ {
+ H5Pclose(fapl);
+ H5Pclose(fcpl);
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ }H5E_END_TRY;
+ if (travt)
+ trav_table_free(travt);
+
+ return -1;
}
/*-------------------------------------------------------------------------
-* Function: Get_hyperslab
-*
-* Purpose: Calulate a hyperslab from a dataset for higher performance.
-* The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
-* Return the hyperslab dimentions and size in byte.
-*
-* Return: 0 - SUCCEED, -1 FAILED
-*
-* Parameters:
-* dcpl_id : [IN] dataset creation property.
-* rank_dset : [IN] dataset rank
-* dims_dset[] : [IN] dataset dimentions
-* size_datum : [IN] size of a data element in byte
-* dims_hslab[] : [OUT] calculated hyperslab dimentions
-* * hslab_nbytes_p : [OUT] total byte of the hyperslab
-*
-* Programmer: Jonathan Kim
-* Date: Feburary, 2012
-* Update:
-* The hyperslab calucation would be depend on if the dataset is chunked
-* or not.
-*
-* There care 3 conditions to cover:
-* 1. If chunked and a chunk fits in buffer, each chunk would be a unit of
-* collection and the boundary would be dataset's dims.
-* 2. If chunked but a chunk doesn't fit in buffer, each data element would
-* be a unit of collection and the boundary would be the chunk itself.
-* 3. If not chunked, each data element would be a unit of collection and
-* the boundary would be dataset's dims.
-*
-* The calulation starts from the last dimention (h5dump dims output).
-*
-* Note:
-* Added for JIRA HDFFV-7862.
-*-----------------------------------------*/
-
-int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
- size_t size_datum,
- hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
-{
- int status = 0;
- int k;
- H5D_layout_t dset_layout;
- int rank_chunk;
- hsize_t dims_chunk[H5S_MAX_RANK];
- hsize_t size_chunk=1;
- hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
- hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
- hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
- hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
- hsize_t hslab_nbytes; /* size of hyperslab in byte */
-
- /* init to set as size of a data element */
- hslab_nbytes = size_datum;
-
- /* get layout of dataset */
- dset_layout = H5Pget_layout(dcpl_id);
-
- /* if dataset is chunked */
- if ( dset_layout == H5D_CHUNKED )
- {
- /* get chunk dims */
- rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
- if (rank_chunk < 0)
- {
- status = -1;
- goto out;
- }
-
- for (k = rank_dset; k > 0; --k)
- size_chunk *= dims_chunk[k-1];
-
- /* figure out how many chunks can fit in the hyperslab buffer */
- nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
-
-
- /* 1. if a chunk fit in hyperslab buffer */
- if (nchunk_fit >= 1)
- {
- /* Calulate a hyperslab that contains as many chunks that can fit
- * in hyperslab buffer. Hyperslab will be increased starting from
- * the last dimention of the dataset (see h5dump's dims output).
- * The calculation boundary is dataset dims.
- * In the loop, used mapping from a datum to a chunk to figure out
- * chunk based hyperslab.
- */
- for (k = rank_dset; k > 0; --k)
- {
- /* map dataset dimentions with a chunk dims */
- chunk_dims_map[k-1]= dims_dset[k-1] / dims_chunk[k-1];
-
- /* if reminder exist, increse by 1 to cover partial edge chunks */
- if (dims_dset[k-1] % dims_chunk[k-1] > 0)
- chunk_dims_map[k-1]++;
-
- /* get mapped hyperslab dims */
- hs_dims_map[k-1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
-
- /* prepare next round */
- nchunk_fit = nchunk_fit / chunk_dims_map[k-1];
- /* if a chunk is bigger than the rest of buffer */
- if (nchunk_fit == 0)
- nchunk_fit=1;
-
- /* get hyperslab dimentions as unmapping to actual size */
- dims_hslab[k-1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k-1];
- }
- }
- /* 2. if a chunk is bigger than hyperslab buffer */
- else
- {
- /* Calulate a hyperslab that contains as many data elements that
- * can fit in hyperslab buffer. Hyperslab will be increased
- * starting from the last dimention of the chunk (see h5dump's dims
- * output).
- * The calculation boundary is a chunk dims.
- */
- for (k = rank_dset; k > 0; --k)
- {
- ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
- /* if a datum is bigger than rest of buffer */
- if ( ndatum_fit == 0)
- ndatum_fit = 1;
- /* get hyperslab dimentions within a chunk boundary */
- dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k - 1];
-
- if (hslab_nbytes <= 0)
- {
- status = -1;
- goto out;
- }
- }
- }
- }
- /* 3. if dataset is not chunked */
- else
- {
- /* Calulate a hyperslab that contains as many data elements that can
- * fit in hyperslab buffer. Hyperslab will be increased starting from
- * the last dimention of the dataset (see h5dump's dims output).
- * The calculation boundary is dataset dims.
- */
- for (k = rank_dset; k > 0; --k)
- {
- ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
- /* if a datum is bigger than rest of buffer */
- if ( ndatum_fit == 0)
- ndatum_fit = 1;
- /* get hyperslab dimentions within dataset boundary */
- dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k - 1];
-
- if (hslab_nbytes <= 0)
- {
- status = -1;
- goto out;
- }
- }
- }
-
- /* pass out the hyperslab size*/
- *hslab_nbytes_p = hslab_nbytes;
+ * Function: Get_hyperslab
+ *
+ * Purpose: Calulate a hyperslab from a dataset for higher performance.
+ * The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
+ * Return the hyperslab dimentions and size in byte.
+ *
+ * Return: 0 - SUCCEED, -1 FAILED
+ *
+ * Parameters:
+ * dcpl_id : [IN] dataset creation property.
+ * rank_dset : [IN] dataset rank
+ * dims_dset[] : [IN] dataset dimentions
+ * size_datum : [IN] size of a data element in byte
+ * dims_hslab[] : [OUT] calculated hyperslab dimentions
+ * * hslab_nbytes_p : [OUT] total byte of the hyperslab
+ *
+ * Programmer: Jonathan Kim
+ * Date: Feburary, 2012
+ * Update:
+ * The hyperslab calucation would be depend on if the dataset is chunked
+ * or not.
+ *
+ * There care 3 conditions to cover:
+ * 1. If chunked and a chunk fits in buffer, each chunk would be a unit of
+ * collection and the boundary would be dataset's dims.
+ * 2. If chunked but a chunk doesn't fit in buffer, each data element would
+ * be a unit of collection and the boundary would be the chunk itself.
+ * 3. If not chunked, each data element would be a unit of collection and
+ * the boundary would be dataset's dims.
+ *
+ * The calulation starts from the last dimention (h5dump dims output).
+ *
+ * Note:
+ * Added for JIRA HDFFV-7862.
+ *-----------------------------------------*/
+
+int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+ size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) {
+ int status = 0;
+ int k;
+ H5D_layout_t dset_layout;
+ int rank_chunk;
+ hsize_t dims_chunk[H5S_MAX_RANK];
+ hsize_t size_chunk = 1;
+ hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
+ hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
+ hsize_t hslab_nbytes; /* size of hyperslab in byte */
+
+ /* init to set as size of a data element */
+ hslab_nbytes = size_datum;
+
+ /* get layout of dataset */
+ dset_layout = H5Pget_layout(dcpl_id);
+
+ /* if dataset is chunked */
+ if (dset_layout == H5D_CHUNKED) {
+ /* get chunk dims */
+ rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
+ if (rank_chunk < 0) {
+ status = -1;
+ goto out;
+ }
+
+ for (k = rank_dset; k > 0; --k)
+ size_chunk *= dims_chunk[k - 1];
+
+ /* figure out how many chunks can fit in the hyperslab buffer */
+ nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
+
+ /* 1. if a chunk fit in hyperslab buffer */
+ if (nchunk_fit >= 1) {
+ /* Calulate a hyperslab that contains as many chunks that can fit
+ * in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ * In the loop, used mapping from a datum to a chunk to figure out
+ * chunk based hyperslab.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ /* map dataset dimentions with a chunk dims */
+ chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];
+
+ /* if reminder exist, increse by 1 to cover partial edge chunks */
+ if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
+ chunk_dims_map[k - 1]++;
+
+ /* get mapped hyperslab dims */
+ hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
+
+ /* prepare next round */
+ nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
+ /* if a chunk is bigger than the rest of buffer */
+ if (nchunk_fit == 0)
+ nchunk_fit = 1;
+
+ /* get hyperslab dimentions as unmapping to actual size */
+ dims_hslab[k - 1] =
+ MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+ }
+ }
+ /* 2. if a chunk is bigger than hyperslab buffer */
+ else {
+ /* Calulate a hyperslab that contains as many data elements that
+ * can fit in hyperslab buffer. Hyperslab will be increased
+ * starting from the last dimention of the chunk (see h5dump's dims
+ * output).
+ * The calculation boundary is a chunk dims.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if (ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within a chunk boundary */
+ dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0) {
+ status = -1;
+ goto out;
+ }
+ }
+ }
+ }
+ /* 3. if dataset is not chunked */
+ else {
+ /* Calulate a hyperslab that contains as many data elements that can
+ * fit in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if (ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within dataset boundary */
+ dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0) {
+ status = -1;
+ goto out;
+ }
+ }
+ }
+
+ /* pass out the hyperslab size*/
+ *hslab_nbytes_p = hslab_nbytes;
out:
- return status;
+ return status;
}
/*-------------------------------------------------------------------------
-* Function: do_copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modifications:
-*
-* July 2004: Introduced the extra EC or NN option for SZIP
-*
-* December 2004: Added a check for H5Dcreate; if the dataset cannot be created
-* with the requested filter, use the input one
-*
-* October 2006: Read/write using the file type by default.
-*
-* October 2006: Read by hyperslabs for big datasets.
-*
-* A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
-* i.e., if the memory needed to read a dataset is greater than this limit,
-* then hyperslab I/O is done instead of one operation I/O
-* For each dataset, the memory needed is calculated according to
-*
-* memory needed = number of elements * size of each element
-*
-* if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-* are done
-*
-* H5Dread( input_dataset1 )
-* H5Dread( input_dataset2 )
-*
-* with all elements in the datasets selected. If the memory needed is greater than
-* H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-* a strip mine is defined for each dimension k (a strip mine is defined as a
-* hyperslab whose size is memory manageable) according to the formula
-*
-* (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
-*
-* where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
-* that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
-* mine size k is simply defined as its dimension k, but for larger datasets the
-* hyperslab size is still memory manageable.
-* a cycle is done until the number of elements in the dataset is reached. In each
-* iteration, two parameters are defined for the function H5Sselect_hyperslab,
-* the start and size of each hyperslab, according to
-*
-* (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
-*
-* where hyperslab_offset [k] is initially set to zero, and later incremented in
-* hyperslab_size[k] offsets. The reason for the operation
-*
-* dimension[k] - hyperslab_offset[k]
-*
-* in (2) is that, when using the strip mine size, it assures that the "remaining" part
-* of the dataset that does not fill an entire strip mine is processed.
-*
-* November 2006: Use H5Ocopy in the copy of objects. The logic for using
-* H5Ocopy or not is if a change of filters or layout is requested by the user
-* then use read/write else use H5Ocopy.
-*
-* May, 1, 2008: Add a printing of the compression ratio of old size / new size
-*
-* Feburary 2012: improve Read/Write by hyperslabs for big datasets.
-* Programmer: Jonathan Kim
-*
-* A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
-* i.e., if the memory needed to read a dataset is greater than this limit,
-* then hyperslab I/O is done instead of one operation I/O
-* For each dataset, the memory needed is calculated according to
-*
-* memory needed = number of elements * size of each element
-*
-* if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-* are done
-*
-* H5Dread( input_dataset )
-* H5Dwrite( output_dataset )
-*
-* with all elements in the datasets selected. If the memory needed is greater than
-* H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-* 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()).
-* 2. Calculate the hyperslab selections as the selection is moving forward.
-* Selection would be same as the hyperslab except for the remaining edge portion
-* of the dataset. The code take care of the remaining portion if exist.
-*
-*-------------------------------------------------------------------------
-*/
-
-int do_copy_objects(hid_t fidin,
- hid_t fidout,
- trav_table_t *travt,
- pack_opt_t *options) /* repack options */
+ * Function: do_copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modifications:
+ *
+ * July 2004: Introduced the extra EC or NN option for SZIP
+ *
+ * December 2004: Added a check for H5Dcreate; if the dataset cannot be created
+ * with the requested filter, use the input one
+ *
+ * October 2006: Read/write using the file type by default.
+ *
+ * October 2006: Read by hyperslabs for big datasets.
+ *
+ * A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
+ * i.e., if the memory needed to read a dataset is greater than this limit,
+ * then hyperslab I/O is done instead of one operation I/O
+ * For each dataset, the memory needed is calculated according to
+ *
+ * memory needed = number of elements * size of each element
+ *
+ * if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ * are done
+ *
+ * H5Dread( input_dataset1 )
+ * H5Dread( input_dataset2 )
+ *
+ * with all elements in the datasets selected. If the memory needed is greater than
+ * H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ * a strip mine is defined for each dimension k (a strip mine is defined as a
+ * hyperslab whose size is memory manageable) according to the formula
+ *
+ * (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
+ *
+ * where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
+ * that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
+ * mine size k is simply defined as its dimension k, but for larger datasets the
+ * hyperslab size is still memory manageable.
+ * a cycle is done until the number of elements in the dataset is reached. In each
+ * iteration, two parameters are defined for the function H5Sselect_hyperslab,
+ * the start and size of each hyperslab, according to
+ *
+ * (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
+ *
+ * where hyperslab_offset [k] is initially set to zero, and later incremented in
+ * hyperslab_size[k] offsets. The reason for the operation
+ *
+ * dimension[k] - hyperslab_offset[k]
+ *
+ * in (2) is that, when using the strip mine size, it assures that the "remaining" part
+ * of the dataset that does not fill an entire strip mine is processed.
+ *
+ * November 2006: Use H5Ocopy in the copy of objects. The logic for using
+ * H5Ocopy or not is if a change of filters or layout is requested by the user
+ * then use read/write else use H5Ocopy.
+ *
+ * May, 1, 2008: Add a printing of the compression ratio of old size / new size
+ *
+ * Feburary 2012: improve Read/Write by hyperslabs for big datasets.
+ * Programmer: Jonathan Kim
+ *
+ * A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
+ * i.e., if the memory needed to read a dataset is greater than this limit,
+ * then hyperslab I/O is done instead of one operation I/O
+ * For each dataset, the memory needed is calculated according to
+ *
+ * memory needed = number of elements * size of each element
+ *
+ * if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ * are done
+ *
+ * H5Dread( input_dataset )
+ * H5Dwrite( output_dataset )
+ *
+ * with all elements in the datasets selected. If the memory needed is greater than
+ * H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ * 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()).
+ * 2. Calculate the hyperslab selections as the selection is moving forward.
+ * Selection would be same as the hyperslab except for the remaining edge portion
+ * of the dataset. The code take care of the remaining portion if exist.
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+ pack_opt_t *options) /* repack options */
{
- hid_t grp_in = -1; /* group ID */
- hid_t grp_out = -1; /* group ID */
- hid_t dset_in = -1; /* read dataset ID */
- hid_t dset_out = -1; /* write dataset ID */
- hid_t gcpl_in = -1; /* group creation property list */
- hid_t gcpl_out = -1; /* group creation property list */
- hid_t type_in = -1; /* named type ID */
- hid_t type_out = -1; /* named type ID */
- hid_t dcpl_in = -1; /* dataset creation property list ID */
- hid_t dcpl_out = -1; /* dataset creation property list ID */
- hid_t f_space_id = -1; /* file space ID */
- hid_t ftype_id = -1; /* file type ID */
- hid_t wtype_id = -1; /* read/write type ID */
- named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
- size_t msize; /* size of type */
- hsize_t nelmts; /* number of elements in dataset */
- H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
- int rank; /* rank of dataset */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- hsize_t dsize_in; /* input dataset size before filter */
- hsize_t dsize_out; /* output dataset size after filter */
- int apply_s; /* flag for apply filter to small dataset sizes */
- int apply_f; /* flag for apply filter to return error on H5Dcreate */
- void *buf=NULL; /* buffer for raw data */
- void *hslab_buf=NULL; /* hyperslab buffer for raw data */
- int has_filter; /* current object has a filter */
- int req_filter; /* there was a request for a filter */
- int req_obj_layout=0; /* request layout to current object */
- unsigned crt_order_flags; /* group creation order flag */
- unsigned i;
- unsigned u;
- int is_ref=0;
- htri_t is_named;
- hbool_t limit_maxdims;
- hsize_t size_dset;
-
-
- /*-------------------------------------------------------------------------
- * copy the suppplied object list
- *-------------------------------------------------------------------------
- */
-
- if (options->verbose)
- {
- printf("-----------------------------------------\n");
- printf(" Type Filter (Compression) Name\n");
- printf("-----------------------------------------\n");
- }
-
- for ( i = 0; i < travt->nobjs; i++)
- {
- /* init variables per obj */
- buf = NULL;
- limit_maxdims = FALSE;
-
- switch ( travt->objs[i].type )
- {
-
- case H5TRAV_TYPE_UNKNOWN:
- HDassert(0);
- break;
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_GROUP
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_GROUP:
-
- if (options->verbose)
- {
- printf(FORMAT_OBJ,"group",travt->objs[i].name );
- }
-
- /* open input group */
- if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
-
- /* get input group creation property list */
- if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
- goto error;
-
- /* query and set the group creation properties */
- if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
- goto error;
-
- /* set up group creation property list */
- if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
- goto error;
-
- if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
- goto error;
-
-
- /*-------------------------------------------------------------------------
- * the root is a special case, we get an ID for the root group
- * and copy its attributes using that ID
- *-------------------------------------------------------------------------
- */
- if(HDstrcmp(travt->objs[i].name, "/") == 0)
- {
- if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
- goto error;
- }
-
- else
- {
-
- if (options->grp_compact>0 || options->grp_indexed>0)
- {
- if(H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
- goto error;
- }
-
- if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
- goto error;
-
- }
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if(copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
- goto error;
-
-
- if(H5Pclose(gcpl_out) < 0)
- goto error;
- if(H5Pclose(gcpl_in) < 0)
- goto error;
- if(H5Gclose(grp_out) < 0)
- goto error;
- if(H5Gclose(grp_in) < 0)
- goto error;
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_DATASET
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_DATASET:
-
- has_filter = 0;
- req_filter = 0;
-
- /* check if global filters were requested */
- if ( options->n_filter_g )
- req_filter = 1;
-
- /* check if filters were requested for individual objects */
- for (u = 0; u < options->op_tbl->nelems; u++) {
-
- if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
- if (options->op_tbl->objs[u].filter->filtn > 0) {
- req_filter = 1;
- }
- }
- }
-
- /* check if layout change requested individual object */
- if (options->layout_g != H5D_LAYOUT_ERROR)
- {
- pack_info_t *pckinfo;
- /* any dataset is specified */
- if (options->op_tbl->nelems > 0)
- {
- /* check if object exist */
- pckinfo = options_get_object (travt->objs[i].name, options->op_tbl);
- if (pckinfo)
- {
- req_obj_layout = 1;
- }
- }
- }
-
- /* early detection of references */
- if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if((ftype_id = H5Dget_type(dset_in)) < 0)
- goto error;
- if(H5T_REFERENCE == H5Tget_class(ftype_id))
- is_ref = 1;
-
- /* Check if the datatype is committed */
- if((is_named = H5Tcommitted(ftype_id)) < 0)
- goto error;
- if(is_named)
- if((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
- goto error;
-
- if(H5Tclose(ftype_id) < 0)
- goto error;
- if(H5Dclose(dset_in) < 0)
- goto error;
-
-
- /*-------------------------------------------------------------------------
- * check if we should use H5Ocopy or not
- * if there is a request for filters/layout, we read/write the object
- * otherwise we do a copy using H5Ocopy
- *-------------------------------------------------------------------------
- */
- if ( options->op_tbl->nelems ||
- options->all_filter == 1 ||
- options->all_layout == 1 ||
- is_ref ||
- is_named)
- {
-
- int j;
-
- if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if((f_space_id = H5Dget_space(dset_in)) < 0)
- goto error;
- if((ftype_id = H5Dget_type(dset_in)) < 0)
- goto error;
- if((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
- goto error;
- if((dcpl_out = H5Pcopy(dcpl_in)) < 0)
- goto error;
- if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
- goto error;
- HDmemset(dims, 0, sizeof dims);
- if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
- goto error;
-
- if(H5Dget_space_status(dset_in, &space_status) < 0)
- goto error;
-
- nelmts = 1;
- for(j = 0; j < rank; j++)
- nelmts *= dims[j];
-
- /* wtype_id will have already been set if using a named dtype */
- if(!is_named) {
- if(options->use_native == 1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
- } /* end if */
-
- if((msize = H5Tget_size(wtype_id)) == 0)
- goto error;
-
- /* size of current dset */
- size_dset = nelmts * msize;
-
- /*-------------------------------------------------------------------------
- * check if the dataset creation property list has filters that
- * are not registered in the current configuration
- * 1) the external filters GZIP and SZIP might not be available
- * 2) the internal filters might be turned off
- *-------------------------------------------------------------------------
- */
- if (h5tools_canreadf((travt->objs[i].name),dcpl_in)==1)
- {
- apply_s=1;
- apply_f=1;
-
- /*-------------------------------------------------------------------------
- * references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- * in a second traversal of the output file
- *-------------------------------------------------------------------------
- */
- if (H5T_REFERENCE!=H5Tget_class(wtype_id))
- {
- /* get the storage size of the input dataset */
- dsize_in=H5Dget_storage_size(dset_in);
-
- /* check for small size datasets (less than 1k) except
- * changing to COMPACT. For the reference, COMPACT is limited
- * by size 64K by library.
- */
- if (options->layout_g != H5D_COMPACT)
- {
- if ( size_dset < options->min_comp )
- apply_s=0;
- }
-
- /* apply the filter */
- if (apply_s)
- {
- if (apply_filters(travt->objs[i].name,
- rank,
- dims,
- msize,
- dcpl_out,
- options,
- &has_filter) < 0)
- goto error;
- }
-
- /* only if layout change requested for entire file or
- * individual obj */
- if (options->all_layout > 0 || req_obj_layout == 1)
- /*-------------------------------------------------
- * Unset the unlimited max dims if convert to other
- * than chunk layouts, because unlimited max dims
- * only can be applied to chunk layout.
