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-rw-r--r--tools/src/h5repack/CMakeLists.txt50
-rw-r--r--tools/src/h5repack/Makefile.am42
-rw-r--r--tools/src/h5repack/h5repack.c942
-rw-r--r--tools/src/h5repack/h5repack.h243
-rw-r--r--tools/src/h5repack/h5repack_copy.c1581
-rw-r--r--tools/src/h5repack/h5repack_filters.c493
-rw-r--r--tools/src/h5repack/h5repack_main.c664
-rw-r--r--tools/src/h5repack/h5repack_opttable.c367
-rw-r--r--tools/src/h5repack/h5repack_parse.c616
-rw-r--r--tools/src/h5repack/h5repack_refs.c877
-rw-r--r--tools/src/h5repack/h5repack_verify.c675
11 files changed, 6550 insertions, 0 deletions
diff --git a/tools/src/h5repack/CMakeLists.txt b/tools/src/h5repack/CMakeLists.txt
new file mode 100644
index 0000000..cb7f5f6
--- /dev/null
+++ b/tools/src/h5repack/CMakeLists.txt
@@ -0,0 +1,50 @@
+cmake_minimum_required (VERSION 3.1.0)
+PROJECT (HDF5_TOOLS_SRC_H5REPACK)
+
+#-----------------------------------------------------------------------------
+# Setup include Directories
+#-----------------------------------------------------------------------------
+INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
+INCLUDE_DIRECTORIES (${HDF5_TEST_SRC_DIR})
+
+# --------------------------------------------------------------------
+# Add h5Repack executables
+# --------------------------------------------------------------------
+set (REPACK_COMMON_SOURCES
+ ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_copy.c
+ ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_filters.c
+ ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_opttable.c
+ ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_parse.c
+ ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_refs.c
+ ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_verify.c
+ ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack.c
+)
+
+add_executable (h5repack ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c)
+TARGET_NAMING (h5repack STATIC)
+TARGET_C_PROPERTIES (h5repack STATIC " " " ")
+target_link_libraries (h5repack ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5repack PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repack")
+
+set (H5_DEP_EXECUTABLES h5repack)
+
+##############################################################################
+##############################################################################
+### I N S T A L L A T I O N ###
+##############################################################################
+##############################################################################
+
+#-----------------------------------------------------------------------------
+# Rules for Installation of tools using make Install target
+#-----------------------------------------------------------------------------
+
+#INSTALL_PROGRAM_PDB (h5repack ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+
+install (
+ TARGETS
+ h5repack
+ EXPORT
+ ${HDF5_EXPORTED_TARGETS}
+ RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+)
diff --git a/tools/src/h5repack/Makefile.am b/tools/src/h5repack/Makefile.am
new file mode 100644
index 0000000..e6e5a56
--- /dev/null
+++ b/tools/src/h5repack/Makefile.am
@@ -0,0 +1,42 @@
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5. The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the files COPYING and Copyright.html. COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page. It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+##
+## Makefile.am
+## Run automake to generate a Makefile.in from this file.
+#
+# HDF5 Library Makefile(.in)
+#
+
+include $(top_srcdir)/config/commence.am
+
+# Include src, test, and tools/lib directories
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
+
+# Our main target, h5repack tool
+bin_PROGRAMS=h5repack
+
+# Add h5repack specific linker flags here
+h5repack_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+
+# Depend on the hdf5 library, the tools library, the test library
+LDADD=$(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
+
+# Source files
+COMMON_SOURCES=h5repack.c h5repack_copy.c h5repack_filters.c \
+ h5repack_opttable.c h5repack_parse.c h5repack_refs.c \
+ h5repack_verify.c
+
+h5repack_SOURCES=$(COMMON_SOURCES) h5repack_main.c
+
+include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
new file mode 100644
index 0000000..ef2085c
--- /dev/null
+++ b/tools/src/h5repack/h5repack.c
@@ -0,0 +1,942 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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>
+#include <ctype.h>
+
+#include "H5private.h"
+#include "h5repack.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+/*-------------------------------------------------------------------------
+ * 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 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_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_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 */
+ unsigned 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 */
+ unsigned 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()
+ * were located in h5repack_copy.c as static prior to bugfix1726.
+ * Made shared functions as copy_attr() was needed in h5repack_refs.c.
+ * However copy_attr() may be obsoleted when H5Acopy is available and put back
+ * 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 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;
+ int 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)
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
+
+ /*-------------------------------------------------------------------------
+ * 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
+
+ /* get name */
+ if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+
+ /* get the file datatype */
+ if ((ftype_id = H5Aget_type(attr_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
+
+ /* Check if the datatype is committed */
+ if ((is_named = H5Tcommitted(ftype_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
+ if (is_named && travt) {
+ hid_t fidout;
+
+ /* Create out file id */
+ if ((fidout = H5Iget_file_id(loc_out)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iget_file_id failed");
+
+ /* Copy named dt */
+ if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
+ H5Fclose(fidout);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
+ } /* end if */
+
+ if (H5Fclose(fidout) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
+ } /* 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed");
+
+ /* get dimensions */
+ if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+
+ nelmts = 1;
+ for (j = 0; j < rank; j++)
+ nelmts *= dims[j];
+
+ if ((msize = H5Tget_size(wtype_id)) == 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+
+ /*-------------------------------------------------------------------------
+ * 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
+ } /* end if */
+ if (H5Aread(attr_id, wtype_id, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
+
+ /*-------------------------------------------------------------------------
+ * copy
+ *-------------------------------------------------------------------------
+ */
+
+ if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed");
+ if (H5Awrite(attr_out, wtype_id, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");
+
+ /*close*/
+ if (H5Aclose(attr_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
+
+ /* 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Tclose(wtype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Sclose(space_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if (H5Aclose(attr_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
+ } /* u */
+
+ return 0;
+
+done:
+ 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 ret_value;
+} /* 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_VIRTUAL:
+ strcpy(slayout, "virtual");
+ 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:
+ 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;
+}
+
+/*-------------------------------------------------------------------------
+ * 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;
+}
+
+/*-------------------------------------------------------------------------
+ * 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;
+
+}
+
+/*-------------------------------------------------------------------------
+ * 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/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h
new file mode 100644
index 0000000..d2ab923
--- /dev/null
+++ b/tools/src/h5repack/h5repack.h
@@ -0,0 +1,243 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+
+#ifndef H5REPACK_H__
+#define H5REPACK_H__
+
+#include "H5private.h"
+#include "