- * Also perform only for targeted dataset
- * Also check for size limit to convert to compact
- *-------------------------------------------------*/
- if (options->layout_g != H5D_CHUNKED)
- {
- /* any dataset is specified */
- if (options->op_tbl->nelems > 0)
- {
- /* if current obj match specified obj */
- if (options_get_object (travt->objs[i].name, options->op_tbl))
- limit_maxdims = TRUE;
- }
- else /* no dataset is specified */
- {
- limit_maxdims = TRUE;
- }
-
- /* if convert to COMPACT */
- if (options->layout_g == H5D_COMPACT)
- {
- /* should be smaller than 64K */
- if ( size_dset > MAX_COMPACT_DSIZE )
- limit_maxdims = FALSE;
- }
-
- /* unset unlimited max dims */
- if (limit_maxdims)
- H5Sset_extent_simple( f_space_id, rank, dims, NULL );
- }
-
- /*-------------------------------------------------------------------------
- * create the output dataset;
- * disable error checking in case the dataset cannot be created with the
- * modified dcpl; in that case use the original instead
- *-------------------------------------------------------------------------
- */
- H5E_BEGIN_TRY {
- dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
- } H5E_END_TRY;
-
- if(dset_out == FAIL)
- {
- if(options->verbose)
- printf(" warning: could not create dataset <%s>. Applying original settings\n",
- travt->objs[i].name);
-
- if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
- goto error;
- apply_f = 0;
- }
-
- /*-------------------------------------------------------------------------
- * read/write
- *-------------------------------------------------------------------------
- */
- if(nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED)
- {
- size_t need = (size_t)(nelmts * msize); /* bytes needed */
-
- /* have to read the whole dataset if there is only one element in the dataset */
- if(need < H5TOOLS_MALLOCSIZE)
- buf = HDmalloc(need);
-
- if(buf != NULL) {
- /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
- CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-
- /* Check if we have VL data in the dataset's
- * datatype that must be reclaimed */
- if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
- if(H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
- goto error;
- }
- else /* possibly not enough memory, read/write by hyperslabs */
- {
- size_t p_type_nbytes = msize; /*size of memory type */
- hsize_t p_nelmts = nelmts; /*total elements */
- hsize_t elmtno; /*counter */
- int carry; /*counter carry value */
- unsigned int vl_data = 0; /*contains VL datatypes */
-
- /* hyperslab info */
- hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
- hsize_t hslab_nbytes; /*bytes per hyperslab */
- hsize_t hslab_nelmts; /*elements per hyperslab*/
- hid_t hslab_space; /*hyperslab data space */
-
- /* hyperslab selection info */
- hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
- hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
- hsize_t hs_select_nelmts; /* selected elements */
- hsize_t zero[8]; /*vector of zeros */
- int k;
- H5D_layout_t dset_layout;
- hid_t dcpl_tmp = -1; /* dataset creation property list ID */
-
- /* check if we have VL data in the dataset's datatype */
- if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
- vl_data = TRUE;
-
-
- /* check first if writing dataset is chunked,
- * if so use its chunk layout for better performance. */
- dset_layout = H5Pget_layout(dcpl_out);
- if (dset_layout == H5D_CHUNKED)
- dcpl_tmp = dcpl_out; /* writing dataset */
- else /* if reading dataset is chunked */
- {
- dset_layout = H5Pget_layout(dcpl_in);
- if (dset_layout == H5D_CHUNKED)
- dcpl_tmp = dcpl_in; /* reading dataset */
- }
-
- /* get hyperslab dims and size in byte */
- if(Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
- goto error;
-
- hslab_buf = HDmalloc((size_t)hslab_nbytes);
-
- hslab_nelmts = hslab_nbytes / p_type_nbytes;
- hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
-
- /* the hyperslab selection loop */
- HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
- HDmemset(zero, 0, sizeof zero);
-
- for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts)
- {
- if (rank > 0)
- {
- /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
- */
- for (k = 0, hs_select_nelmts = 1; k < rank; k++)
- {
- /* MIN() is used to get the remaining edge portion if exist.
- * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
- hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
- hs_select_nelmts *= hs_sel_count[k];
- }
-
- if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
- goto error;
- if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
- goto error;
- }
- else
- {
- H5Sselect_all(f_space_id);
- H5Sselect_all(hslab_space);
- hs_select_nelmts = 1;
- } /* rank */
-
- /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
- CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-
- /* reclaim any VL memory, if necessary */
- if(vl_data)
- H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
-
- /* calculate the next hyperslab offset */
- for (k = rank, carry = 1; k > 0 && carry; --k)
- {
- hs_sel_offset[k - 1] += hs_sel_count[k - 1];
- /* if reached the end of a dim */
- if (hs_sel_offset[k - 1] == dims[k - 1])
- hs_sel_offset[k - 1] = 0;
- else
- carry = 0;
- } /* k */
- } /* elmtno */
-
- H5Sclose(hslab_space);
- /* free */
- if (hslab_buf!=NULL)
- {
- HDfree(hslab_buf);
- hslab_buf=NULL;
- }
- } /* hyperslab read */
- } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
-
- /*-------------------------------------------------------------------------
- * amount of compression used
- *-------------------------------------------------------------------------
- */
- if (options->verbose)
- {
- double ratio=0;
-
- /* only print the compression ration if there was a filter request */
- if (apply_s && apply_f && req_filter)
- {
- /* get the storage size of the output dataset */
- dsize_out=H5Dget_storage_size(dset_out);
-
- /* compression ratio = uncompressed size / compressed size */
- if (dsize_out!=0)
- ratio = (double) dsize_in / (double) dsize_out;
-
- print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1);
- }
- else
- print_dataset_info(dcpl_in,travt->objs[i].name,ratio,0);
-
- /* print a message that the filter was not applied
- (in case there was a filter)
- */
- if ( has_filter && apply_s == 0 )
- printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
- travt->objs[i].name,
- (int)options->min_comp);
-
- if ( has_filter && apply_f == 0 )
- printf(" <warning: could not apply the filter to %s>\n",
- travt->objs[i].name);
-
- } /* verbose */
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
- goto error;
-
- /*close */
- if (H5Dclose(dset_out) < 0)
- goto error;
-
- }/*!H5T_REFERENCE*/
- }/*h5tools_canreadf*/
-
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
- if (H5Tclose(ftype_id) < 0)
- goto error;
- if (H5Tclose(wtype_id) < 0)
- goto error;
- if (H5Pclose(dcpl_in) < 0)
- goto error;
- if (H5Pclose(dcpl_out) < 0)
- goto error;
- if (H5Sclose(f_space_id) < 0)
- goto error;
- if (H5Dclose(dset_in) < 0)
- goto error;
-
- }
- /*-------------------------------------------------------------------------
- * we do not have request for filter/chunking use H5Ocopy instead
- *-------------------------------------------------------------------------
- */
- else
- {
- hid_t pid;
-
- /* create property to pass copy options */
- if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
- goto error;
-
- /* set options for object copy */
- if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
-
- if(H5Ocopy(fidin, /* Source file or group identifier */
- travt->objs[i].name, /* Name of the source object to be copied */
- fidout, /* Destination file or group identifier */
- travt->objs[i].name, /* Name of the destination object */
- pid, /* Properties which apply to the copy */
- H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
- goto error;
-
- /* close property */
- if(H5Pclose(pid) < 0)
- goto error;
-
-
- /*-------------------------------------------------------------------------
- * copy attrs manually
- *-------------------------------------------------------------------------
- */
- if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
- goto error;
- if(H5Dclose(dset_in) < 0)
- goto error;
- if(H5Dclose(dset_out) < 0)
- goto error;
-
-
- if (options->verbose)
- printf(FORMAT_OBJ,"dset",travt->objs[i].name );
-
-
- } /* end do we have request for filter/chunking */
-
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_NAMED_DATATYPE
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_NAMED_DATATYPE:
-
- if(options->verbose)
- printf(FORMAT_OBJ, "type", travt->objs[i].name);
-
- if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
-
- /* Copy the datatype anonymously */
- if((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
- travt, options)) < 0)
- goto error;
-
- /* Link in to group structure */
- if(H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
- H5P_DEFAULT, H5P_DEFAULT) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if(copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
- goto error;
-
- if(H5Tclose(type_in) < 0)
- goto error;
- if(H5Tclose(type_out) < 0)
- goto error;
-
-
-
- break;
-
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_LINK
- * H5TRAV_TYPE_UDLINK
- *
- * Only handles external links; H5Lcopy will fail for other UD link types
- * since we don't have creation or copy callbacks for them.
- *-------------------------------------------------------------------------
- */
-
- case H5TRAV_TYPE_LINK:
- case H5TRAV_TYPE_UDLINK:
- {
-
- if(options->verbose)
- printf(FORMAT_OBJ, "link", travt->objs[i].name);
-
- if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
- goto error;
-
- if (options->verbose)
- printf(FORMAT_OBJ,"link",travt->objs[i].name );
-
- }
- break;
-
- default:
- goto error;
- } /* switch */
-
- /* free */
- if (buf!=NULL)
- {
- HDfree(buf);
- buf=NULL;
- }
-
- } /* i */
-
- /* Finalize (link) the stack of named datatypes (if any) */
- named_datatype_free(&named_dt_head, 0);
-
- return 0;
+ hid_t grp_in = -1; /* group ID */
+ hid_t grp_out = -1; /* group ID */
+ hid_t dset_in = -1; /* read dataset ID */
+ hid_t dset_out = -1; /* write dataset ID */
+ hid_t gcpl_in = -1; /* group creation property list */
+ hid_t gcpl_out = -1; /* group creation property list */
+ hid_t type_in = -1; /* named type ID */
+ hid_t type_out = -1; /* named type ID */
+ hid_t dcpl_in = -1; /* dataset creation property list ID */
+ hid_t dcpl_out = -1; /* dataset creation property list ID */
+ hid_t f_space_id = -1; /* file space ID */
+ hid_t ftype_id = -1; /* file type ID */
+ hid_t wtype_id = -1; /* read/write type ID */
+ named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
+ size_t msize; /* size of type */
+ hsize_t nelmts; /* number of elements in dataset */
+ H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
+ int rank; /* rank of dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ hsize_t dsize_in; /* input dataset size before filter */
+ hsize_t dsize_out; /* output dataset size after filter */
+ int apply_s; /* flag for apply filter to small dataset sizes */
+ int apply_f; /* flag for apply filter to return error on H5Dcreate */
+ void *buf = NULL; /* buffer for raw data */
+ void *hslab_buf = NULL; /* hyperslab buffer for raw data */
+ int has_filter; /* current object has a filter */
+ int req_filter; /* there was a request for a filter */
+ int req_obj_layout = 0; /* request layout to current object */
+ unsigned crt_order_flags; /* group creation order flag */
+ unsigned i;
+ unsigned u;
+ int is_ref = 0;
+ htri_t is_named;
+ hbool_t limit_maxdims;
+ hsize_t size_dset;
+
+ /*-------------------------------------------------------------------------
+ * copy the suppplied object list
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->verbose) {
+ printf("-----------------------------------------\n");
+ printf(" Type Filter (Compression) Name\n");
+ printf("-----------------------------------------\n");
+ }
+
+ for (i = 0; i < travt->nobjs; i++) {
+ /* init variables per obj */
+ buf = NULL;
+ limit_maxdims = FALSE;
+
+ switch (travt->objs[i].type) {
+
+ case H5TRAV_TYPE_UNKNOWN:
+ HDassert(0);
+ break;
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_GROUP
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_GROUP:
+
+ if (options->verbose) {
+ printf(FORMAT_OBJ, "group", travt->objs[i].name);
+ }
+
+ /* open input group */
+ if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+
+ /* get input group creation property list */
+ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+ goto error;
+
+ /* query and set the group creation properties */
+ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+ goto error;
+
+ /* set up group creation property list */
+ if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+ goto error;
+
+ if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * the root is a special case, we get an ID for the root group
+ * and copy its attributes using that ID
+ *-------------------------------------------------------------------------
+ */
+ if (HDstrcmp(travt->objs[i].name, "/") == 0) {
+ if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
+ goto error;
+ }
+ else {
+
+ if (options->grp_compact > 0 || options->grp_indexed > 0) {
+ if (H5Pset_link_phase_change(gcpl_out,
+ (unsigned) options->grp_compact,
+ (unsigned) options->grp_indexed) < 0)
+ goto error;
+ }
+
+ if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name,
+ H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
+ goto error;
+
+ }
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
+ goto error;
+
+ if (H5Pclose(gcpl_out) < 0)
+ goto error;
+ if (H5Pclose(gcpl_in) < 0)
+ goto error;
+ if (H5Gclose(grp_out) < 0)
+ goto error;
+ if (H5Gclose(grp_in) < 0)
+ goto error;
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_DATASET
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_DATASET:
+
+ has_filter = 0;
+ req_filter = 0;
+
+ /* check if global filters were requested */
+ if (options->n_filter_g)
+ req_filter = 1;
+
+ /* check if filters were requested for individual objects */
+ for (u = 0; u < options->op_tbl->nelems; u++) {
+
+ if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
+ if (options->op_tbl->objs[u].filter->filtn > 0) {
+ req_filter = 1;
+ }
+ }
+ }
+
+ /* check if layout change requested individual object */
+ if (options->layout_g != H5D_LAYOUT_ERROR) {
+ pack_info_t *pckinfo;
+ /* any dataset is specified */
+ if (options->op_tbl->nelems > 0) {
+ /* check if object exist */
+ pckinfo = options_get_object(travt->objs[i].name,
+ options->op_tbl);
+ if (pckinfo) {
+ req_obj_layout = 1;
+ }
+ }
+ }
+
+ /* early detection of references */
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ goto error;
+ if (H5T_REFERENCE == H5Tget_class(ftype_id))
+ is_ref = 1;
+
+ /* Check if the datatype is committed */
+ if ((is_named = H5Tcommitted(ftype_id)) < 0)
+ goto error;
+ if (is_named)
+ if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+ &named_dt_head, travt, options)) < 0)
+ goto error;
+
+ if (H5Tclose(ftype_id) < 0)
+ goto error;
+ if (H5Dclose(dset_in) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * check if we should use H5Ocopy or not
+ * if there is a request for filters/layout, we read/write the object
+ * otherwise we do a copy using H5Ocopy
+ *-------------------------------------------------------------------------
+ */
+ if (options->op_tbl->nelems || options->all_filter == 1
+ || options->all_layout == 1 || is_ref || is_named) {
+
+ int j;
+
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ goto error;
+ if ((f_space_id = H5Dget_space(dset_in)) < 0)
+ goto error;
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ goto error;
+ if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
+ goto error;
+ if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
+ goto error;
+ if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
+ goto error;
+ HDmemset(dims, 0, sizeof dims);
+ if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
+ goto error;
+
+ if (H5Dget_space_status(dset_in, &space_status) < 0)
+ goto error;
+
+ nelmts = 1;
+ for (j = 0; j < rank; j++)
+ nelmts *= dims[j];
+
+ /* wtype_id will have already been set if using a named dtype */
+ if (!is_named) {
+ if (options->use_native == 1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
+ } /* end if */
+
+ if ((msize = H5Tget_size(wtype_id)) == 0)
+ goto error;
+
+ /* size of current dset */
+ size_dset = nelmts * msize;
+
+ /*-------------------------------------------------------------------------
+ * check if the dataset creation property list has filters that
+ * are not registered in the current configuration
+ * 1) the external filters GZIP and SZIP might not be available
+ * 2) the internal filters might be turned off
+ *-------------------------------------------------------------------------
+ */
+ if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
+ apply_s = 1;
+ apply_f = 1;
+
+ /*-------------------------------------------------------------------------
+ * references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ * in a second traversal of the output file
+ *-------------------------------------------------------------------------
+ */
+ if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
+ /* get the storage size of the input dataset */
+ dsize_in = H5Dget_storage_size(dset_in);
+
+ /* check for small size datasets (less than 1k) except
+ * changing to COMPACT. For the reference, COMPACT is limited
+ * by size 64K by library.
+ */
+ if (options->layout_g != H5D_COMPACT) {
+ if (size_dset < options->min_comp)
+ apply_s = 0;
+ }
+
+ /* apply the filter */
+ if (apply_s) {
+ if (apply_filters(travt->objs[i].name, rank, dims,
+ msize, dcpl_out, options, &has_filter) < 0)
+ goto error;
+ }
+
+ /* only if layout change requested for entire file or
+ * individual obj */
+ if (options->all_layout > 0 || req_obj_layout == 1)
+ /*-------------------------------------------------
+ * Unset the unlimited max dims if convert to other
+ * than chunk layouts, because unlimited max dims
+ * only can be applied to chunk layout.
+ * Also perform only for targeted dataset
+ * Also check for size limit to convert to compact
+ *-------------------------------------------------*/
+ if (options->layout_g != H5D_CHUNKED) {
+ /* any dataset is specified */
+ if (options->op_tbl->nelems > 0) {
+ /* if current obj match specified obj */
+ if (options_get_object(travt->objs[i].name,
+ options->op_tbl))
+ limit_maxdims = TRUE;
+ }
+ else { /* no dataset is specified */
+ limit_maxdims = TRUE;
+ }
+
+ /* if convert to COMPACT */
+ if (options->layout_g == H5D_COMPACT) {
+ /* should be smaller than 64K */
+ if (size_dset > MAX_COMPACT_DSIZE)
+ limit_maxdims = FALSE;
+ }
+
+ /* unset unlimited max dims */
+ if (limit_maxdims)
+ H5Sset_extent_simple(f_space_id, rank, dims,
+ NULL);
+ }
+
+ /*-------------------------------------------------------------------------
+ * create the output dataset;
+ * disable error checking in case the dataset cannot be created with the
+ * modified dcpl; in that case use the original instead
+ *-------------------------------------------------------------------------
+ */
+ H5E_BEGIN_TRY
+ {
+ dset_out = H5Dcreate2(fidout,
+ travt->objs[i].name, wtype_id,
+ f_space_id, H5P_DEFAULT, dcpl_out,
+ H5P_DEFAULT);
+ }H5E_END_TRY;
+
+ if (dset_out == FAIL) {
+ if (options->verbose)
+ printf(
+ " warning: could not create dataset <%s>. Applying original settings\n",
+ travt->objs[i].name);
+
+ if ((dset_out = H5Dcreate2(fidout,
+ travt->objs[i].name, wtype_id, f_space_id,
+ H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
+ goto error;
+ apply_f = 0;
+ }
+
+ /*-------------------------------------------------------------------------
+ * read/write
+ *-------------------------------------------------------------------------
+ */
+ if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
+ size_t need = (size_t)(nelmts * msize); /* bytes needed */
+
+ /* have to read the whole dataset if there is only one element in the dataset */
+ if (need < H5TOOLS_MALLOCSIZE)
+ buf = HDmalloc(need);
+
+ if (buf != NULL) {
+ /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+ CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id,
+ H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id,
+ H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+
+ /* Check if we have VL data in the dataset's
+ * datatype that must be reclaimed */
+ if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+ if (H5Dvlen_reclaim(wtype_id, f_space_id,
+ H5P_DEFAULT, buf) < 0)
+ goto error;
+ }
+ else { /* possibly not enough memory, read/write by hyperslabs */
+ size_t p_type_nbytes = msize; /*size of memory type */
+ hsize_t p_nelmts = nelmts; /*total elements */
+ hsize_t elmtno; /*counter */
+ int carry; /*counter carry value */
+ unsigned int vl_data = 0; /*contains VL datatypes */
+
+ /* hyperslab info */
+ hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
+ hsize_t hslab_nbytes; /*bytes per hyperslab */
+ hsize_t hslab_nelmts; /*elements per hyperslab*/
+ hid_t hslab_space; /*hyperslab data space */
+
+ /* hyperslab selection info */
+ hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
+ hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
+ hsize_t hs_select_nelmts; /* selected elements */
+ hsize_t zero[8]; /*vector of zeros */
+ int k;
+ H5D_layout_t dset_layout;
+ hid_t dcpl_tmp = -1; /* dataset creation property list ID */
+
+ /* check if we have VL data in the dataset's datatype */
+ if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
+ vl_data = TRUE;
+
+ /* check first if writing dataset is chunked,
+ * if so use its chunk layout for better performance. */
+ dset_layout = H5Pget_layout(dcpl_out);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_out; /* writing dataset */
+ else { /* if reading dataset is chunked */
+ dset_layout = H5Pget_layout(dcpl_in);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_in; /* reading dataset */
+ }
+
+ /* get hyperslab dims and size in byte */
+ if (Get_hyperslab(dcpl_tmp, rank, dims,
+ p_type_nbytes, hslab_dims,
+ &hslab_nbytes) < 0)
+ goto error;
+
+ hslab_buf = HDmalloc((size_t)hslab_nbytes);
+
+ hslab_nelmts = hslab_nbytes / p_type_nbytes;
+ hslab_space = H5Screate_simple(1, &hslab_nelmts,
+ NULL);
+
+ /* the hyperslab selection loop */
+ HDmemset(hs_sel_offset, 0,
+ sizeof hs_sel_offset);
+ HDmemset(zero, 0, sizeof zero);
+
+ for (elmtno = 0; elmtno < p_nelmts; elmtno +=
+ hs_select_nelmts) {
+ if (rank > 0) {
+ /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
+ */
+ for (k = 0, hs_select_nelmts = 1;
+ k < rank; k++) {
+ /* MIN() is used to get the remaining edge portion if exist.
+ * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
+ hs_sel_count[k] =
+ MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
+ hs_select_nelmts *= hs_sel_count[k];
+ }
+
+ if (H5Sselect_hyperslab(f_space_id,
+ H5S_SELECT_SET, hs_sel_offset,
+ NULL, hs_sel_count, NULL) < 0)
+ goto error;
+ if (H5Sselect_hyperslab(hslab_space,
+ H5S_SELECT_SET, zero, NULL,
+ &hs_select_nelmts, NULL) < 0)
+ goto error;
+ }
+ else {
+ H5Sselect_all(f_space_id);
+ H5Sselect_all(hslab_space);
+ hs_select_nelmts = 1;
+ } /* rank */
+
+ /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+ CHECK_H5DRW_ERROR(H5Dread, dset_in,
+ wtype_id, hslab_space, f_space_id,
+ H5P_DEFAULT, hslab_buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, dset_out,
+ wtype_id, hslab_space, f_space_id,
+ H5P_DEFAULT, hslab_buf);
+
+ /* reclaim any VL memory, if necessary */
+ if (vl_data)
+ H5Dvlen_reclaim(wtype_id, hslab_space,
+ H5P_DEFAULT, hslab_buf);
+
+ /* calculate the next hyperslab offset */
+ for (k = rank, carry = 1; k > 0 && carry;
+ --k) {
+ hs_sel_offset[k - 1] += hs_sel_count[k
+ - 1];
+ /* if reached the end of a dim */
+ if (hs_sel_offset[k - 1] == dims[k - 1])
+ hs_sel_offset[k - 1] = 0;
+ else
+ carry = 0;
+ } /* k */
+ } /* elmtno */
+
+ H5Sclose(hslab_space);
+ /* free */
+ if (hslab_buf != NULL) {
+ HDfree(hslab_buf);
+ hslab_buf = NULL;
+ }
+ } /* hyperslab read */
+ } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
+
+ /*-------------------------------------------------------------------------
+ * amount of compression used
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose) {
+ double ratio = 0;
+
+ /* only print the compression ration if there was a filter request */
+ if (apply_s && apply_f && req_filter) {
+ /* get the storage size of the output dataset */
+ dsize_out = H5Dget_storage_size(dset_out);
+
+ /* compression ratio = uncompressed size / compressed size */
+ if (dsize_out != 0)
+ ratio = (double) dsize_in
+ / (double) dsize_out;
+
+ print_dataset_info(dcpl_out,
+ travt->objs[i].name, ratio, 1);
+ }
+ else
+ print_dataset_info(dcpl_in, travt->objs[i].name,
+ ratio, 0);
+
+ /* print a message that the filter was not applied
+ (in case there was a filter)
+ */
+ if (has_filter && apply_s == 0)
+ printf(
+ " <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
+ travt->objs[i].name,
+ (int) options->min_comp);
+
+ if (has_filter && apply_f == 0)
+ printf(
+ " <warning: could not apply the filter to %s>\n",
+ travt->objs[i].name);
+
+ } /* verbose */
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt,
+ options) < 0)
+ goto error;
+ /*close */
+ if (H5Dclose(dset_out) < 0)
+ goto error;
+
+ }/*!H5T_REFERENCE*/
+ }/*h5tools_canreadf*/
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Tclose(ftype_id) < 0)
+ goto error;
+ if (H5Tclose(wtype_id) < 0)
+ goto error;
+ if (H5Pclose(dcpl_in) < 0)
+ goto error;
+ if (H5Pclose(dcpl_out) < 0)
+ goto error;
+ if (H5Sclose(f_space_id) < 0)
+ goto error;
+ if (H5Dclose(dset_in) < 0)
+ goto error;
+
+ }
+ /*-------------------------------------------------------------------------
+ * we do not have request for filter/chunking use H5Ocopy instead
+ *-------------------------------------------------------------------------
+ */
+ else {
+ hid_t pid;
+
+ /* create property to pass copy options */
+ if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
+ goto error;
+
+ /* set options for object copy */
+ if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Ocopy(fidin, /* Source file or group identifier */
+ travt->objs[i].name, /* Name of the source object to be copied */
+ fidout, /* Destination file or group identifier */
+ travt->objs[i].name, /* Name of the destination object */
+ pid, /* Properties which apply to the copy */
+ H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
+ goto error;
+
+ /* close property */
+ if (H5Pclose(pid) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy attrs manually
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+ if ((dset_out = H5Dopen2(fidout, travt->objs[i].name,
+ H5P_DEFAULT)) < 0)
+ goto error;
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options)
+ < 0)
+ goto error;
+ if (H5Dclose(dset_in) < 0)
+ goto error;
+ if (H5Dclose(dset_out) < 0)
+ goto error;
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+
+ } /* end do we have request for filter/chunking */
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_NAMED_DATATYPE
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_NAMED_DATATYPE:
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "type", travt->objs[i].name);
+
+ if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+
+ /* Copy the datatype anonymously */
+ if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
+ travt, options)) < 0)
+ goto error;
+
+ /* Link in to group structure */
+ if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
+ H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(type_in, type_out, &named_dt_head, travt, options)
+ < 0)
+ goto error;
+
+ if (H5Tclose(type_in) < 0)
+ goto error;
+ if (H5Tclose(type_out) < 0)
+ goto error;
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_LINK
+ * H5TRAV_TYPE_UDLINK
+ *
+ * Only handles external links; H5Lcopy will fail for other UD link types
+ * since we don't have creation or copy callbacks for them.
+ *-------------------------------------------------------------------------
+ */
+
+ case H5TRAV_TYPE_LINK:
+ case H5TRAV_TYPE_UDLINK: {
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+ if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name,
+ H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto error;
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+ }
+ break;
+
+ default:
+ goto error;
+ } /* switch */
+
+ /* free */
+ if (buf != NULL) {
+ HDfree(buf);
+ buf = NULL;
+ }
+
+ } /* i */
+
+ /* Finalize (link) the stack of named datatypes (if any) */
+ named_datatype_free(&named_dt_head, 0);
+
+ return 0;
error:
- H5E_BEGIN_TRY {
- H5Gclose(grp_in);
- H5Gclose(grp_out);
- H5Pclose(dcpl_in);
- H5Pclose(gcpl_in);
- H5Pclose(gcpl_out);
- H5Sclose(f_space_id);
- H5Dclose(dset_in);
- H5Dclose(dset_out);
- H5Tclose(ftype_id);
- H5Tclose(wtype_id);
- H5Tclose(type_in);
- H5Tclose(type_out);
- named_datatype_free(&named_dt_head, 1);
- } H5E_END_TRY;
- /* free */
- if (buf!=NULL)
- HDfree(buf);
- if (hslab_buf!=NULL)
- HDfree(hslab_buf);
- return -1;
+ H5E_BEGIN_TRY
+ {
+ H5Gclose(grp_in);
+ H5Gclose(grp_out);
+ H5Pclose(dcpl_in);
+ H5Pclose(gcpl_in);
+ H5Pclose(gcpl_out);
+ H5Sclose(f_space_id);
+ H5Dclose(dset_in);
+ H5Dclose(dset_out);
+ H5Tclose(ftype_id);
+ H5Tclose(wtype_id);
+ H5Tclose(type_in);
+ H5Tclose(type_out);
+ named_datatype_free(&named_dt_head, 1);
+ }H5E_END_TRY;
+ /* free */
+ if (buf != NULL)
+ HDfree(buf);
+ if (hslab_buf != NULL)
+ HDfree(hslab_buf);
+ return -1;
}
-
/*-------------------------------------------------------------------------
-* Function: print_dataset_info
-*
-* Purpose: print name, filters, percentage compression of a dataset
-*
-*-------------------------------------------------------------------------
-*/
-static void print_dataset_info(hid_t dcpl_id,
- char *objname,
- double ratio,
- int pr)
-{
- char strfilter[255];
+ * Function: print_dataset_info
+ *
+ * Purpose: print name, filters, percentage compression of a dataset
+ *
+ *-------------------------------------------------------------------------
+ */
+static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
+ int pr) {
+ char strfilter[255];
#if defined (PRINT_DEBUG )
- char temp[255];
+ char temp[255];
#endif
- int nfilters; /* number of filters */
- unsigned filt_flags; /* filter flags */
- H5Z_filter_t filtn; /* filter identification number */
- unsigned cd_values[20]; /* filter client data values */
- size_t cd_nelmts; /* filter client number of values */
- char f_objname[256]; /* filter objname */
- int i;
+ int nfilters; /* number of filters */
+ unsigned filt_flags; /* filter flags */
+ H5Z_filter_t filtn; /* filter identification number */
+ unsigned cd_values[20]; /* filter client data values */
+ size_t cd_nelmts; /* filter client number of values */
+ char f_objname[256]; /* filter objname */
+ int i;
+ HDstrcpy(strfilter, "\0");
- HDstrcpy(strfilter,"\0");
+ /* get information about input filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
+ return;
- /* get information about input filters */
- if((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
- return;
+ for (i = 0; i < nfilters; i++) {
+ cd_nelmts = NELMTS(cd_values);
- for(i = 0; i < nfilters; i++) {
- cd_nelmts = NELMTS(cd_values);
+ filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
+ cd_values, sizeof(f_objname), f_objname, NULL);
- filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts,
- cd_values, sizeof(f_objname), f_objname, NULL);
+ switch (filtn) {
- switch(filtn) {
- default:
- break;
+ case H5Z_FILTER_NONE:
+ HDstrcat(strfilter, "NONE ");
+ break;
- case H5Z_FILTER_DEFLATE:
- HDstrcat(strfilter,"GZIP ");
+ case H5Z_FILTER_DEFLATE:
+ HDstrcat(strfilter, "GZIP ");
#if defined (PRINT_DEBUG)
- {
- unsigned level=cd_values[0];
- sprintf(temp,"(%d)",level);
- HDstrcat(strfilter,temp);
- }
+ {
+ unsigned level=cd_values[0];
+ sprintf(temp,"(%d)",level);
+ HDstrcat(strfilter,temp);
+ }
#endif
- break;
+ break;
- case H5Z_FILTER_SZIP:
- HDstrcat(strfilter,"SZIP ");
+ case H5Z_FILTER_SZIP:
+ HDstrcat(strfilter, "SZIP ");
#if defined (PRINT_DEBUG)
- {
- unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
- unsigned ppb=cd_values[1];
- sprintf(temp,"(%d,",ppb);
- HDstrcat(strfilter,temp);
- if (options_mask & H5_SZIP_EC_OPTION_MASK)
- HDstrcpy(temp,"EC) ");
- else if (options_mask & H5_SZIP_NN_OPTION_MASK)
- HDstrcpy(temp,"NN) ");
- }
- HDstrcat(strfilter,temp);
+ {
+ unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
+ unsigned ppb=cd_values[1];
+ sprintf(temp,"(%d,",ppb);
+ HDstrcat(strfilter,temp);
+ if (options_mask & H5_SZIP_EC_OPTION_MASK)
+ HDstrcpy(temp,"EC) ");
+ else if (options_mask & H5_SZIP_NN_OPTION_MASK)
+ HDstrcpy(temp,"NN) ");
+ }
+ HDstrcat(strfilter,temp);
#endif
- break;
-
- case H5Z_FILTER_SHUFFLE:
- HDstrcat(strfilter,"SHUF ");
- break;
-
- case H5Z_FILTER_FLETCHER32:
- HDstrcat(strfilter,"FLET ");
- break;
-
- case H5Z_FILTER_NBIT:
- HDstrcat(strfilter,"NBIT ");
- break;
-
- case H5Z_FILTER_SCALEOFFSET:
- HDstrcat(strfilter,"SCALEOFFSET ");
- break;
- } /* switch */
- }/*i*/
-
- if(!pr)
- printf(FORMAT_OBJ,"dset",objname );
- else
- {
- char str[255], temp[28];
- HDstrcpy(str,"dset ");
- HDstrcat(str,strfilter);
- sprintf(temp," (%.3f:1)",ratio);
- HDstrcat(str,temp);
- printf(FORMAT_OBJ,str,objname);
- }
+ break;
+
+ case H5Z_FILTER_SHUFFLE:
+ HDstrcat(strfilter, "SHUF ");
+ break;
+
+ case H5Z_FILTER_FLETCHER32:
+ HDstrcat(strfilter, "FLET ");
+ break;
+
+ case H5Z_FILTER_NBIT:
+ HDstrcat(strfilter, "NBIT ");
+ break;
+
+ case H5Z_FILTER_SCALEOFFSET:
+ HDstrcat(strfilter, "SCALEOFFSET ");
+ break;
+
+ default:
+ HDstrcat(strfilter, "UD ");
+ break;
+ } /* switch */
+ }/*i*/
+
+ if (!pr)
+ printf(FORMAT_OBJ, "dset", objname);
+ else {
+ char str[255], temp[28];
+ HDstrcpy(str, "dset ");
+ HDstrcat(str, strfilter);
+ sprintf(temp, " (%.3f:1)", ratio);
+ HDstrcat(str, temp);
+ printf(FORMAT_OBJ, str, objname);
+ }
}
-
/*-------------------------------------------------------------------------
-* Function: copy_user_block
-*
-* Purpose: copy user block from one file to another
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Peter Cao
-*
-* Date: October, 25, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int
-copy_user_block(const char *infile, const char *outfile, hsize_t size)
-{
- int infid = -1, outfid = -1; /* File descriptors */
- int status = 0; /* Return value */
-
- /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
- HDassert(size > 0);
-
- /* Open files */
- if((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
- status = -1;
- goto done;
- }
- if((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
- status = -1;
- goto done;
- }
-
- /* Copy the userblock from the input file to the output file */
- while(size > 0) {
- ssize_t nread, nbytes; /* # of bytes transfered, etc. */
- char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
- const char *wbuf; /* Pointer into buffer, for writing */
-
- /* Read buffer from source file */
- if(size > USERBLOCK_XFER_SIZE)
- nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
- else
- nread = HDread(infid, rbuf, (size_t)size);
- if(nread < 0) {
- status = -1;
- goto done;
- } /* end if */
-
- /* Write buffer to destination file */
- /* (compensating for interrupted writes & checking for errors, etc.) */
- nbytes = nread;
- wbuf = rbuf;
- while(nbytes > 0) {
- ssize_t nwritten; /* # of bytes written */
-
- do {
- nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
- } while(-1 == nwritten && EINTR == errno);
- if(-1 == nwritten) { /* error */
- status = -1;
- goto done;
- } /* end if */
- HDassert(nwritten > 0);
- HDassert(nwritten <= nbytes);
-
- /* Update # of bytes left & offset in buffer */
- nbytes -= nwritten;
- wbuf += nwritten;
- HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
- } /* end while */
-
- /* Update size of userblock left to transfer */
- size = size - (hsize_t)nread;
- } /* end while */
+ * Function: copy_user_block
+ *
+ * Purpose: copy user block from one file to another
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Peter Cao
+ *
+ * Date: October, 25, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int copy_user_block(const char *infile, const char *outfile,
+ hsize_t size) {
+ int infid = -1, outfid = -1; /* File descriptors */
+ int status = 0; /* Return value */
+
+ /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
+ HDassert(size > 0);
+
+ /* Open files */
+ if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
+ status = -1;
+ goto done;
+ }
+ if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
+ status = -1;
+ goto done;
+ }
+
+ /* Copy the userblock from the input file to the output file */
+ while (size > 0) {
+ ssize_t nread, nbytes; /* # of bytes transfered, etc. */
+ char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
+ const char *wbuf; /* Pointer into buffer, for writing */
+
+ /* Read buffer from source file */
+ if (size > USERBLOCK_XFER_SIZE)
+ nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+ else
+ nread = HDread(infid, rbuf, (size_t)size);
+ if (nread < 0) {
+ status = -1;
+ goto done;
+ } /* end if */
+
+ /* Write buffer to destination file */
+ /* (compensating for interrupted writes & checking for errors, etc.) */
+ nbytes = nread;
+ wbuf = rbuf;
+ while (nbytes > 0) {
+ ssize_t nwritten; /* # of bytes written */
+
+ do {
+ nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
+ } while (-1 == nwritten && EINTR == errno);
+ if (-1 == nwritten) { /* error */
+ status = -1;
+ goto done;
+ } /* end if */
+ HDassert(nwritten > 0);
+ HDassert(nwritten <= nbytes);
+
+ /* Update # of bytes left & offset in buffer */
+ nbytes -= nwritten;
+ wbuf += nwritten;
+ HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
+ } /* end while */
+
+ /* Update size of userblock left to transfer */
+ size = size - (hsize_t) nread;
+ } /* end while */
done:
- if(infid > 0)
- HDclose(infid);
- if(outfid > 0)
- HDclose(outfid);
+ if (infid > 0)
+ HDclose(infid);
+ if (outfid > 0)
+ HDclose(outfid);
- return status;
+ return status;
}
-
-
/*-------------------------------------------------------------------------
-* Function: print_user_block
-*
-* Purpose: print user block
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente
-*
-* Date: August, 20, 2008
-*
-*-------------------------------------------------------------------------
-*/
+ * Function: print_user_block
+ *
+ * Purpose: print user block
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente
+ *
+ * Date: August, 20, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static
void print_user_block(const char *filename, hid_t fid)
{
- int fh; /* file handle */
- hsize_t ub_size; /* user block size */
- hsize_t size; /* size read */
- hid_t fcpl; /* file creation property list ID for HDF5 file */
- int i;
-
- /* get user block size */
- if(( fcpl = H5Fget_create_plist(fid)) < 0)
- {
- error_msg("failed to retrieve file creation property list\n");
- goto done;
- }
-
- if(H5Pget_userblock(fcpl, &ub_size) < 0)
- {
- error_msg("failed to retrieve userblock size\n");
- goto done;
- }
-
- if(H5Pclose(fcpl) < 0)
- {
- error_msg("failed to close property list\n");
- goto done;
- }
-
- /* open file */
- if((fh = HDopen(filename, O_RDONLY, 0)) < 0)
- {
- goto done;
- }
-
- size = ub_size;
-
- /* read file */
- while(size > 0)
- {
- ssize_t nread; /* # of bytes read */
- char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
-
- /* read buffer */
- if(size > USERBLOCK_XFER_SIZE)
- nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
- else
- nread = HDread(fh, rbuf, (size_t)size);
-
- for(i = 0; i < nread; i++)
- {
-
- printf("%c ", rbuf[i]);
-
- }
- printf("\n");
-
- if(nread < 0)
- {
- goto done;
- }
-
-
- /* update size of userblock left to transfer */
- size -= nread;
- }
+ int fh; /* file handle */
+ hsize_t ub_size; /* user block size */
+ hsize_t size; /* size read */
+ hid_t fcpl; /* file creation property list ID for HDF5 file */
+ int i;
-done:
- if(fh > 0)
- HDclose(fh);
+ /* get user block size */
+ if(( fcpl = H5Fget_create_plist(fid)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
+ goto done;
+ }
+
+ if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
+ goto done;
+ }
+
+ if(H5Pclose(fcpl) < 0) {
+ error_msg("failed to close property list\n");
+ goto done;
+ }
+
+ /* open file */
+ if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
+ goto done;
+ }
+ size = ub_size;
+
+ /* read file */
+ while(size > 0) {
+ ssize_t nread; /* # of bytes read */
+ char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
+
+ /* read buffer */
+ if(size > USERBLOCK_XFER_SIZE)
+ nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+ else
+ nread = HDread(fh, rbuf, (size_t)size);
+
+ for(i = 0; i < nread; i++) {
+
+ printf("%c ", rbuf[i]);
+
+ }
+ printf("\n");
+
+ if(nread < 0) {
+ goto done;
+ }
+
+ /* update size of userblock left to transfer */
+ size -= nread;
+ }
+
+done:
+ if(fh > 0)
+ HDclose(fh);
- return;
+ return;
}
#endif
diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
index 6c7bc65..56e08ef 100644
--- a/tools/h5repack/h5repack_filters.c
+++ b/tools/h5repack/h5repack_filters.c
@@ -345,8 +345,13 @@ int apply_filters(const char* name, /* object name from traverse list */
{
switch (obj.filter[i].filtn)
{
- default:
- break;
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_NONE 0 , uncompress if compressed
+ *-------------------------------------------------------------------------
+ */
+ case H5Z_FILTER_NONE:
+ break;
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE 1 , deflation like gzip
@@ -436,6 +441,14 @@ int apply_filters(const char* name, /* object name from traverse list */
return -1;
}
break;
+ default:
+ {
+ if (H5Pset_filter (dcpl_id, obj.filter[i].filtn, H5Z_FLAG_MANDATORY, obj.filter[i].cd_nelmts, obj.filter[i].cd_values)<0)
+ return -1;
+ if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+ return -1;
+ }
+ break;
} /* switch */
}/*i*/
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 05ff447..d7bfd02 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -20,259 +20,346 @@
/* Name of tool */
#define PROGRAMNAME "h5repack"
-static void usage(const char *prog);
-static void parse_command_line(int argc, const char **argv, pack_opt_t* options);
-static void read_info(const char *filename,pack_opt_t *options);
-
+static int parse_command_line(int argc, const char **argv, pack_opt_t* options);
/* module-scoped variables */
-static int has_i_o = 0;
-const char *infile = NULL;
-const char *outfile = NULL;
-
+static int has_i_o = 0;
+const char *infile = NULL;
+const char *outfile = NULL;
/*
* Command-line options: The user can specify short or long-named
* parameters.
*/
static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:T:";
-static struct long_options l_opts[] = {
- { "help", no_arg, 'h' },
- { "version", no_arg, 'V' },
- { "verbose", no_arg, 'v' },
- { "filter", require_arg, 'f' },
- { "layout", require_arg, 'l' },
- { "minimum", require_arg, 'm' },
- { "file", require_arg, 'e' },
- { "native", no_arg, 'n' },
- { "latest", no_arg, 'L' },
- { "compact", require_arg, 'c' },
- { "indexed", require_arg, 'd' },
- { "ssize", require_arg, 's' },
- { "ublock", require_arg, 'u' },
- { "block", require_arg, 'b' },
- { "metadata_block_size", require_arg, 'M' },
- { "threshold", require_arg, 't' },
- { "alignment", require_arg, 'a' },
- { "infile", require_arg, 'i' }, /* -i for backward compability */
- { "outfile", require_arg, 'o' }, /* -o for backward compability */
- { "fs_strategy", require_arg, 'S' },
- { "fs_threshold", require_arg, 'T' },
- { NULL, 0, '\0' }
-};
-
-
-
+static struct long_options l_opts[] = { { "help", no_arg, 'h' }, { "version",
+ no_arg, 'V' }, { "verbose", no_arg, 'v' },
+ { "filter", require_arg, 'f' }, { "layout", require_arg, 'l' }, {
+ "minimum", require_arg, 'm' }, { "file", require_arg, 'e' }, {
+ "native", no_arg, 'n' }, { "latest", no_arg, 'L' }, { "compact",
+ require_arg, 'c' }, { "indexed", require_arg, 'd' }, { "ssize",
+ require_arg, 's' }, { "ublock", require_arg, 'u' }, { "block",
+ require_arg, 'b' }, { "metadata_block_size", require_arg, 'M' },
+ { "threshold", require_arg, 't' }, { "alignment", require_arg, 'a' }, {
+ "infile", require_arg, 'i' }, /* -i for backward compability */
+ { "outfile", require_arg, 'o' }, /* -o for backward compability */
+ { "fs_strategy", require_arg, 'S' },
+ { "fs_threshold", require_arg, 'T' }, { NULL, 0, '\0' } };
/*-------------------------------------------------------------------------
- * Function: main
+ * Function: usage
*
- * Purpose: h5repack main program
+ * Purpose: print usage
*
- * Return: Success: EXIT_SUCCESS(0)
+ * Return: void
*
- * Failure: EXIT_FAILURE(1)
+ *-------------------------------------------------------------------------
+ */
+static void usage(const char *prog) {
+ printf("usage: %s [OPTIONS] file1 file2\n", prog);
+ printf(" file1 Input HDF5 File\n");
+ printf(" file2 Output HDF5 File\n");
+ printf(" OPTIONS\n");
+ printf(" -h, --help Print a usage message and exit\n");
+ printf(
+ " -v, --verbose Verbose mode, print object information\n");
+ printf(" -V, --version Print version number and exit\n");
+ printf(
+ " -n, --native Use a native HDF5 type when repacking\n");
+ printf(" -L, --latest Use latest version of file format\n");
+ printf(
+ " -c L1, --compact=L1 Maximum number of links in header messages\n");
+ printf(
+ " -d L2, --indexed=L2 Minimum number of links in the indexed format\n");
+ printf(
+ " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
+ printf(
+ " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n");
+ printf(
+ " -e E, --file=E Name of file E with the -f and -l options\n");
+ printf(
+ " -u U, --ublock=U Name of file U with user block data to be added\n");
+ printf(" -b B, --block=B Size of user block to be added\n");
+ printf(
+ " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n");
+ printf(" -t T, --threshold=T Threshold value for H5Pset_alignment\n");
+ printf(" -a A, --alignment=A Alignment value for H5Pset_alignment\n");
+ printf(" -f FILT, --filter=FILT Filter type\n");
+ printf(" -l LAYT, --layout=LAYT Layout type\n");
+ printf(
+ " -S FS_STRGY, --fs_strategy=FS_STRGY File space management strategy\n");
+ printf(
+ " -T FS_THRD, --fs_threshold=FS_THRD Free-space section threshold\n");
+
+ printf("\n");
+
+ printf(
+ " M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
+ printf(" E - is a filename.\n");
+ printf(" S - is an integer\n");
+ printf(" U - is a filename.\n");
+ printf(" T - is an integer\n");
+ printf(" A - is an integer greater than zero\n");
+ printf(
+ " B - is the user block size, any value that is 512 or greater and is\n");
+ printf(" a power of 2 (1024 default)\n");
+ printf(
+ " F - is the shared object header message type, any of <dspace|dtype|fill|\n");
+ printf(
+ " pline|attr>. If F is not specified, S applies to all messages\n");
+ printf("\n");
+ printf(
+ " FS_STRGY is the file space management strategy to use for the output file.\n");
+ printf(" It is a string as listed below:\n");
+ printf(
+ " ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n");
+ printf(" for file space allocation\n");
+ printf(
+ " ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n");
+ printf(" for file space allocation\n");
+ printf(
+ " AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n");
+ printf(" VFD - Use virtual file driver for file space allocation\n");
+ printf("\n");
+ printf(
+ " FS_THRD is the free-space section threshold to use for the output file.\n");
+ printf(
+ " It is the minimum size (in bytes) of free-space sections to be tracked\n");
+ printf(" by the the library's free-space managers.\n");
+ printf("\n");
+
+ printf(" FILT - is a string with the format:\n");
+ printf("\n");
+ printf(" <list of objects>:<name of filter>=<filter parameters>\n");
+ printf("\n");
+ printf(
+ " <list of objects> is a comma separated list of object names, meaning apply\n");
+ printf(
+ " compression only to those objects. If no names are specified, the filter\n");
+ printf(" is applied to all objects\n");
+ printf(" <name of filter> can be:\n");
+ printf(" GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
+ printf(" SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
+ printf(" SHUF, to apply the HDF5 shuffle filter\n");
+ printf(" FLET, to apply the HDF5 checksum filter\n");
+ printf(" NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
+ printf(" SOFF, to apply the HDF5 Scale/Offset filter\n");
+ printf(" UD, to apply a user defined filter\n");
+ printf(" NONE, to remove all filters\n");
+ printf(
+ " <filter parameters> is optional filter parameter information\n");
+ printf(" GZIP=<deflation level> from 1-9\n");
+ printf(
+ " SZIP=<pixels per block,coding> pixels per block is a even number in\n");
+ printf(" 2-32 and coding method is either EC or NN\n");
+ printf(" SHUF (no parameter)\n");
+ printf(" FLET (no parameter)\n");
+ printf(" NBIT (no parameter)\n");
+ printf(
+ " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
+ printf(" is either IN or DS\n");
+ printf(
+ " UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
+ printf(
+ " required values for filter_number,cd_value_count,value_1\n");
+ printf(" optional values for value_2 to value_N\n");
+ printf(" NONE (no parameter)\n");
+ printf("\n");
+ printf(" LAYT - is a string with the format:\n");
+ printf("\n");
+ printf(" <list of objects>:<layout type>=<layout parameters>\n");
+ printf("\n");
+ printf(
+ " <list of objects> is a comma separated list of object names, meaning that\n");
+ printf(
+ " layout information is supplied for those objects. If no names are\n");
+ printf(" specified, the layout type is applied to all objects\n");
+ printf(" <layout type> can be:\n");
+ printf(" CHUNK, to apply chunking layout\n");
+ printf(" COMPA, to apply compact layout\n");
+ printf(" CONTI, to apply contiguous layout\n");
+ printf(" <layout parameters> is optional layout information\n");
+ printf(
+ " CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
+ printf(" COMPA (no parameter)\n");
+ printf(" CONTI (no parameter)\n");
+ printf("\n");
+ printf("Examples of use:\n");
+ printf("\n");
+ printf("1) h5repack -v -f GZIP=1 file1 file2\n");
+ printf("\n");
+ printf(" GZIP compression with level 1 to all objects\n");
+ printf("\n");
+ printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
+ printf("\n");
+ printf(
+ " SZIP compression with 8 pixels per block and NN coding method to object A\n");
+ printf("\n");
+ printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
+ printf("\n");
+ printf(
+ " Chunked layout, with a layout size of 20x10, to objects A and B\n");
+ printf(" and remove filters to objects C, D, F\n");
+ printf("\n");
+ printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
+ printf("\n");
+ printf(
+ " Using latest file format with maximum compact group size of 10 and\n");
+ printf(" and minimum shared datatype size of 20\n");
+ printf("\n");
+ printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
+ printf("\n");
+ printf(" Add both filters SHUF and GZIP in this order to all datasets\n");
+ printf("\n");
+ printf("6) h5repack -f UD=307,1,9 file1 file2 \n");
+ printf("\n");
+ printf(" Add bzip2 filter to all datasets\n");
+ printf("\n");
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: leave
*
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * Purpose: Shutdown MPI & HDF5 and call exit()
*
- * Date: May 9, 2003
+ * Return: Does not return
*
- * Comments:
+ * Programmer: Quincey Koziol
+ * Saturday, 31. January 2004
+ *
+ * Modifications:
*
*-------------------------------------------------------------------------
*/
-int main(int argc, const char **argv)
-{
-
- pack_opt_t options; /*the global options */
- int ret=-1;
-
- h5tools_setprogname(PROGRAMNAME);
- h5tools_setstatus(EXIT_SUCCESS);
-
- /* Initialize h5tools lib */
- h5tools_init();
-
- /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
- if ( h5tools_getenv_update_hyperslab_bufsize() < 0)
- HDexit(EXIT_FAILURE);
-
- /* initialize options */
- h5repack_init(&options, 0, FALSE, H5F_FILE_SPACE_DEFAULT, (hsize_t)0);
-
- parse_command_line(argc, argv, &options);
-
- /* get file names if they were not yet got */
- if ( has_i_o == 0 )
- {
-
- if ( argv[ opt_ind ] != NULL && argv[ opt_ind + 1 ] != NULL )
- {
- infile = argv[ opt_ind ];
- outfile = argv[ opt_ind + 1 ];
-
- if ( HDstrcmp( infile, outfile ) == 0 )
- {
- error_msg("file names cannot be the same\n");
- usage(h5tools_getprogname());
- HDexit(EXIT_FAILURE);
-
- }
- }
-
- else
- {
- error_msg("file names missing\n");
- usage(h5tools_getprogname());
- HDexit(EXIT_FAILURE);
- }
- }
-
-
- /* pack it */
- ret=h5repack(infile,outfile,&options);
+static void leave(int ret) {
+ h5tools_close();
- /* free tables */
- h5repack_end(&options);
-
- if (ret==-1)
- return 1;
- else
- return 0;
+ HDexit(ret);
}
-
-
/*-------------------------------------------------------------------------
- * Function: usage
+ * Function: read_info
*
- * Purpose: print usage
+ * Purpose: read comp and chunk options from a file
*
- * Return: void
+ * Return: void, exit on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
*
*-------------------------------------------------------------------------
*/
-static void usage(const char *prog)
-{
- printf("usage: %s [OPTIONS] file1 file2\n", prog);
- printf(" file1 Input HDF5 File\n");
- printf(" file2 Output HDF5 File\n");
- printf(" OPTIONS\n");
- printf(" -h, --help Print a usage message and exit\n");
- printf(" -v, --verbose Verbose mode, print object information\n");
- printf(" -V, --version Print version number and exit\n");
- printf(" -n, --native Use a native HDF5 type when repacking\n");
- printf(" -L, --latest Use latest version of file format\n");
- printf(" -c L1, --compact=L1 Maximum number of links in header messages\n");
- printf(" -d L2, --indexed=L2 Minimum number of links in the indexed format\n");
- printf(" -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
- printf(" -m M, --minimum=M Do not apply the filter to datasets smaller than M\n");
- printf(" -e E, --file=E Name of file E with the -f and -l options\n");
- printf(" -u U, --ublock=U Name of file U with user block data to be added\n");
- printf(" -b B, --block=B Size of user block to be added\n");
- printf(" -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n");
- printf(" -t T, --threshold=T Threshold value for H5Pset_alignment\n");
- printf(" -a A, --alignment=A Alignment value for H5Pset_alignment\n");
- printf(" -f FILT, --filter=FILT Filter type\n");
- printf(" -l LAYT, --layout=LAYT Layout type\n");
- printf(" -S FS_STRGY, --fs_strategy=FS_STRGY File space management strategy\n");
- printf(" -T FS_THRD, --fs_threshold=FS_THRD Free-space section threshold\n");
-
- printf("\n");
-
- printf(" M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
- printf(" E - is a filename.\n");
- printf(" S - is an integer\n");
- printf(" U - is a filename.\n");
- printf(" T - is an integer\n");
- printf(" A - is an integer greater than zero\n");
- printf(" B - is the user block size, any value that is 512 or greater and is\n");
- printf(" a power of 2 (1024 default)\n");
- printf(" F - is the shared object header message type, any of <dspace|dtype|fill|\n");
- printf(" pline|attr>. If F is not specified, S applies to all messages\n");
- printf("\n");
- printf(" FS_STRGY is the file space management strategy to use for the output file.\n");
- printf(" It is a string as listed below:\n");
- printf(" ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n");
- printf(" for file space allocation\n");
- printf(" ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n");
- printf(" for file space allocation\n");
- printf(" AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n");
- printf(" VFD - Use virtual file driver for file space allocation\n");
- printf("\n");
- printf(" FS_THRD is the free-space section threshold to use for the output file.\n");
- printf(" It is the minimum size (in bytes) of free-space sections to be tracked\n");
- printf(" by the the library's free-space managers.\n");
- printf("\n");
-
- printf(" FILT - is a string with the format:\n");
- printf("\n");
- printf(" <list of objects>:<name of filter>=<filter parameters>\n");
- printf("\n");
- printf(" <list of objects> is a comma separated list of object names, meaning apply\n");
- printf(" compression only to those objects. If no names are specified, the filter\n");
- printf(" is applied to all objects\n");
- printf(" <name of filter> can be:\n");
- printf(" GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
- printf(" SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
- printf(" SHUF, to apply the HDF5 shuffle filter\n");
- printf(" FLET, to apply the HDF5 checksum filter\n");
- printf(" NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
- printf(" SOFF, to apply the HDF5 Scale/Offset filter\n");
- printf(" NONE, to remove all filters\n");
- printf(" <filter parameters> is optional filter parameter information\n");
- printf(" GZIP=<deflation level> from 1-9\n");
- printf(" SZIP=<pixels per block,coding> pixels per block is a even number in\n");
- printf(" 2-32 and coding method is either EC or NN\n");
- printf(" SHUF (no parameter)\n");
- printf(" FLET (no parameter)\n");
- printf(" NBIT (no parameter)\n");
- printf(" SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
- printf(" is either IN or DS\n");
- printf(" NONE (no parameter)\n");
- printf("\n");
- printf(" LAYT - is a string with the format:\n");
- printf("\n");
- printf(" <list of objects>:<layout type>=<layout parameters>\n");
- printf("\n");
- printf(" <list of objects> is a comma separated list of object names, meaning that\n");
- printf(" layout information is supplied for those objects. If no names are\n");
- printf(" specified, the layout type is applied to all objects\n");
- printf(" <layout type> can be:\n");
- printf(" CHUNK, to apply chunking layout\n");
- printf(" COMPA, to apply compact layout\n");
- printf(" CONTI, to apply contiguous layout\n");
- printf(" <layout parameters> is optional layout information\n");
- printf(" CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
- printf(" COMPA (no parameter)\n");
- printf(" CONTI (no parameter)\n");
- printf("\n");
- printf("Examples of use:\n");
- printf("\n");
- printf("1) h5repack -v -f GZIP=1 file1 file2\n");
- printf("\n");
- printf(" GZIP compression with level 1 to all objects\n");
- printf("\n");
- printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
- printf("\n");
- printf(" SZIP compression with 8 pixels per block and NN coding method to object A\n");
- printf("\n");
- printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
- printf("\n");
- printf(" Chunked layout, with a layout size of 20x10, to objects A and B\n");
- printf(" and remove filters to objects C, D, F\n");
- printf("\n");
- printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
- printf("\n");
- printf(" Using latest file format with maximum compact group size of 10 and\n");
- printf(" and minimum shared datatype size of 20\n");
- printf("\n");
- printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
- printf("\n");
- printf(" Add both filters SHUF and GZIP in this order to all datasets\n");
- printf("\n");
-}
+static
+int read_info(const char *filename, pack_opt_t *options) {
+
+ char stype[10];
+ char comp_info[1024];
+ FILE *fp = NULL;
+ char c;
+ int i, rc = 1;
+ int ret_value = EXIT_SUCCESS;
+
+ if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
+ error_msg("cannot open options file %s\n", filename);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+
+ /* cycle until end of file reached */
+ while (1) {
+ rc = fscanf(fp, "%s", stype);
+ if (rc == -1)
+ break;
+
+ /*-------------------------------------------------------------------------
+ * filter
+ *-------------------------------------------------------------------------
+ */
+ if (HDstrcmp(stype,"-f") == 0) {
+ /* find begining of info */
+ i = 0;
+ c = '0';
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ if (HDfeof(fp))
+ break;
+ }
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ comp_info[i] = c;
+ i++;
+ if (HDfeof(fp))
+ break;
+ if (c == 10 /*eol*/)
+ break;
+ }
+ comp_info[i - 1] = '\0'; /*cut the last " */
+
+ if (h5repack_addfilter(comp_info, options) == -1) {
+ error_msg("could not add compression option\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * layout
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(stype,"-l") == 0) {
+
+ /* find begining of info */
+ i = 0;
+ c = '0';
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ if (HDfeof(fp))
+ break;
+ }
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ comp_info[i] = c;
+ i++;
+ if (HDfeof(fp))
+ break;
+ if (c == 10 /*eol*/)
+ break;
+ }
+ comp_info[i - 1] = '\0'; /*cut the last " */
+
+ if (h5repack_addlayout(comp_info, options) == -1) {
+ error_msg("could not add chunck option\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * not valid
+ *-------------------------------------------------------------------------
+ */
+ else {
+ error_msg("bad file format for %s", filename);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+ }
+
+done:
+ if (fp)
+ HDfclose(fp);
+
+ return ret_value;
+}
/*-------------------------------------------------------------------------
* Function: parse_command_line
@@ -283,306 +370,275 @@ static void usage(const char *prog)
*/
static
-void parse_command_line(int argc, const char **argv, pack_opt_t* options)
-{
-
- int opt;
-
- /* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
- {
- switch ((char)opt)
- {
-
- /* -i for backward compability */
- case 'i':
- infile = opt_arg;
- has_i_o = 1;
- break;
- /* -o for backward compability */
- case 'o':
- outfile = opt_arg;
- has_i_o = 1;
- break;
-
-
- case 'h':
- usage(h5tools_getprogname());
- HDexit(EXIT_SUCCESS);
- case 'V':
- print_version(h5tools_getprogname());
- HDexit(EXIT_SUCCESS);
- case 'v':
- options->verbose = 1;
- break;
- case 'f':
-
- /* parse the -f filter option */
- if (h5repack_addfilter( opt_arg, options)<0)
- {
- error_msg("in parsing filter\n");
- HDexit(EXIT_FAILURE);
- }
- break;
- case 'l':
-
- /* parse the -l layout option */
- if (h5repack_addlayout( opt_arg, options)<0)
- {
- error_msg("in parsing layout\n");
- HDexit(EXIT_FAILURE);
- }
- break;
-
-
- case 'm':
-
- options->min_comp = HDatoi( opt_arg );
- if ((int)options->min_comp<=0)
- {
- error_msg("invalid minimum compress size <%s>\n", opt_arg );
- HDexit(EXIT_FAILURE);
- }
- break;
-
- case 'e':
- read_info( opt_arg, options);
- break;
-
- case 'n':
- options->use_native = 1;
- break;
-
- case 'L':
- options->latest = TRUE;
- break;
-
- case 'c':
- options->grp_compact = HDatoi( opt_arg );
- if (options->grp_compact > 0)
- options->latest = TRUE; /* must use latest format */
- break;
-
-
- case 'd':
- options->grp_indexed = HDatoi( opt_arg );
- if (options->grp_indexed > 0)
- options->latest = TRUE; /* must use latest format */
- break;
-
- case 's':
- {
- int idx = 0;
- int ssize = 0;
- char *msgPtr = HDstrchr(opt_arg, ':');
- options->latest = TRUE; /* must use latest format */
- if (msgPtr == NULL)
- {
- ssize = HDatoi( opt_arg );
- for(idx = 0; idx < 5; idx++)
- options->msg_size[idx] = ssize;
- }
- else
- {
- char msgType[10];
- HDstrcpy(msgType, msgPtr+1);
- msgPtr[0] = '\0';
- ssize = HDatoi( opt_arg );
- if(HDstrncmp(msgType, "dspace",6) == 0)
- options->msg_size[0] = ssize;
- else if (HDstrncmp(msgType, "dtype", 5) == 0)
- options->msg_size[1] = ssize;
- else if (HDstrncmp(msgType, "fill", 4) == 0)
- options->msg_size[2] = ssize;
- else if (HDstrncmp(msgType, "pline", 5) == 0)
- options->msg_size[3] = ssize;
- else if (HDstrncmp(msgType, "attr", 4) == 0)
- options->msg_size[4] = ssize;
- }
- }
- break;
-
- case 'u':
-
- options->ublock_filename = opt_arg;
- break;
-
- case 'b':
-
- options->ublock_size = (hsize_t)HDatol( opt_arg );
- break;
-
- case 'M':
-
- options->meta_block_size = (hsize_t)HDatol( opt_arg );
- break;
-
- case 't':
-
- options->threshold = (hsize_t)HDatol( opt_arg );
- break;
-
- case 'a':
-
- options->alignment = HDatol( opt_arg );
- if ( options->alignment < 1 )
- {
- error_msg("invalid alignment size\n", opt_arg );
- HDexit(EXIT_FAILURE);
- }
- break;
-
- case 'S':
- {
- char strategy[MAX_NC_NAME];
-
- HDstrcpy(strategy, opt_arg);
- if(!HDstrcmp(strategy, "ALL_PERSIST"))
- options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST;
- else if(!HDstrcmp(strategy, "ALL"))
- options->fs_strategy = H5F_FILE_SPACE_ALL;
- else if(!HDstrcmp(strategy, "AGGR_VFD"))
- options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD;
- else if(!HDstrcmp(strategy, "VFD"))
- options->fs_strategy = H5F_FILE_SPACE_VFD;
- else {
- error_msg("invalid file space management strategy\n", opt_arg );
- HDexit(EXIT_FAILURE);
- }
- break;
- }
-
- case 'T':
-
- options->fs_threshold = (hsize_t)HDatol( opt_arg );
- break;
- default:
- break;
- } /* switch */
-
-
- } /* while */
-
- if ( has_i_o == 0 )
- {
- /* check for file names to be processed */
- if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL)
- {
- error_msg("missing file names\n");
- usage(h5tools_getprogname());
- HDexit(EXIT_FAILURE);
- }
- }
-
+int parse_command_line(int argc, const char **argv, pack_opt_t* options) {
+
+ int opt;
+ int ret_value = 0;
+
+ /* parse command line options */
+ while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ switch ((char) opt) {
+
+ /* -i for backward compability */
+ case 'i':
+ infile = opt_arg;
+ has_i_o = 1;
+ break;
+
+ /* -o for backward compability */
+ case 'o':
+ outfile = opt_arg;
+ has_i_o = 1;
+ break;
+
+ case 'h':
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_SUCCESS);
+ ret_value = -1;
+ goto done;
+
+ case 'V':
+ print_version(h5tools_getprogname());
+ h5tools_setstatus(EXIT_SUCCESS);
+ ret_value = -1;
+ goto done;
+
+ case 'v':
+ options->verbose = 1;
+ break;
+
+ case 'f':
+ /* parse the -f filter option */
+ if (h5repack_addfilter(opt_arg, options) < 0) {
+ error_msg("in parsing filter\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'l':
+ /* parse the -l layout option */
+ if (h5repack_addlayout(opt_arg, options) < 0) {
+ error_msg("in parsing layout\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'm':
+ options->min_comp = HDatoi( opt_arg );
+ if ((int) options->min_comp <= 0) {
+ error_msg("invalid minimum compress size <%s>\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'e':
+ ret_value = read_info(opt_arg, options);
+ if (ret_value < 0)
+ goto done;
+ break;
+
+ case 'n':
+ options->use_native = 1;
+ break;
+
+ case 'L':
+ options->latest = TRUE;
+ break;
+
+ case 'c':
+ options->grp_compact = HDatoi( opt_arg );
+ if (options->grp_compact > 0)
+ options->latest = TRUE; /* must use latest format */
+ break;
+
+ case 'd':
+ options->grp_indexed = HDatoi( opt_arg );
+ if (options->grp_indexed > 0)
+ options->latest = TRUE; /* must use latest format */
+ break;
+
+ case 's':
+ {
+ int idx = 0;
+ int ssize = 0;
+ char *msgPtr = HDstrchr( opt_arg, ':');
+ options->latest = TRUE; /* must use latest format */
+ if (msgPtr == NULL) {
+ ssize = HDatoi( opt_arg );
+ for (idx = 0; idx < 5; idx++)
+ options->msg_size[idx] = ssize;
+ }
+ else {
+ char msgType[10];
+ HDstrcpy(msgType, msgPtr + 1);
+ msgPtr[0] = '\0';
+ ssize = HDatoi( opt_arg );
+ if (HDstrncmp(msgType, "dspace",6) == 0) {
+ options->msg_size[0] = ssize;
+ }
+ else if (HDstrncmp(msgType, "dtype", 5) == 0) {
+ options->msg_size[1] = ssize;
+ }
+ else if (HDstrncmp(msgType, "fill", 4) == 0) {
+ options->msg_size[2] = ssize;
+ }
+ else if (HDstrncmp(msgType, "pline", 5) == 0) {
+ options->msg_size[3] = ssize;
+ }
+ else if (HDstrncmp(msgType, "attr", 4) == 0) {
+ options->msg_size[4] = ssize;
+ }
+ }
+ }
+ break;
+
+ case 'u':
+ options->ublock_filename = opt_arg;
+ break;
+
+ case 'b':
+ options->ublock_size = (hsize_t) HDatol( opt_arg );
+ break;
+
+ case 'M':
+ options->meta_block_size = (hsize_t) HDatol( opt_arg );
+ break;
+
+ case 't':
+ options->threshold = (hsize_t) HDatol( opt_arg );
+ break;
+
+ case 'a':
+ options->alignment = HDatol( opt_arg );
+ if (options->alignment < 1) {
+ error_msg("invalid alignment size\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'S':
+ {
+ char strategy[MAX_NC_NAME];
+
+ HDstrcpy(strategy, opt_arg);
+ if (!HDstrcmp(strategy, "ALL_PERSIST"))
+ options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST;
+ else if (!HDstrcmp(strategy, "ALL"))
+ options->fs_strategy = H5F_FILE_SPACE_ALL;
+ else if (!HDstrcmp(strategy, "AGGR_VFD"))
+ options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD;
+ else if (!HDstrcmp(strategy, "VFD"))
+ options->fs_strategy = H5F_FILE_SPACE_VFD;
+ else {
+ error_msg("invalid file space management strategy\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ }
+ break;
+
+ case 'T':
+ options->fs_threshold = (hsize_t) HDatol( opt_arg );
+ break;
+
+ default:
+ break;
+ } /* switch */
+
+ } /* while */
+
+ if (has_i_o == 0) {
+ /* check for file names to be processed */
+ if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
+ error_msg("missing file names\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
+ }
+
+done:
+ return ret_value;
}
/*-------------------------------------------------------------------------
- * Function: read_info
+ * Function: main
*
- * Purpose: read comp and chunk options from a file
+ * Purpose: h5repack main program
*
- * Return: void, exit on error
+ * Return: Success: EXIT_SUCCESS(0)
*
- * Programmer: pvn@ncsa.uiuc.edu
+ * Failure: EXIT_FAILURE(1)
*
- * Date: September, 22, 2003
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
*
*-------------------------------------------------------------------------
*/
-
-static
-void read_info(const char *filename,
- pack_opt_t *options)
-{
-
- char stype[10];
- char comp_info[1024];
- FILE *fp;
- char c;
- int i, rc=1;
-
- if ((fp = HDfopen(filename, "r")) == (FILE *)NULL) {
- error_msg("cannot open options file %s\n", filename);
- HDexit(EXIT_FAILURE);
- }
-
- /* cycle until end of file reached */
- while( 1 )
- {
- rc=fscanf(fp, "%s", stype);
- if (rc==-1)
- break;
-
- /*-------------------------------------------------------------------------
- * filter
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(stype,"-f") == 0) {
-
- /* find begining of info */
- i=0; c='0';
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- if (HDfeof(fp)) break;
- }
- c='0';
- /* go until end */
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- comp_info[i]=c;
- i++;
- if (HDfeof(fp)) break;
- if (c==10 /*eol*/) break;
- }
- comp_info[i-1]='\0'; /*cut the last " */
-
- if (h5repack_addfilter(comp_info,options)==-1){
- error_msg("could not add compression option\n");
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * layout
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(stype,"-l") == 0) {
-
- /* find begining of info */
- i=0; c='0';
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- if (HDfeof(fp)) break;
- }
- c='0';
- /* go until end */
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- comp_info[i]=c;
- i++;
- if (HDfeof(fp)) break;
- if (c==10 /*eol*/) break;
- }
- comp_info[i-1]='\0'; /*cut the last " */
-
- if (h5repack_addlayout(comp_info,options)==-1){
- error_msg("could not add chunck option\n");
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * not valid
- *-------------------------------------------------------------------------
- */
- else {
- error_msg("bad file format for %s", filename);
- HDexit(EXIT_FAILURE);
- }
- }
-
- HDfclose(fp);
- return;
+int main(int argc, const char **argv) {
+
+ pack_opt_t options; /*the global options */
+ int ret = -1;
+
+ h5tools_setprogname(PROGRAMNAME);
+ h5tools_setstatus(EXIT_SUCCESS);
+
+ /* Initialize h5tools lib */
+ h5tools_init();
+
+ /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
+ if (h5tools_getenv_update_hyperslab_bufsize() < 0) {
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+
+ /* initialize options */
+ h5repack_init(&options, 0, FALSE, H5F_FILE_SPACE_DEFAULT, (hsize_t) 0);
+
+ if (parse_command_line(argc, argv, &options) < 0)
+ goto done;
+
+ /* get file names if they were not yet got */
+ if (has_i_o == 0) {
+
+ if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
+ infile = argv[opt_ind];
+ outfile = argv[opt_ind + 1];
+
+ if ( HDstrcmp( infile, outfile ) == 0) {
+ error_msg("file names cannot be the same\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+ }
+ else {
+ error_msg("file names missing\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+ }
+
+ /* pack it */
+ h5tools_setstatus(h5repack(infile, outfile, &options));
+
+done:
+ /* free tables */
+ h5repack_end(&options);
+
+ leave(h5tools_getstatus());
}
+
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index bcddbb9..b54e887 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -1,4 +1,4 @@
- /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
@@ -27,21 +27,19 @@
*-------------------------------------------------------------------------
*/
-void init_packobject(pack_info_t *obj)
-{
- int j, k;
-
- HDstrcpy(obj->path,"\0");
- for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
- {
- obj->filter[j].filtn = -1;
- for ( k=0; k<CD_VALUES; k++)
- obj->filter[j].cd_values[k] = 0;
- }
- obj->chunk.rank = -1;
- obj->refobj_id = -1;
- obj->layout = H5D_LAYOUT_ERROR;
- obj->nfilters = 0;
+void init_packobject(pack_info_t *obj) {
+ int j, k;
+
+ HDstrcpy(obj->path, "\0");
+ for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) {
+ obj->filter[j].filtn = -1;
+ for (k = 0; k < CD_VALUES; k++)
+ obj->filter[j].cd_values[k] = 0;
+ }
+ obj->chunk.rank = -1;
+ obj->refobj_id = -1;
+ obj->layout = H5D_LAYOUT_ERROR;
+ obj->nfilters = 0;
}
/*-------------------------------------------------------------------------
@@ -54,19 +52,16 @@ void init_packobject(pack_info_t *obj)
*-------------------------------------------------------------------------
*/
-static void aux_tblinsert_filter(pack_opttbl_t *table,
- unsigned int I,
- filter_info_t filt)
-{
- if (table->objs[ I ].nfilters<H5_REPACK_MAX_NFILTERS)
- {
- table->objs[ I ].filter[ table->objs[ I ].nfilters++ ] = filt;
- }
- else
- {
- error_msg("cannot insert the filter in this object.\
+static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I,
+ filter_info_t filt) {
+ if (table->objs[I].nfilters < H5_REPACK_MAX_NFILTERS) {
+ table->objs[I].filter[table->objs[I].nfilters++] = filt;
+ }
+ else {
+ error_msg(
+ "cannot insert the filter in this object.\
Maximum capacity exceeded\n");
- }
+ }
}
/*-------------------------------------------------------------------------
@@ -79,33 +74,28 @@ static void aux_tblinsert_filter(pack_opttbl_t *table,
*-------------------------------------------------------------------------
*/
-static void aux_tblinsert_layout(pack_opttbl_t *table,
- unsigned int I,
- pack_info_t *pack)
-{
- int k;
-
- table->objs[I].layout = pack->layout;
- if (H5D_CHUNKED==pack->layout)
- {
- /* -2 means the NONE option, remove chunking
- and set the layout to contiguous */
- if (pack->chunk.rank==-2)
- {
- table->objs[I].layout = H5D_CONTIGUOUS;
- table->objs[I].chunk.rank = -2;
- }
- /* otherwise set the chunking type */
- else
- {
- table->objs[I].chunk.rank = pack->chunk.rank;
- for (k = 0; k < pack->chunk.rank; k++)
- table->objs[I].chunk.chunk_lengths[k] = pack->chunk.chunk_lengths[k];
- }
- }
+static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I,
+ pack_info_t *pack) {
+ int k;
+
+ table->objs[I].layout = pack->layout;
+ if (H5D_CHUNKED == pack->layout) {
+ /* -2 means the NONE option, remove chunking
+ and set the layout to contiguous */
+ if (pack->chunk.rank == -2) {
+ table->objs[I].layout = H5D_CONTIGUOUS;
+ table->objs[I].chunk.rank = -2;
+ }
+ /* otherwise set the chunking type */
+ else {
+ table->objs[I].chunk.rank = pack->chunk.rank;
+ for (k = 0; k < pack->chunk.rank; k++)
+ table->objs[I].chunk.chunk_lengths[k] =
+ pack->chunk.chunk_lengths[k];
+ }
+ }
}
-
/*-------------------------------------------------------------------------
* Function: aux_inctable
*
@@ -116,21 +106,20 @@ static void aux_tblinsert_layout(pack_opttbl_t *table,
*-------------------------------------------------------------------------
*/
-static int aux_inctable(pack_opttbl_t *table, int n_objs )
-{
- unsigned int i;
-
- table->size += n_objs;
- table->objs = (pack_info_t*)HDrealloc(table->objs, table->size * sizeof(pack_info_t));
- if (table->objs==NULL) {
- error_msg("not enough memory for options table\n");
- return -1;
- }
- for (i = table->nelems; i < table->size; i++)
- {
- init_packobject(&table->objs[i]);
- }
- return 0;
+static int aux_inctable(pack_opttbl_t *table, int n_objs) {
+ unsigned int i;
+
+ table->size += n_objs;
+ table->objs =
+ (pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t));
+ if (table->objs == NULL) {
+ error_msg("not enough memory for options table\n");
+ return -1;
+ }
+ for (i = table->nelems; i < table->size; i++) {
+ init_packobject(&table->objs[i]);
+ }
+ return 0;
}
@@ -143,31 +132,29 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs )
*
*-------------------------------------------------------------------------
*/
-int options_table_init( pack_opttbl_t **tbl )
-{
- unsigned int i;
- pack_opttbl_t *table;
-
- if(NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t))))
- {
- error_msg("not enough memory for options table\n");
- return -1;
- }
-
- table->size = 30;
- table->nelems = 0;
- if(NULL == (table->objs = (pack_info_t*)HDmalloc(table->size * sizeof(pack_info_t))))
- {
- error_msg("not enough memory for options table\n");
- HDfree(table);
- return -1;
- }
-
- for(i = 0; i < table->size; i++)
- init_packobject(&table->objs[i]);
-
- *tbl = table;
- return 0;
+int options_table_init(pack_opttbl_t **tbl) {
+ unsigned int i;
+ pack_opttbl_t *table;
+
+ if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) {
+ error_msg("not enough memory for options table\n");
+ return -1;
+ }
+
+ table->size = 30;
+ table->nelems = 0;
+ if (NULL == (table->objs =
+ (pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) {
+ error_msg("not enough memory for options table\n");
+ HDfree(table);
+ return -1;
+ }
+
+ for (i = 0; i < table->size; i++)
+ init_packobject(&table->objs[i]);
+
+ *tbl = table;
+ return 0;
}
@@ -181,11 +168,10 @@ int options_table_init( pack_opttbl_t **tbl )
*-------------------------------------------------------------------------
*/
-int options_table_free( pack_opttbl_t *table )
-{
- HDfree(table->objs);
- HDfree(table);
- return 0;
+int options_table_free(pack_opttbl_t *table) {
+ HDfree(table->objs);
+ HDfree(table);
+ return 0;
}
/*-------------------------------------------------------------------------
@@ -198,95 +184,81 @@ int options_table_free( pack_opttbl_t *table )
*-------------------------------------------------------------------------
*/
-
-int options_add_layout( obj_list_t *obj_list,
- int n_objs,
- pack_info_t *pack,
- pack_opttbl_t *table )
-{
- unsigned int i, I;
- int j, added=0, found=0;
-
- /* increase the size of the collection by N_OBJS if necessary */
- if (table->nelems+n_objs >= table->size)
- {
- if (aux_inctable(table,n_objs)<0)
- return -1;
- }
-
- /* search if this object is already in the table; "path" is the key */
- if (table->nelems>0)
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- /* linear table search */
- for (i = 0; i < table->nelems; i++)
- {
- /*already on the table */
- if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
- {
- /* already chunk info inserted for this one; exit */
- if (table->objs[i].chunk.rank>0)
- {
- error_msg("chunk information already inserted for <%s>\n",obj_list[j].obj);
- HDexit(EXIT_FAILURE);
- }
- /* insert the layout info */
- else
- {
- aux_tblinsert_layout(table,i,pack);
- found=1;
- break;
- }
- } /* if */
- } /* i */
-
- if (found==0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_layout(table,I,pack);
- }
- /* cases where we have an already inserted name but there is a new name also
- example:
- -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
- dset1 is already inserted, but dset2 must also be
- */
- else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_layout(table,I,pack);
- }
- } /* j */
- }
-
- /* first time insertion */
- else
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_layout(table,I,pack);
-
- }
- }
-
- table->nelems+= added;
-
- return 0;
+int options_add_layout(obj_list_t *obj_list, int n_objs, pack_info_t *pack,
+ pack_opttbl_t *table) {
+ unsigned int i, I;
+ int j, added = 0, found = 0;
+
+ /* increase the size of the collection by N_OBJS if necessary */
+ if (table->nelems + n_objs >= table->size) {
+ if (aux_inctable(table, n_objs) < 0)
+ return -1;
+ }
+
+ /* search if this object is already in the table; "path" is the key */
+ if (table->nelems > 0) {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ /* linear table search */
+ for (i = 0; i < table->nelems; i++) {
+ /*already on the table */
+ if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+ /* already chunk info inserted for this one; exit */
+ if (table->objs[i].chunk.rank > 0) {
+ error_msg(
+ "chunk information already inserted for <%s>\n",
+ obj_list[j].obj);
+ HDexit(EXIT_FAILURE);
+ }
+ /* insert the layout info */
+ else {
+ aux_tblinsert_layout(table, i, pack);
+ found = 1;
+ break;
+ }
+ } /* if */
+ } /* i */
+
+ if (found == 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_layout(table, I, pack);
+ }
+ /* cases where we have an already inserted name but there is a new name also
+ example:
+ -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
+ dset1 is already inserted, but dset2 must also be
+ */
+ else if (found == 1
+ && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_layout(table, I, pack);
+ }
+ } /* j */
+ }
+
+ /* first time insertion */
+ else {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_layout(table, I, pack);
+
+ }
+ }
+
+ table->nelems += added;
+
+ return 0;
}
-
-
/*-------------------------------------------------------------------------
* Function: options_add_filter
*
@@ -297,81 +269,70 @@ int options_add_layout( obj_list_t *obj_list,
*-------------------------------------------------------------------------
*/
-int options_add_filter(obj_list_t *obj_list,
- int n_objs,
- filter_info_t filt,
- pack_opttbl_t *table )
-{
-
- unsigned int i, I;
- int j, added=0, found=0;
-
- /* increase the size of the collection by N_OBJS if necessary */
- if (table->nelems+n_objs >= table->size)
- {
- if (aux_inctable(table,n_objs)<0)
- return -1;
- }
-
- /* search if this object is already in the table; "path" is the key */
- if (table->nelems>0)
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- /* linear table search */
- for (i = 0; i < table->nelems; i++)
- {
- /*already on the table */
- if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
- {
- /* insert */
- aux_tblinsert_filter(table,i,filt);
- found=1;
- break;
- } /* if */
- } /* i */
-
- if (found==0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_filter(table,I,filt);
- }
- /* cases where we have an already inserted name but there is a new name also
- example:
- -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
- dset1 is already inserted, but dset2 must also be
- */
- else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_filter(table,I,filt);
- }
- } /* j */
- }
-
- /* first time insertion */
- else
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_filter(table,I,filt);
- }
- }
-
- table->nelems+= added;
-
- return 0;
+int options_add_filter(obj_list_t *obj_list, int n_objs, filter_info_t filt,
+ pack_opttbl_t *table) {
+
+ unsigned int i, I;
+ int j, added = 0, found = 0;
+
+ /* increase the size of the collection by N_OBJS if necessary */
+ if (table->nelems + n_objs >= table->size) {
+ if (aux_inctable(table, n_objs) < 0)
+ return -1;
+ }
+
+ /* search if this object is already in the table; "path" is the key */
+ if (table->nelems > 0) {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ /* linear table search */
+ for (i = 0; i < table->nelems; i++) {
+ /*already on the table */
+ if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+ /* insert */
+ aux_tblinsert_filter(table, i, filt);
+ found = 1;
+ break;
+ } /* if */
+ } /* i */
+
+ if (found == 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_filter(table, I, filt);
+ }
+ /* cases where we have an already inserted name but there is a new name also
+ example:
+ -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
+ dset1 is already inserted, but dset2 must also be
+ */
+ else if (found == 1
+ && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_filter(table, I, filt);
+ }
+ } /* j */
+ }
+
+ /* first time insertion */
+ else {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_filter(table, I, filt);
+ }
+ }
+
+ table->nelems += added;
+
+ return 0;
}
/*-------------------------------------------------------------------------
@@ -384,34 +345,25 @@ int options_add_filter(obj_list_t *obj_list,
*-------------------------------------------------------------------------
*/
-pack_info_t* options_get_object( const char *path,
- pack_opttbl_t *table )
-{
- unsigned int i;
- char tbl_path[MAX_NC_NAME+1]; /* +1 for start with "/" case */
-
-
- for ( i = 0; i < table->nelems; i++)
- {
- /* make full path (start with "/") to compare correctly */
- if (HDstrncmp(table->objs[i].path, "/", 1))
- {
- HDstrcpy(tbl_path, "/");
- HDstrcat(tbl_path, table->objs[i].path);
- }
- else
- HDstrcpy(tbl_path, table->objs[i].path);
-
- /* found it */
- if (HDstrcmp(tbl_path, path)==0)
- {
- return (&table->objs[i]);
- }
- }
-
- return NULL;
+pack_info_t* options_get_object(const char *path, pack_opttbl_t *table) {
+ unsigned int i;
+ char tbl_path[MAX_NC_NAME + 1]; /* +1 for start with "/" case */
+
+ for (i = 0; i < table->nelems; i++) {
+ /* make full path (start with "/") to compare correctly */
+ if (HDstrncmp(table->objs[i].path, "/", 1)) {
+ HDstrcpy(tbl_path, "/");
+ HDstrcat(tbl_path, table->objs[i].path);
+ }
+ else
+ HDstrcpy(tbl_path, table->objs[i].path);
+
+ /* found it */
+ if (HDstrcmp(tbl_path, path) == 0) {
+ return (&table->objs[i]);
+ }
+ }
+
+ return NULL;
}
-
-
-
diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
index 9f798e9..8a297a7 100644
--- a/tools/h5repack/h5repack_parse.c
+++ b/tools/h5repack/h5repack_parse.c
@@ -31,6 +31,7 @@
* FLET, to apply the HDF5 checksum filter
* NBIT, to apply the HDF5 NBIT filter (NBIT compression)
* SOFF, to apply the HDF5 scale+offset filter (compression)
+ * UD, to apply a User Defined filter k, m, n1[,…,nm]
* NONE, to remove the filter
*
* Examples:
@@ -51,402 +52,468 @@ obj_list_t* parse_filter(const char *str,
pack_opt_t *options,
int *is_glb)
{
- unsigned i, u;
- char c;
- size_t len=HDstrlen(str);
- int j, m, n, k, l, end_obj=-1, no_param=0;
- char sobj[MAX_NC_NAME];
- char scomp[10];
- char stype[5];
- char smask[3];
- obj_list_t* obj_list=NULL;
- unsigned pixels_per_block;
-
-
- /* initialize compression info */
- HDmemset(filt,0,sizeof(filter_info_t));
- *is_glb = 0;
-
- /* check for the end of object list and number of objects */
- for ( i = 0, n = 0; i < len; i++)
- {
- c = str[i];
- if ( c==':' )
- {
- end_obj=i;
- }
- if ( c==',' )
- {
- n++;
- }
- }
-
- if (end_obj==-1) /* missing : */
- {
- /* apply to all objects */
- options->all_filter=1;
- *is_glb = 1;
- }
-
- n++;
- obj_list = (obj_list_t*) HDmalloc(n*sizeof(obj_list_t));
- if (obj_list==NULL)
- {
- error_msg("could not allocate object list\n");
- return NULL;
- }
- *n_objs=n;
-
- /* get object list */
- for ( j = 0, k = 0, n = 0; j < end_obj; j++, k++)
- {
- c = str[j];
- sobj[k] = c;
- if ( c==',' || j==end_obj-1)
- {
- if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
- HDstrcpy(obj_list[n].obj,sobj);
- HDmemset(sobj,0,sizeof(sobj));
- n++;
- k=-1;
- }
- }
- /* nothing after : */
- if (end_obj+1==(int)len)
- {
- if (obj_list) HDfree(obj_list);
- error_msg("input Error: Invalid compression type in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
-
-
- /* get filter additional parameters */
- m=0;
- for ( i=end_obj+1, k=0, j=0; i<len; i++,k++)
- {
- c = str[i];
- scomp[k]=c;
- if ( c=='=' || i==len-1)
- {
- if ( c=='=') /*one more parameter */
- {
- scomp[k]='\0'; /*cut space */
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SZIP
- * szip has the format SZIP=<pixels per block,coding>
- * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN'
- * example SZIP=8,NN
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(scomp,"SZIP")==0)
- {
- l=-1; /* mask index check */
- for ( m=0,u=i+1; u<len; u++,m++)
- {
- if (str[u]==',')
- {
- stype[m]='\0'; /* end digit of szip */
- l=0; /* start EC or NN search */
- u++; /* skip ',' */
- }
- c = str[u];
- if (!isdigit(c) && l==-1){
- if (obj_list) HDfree(obj_list);
- error_msg("compression parameter not digit in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- if (l==-1)
- stype[m]=c;
- else
- {
- smask[l]=c;
- l++;
- if (l==2)
- {
- smask[l]='\0';
- i=len-1; /* end */
- (*n_objs)--; /* we counted an extra ',' */
- if (HDstrcmp(smask,"NN")==0)
- filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK;
- else if (HDstrcmp(smask,"EC")==0)
- filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK;
- else
- {
- error_msg("szip mask must be 'NN' or 'EC' \n");
- HDexit(EXIT_FAILURE);
- }
-
-
- }
- }
-
- } /* u */
- } /*if */
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SCALEOFFSET
- * scaleoffset has the format SOFF=<scale_factor,scale_type>
- * scale_type can be
- * integer datatype, H5Z_SO_INT (IN)
- * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS)
- * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented
- * for integer datatypes, scale_factor denotes Minimum Bits
- * for float datatypes, scale_factor denotes decimal scale factor
- * examples
- * SOFF=31,IN
- * SOFF=3,DF
- *-------------------------------------------------------------------------
- */
-
- else if (HDstrcmp(scomp,"SOFF")==0)
- {
- l=-1; /* mask index check */
- for ( m=0,u=i+1; u<len; u++,m++)
- {
- if (str[u]==',')
- {
- stype[m]='\0'; /* end digit */
- l=0; /* start 'IN' , 'DS', or 'ES' search */
- u++; /* skip ',' */
- }
- c = str[u];
- if (!isdigit(c) && l==-1){
- if (obj_list) HDfree(obj_list);
- error_msg("compression parameter is not a digit in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- if (l==-1)
- stype[m]=c;
- else
- {
- smask[l]=c;
- l++;
- if (l==2)
- {
- smask[l]='\0';
- i=len-1; /* end */
- (*n_objs)--; /* we counted an extra ',' */
- if (HDstrcmp(smask,"IN")==0)
- filt->cd_values[j++]=H5Z_SO_INT;
- else if (HDstrcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE)
- filt->cd_values[j++]=H5Z_SO_FLOAT_DSCALE;
- else
- {
- error_msg("scale type must be 'IN' or 'DS' \n");
- HDexit(EXIT_FAILURE);
- }
-
- }
- }
-
- } /* u */
- } /*if */
-
-
- /*-------------------------------------------------------------------------
- * all other filters
- *-------------------------------------------------------------------------
- */
-
- else
- {
- /* here we could have 1 or 2 digits */
- for ( m=0,u=i+1; u<len; u++,m++)
- {
- c = str[u];
- if (!isdigit(c)){
- if (obj_list) HDfree(obj_list);
- error_msg("compression parameter is not a digit in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- stype[m]=c;
- } /* u */
-
- stype[m]='\0';
- } /*if */
-
-
-
- filt->cd_values[j++]=atoi(stype);
- i+=m; /* jump */
- }
- else if (i==len-1)
- { /*no more parameters */
- scomp[k+1]='\0';
- no_param=1;
- }
-
- /*-------------------------------------------------------------------------
- * translate from string to filter symbol
- *-------------------------------------------------------------------------
- */
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_NONE
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(scomp,"NONE")==0)
- {
- filt->filtn=H5Z_FILTER_NONE;
- filt->cd_nelmts = 0;
- }
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_DEFLATE
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp,"GZIP")==0)
- {
- filt->filtn=H5Z_FILTER_DEFLATE;
- filt->cd_nelmts = 1;
- if (no_param)
- { /*no more parameters, GZIP must have parameter */
- if (obj_list) HDfree(obj_list);
- error_msg("missing compression parameter in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- }
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SZIP
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp,"SZIP")==0)
- {
- filt->filtn=H5Z_FILTER_SZIP;
- filt->cd_nelmts = 2;
- if (no_param)
- { /*no more parameters, SZIP must have parameter */
- if (obj_list) HDfree(obj_list);
- error_msg("missing compression parameter in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- }
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SHUFFLE
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp,"SHUF")==0)
- {
- filt->filtn=H5Z_FILTER_SHUFFLE;
- filt->cd_nelmts = 0;
- if (m>0)
- { /*shuffle does not have parameter */
- if (obj_list) HDfree(obj_list);
- error_msg("extra parameter in SHUF <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_FLETCHER32
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp,"FLET")==0)
- {
- filt->filtn=H5Z_FILTER_FLETCHER32;
- filt->cd_nelmts = 0;
- if (m>0)
- { /*shuffle does not have parameter */
- if (obj_list) HDfree(obj_list);
- error_msg("extra parameter in FLET <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_NBIT
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp,"NBIT")==0)
- {
- filt->filtn=H5Z_FILTER_NBIT;
- filt->cd_nelmts = 0;
- if (m>0)
- { /*nbit does not have parameter */
- if (obj_list) HDfree(obj_list);
- error_msg("extra parameter in NBIT <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SCALEOFFSET
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp,"SOFF")==0)
- {
- filt->filtn=H5Z_FILTER_SCALEOFFSET;
- filt->cd_nelmts = 2;
- if (no_param)
- { /*no more parameters, SOFF must have parameter */
- if (obj_list) HDfree(obj_list);
- error_msg("missing compression parameter in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- }
- else {
- if (obj_list) HDfree(obj_list);
- error_msg("invalid filter type in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- }
- } /*i*/
-
- /*-------------------------------------------------------------------------
- * check valid parameters
- *-------------------------------------------------------------------------
- */
-
- switch (filt->filtn)
- {
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_DEFLATE
- *-------------------------------------------------------------------------
- */
-
- case H5Z_FILTER_DEFLATE:
- if (filt->cd_values[0]>9 )
- {
- if (obj_list) HDfree(obj_list);
- error_msg("invalid compression parameter in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- break;
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SZIP
- *-------------------------------------------------------------------------
- */
-
- case H5Z_FILTER_SZIP:
- pixels_per_block=filt->cd_values[0];
- if ((pixels_per_block%2)==1)
- {
- if (obj_list) HDfree(obj_list);
- error_msg("pixels_per_block is not even in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- if (pixels_per_block>H5_SZIP_MAX_PIXELS_PER_BLOCK)
- {
- if (obj_list) HDfree(obj_list);
- error_msg("pixels_per_block is too large in <%s>\n",str);
- HDexit(EXIT_FAILURE);
- }
- if ( (HDstrcmp(smask,"NN")!=0) && (HDstrcmp(smask,"EC")!=0) )
- {
- if (obj_list) HDfree(obj_list);
- error_msg("szip mask must be 'NN' or 'EC' \n");
- HDexit(EXIT_FAILURE);
- }
- break;
- default:
- break;
-
-
- };
-
- return obj_list;
+ unsigned i, u;
+ char c;
+ size_t len=HDstrlen(str);
+ int j, m, n, k, l, p, r, q, end_obj=-1, no_param=0;
+ char sobj[MAX_NC_NAME];
+ char scomp[10];
+ char stype[5];
+ char smask[3];
+ obj_list_t* obj_list=NULL;
+ unsigned pixels_per_block;
+
+
+ /* initialize compression info */
+ HDmemset(filt,0,sizeof(filter_info_t));
+ *is_glb = 0;
+
+ /* check for the end of object list and number of objects */
+ for ( i = 0, n = 0; i < len; i++)
+ {
+ c = str[i];
+ if ( c==':' )
+ {
+ end_obj=i;
+ }
+ if ( c==',' )
+ {
+ n++;
+ }
+ }
+
+ if (end_obj==-1) /* missing : */
+ {
+ /* apply to all objects */
+ options->all_filter=1;
+ *is_glb = 1;
+ }
+
+ n++;
+ obj_list = (obj_list_t*) HDmalloc(n*sizeof(obj_list_t));
+ if (obj_list==NULL)
+ {
+ error_msg("could not allocate object list\n");
+ return NULL;
+ }
+ *n_objs=n;
+
+ /* get object list */
+ for ( j = 0, k = 0, n = 0; j < end_obj; j++, k++)
+ {
+ c = str[j];
+ sobj[k] = c;
+ if ( c==',' || j==end_obj-1)
+ {
+ if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
+ HDstrcpy(obj_list[n].obj,sobj);
+ HDmemset(sobj,0,sizeof(sobj));
+ n++;
+ k=-1;
+ }
+ }
+ /* nothing after : */
+ if (end_obj+1==(int)len)
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("input Error: Invalid compression type in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+
+
+ /* get filter additional parameters */
+ m=0;
+ for ( i=end_obj+1, k=0, j=0; i<len; i++,k++)
+ {
+ c = str[i];
+ scomp[k]=c;
+ if ( c=='=' || i==len-1)
+ {
+ if ( c=='=') /*one more parameter */
+ {
+ scomp[k]='\0'; /*cut space */
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SZIP
+ * szip has the format SZIP=<pixels per block,coding>
+ * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN'
+ * example SZIP=8,NN
+ *-------------------------------------------------------------------------
+ */
+ if (HDstrcmp(scomp,"SZIP")==0)
+ {
+ l=-1; /* mask index check */
+ for ( m=0,u=i+1; u<len; u++,m++)
+ {
+ if (str[u]==',')
+ {
+ stype[m]='\0'; /* end digit of szip */
+ l=0; /* start EC or NN search */
+ u++; /* skip ',' */
+ }
+ c = str[u];
+ if (!isdigit(c) && l==-1)
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("compression parameter not digit in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ if (l==-1)
+ stype[m]=c;
+ else
+ {
+ smask[l]=c;
+ l++;
+ if (l==2)
+ {
+ smask[l]='\0';
+ i=len-1; /* end */
+ (*n_objs)--; /* we counted an extra ',' */
+ if (HDstrcmp(smask,"NN")==0)
+ filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK;
+ else if (HDstrcmp(smask,"EC")==0)
+ filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK;
+ else
+ {
+ error_msg("szip mask must be 'NN' or 'EC' \n");
+ HDexit(EXIT_FAILURE);
+ }
+
+
+ }
+ }
+
+ } /* u */
+ } /*if */
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SCALEOFFSET
+ * scaleoffset has the format SOFF=<scale_factor,scale_type>
+ * scale_type can be
+ * integer datatype, H5Z_SO_INT (IN)
+ * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS)
+ * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented
+ * for integer datatypes, scale_factor denotes Minimum Bits
+ * for float datatypes, scale_factor denotes decimal scale factor
+ * examples
+ * SOFF=31,IN
+ * SOFF=3,DF
+ *-------------------------------------------------------------------------
+ */
+
+ else if (HDstrcmp(scomp,"SOFF")==0)
+ {
+ l=-1; /* mask index check */
+ for ( m=0,u=i+1; u<len; u++,m++)
+ {
+ if (str[u]==',')
+ {
+ stype[m]='\0'; /* end digit */
+ l=0; /* start 'IN' , 'DS', or 'ES' search */
+ u++; /* skip ',' */
+ }
+ c = str[u];
+ if (!isdigit(c) && l==-1)
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("compression parameter is not a digit in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ if (l==-1)
+ stype[m]=c;
+ else
+ {
+ smask[l]=c;
+ l++;
+ if (l==2)
+ {
+ smask[l]='\0';
+ i=len-1; /* end */
+ (*n_objs)--; /* we counted an extra ',' */
+ if (HDstrcmp(smask,"IN")==0)
+ filt->cd_values[j++]=H5Z_SO_INT;
+ else if (HDstrcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE)
+ filt->cd_values[j++]=H5Z_SO_FLOAT_DSCALE;
+ else
+ {
+ error_msg("scale type must be 'IN' or 'DS' \n");
+ HDexit(EXIT_FAILURE);
+ }
+
+ }
+ }
+
+ } /* u */
+ } /*if */
+ /*-------------------------------------------------------------------------
+ * User Defined
+ * has the format UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
+ * BZIP2 example
+ * UD=307,1,9
+ *-------------------------------------------------------------------------
+ */
+
+ else if (HDstrcmp(scomp,"UD")==0)
+ {
+ l=-1; /* filter number index check */
+ p=-1; /* CD_VAL count check */
+ r=-1; /* CD_VAL check */
+ for ( m=0,q=0,u=i+1; u<len; u++,m++,q++)
+ {
+ if (str[u]==',')
+ {
+ stype[q]='\0'; /* end digit */
+ if (l==-1)
+ {
+ filt->filtn=atoi(stype);
+ l=0;
+ }
+ else if (p==-1)
+ {
+ filt->cd_nelmts=atoi(stype);
+ p=0;
+ }
+ else
+ r=0;
+ q=0;
+ u++; /* skip ',' */
+ }
+ c = str[u];
+ if (!isdigit(c) && l==-1)
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("filter number parameter is not a digit in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ stype[q]=c;
+ if (l==0 && p==0)
+ {
+ if (r==0)
+ filt->cd_values[j++]=atoi(stype);
+ }
+
+ } /* u */
+
+ stype[q]='\0';
+ } /*if */
+
+
+ /*-------------------------------------------------------------------------
+ * all other filters
+ *-------------------------------------------------------------------------
+ */
+
+ else
+ {
+ /* here we could have 1 or 2 digits */
+ for ( m=0,u=i+1; u<len; u++,m++)
+ {
+ c = str[u];
+ if (!isdigit(c)){
+ if (obj_list) HDfree(obj_list);
+ error_msg("compression parameter is not a digit in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ stype[m]=c;
+ } /* u */
+
+ stype[m]='\0';
+ } /*if */
+
+
+
+ filt->cd_values[j++]=atoi(stype);
+ i+=m; /* jump */
+ }
+ else if (i==len-1)
+ { /*no more parameters */
+ scomp[k+1]='\0';
+ no_param=1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * translate from string to filter symbol
+ *-------------------------------------------------------------------------
+ */
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_NONE
+ *-------------------------------------------------------------------------
+ */
+ if (HDstrcmp(scomp,"NONE")==0)
+ {
+ filt->filtn=H5Z_FILTER_NONE;
+ filt->cd_nelmts = 0;
+ }
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_DEFLATE
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(scomp,"GZIP")==0)
+ {
+ filt->filtn=H5Z_FILTER_DEFLATE;
+ filt->cd_nelmts = 1;
+ if (no_param)
+ { /*no more parameters, GZIP must have parameter */
+ if (obj_list) HDfree(obj_list);
+ error_msg("missing compression parameter in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SZIP
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(scomp,"SZIP")==0)
+ {
+ filt->filtn=H5Z_FILTER_SZIP;
+ filt->cd_nelmts = 2;
+ if (no_param)
+ { /*no more parameters, SZIP must have parameter */
+ if (obj_list) HDfree(obj_list);
+ error_msg("missing compression parameter in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SHUFFLE
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(scomp,"SHUF")==0)
+ {
+ filt->filtn=H5Z_FILTER_SHUFFLE;
+ filt->cd_nelmts = 0;
+ if (m>0)
+ { /*shuffle does not have parameter */
+ if (obj_list) HDfree(obj_list);
+ error_msg("extra parameter in SHUF <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_FLETCHER32
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(scomp,"FLET")==0)
+ {
+ filt->filtn=H5Z_FILTER_FLETCHER32;
+ filt->cd_nelmts = 0;
+ if (m>0)
+ { /*shuffle does not have parameter */
+ if (obj_list) HDfree(obj_list);
+ error_msg("extra parameter in FLET <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_NBIT
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(scomp,"NBIT")==0)
+ {
+ filt->filtn=H5Z_FILTER_NBIT;
+ filt->cd_nelmts = 0;
+ if (m>0)
+ { /*nbit does not have parameter */
+ if (obj_list) HDfree(obj_list);
+ error_msg("extra parameter in NBIT <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SCALEOFFSET
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(scomp,"SOFF")==0)
+ {
+ filt->filtn=H5Z_FILTER_SCALEOFFSET;
+ filt->cd_nelmts = 2;
+ if (no_param)
+ { /*no more parameters, SOFF must have parameter */
+ if (obj_list) HDfree(obj_list);
+ error_msg("missing compression parameter in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * User Defined Filter
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(scomp,"UD")==0)
+ {
+ if (filt->cd_nelmts != j)
+ { /* parameters does not match count */
+ if (obj_list) HDfree(obj_list);
+ error_msg("incorrect number of compression parameters in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+ else {
+ if (obj_list) HDfree(obj_list);
+ error_msg("invalid filter type in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+ } /*i*/
+
+ /*-------------------------------------------------------------------------
+ * check valid parameters
+ *-------------------------------------------------------------------------
+ */
+
+ switch (filt->filtn)
+ {
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_DEFLATE
+ *-------------------------------------------------------------------------
+ */
+
+ case H5Z_FILTER_DEFLATE:
+ if (filt->cd_values[0]>9 )
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("invalid compression parameter in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SZIP
+ *-------------------------------------------------------------------------
+ */
+
+ case H5Z_FILTER_SZIP:
+ pixels_per_block=filt->cd_values[0];
+ if ((pixels_per_block%2)==1)
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("pixels_per_block is not even in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ if (pixels_per_block>H5_SZIP_MAX_PIXELS_PER_BLOCK)
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("pixels_per_block is too large in <%s>\n",str);
+ HDexit(EXIT_FAILURE);
+ }
+ if ( (HDstrcmp(smask,"NN")!=0) && (HDstrcmp(smask,"EC")!=0) )
+ {
+ if (obj_list) HDfree(obj_list);
+ error_msg("szip mask must be 'NN' or 'EC' \n");
+ HDexit(EXIT_FAILURE);
+ }
+ break;
+ default:
+ break;
+
+
+ };
+
+ return obj_list;
}
diff --git a/tools/h5repack/h5repack_plugin.sh.in b/tools/h5repack/h5repack_plugin.sh.in
new file mode 100644
index 0000000..e8ba83e
--- /dev/null
+++ b/tools/h5repack/h5repack_plugin.sh.in
@@ -0,0 +1,238 @@
+#! /bin/sh
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5. The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the 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 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.
+#
+srcdir=@srcdir@
+TOP_BUILDDIR=@top_builddir@
+
+# Determine backward compatibility options enabled
+DEPRECATED_SYMBOLS="@DEPRECATED_SYMBOLS@"
+
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+H5REPACK=h5repack # The tool name
+H5REPACK_BIN=`pwd`/$H5REPACK # The path of the tool binary
+
+H5DUMP=../h5dump/h5dump # The h5dump tool name
+H5DUMP_BIN=`pwd`/$H5DUMP # The path of the h5dump tool binary
+
+nerrors=0
+verbose=yes
+exit_code=$EXIT_SUCCESS
+
+TEST_NAME=ud_plugin
+FROM_DIR=`pwd`/.libs
+PLUGIN_LIB="$FROM_DIR/libdynlibadd.*"
+PLUGIN_LIBDIR=testdir3
+RM="rm -rf"
+
+GREP='grep'
+CP='cp'
+DIRNAME='dirname'
+LS='ls'
+AWK='awk'
+
+# source dirs
+SRC_TOOLS="$srcdir/.."
+
+# testfiles source dirs for tools
+SRC_H5REPACK_TESTFILES="$SRC_TOOLS/h5repack/testfiles"
+
+TESTDIR=testfiles
+test -d $TESTDIR || mkdir $TESTDIR
+
+######################################################################
+# test files
+# --------------------------------------------------------------------
+# All the test files copy from source directory to test directory
+# NOTE: Keep this framework to add/remove test files.
+# Any test files from other tools can be used in this framework.
+# This list are also used for checking exist.
+# Comment '#' without space can be used.
+# --------------------------------------------------------------------
+LIST_HDF5_TEST_FILES="
+$SRC_H5REPACK_TESTFILES/h5repack_layout.h5
+$SRC_H5REPACK_TESTFILES/h5repack_layout.h5-plugin_test.ddl
+$SRC_H5REPACK_TESTFILES/plugin_test.h5repack_layout.h5.tst
+"
+
+#
+# copy test files and expected output files from source dirs to test dir
+#
+COPY_TESTFILES="$LIST_HDF5_TEST_FILES"
+
+# Main Body
+# Create test directories if not exists yet.
+test -d $PLUGIN_LIBDIR || mkdir -p $PLUGIN_LIBDIR
+if [ $? != 0 ]; then
+ echo "Failed to create test directory($PLUGIN_LIBDIR)"
+ exit $EXIT_FAILURE
+fi
+
+# copy plugin library for test
+$CP $PLUGIN_LIB $PLUGIN_LIBDIR
+if [ $? != 0 ]; then
+ echo "Failed to copy plugin library ($PLUGIN_LIB) for test."
+ exit $EXIT_FAILURE
+fi
+
+# setup plugin path
+ENVCMD="env HDF5_PLUGIN_PATH=${PLUGIN_LIBDIR}"
+
+COPY_TESTFILES_TO_TESTDIR()
+{
+ # copy test files. Used -f to make sure get a new copy
+ for tstfile in $COPY_TESTFILES
+ 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 $TESTDIR
+ if [ $? -ne 0 ]; then
+ echo "Error: FAILED to copy $tstfile ."
+
+ # Comment out this to CREATE expected file
+ exit $EXIT_FAILURE
+ fi
+ fi
+ fi
+ done
+}
+
+# Print a $* message left justified in a field of 70 characters
+#
+MESSAGE() {
+ SPACES=" "
+ echo "$* $SPACES" | cut -c1-70 | tr -d '\012'
+}
+
+# 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'
+}
+
+# Print a line-line message left justified in a field of 70 characters
+# beginning with the word "Verifying".
+#
+VERIFY() {
+ MESSAGE "Verifying $*"
+}
+
+# This is different from $srcdir/../../bin/output_filter.sh
+STDOUT_FILTER() {
+ result_file=$1
+ tmp_file=/tmp/h5test_tmp_$$
+ # Filter name of files.
+ cp $result_file $tmp_file
+ sed -e '/^Opening file/d' -e '/^Making file/d' \
+ < $tmp_file > $result_file
+ # cleanup
+ rm -f $tmp_file
+}
+
+# This runs h5repack comparing output with h5dump output
+# from -pH option
+#
+TOOLTEST_DUMP()
+{
+ echo $@
+ infile=$TESTDIR/$2
+ outfile=$TESTDIR/out-$1.$2
+ expect1="$TESTDIR/$1.$2.tst"
+ actual1="$TESTDIR/$1.$2.out"
+ actual1_err="$TESTDIR/$1.$2.err"
+ expect2="$TESTDIR/$2-$1.ddl"
+ actual2="$TESTDIR/$2-$1.out"
+ actual2_err="$TESTDIR/$2-$1.err"
+
+ shift
+ shift
+
+ # Run test.
+ TESTING $H5REPACK $@
+ (
+ $ENVCMD $H5REPACK_BIN "$@" $infile $outfile
+ ) >$actual1 2>$actual1_err
+ RET=$?
+ STDOUT_FILTER $actual1
+ cat $actual1_err >> $actual1
+ if [ $RET != 0 ] ; then
+ echo "*FAILED*"
+ nerrors="`expr $nerrors + 1`"
+ else
+ echo " PASSED"
+ if cmp -s $expect1 $actual1; then
+ echo " PASSED"
+ else
+ echo "*FAILED*"
+ echo " Expected result (*.tst) differs from actual result (*.out)"
+ nerrors="`expr $nerrors + 1`"
+ test yes = "$verbose" && diff -c $expect1 $actual1 |sed 's/^/ /'
+ fi
+ VERIFY h5dump output -pH $outfile
+ (
+ $ENVCMD $H5DUMP_BIN -pH $outfile
+ ) >$actual2 2>$actual2_err
+ RET=$?
+ cat $actual2_err >> $actual2
+
+ if cmp -s $expect2 $actual2; then
+ echo " PASSED"
+ else
+ echo "*FAILED*"
+ echo " Expected result (*.ddl) differs from actual result (*.out)"
+ nerrors="`expr $nerrors + 1`"
+ test yes = "$verbose" && diff -c $expect2 $actual2 |sed 's/^/ /'
+ fi
+
+ fi
+
+
+ rm -f $actual1 $actual1_err $actual2 $actual2_err
+ rm -f $outfile
+}
+
+##############################################################################
+### T H E T E S T S
+##############################################################################
+# prepare for test
+COPY_TESTFILES_TO_TESTDIR
+
+# Run the test
+arg="h5repack_layout.h5 -v -f UD=257,1,9"
+#TOOLTEST_DUMP plugin_test $arg
+
+# print results
+if test $nerrors -ne 0 ; then
+ echo "$nerrors errors encountered"
+ exit_code=$EXIT_FAILURE
+else
+ echo "All Plugin API tests passed."
+ exit_code=$EXIT_SUCCESS
+fi
+
+# Clean up temporary files/directories and leave
+$RM $PLUGIN_LIBDIR
+exit $exit_code
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index a57295b..42799f9 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -601,6 +601,9 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
switch (filtn)
{
+ case H5Z_FILTER_NONE:
+ break;
+
case H5Z_FILTER_SHUFFLE:
/* 1 private client value is returned by DCPL */
@@ -677,7 +680,17 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
break;
default:
- /* filter has no local values */
+ if ( cd_nelmts != filter[i].cd_nelmts)
+ return 0;
+
+ for( j = 0; j < cd_nelmts; j++)
+ {
+ if (cd_values[j] != filter[i].cd_values[j])
+ {
+ return 0;
+ }
+
+ }
break;
} /* switch */
diff --git a/tools/h5repack/testfiles/deflate_limit.h5repack_layout.h5.ddl b/tools/h5repack/testfiles/deflate_limit.h5repack_layout.h5.ddl
new file mode 100644
index 0000000..d380201
--- /dev/null
+++ b/tools/h5repack/testfiles/deflate_limit.h5repack_layout.h5.ddl
@@ -0,0 +1,130 @@
+HDF5 "./testfiles/out-deflate_limit.h5repack_layout.h5" {
+GROUP "/" {
+ DATASET "dset1" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 1150 (2.783:1 COMPRESSION)
+ }
+ FILTERS {
+ COMPRESSION DEFLATE { LEVEL 1 }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset2" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 1150 (2.783:1 COMPRESSION)
+ }
+ FILTERS {
+ COMPRESSION DEFLATE { LEVEL 1 }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset3" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 1150 (2.783:1 COMPRESSION)
+ }
+ FILTERS {
+ COMPRESSION DEFLATE { LEVEL 1 }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset4" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 1150 (2.783:1 COMPRESSION)
+ }
+ FILTERS {
+ COMPRESSION DEFLATE { LEVEL 1 }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset_chunk" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, H5S_UNLIMITED ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 20, 10 )
+ SIZE 1283 (2.494:1 COMPRESSION)
+ }
+ FILTERS {
+ COMPRESSION DEFLATE { LEVEL 1 }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset_compact" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 1150 (2.783:1 COMPRESSION)
+ }
+ FILTERS {
+ COMPRESSION DEFLATE { LEVEL 1 }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset_contiguous" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 1150 (2.783:1 COMPRESSION)
+ }
+ FILTERS {
+ COMPRESSION DEFLATE { LEVEL 1 }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+}
+}
diff --git a/tools/h5repack/testfiles/h5repack-help.txt b/tools/h5repack/testfiles/h5repack-help.txt
new file mode 100644
index 0000000..6de1eb4
--- /dev/null
+++ b/tools/h5repack/testfiles/h5repack-help.txt
@@ -0,0 +1,122 @@
+usage: h5repack [OPTIONS] file1 file2
+ file1 Input HDF5 File
+ file2 Output HDF5 File
+ OPTIONS
+ -h, --help Print a usage message and exit
+ -v, --verbose Verbose mode, print object information
+ -V, --version Print version number and exit
+ -n, --native Use a native HDF5 type when repacking
+ -L, --latest Use latest version of file format
+ -c L1, --compact=L1 Maximum number of links in header messages
+ -d L2, --indexed=L2 Minimum number of links in the indexed format
+ -s S[:F], --ssize=S[:F] Shared object header message minimum size
+ -m M, --minimum=M Do not apply the filter to datasets smaller than M
+ -e E, --file=E Name of file E with the -f and -l options
+ -u U, --ublock=U Name of file U with user block data to be added
+ -b B, --block=B Size of user block to be added
+ -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size
+ -t T, --threshold=T Threshold value for H5Pset_alignment
+ -a A, --alignment=A Alignment value for H5Pset_alignment
+ -f FILT, --filter=FILT Filter type
+ -l LAYT, --layout=LAYT Layout type
+ -S FS_STRGY, --fs_strategy=FS_STRGY File space management strategy
+ -T FS_THRD, --fs_threshold=FS_THRD Free-space section threshold
+
+ M - is an integer greater than 1, size of dataset in bytes (default is 0)
+ E - is a filename.
+ S - is an integer
+ U - is a filename.
+ T - is an integer
+ A - is an integer greater than zero
+ B - is the user block size, any value that is 512 or greater and is
+ a power of 2 (1024 default)
+ F - is the shared object header message type, any of <dspace|dtype|fill|
+ pline|attr>. If F is not specified, S applies to all messages
+
+ FS_STRGY is the file space management strategy to use for the output file.
+ It is a string as listed below:
+ ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver
+ for file space allocation
+ ALL - Use non-persistent free-space managers, aggregators and virtual file driver
+ for file space allocation
+ AGGR_VFD - Use aggregators and virtual file driver for file space allocation
+ VFD - Use virtual file driver for file space allocation
+
+ FS_THRD is the free-space section threshold to use for the output file.
+ It is the minimum size (in bytes) of free-space sections to be tracked
+ by the the library's free-space managers.
+
+ FILT - is a string with the format:
+
+ <list of objects>:<name of filter>=<filter parameters>
+
+ <list of objects> is a comma separated list of object names, meaning apply
+ compression only to those objects. If no names are specified, the filter
+ is applied to all objects
+ <name of filter> can be:
+ GZIP, to apply the HDF5 GZIP filter (GZIP compression)
+ SZIP, to apply the HDF5 SZIP filter (SZIP compression)
+ SHUF, to apply the HDF5 shuffle filter
+ FLET, to apply the HDF5 checksum filter
+ NBIT, to apply the HDF5 NBIT filter (NBIT compression)
+ SOFF, to apply the HDF5 Scale/Offset filter
+ UD, to apply a user defined filter
+ NONE, to remove all filters
+ <filter parameters> is optional filter parameter information
+ GZIP=<deflation level> from 1-9
+ SZIP=<pixels per block,coding> pixels per block is a even number in
+ 2-32 and coding method is either EC or NN
+ SHUF (no parameter)
+ FLET (no parameter)
+ NBIT (no parameter)
+ SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type
+ is either IN or DS
+ UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
+ required values for filter_number,cd_value_count,value_1
+ optional values for value_2 to value_N
+ NONE (no parameter)
+
+ LAYT - is a string with the format:
+
+ <list of objects>:<layout type>=<layout parameters>
+
+ <list of objects> is a comma separated list of object names, meaning that
+ layout information is supplied for those objects. If no names are
+ specified, the layout type is applied to all objects
+ <layout type> can be:
+ CHUNK, to apply chunking layout
+ COMPA, to apply compact layout
+ CONTI, to apply contiguous layout
+ <layout parameters> is optional layout information
+ CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension
+ COMPA (no parameter)
+ CONTI (no parameter)
+
+Examples of use:
+
+1) h5repack -v -f GZIP=1 file1 file2
+
+ GZIP compression with level 1 to all objects
+
+2) h5repack -v -f A:SZIP=8,NN file1 file2
+
+ SZIP compression with 8 pixels per block and NN coding method to object A
+
+3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2
+
+ Chunked layout, with a layout size of 20x10, to objects A and B
+ and remove filters to objects C, D, F
+
+4) h5repack -L -c 10 -s 20:dtype file1 file2
+
+ Using latest file format with maximum compact group size of 10 and
+ and minimum shared datatype size of 20
+
+5) h5repack -f SHUF -f GZIP=1 file1 file2
+
+ Add both filters SHUF and GZIP in this order to all datasets
+
+6) h5repack -f UD=307,1,9 file1 file2
+
+ Add bzip2 filter to all datasets
+
diff --git a/tools/h5repack/testfiles/h5repack_filters.h5.tst b/tools/h5repack/testfiles/h5repack_filters.h5.tst
new file mode 100644
index 0000000..36e65b9
--- /dev/null
+++ b/tools/h5repack/testfiles/h5repack_filters.h5.tst
@@ -0,0 +1,13 @@
+Objects to modify layout are...
+Objects to apply filter are...
+ </dset_deflate> with GZIP filter
+ </dset_deflate>...Found
+-----------------------------------------
+ Type Filter (Compression) Name
+-----------------------------------------
+ group /
+ dset /dset_all
+ dset GZIP (0.995:1) /dset_deflate
+ dset /dset_fletcher32
+ dset /dset_nbit
+ dset /dset_shuffle
diff --git a/tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl
new file mode 100644
index 0000000..a7ba967
--- /dev/null
+++ b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl
@@ -0,0 +1,158 @@
+HDF5 "testfiles/out-plugin_test.h5repack_layout.h5" {
+GROUP "/" {
+ DATASET "dset1" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 3200 (1.000:1 COMPRESSION)
+ }
+ FILTERS {
+ USER_DEFINED_FILTER {
+ FILTER_ID 257
+ COMMENT dynlib1
+ PARAMS { 9 }
+ }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset2" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 3200 (1.000:1 COMPRESSION)
+ }
+ FILTERS {
+ USER_DEFINED_FILTER {
+ FILTER_ID 257
+ COMMENT dynlib1
+ PARAMS { 9 }
+ }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset3" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 3200 (1.000:1 COMPRESSION)
+ }
+ FILTERS {
+ USER_DEFINED_FILTER {
+ FILTER_ID 257
+ COMMENT dynlib1
+ PARAMS { 9 }
+ }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset4" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 3200 (1.000:1 COMPRESSION)
+ }
+ FILTERS {
+ USER_DEFINED_FILTER {
+ FILTER_ID 257
+ COMMENT dynlib1
+ PARAMS { 9 }
+ }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset_chunk" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, H5S_UNLIMITED ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 20, 10 )
+ SIZE 3200 (1.000:1 COMPRESSION)
+ }
+ FILTERS {
+ USER_DEFINED_FILTER {
+ FILTER_ID 257
+ COMMENT dynlib1
+ PARAMS { 9 }
+ }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset_compact" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 3200 (1.000:1 COMPRESSION)
+ }
+ FILTERS {
+ USER_DEFINED_FILTER {
+ FILTER_ID 257
+ COMMENT dynlib1
+ PARAMS { 9 }
+ }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+ DATASET "dset_contiguous" {
+ DATATYPE H5T_STD_I32LE
+ DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+ STORAGE_LAYOUT {
+ CHUNKED ( 40, 20 )
+ SIZE 3200 (1.000:1 COMPRESSION)
+ }
+ FILTERS {
+ USER_DEFINED_FILTER {
+ FILTER_ID 257
+ COMMENT dynlib1
+ PARAMS { 9 }
+ }
+ }
+ FILLVALUE {
+ FILL_TIME H5D_FILL_TIME_IFSET
+ VALUE 0
+ }
+ ALLOCATION_TIME {
+ H5D_ALLOC_TIME_INCR
+ }
+ }
+}
+}
diff --git a/tools/h5repack/testfiles/h5repack_layout.h5.ddl b/tools/h5repack/testfiles/h5repack_layout.h5.ddl
index d380201..00c74f4 100644
--- a/tools/h5repack/testfiles/h5repack_layout.h5.ddl
+++ b/tools/h5repack/testfiles/h5repack_layout.h5.ddl
@@ -1,129 +1,605 @@
-HDF5 "./testfiles/out-deflate_limit.h5repack_layout.h5" {
+HDF5 "h5repack_layout.h5" {
GROUP "/" {
DATASET "dset1" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
- STORAGE_LAYOUT {
- CHUNKED ( 40, 20 )
- SIZE 1150 (2.783:1 COMPRESSION)
- }
- FILTERS {
- COMPRESSION DEFLATE { LEVEL 1 }
- }
- FILLVALUE {
- FILL_TIME H5D_FILL_TIME_IFSET
- VALUE 0
- }
- ALLOCATION_TIME {
- H5D_ALLOC_TIME_INCR
+ DATA {
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+ (0,18): 18, 19,
+ (1,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
+ (1,16): 36, 37, 38, 39,
+ (2,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
+ (2,16): 56, 57, 58, 59,
+ (3,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
+ (3,16): 76, 77, 78, 79,
+ (4,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
+ (4,16): 96, 97, 98, 99,
+ (5,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
+ (5,13): 113, 114, 115, 116, 117, 118, 119,
+ (6,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ (6,13): 133, 134, 135, 136, 137, 138, 139,
+ (7,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
+ (7,13): 153, 154, 155, 156, 157, 158, 159,
+ (8,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ (8,13): 173, 174, 175, 176, 177, 178, 179,
+ (9,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192,
+ (9,13): 193, 194, 195, 196, 197, 198, 199,
+ (10,0): 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211,
+ (10,12): 212, 213, 214, 215, 216, 217, 218, 219,
+ (11,0): 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,
+ (11,12): 232, 233, 234, 235, 236, 237, 238, 239,
+ (12,0): 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+ (12,12): 252, 253, 254, 255, 256, 257, 258, 259,
+ (13,0): 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
+ (13,12): 272, 273, 274, 275, 276, 277, 278, 279,
+ (14,0): 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
+ (14,12): 292, 293, 294, 295, 296, 297, 298, 299,
+ (15,0): 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
+ (15,12): 312, 313, 314, 315, 316, 317, 318, 319,
+ (16,0): 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
+ (16,12): 332, 333, 334, 335, 336, 337, 338, 339,
+ (17,0): 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,
+ (17,12): 352, 353, 354, 355, 356, 357, 358, 359,
+ (18,0): 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,
+ (18,12): 372, 373, 374, 375, 376, 377, 378, 379,
+ (19,0): 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+ (19,12): 392, 393, 394, 395, 396, 397, 398, 399,
+ (20,0): 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411,
+ (20,12): 412, 413, 414, 415, 416, 417, 418, 419,
+ (21,0): 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431,
+ (21,12): 432, 433, 434, 435, 436, 437, 438, 439,
+ (22,0): 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451,
+ (22,12): 452, 453, 454, 455, 456, 457, 458, 459,
+ (23,0): 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471,
+ (23,12): 472, 473, 474, 475, 476, 477, 478, 479,
+ (24,0): 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491,
+ (24,12): 492, 493, 494, 495, 496, 497, 498, 499,
+ (25,0): 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511,
+ (25,12): 512, 513, 514, 515, 516, 517, 518, 519,
+ (26,0): 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+ (26,12): 532, 533, 534, 535, 536, 537, 538, 539,
+ (27,0): 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551,
+ (27,12): 552, 553, 554, 555, 556, 557, 558, 559,
+ (28,0): 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571,
+ (28,12): 572, 573, 574, 575, 576, 577, 578, 579,
+ (29,0): 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591,
+ (29,12): 592, 593, 594, 595, 596, 597, 598, 599,
+ (30,0): 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611,
+ (30,12): 612, 613, 614, 615, 616, 617, 618, 619,
+ (31,0): 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631,
+ (31,12): 632, 633, 634, 635, 636, 637, 638, 639,
+ (32,0): 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,
+ (32,12): 652, 653, 654, 655, 656, 657, 658, 659,
+ (33,0): 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671,
+ (33,12): 672, 673, 674, 675, 676, 677, 678, 679,
+ (34,0): 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691,
+ (34,12): 692, 693, 694, 695, 696, 697, 698, 699,
+ (35,0): 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711,
+ (35,12): 712, 713, 714, 715, 716, 717, 718, 719,
+ (36,0): 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731,
+ (36,12): 732, 733, 734, 735, 736, 737, 738, 739,
+ (37,0): 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751,
+ (37,12): 752, 753, 754, 755, 756, 757, 758, 759,
+ (38,0): 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771,
+ (38,12): 772, 773, 774, 775, 776, 777, 778, 779,
+ (39,0): 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791,
+ (39,12): 792, 793, 794, 795, 796, 797, 798, 799
}
}
DATASET "dset2" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
- STORAGE_LAYOUT {
- CHUNKED ( 40, 20 )
- SIZE 1150 (2.783:1 COMPRESSION)
- }
- FILTERS {
- COMPRESSION DEFLATE { LEVEL 1 }
- }
- FILLVALUE {
- FILL_TIME H5D_FILL_TIME_IFSET
- VALUE 0
- }
- ALLOCATION_TIME {
- H5D_ALLOC_TIME_INCR
+ DATA {
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+ (0,18): 18, 19,
+ (1,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
+ (1,16): 36, 37, 38, 39,
+ (2,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
+ (2,16): 56, 57, 58, 59,
+ (3,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
+ (3,16): 76, 77, 78, 79,
+ (4,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
+ (4,16): 96, 97, 98, 99,
+ (5,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
+ (5,13): 113, 114, 115, 116, 117, 118, 119,
+ (6,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ (6,13): 133, 134, 135, 136, 137, 138, 139,
+ (7,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
+ (7,13): 153, 154, 155, 156, 157, 158, 159,
+ (8,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ (8,13): 173, 174, 175, 176, 177, 178, 179,
+ (9,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192,
+ (9,13): 193, 194, 195, 196, 197, 198, 199,
+ (10,0): 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211,
+ (10,12): 212, 213, 214, 215, 216, 217, 218, 219,
+ (11,0): 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,
+ (11,12): 232, 233, 234, 235, 236, 237, 238, 239,
+ (12,0): 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+ (12,12): 252, 253, 254, 255, 256, 257, 258, 259,
+ (13,0): 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
+ (13,12): 272, 273, 274, 275, 276, 277, 278, 279,
+ (14,0): 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
+ (14,12): 292, 293, 294, 295, 296, 297, 298, 299,
+ (15,0): 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
+ (15,12): 312, 313, 314, 315, 316, 317, 318, 319,
+ (16,0): 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
+ (16,12): 332, 333, 334, 335, 336, 337, 338, 339,
+ (17,0): 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,
+ (17,12): 352, 353, 354, 355, 356, 357, 358, 359,
+ (18,0): 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,
+ (18,12): 372, 373, 374, 375, 376, 377, 378, 379,
+ (19,0): 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+ (19,12): 392, 393, 394, 395, 396, 397, 398, 399,
+ (20,0): 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411,
+ (20,12): 412, 413, 414, 415, 416, 417, 418, 419,
+ (21,0): 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431,
+ (21,12): 432, 433, 434, 435, 436, 437, 438, 439,
+ (22,0): 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451,
+ (22,12): 452, 453, 454, 455, 456, 457, 458, 459,
+ (23,0): 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471,
+ (23,12): 472, 473, 474, 475, 476, 477, 478, 479,
+ (24,0): 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491,
+ (24,12): 492, 493, 494, 495, 496, 497, 498, 499,
+ (25,0): 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511,
+ (25,12): 512, 513, 514, 515, 516, 517, 518, 519,
+ (26,0): 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+ (26,12): 532, 533, 534, 535, 536, 537, 538, 539,
+ (27,0): 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551,
+ (27,12): 552, 553, 554, 555, 556, 557, 558, 559,
+ (28,0): 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571,
+ (28,12): 572, 573, 574, 575, 576, 577, 578, 579,
+ (29,0): 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591,
+ (29,12): 592, 593, 594, 595, 596, 597, 598, 599,
+ (30,0): 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611,
+ (30,12): 612, 613, 614, 615, 616, 617, 618, 619,
+ (31,0): 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631,
+ (31,12): 632, 633, 634, 635, 636, 637, 638, 639,
+ (32,0): 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,
+ (32,12): 652, 653, 654, 655, 656, 657, 658, 659,
+ (33,0): 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671,
+ (33,12): 672, 673, 674, 675, 676, 677, 678, 679,
+ (34,0): 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691,
+ (34,12): 692, 693, 694, 695, 696, 697, 698, 699,
+ (35,0): 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711,
+ (35,12): 712, 713, 714, 715, 716, 717, 718, 719,
+ (36,0): 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731,
+ (36,12): 732, 733, 734, 735, 736, 737, 738, 739,
+ (37,0): 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751,
+ (37,12): 752, 753, 754, 755, 756, 757, 758, 759,
+ (38,0): 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771,
+ (38,12): 772, 773, 774, 775, 776, 777, 778, 779,
+ (39,0): 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791,
+ (39,12): 792, 793, 794, 795, 796, 797, 798, 799
}
}
DATASET "dset3" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
- STORAGE_LAYOUT {
- CHUNKED ( 40, 20 )
- SIZE 1150 (2.783:1 COMPRESSION)
- }
- FILTERS {
- COMPRESSION DEFLATE { LEVEL 1 }
- }
- FILLVALUE {
- FILL_TIME H5D_FILL_TIME_IFSET
- VALUE 0
- }
- ALLOCATION_TIME {
- H5D_ALLOC_TIME_INCR
+ DATA {
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+ (0,18): 18, 19,
+ (1,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
+ (1,16): 36, 37, 38, 39,
+ (2,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
+ (2,16): 56, 57, 58, 59,
+ (3,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
+ (3,16): 76, 77, 78, 79,
+ (4,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
+ (4,16): 96, 97, 98, 99,
+ (5,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
+ (5,13): 113, 114, 115, 116, 117, 118, 119,
+ (6,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ (6,13): 133, 134, 135, 136, 137, 138, 139,
+ (7,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
+ (7,13): 153, 154, 155, 156, 157, 158, 159,
+ (8,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ (8,13): 173, 174, 175, 176, 177, 178, 179,
+ (9,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192,
+ (9,13): 193, 194, 195, 196, 197, 198, 199,
+ (10,0): 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211,
+ (10,12): 212, 213, 214, 215, 216, 217, 218, 219,
+ (11,0): 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,
+ (11,12): 232, 233, 234, 235, 236, 237, 238, 239,
+ (12,0): 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+ (12,12): 252, 253, 254, 255, 256, 257, 258, 259,
+ (13,0): 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
+ (13,12): 272, 273, 274, 275, 276, 277, 278, 279,
+ (14,0): 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
+ (14,12): 292, 293, 294, 295, 296, 297, 298, 299,
+ (15,0): 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
+ (15,12): 312, 313, 314, 315, 316, 317, 318, 319,
+ (16,0): 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
+ (16,12): 332, 333, 334, 335, 336, 337, 338, 339,
+ (17,0): 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,
+ (17,12): 352, 353, 354, 355, 356, 357, 358, 359,
+ (18,0): 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,
+ (18,12): 372, 373, 374, 375, 376, 377, 378, 379,
+ (19,0): 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+ (19,12): 392, 393, 394, 395, 396, 397, 398, 399,
+ (20,0): 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411,
+ (20,12): 412, 413, 414, 415, 416, 417, 418, 419,
+ (21,0): 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431,
+ (21,12): 432, 433, 434, 435, 436, 437, 438, 439,
+ (22,0): 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451,
+ (22,12): 452, 453, 454, 455, 456, 457, 458, 459,
+ (23,0): 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471,
+ (23,12): 472, 473, 474, 475, 476, 477, 478, 479,
+ (24,0): 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491,
+ (24,12): 492, 493, 494, 495, 496, 497, 498, 499,
+ (25,0): 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511,
+ (25,12): 512, 513, 514, 515, 516, 517, 518, 519,
+ (26,0): 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+ (26,12): 532, 533, 534, 535, 536, 537, 538, 539,
+ (27,0): 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551,
+ (27,12): 552, 553, 554, 555, 556, 557, 558, 559,
+ (28,0): 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571,
+ (28,12): 572, 573, 574, 575, 576, 577, 578, 579,
+ (29,0): 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591,
+ (29,12): 592, 593, 594, 595, 596, 597, 598, 599,
+ (30,0): 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611,
+ (30,12): 612, 613, 614, 615, 616, 617, 618, 619,
+ (31,0): 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631,
+ (31,12): 632, 633, 634, 635, 636, 637, 638, 639,
+ (32,0): 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,
+ (32,12): 652, 653, 654, 655, 656, 657, 658, 659,
+ (33,0): 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671,
+ (33,12): 672, 673, 674, 675, 676, 677, 678, 679,
+ (34,0): 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691,
+ (34,12): 692, 693, 694, 695, 696, 697, 698, 699,
+ (35,0): 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711,
+ (35,12): 712, 713, 714, 715, 716, 717, 718, 719,
+ (36,0): 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731,
+ (36,12): 732, 733, 734, 735, 736, 737, 738, 739,
+ (37,0): 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751,
+ (37,12): 752, 753, 754, 755, 756, 757, 758, 759,
+ (38,0): 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771,
+ (38,12): 772, 773, 774, 775, 776, 777, 778, 779,
+ (39,0): 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791,
+ (39,12): 792, 793, 794, 795, 796, 797, 798, 799
}
}
DATASET "dset4" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
- STORAGE_LAYOUT {
- CHUNKED ( 40, 20 )
- SIZE 1150 (2.783:1 COMPRESSION)
- }
- FILTERS {
- COMPRESSION DEFLATE { LEVEL 1 }
- }
- FILLVALUE {
- FILL_TIME H5D_FILL_TIME_IFSET
- VALUE 0
- }
- ALLOCATION_TIME {
- H5D_ALLOC_TIME_INCR
+ DATA {
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+ (0,18): 18, 19,
+ (1,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
+ (1,16): 36, 37, 38, 39,
+ (2,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
+ (2,16): 56, 57, 58, 59,
+ (3,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
+ (3,16): 76, 77, 78, 79,
+ (4,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
+ (4,16): 96, 97, 98, 99,
+ (5,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
+ (5,13): 113, 114, 115, 116, 117, 118, 119,
+ (6,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ (6,13): 133, 134, 135, 136, 137, 138, 139,
+ (7,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
+ (7,13): 153, 154, 155, 156, 157, 158, 159,
+ (8,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ (8,13): 173, 174, 175, 176, 177, 178, 179,
+ (9,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192,
+ (9,13): 193, 194, 195, 196, 197, 198, 199,
+ (10,0): 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211,
+ (10,12): 212, 213, 214, 215, 216, 217, 218, 219,
+ (11,0): 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,
+ (11,12): 232, 233, 234, 235, 236, 237, 238, 239,
+ (12,0): 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+ (12,12): 252, 253, 254, 255, 256, 257, 258, 259,
+ (13,0): 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
+ (13,12): 272, 273, 274, 275, 276, 277, 278, 279,
+ (14,0): 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
+ (14,12): 292, 293, 294, 295, 296, 297, 298, 299,
+ (15,0): 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
+ (15,12): 312, 313, 314, 315, 316, 317, 318, 319,
+ (16,0): 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
+ (16,12): 332, 333, 334, 335, 336, 337, 338, 339,
+ (17,0): 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,
+ (17,12): 352, 353, 354, 355, 356, 357, 358, 359,
+ (18,0): 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,
+ (18,12): 372, 373, 374, 375, 376, 377, 378, 379,
+ (19,0): 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+ (19,12): 392, 393, 394, 395, 396, 397, 398, 399,
+ (20,0): 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411,
+ (20,12): 412, 413, 414, 415, 416, 417, 418, 419,
+ (21,0): 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431,
+ (21,12): 432, 433, 434, 435, 436, 437, 438, 439,
+ (22,0): 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451,
+ (22,12): 452, 453, 454, 455, 456, 457, 458, 459,
+ (23,0): 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471,
+ (23,12): 472, 473, 474, 475, 476, 477, 478, 479,
+ (24,0): 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491,
+ (24,12): 492, 493, 494, 495, 496, 497, 498, 499,
+ (25,0): 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511,
+ (25,12): 512, 513, 514, 515, 516, 517, 518, 519,
+ (26,0): 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+ (26,12): 532, 533, 534, 535, 536, 537, 538, 539,
+ (27,0): 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551,
+ (27,12): 552, 553, 554, 555, 556, 557, 558, 559,
+ (28,0): 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571,
+ (28,12): 572, 573, 574, 575, 576, 577, 578, 579,
+ (29,0): 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591,
+ (29,12): 592, 593, 594, 595, 596, 597, 598, 599,
+ (30,0): 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611,
+ (30,12): 612, 613, 614, 615, 616, 617, 618, 619,
+ (31,0): 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631,
+ (31,12): 632, 633, 634, 635, 636, 637, 638, 639,
+ (32,0): 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,
+ (32,12): 652, 653, 654, 655, 656, 657, 658, 659,
+ (33,0): 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671,
+ (33,12): 672, 673, 674, 675, 676, 677, 678, 679,
+ (34,0): 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691,
+ (34,12): 692, 693, 694, 695, 696, 697, 698, 699,
+ (35,0): 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711,
+ (35,12): 712, 713, 714, 715, 716, 717, 718, 719,
+ (36,0): 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731,
+ (36,12): 732, 733, 734, 735, 736, 737, 738, 739,
+ (37,0): 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751,
+ (37,12): 752, 753, 754, 755, 756, 757, 758, 759,
+ (38,0): 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771,
+ (38,12): 772, 773, 774, 775, 776, 777, 778, 779,
+ (39,0): 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791,
+ (39,12): 792, 793, 794, 795, 796, 797, 798, 799
}
}
DATASET "dset_chunk" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, H5S_UNLIMITED ) }
- STORAGE_LAYOUT {
- CHUNKED ( 20, 10 )
- SIZE 1283 (2.494:1 COMPRESSION)
- }
- FILTERS {
- COMPRESSION DEFLATE { LEVEL 1 }
- }
- FILLVALUE {
- FILL_TIME H5D_FILL_TIME_IFSET
- VALUE 0
- }
- ALLOCATION_TIME {
- H5D_ALLOC_TIME_INCR
+ DATA {
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+ (0,18): 18, 19,
+ (1,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
+ (1,16): 36, 37, 38, 39,
+ (2,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
+ (2,16): 56, 57, 58, 59,
+ (3,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
+ (3,16): 76, 77, 78, 79,
+ (4,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
+ (4,16): 96, 97, 98, 99,
+ (5,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
+ (5,13): 113, 114, 115, 116, 117, 118, 119,
+ (6,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ (6,13): 133, 134, 135, 136, 137, 138, 139,
+ (7,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
+ (7,13): 153, 154, 155, 156, 157, 158, 159,
+ (8,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ (8,13): 173, 174, 175, 176, 177, 178, 179,
+ (9,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192,
+ (9,13): 193, 194, 195, 196, 197, 198, 199,
+ (10,0): 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211,
+ (10,12): 212, 213, 214, 215, 216, 217, 218, 219,
+ (11,0): 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,
+ (11,12): 232, 233, 234, 235, 236, 237, 238, 239,
+ (12,0): 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+ (12,12): 252, 253, 254, 255, 256, 257, 258, 259,
+ (13,0): 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
+ (13,12): 272, 273, 274, 275, 276, 277, 278, 279,
+ (14,0): 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
+ (14,12): 292, 293, 294, 295, 296, 297, 298, 299,
+ (15,0): 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
+ (15,12): 312, 313, 314, 315, 316, 317, 318, 319,
+ (16,0): 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
+ (16,12): 332, 333, 334, 335, 336, 337, 338, 339,
+ (17,0): 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,
+ (17,12): 352, 353, 354, 355, 356, 357, 358, 359,
+ (18,0): 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,
+ (18,12): 372, 373, 374, 375, 376, 377, 378, 379,
+ (19,0): 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+ (19,12): 392, 393, 394, 395, 396, 397, 398, 399,
+ (20,0): 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411,
+ (20,12): 412, 413, 414, 415, 416, 417, 418, 419,
+ (21,0): 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431,
+ (21,12): 432, 433, 434, 435, 436, 437, 438, 439,
+ (22,0): 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451,
+ (22,12): 452, 453, 454, 455, 456, 457, 458, 459,
+ (23,0): 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471,
+ (23,12): 472, 473, 474, 475, 476, 477, 478, 479,
+ (24,0): 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491,
+ (24,12): 492, 493, 494, 495, 496, 497, 498, 499,
+ (25,0): 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511,
+ (25,12): 512, 513, 514, 515, 516, 517, 518, 519,
+ (26,0): 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+ (26,12): 532, 533, 534, 535, 536, 537, 538, 539,
+ (27,0): 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551,
+ (27,12): 552, 553, 554, 555, 556, 557, 558, 559,
+ (28,0): 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571,
+ (28,12): 572, 573, 574, 575, 576, 577, 578, 579,
+ (29,0): 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591,
+ (29,12): 592, 593, 594, 595, 596, 597, 598, 599,
+ (30,0): 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611,
+ (30,12): 612, 613, 614, 615, 616, 617, 618, 619,
+ (31,0): 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631,
+ (31,12): 632, 633, 634, 635, 636, 637, 638, 639,
+ (32,0): 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,
+ (32,12): 652, 653, 654, 655, 656, 657, 658, 659,
+ (33,0): 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671,
+ (33,12): 672, 673, 674, 675, 676, 677, 678, 679,
+ (34,0): 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691,
+ (34,12): 692, 693, 694, 695, 696, 697, 698, 699,
+ (35,0): 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711,
+ (35,12): 712, 713, 714, 715, 716, 717, 718, 719,
+ (36,0): 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731,
+ (36,12): 732, 733, 734, 735, 736, 737, 738, 739,
+ (37,0): 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751,
+ (37,12): 752, 753, 754, 755, 756, 757, 758, 759,
+ (38,0): 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771,
+ (38,12): 772, 773, 774, 775, 776, 777, 778, 779,
+ (39,0): 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791,
+ (39,12): 792, 793, 794, 795, 796, 797, 798, 799
}
}
DATASET "dset_compact" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
- STORAGE_LAYOUT {
- CHUNKED ( 40, 20 )
- SIZE 1150 (2.783:1 COMPRESSION)
- }
- FILTERS {
- COMPRESSION DEFLATE { LEVEL 1 }
- }
- FILLVALUE {
- FILL_TIME H5D_FILL_TIME_IFSET
- VALUE 0
- }
- ALLOCATION_TIME {
- H5D_ALLOC_TIME_INCR
+ DATA {
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+ (0,18): 18, 19,
+ (1,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
+ (1,16): 36, 37, 38, 39,
+ (2,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
+ (2,16): 56, 57, 58, 59,
+ (3,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
+ (3,16): 76, 77, 78, 79,
+ (4,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
+ (4,16): 96, 97, 98, 99,
+ (5,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
+ (5,13): 113, 114, 115, 116, 117, 118, 119,
+ (6,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ (6,13): 133, 134, 135, 136, 137, 138, 139,
+ (7,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
+ (7,13): 153, 154, 155, 156, 157, 158, 159,
+ (8,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ (8,13): 173, 174, 175, 176, 177, 178, 179,
+ (9,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192,
+ (9,13): 193, 194, 195, 196, 197, 198, 199,
+ (10,0): 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211,
+ (10,12): 212, 213, 214, 215, 216, 217, 218, 219,
+ (11,0): 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,
+ (11,12): 232, 233, 234, 235, 236, 237, 238, 239,
+ (12,0): 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+ (12,12): 252, 253, 254, 255, 256, 257, 258, 259,
+ (13,0): 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
+ (13,12): 272, 273, 274, 275, 276, 277, 278, 279,
+ (14,0): 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
+ (14,12): 292, 293, 294, 295, 296, 297, 298, 299,
+ (15,0): 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
+ (15,12): 312, 313, 314, 315, 316, 317, 318, 319,
+ (16,0): 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
+ (16,12): 332, 333, 334, 335, 336, 337, 338, 339,
+ (17,0): 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,
+ (17,12): 352, 353, 354, 355, 356, 357, 358, 359,
+ (18,0): 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,
+ (18,12): 372, 373, 374, 375, 376, 377, 378, 379,
+ (19,0): 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+ (19,12): 392, 393, 394, 395, 396, 397, 398, 399,
+ (20,0): 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411,
+ (20,12): 412, 413, 414, 415, 416, 417, 418, 419,
+ (21,0): 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431,
+ (21,12): 432, 433, 434, 435, 436, 437, 438, 439,
+ (22,0): 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451,
+ (22,12): 452, 453, 454, 455, 456, 457, 458, 459,
+ (23,0): 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471,
+ (23,12): 472, 473, 474, 475, 476, 477, 478, 479,
+ (24,0): 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491,
+ (24,12): 492, 493, 494, 495, 496, 497, 498, 499,
+ (25,0): 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511,
+ (25,12): 512, 513, 514, 515, 516, 517, 518, 519,
+ (26,0): 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+ (26,12): 532, 533, 534, 535, 536, 537, 538, 539,
+ (27,0): 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551,
+ (27,12): 552, 553, 554, 555, 556, 557, 558, 559,
+ (28,0): 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571,
+ (28,12): 572, 573, 574, 575, 576, 577, 578, 579,
+ (29,0): 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591,
+ (29,12): 592, 593, 594, 595, 596, 597, 598, 599,
+ (30,0): 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611,
+ (30,12): 612, 613, 614, 615, 616, 617, 618, 619,
+ (31,0): 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631,
+ (31,12): 632, 633, 634, 635, 636, 637, 638, 639,
+ (32,0): 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,
+ (32,12): 652, 653, 654, 655, 656, 657, 658, 659,
+ (33,0): 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671,
+ (33,12): 672, 673, 674, 675, 676, 677, 678, 679,
+ (34,0): 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691,
+ (34,12): 692, 693, 694, 695, 696, 697, 698, 699,
+ (35,0): 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711,
+ (35,12): 712, 713, 714, 715, 716, 717, 718, 719,
+ (36,0): 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731,
+ (36,12): 732, 733, 734, 735, 736, 737, 738, 739,
+ (37,0): 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751,
+ (37,12): 752, 753, 754, 755, 756, 757, 758, 759,
+ (38,0): 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771,
+ (38,12): 772, 773, 774, 775, 776, 777, 778, 779,
+ (39,0): 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791,
+ (39,12): 792, 793, 794, 795, 796, 797, 798, 799
}
}
DATASET "dset_contiguous" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
- STORAGE_LAYOUT {
- CHUNKED ( 40, 20 )
- SIZE 1150 (2.783:1 COMPRESSION)
- }
- FILTERS {
- COMPRESSION DEFLATE { LEVEL 1 }
- }
- FILLVALUE {
- FILL_TIME H5D_FILL_TIME_IFSET
- VALUE 0
- }
- ALLOCATION_TIME {
- H5D_ALLOC_TIME_INCR
+ DATA {
+ (0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
+ (0,18): 18, 19,
+ (1,0): 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
+ (1,16): 36, 37, 38, 39,
+ (2,0): 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
+ (2,16): 56, 57, 58, 59,
+ (3,0): 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
+ (3,16): 76, 77, 78, 79,
+ (4,0): 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
+ (4,16): 96, 97, 98, 99,
+ (5,0): 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
+ (5,13): 113, 114, 115, 116, 117, 118, 119,
+ (6,0): 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,
+ (6,13): 133, 134, 135, 136, 137, 138, 139,
+ (7,0): 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,
+ (7,13): 153, 154, 155, 156, 157, 158, 159,
+ (8,0): 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172,
+ (8,13): 173, 174, 175, 176, 177, 178, 179,
+ (9,0): 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192,
+ (9,13): 193, 194, 195, 196, 197, 198, 199,
+ (10,0): 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211,
+ (10,12): 212, 213, 214, 215, 216, 217, 218, 219,
+ (11,0): 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,
+ (11,12): 232, 233, 234, 235, 236, 237, 238, 239,
+ (12,0): 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251,
+ (12,12): 252, 253, 254, 255, 256, 257, 258, 259,
+ (13,0): 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
+ (13,12): 272, 273, 274, 275, 276, 277, 278, 279,
+ (14,0): 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
+ (14,12): 292, 293, 294, 295, 296, 297, 298, 299,
+ (15,0): 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
+ (15,12): 312, 313, 314, 315, 316, 317, 318, 319,
+ (16,0): 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331,
+ (16,12): 332, 333, 334, 335, 336, 337, 338, 339,
+ (17,0): 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,
+ (17,12): 352, 353, 354, 355, 356, 357, 358, 359,
+ (18,0): 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,
+ (18,12): 372, 373, 374, 375, 376, 377, 378, 379,
+ (19,0): 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391,
+ (19,12): 392, 393, 394, 395, 396, 397, 398, 399,
+ (20,0): 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411,
+ (20,12): 412, 413, 414, 415, 416, 417, 418, 419,
+ (21,0): 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431,
+ (21,12): 432, 433, 434, 435, 436, 437, 438, 439,
+ (22,0): 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451,
+ (22,12): 452, 453, 454, 455, 456, 457, 458, 459,
+ (23,0): 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471,
+ (23,12): 472, 473, 474, 475, 476, 477, 478, 479,
+ (24,0): 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491,
+ (24,12): 492, 493, 494, 495, 496, 497, 498, 499,
+ (25,0): 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511,
+ (25,12): 512, 513, 514, 515, 516, 517, 518, 519,
+ (26,0): 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531,
+ (26,12): 532, 533, 534, 535, 536, 537, 538, 539,
+ (27,0): 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551,
+ (27,12): 552, 553, 554, 555, 556, 557, 558, 559,
+ (28,0): 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571,
+ (28,12): 572, 573, 574, 575, 576, 577, 578, 579,
+ (29,0): 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591,
+ (29,12): 592, 593, 594, 595, 596, 597, 598, 599,
+ (30,0): 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611,
+ (30,12): 612, 613, 614, 615, 616, 617, 618, 619,
+ (31,0): 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631,
+ (31,12): 632, 633, 634, 635, 636, 637, 638, 639,
+ (32,0): 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,
+ (32,12): 652, 653, 654, 655, 656, 657, 658, 659,
+ (33,0): 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671,
+ (33,12): 672, 673, 674, 675, 676, 677, 678, 679,
+ (34,0): 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691,
+ (34,12): 692, 693, 694, 695, 696, 697, 698, 699,
+ (35,0): 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711,
+ (35,12): 712, 713, 714, 715, 716, 717, 718, 719,
+ (36,0): 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731,
+ (36,12): 732, 733, 734, 735, 736, 737, 738, 739,
+ (37,0): 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751,
+ (37,12): 752, 753, 754, 755, 756, 757, 758, 759,
+ (38,0): 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771,
+ (38,12): 772, 773, 774, 775, 776, 777, 778, 779,
+ (39,0): 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791,
+ (39,12): 792, 793, 794, 795, 796, 797, 798, 799
}
}
}
diff --git a/tools/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst b/tools/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst
new file mode 100644
index 0000000..7f9bd6e
--- /dev/null
+++ b/tools/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst
@@ -0,0 +1,14 @@
+Objects to modify layout are...
+Objects to apply filter are...
+ User Defined 257
+-----------------------------------------
+ Type Filter (Compression) Name
+-----------------------------------------
+ group /
+ dset UD (1.000:1) /dset1
+ dset UD (1.000:1) /dset2
+ dset UD (1.000:1) /dset3
+ dset UD (1.000:1) /dset4
+ dset UD (1.000:1) /dset_chunk
+ dset UD (1.000:1) /dset_compact
+ dset UD (1.000:1) /dset_contiguous
generated by cgit v0.12 at 2024-11-18 04:56:11 (GMT)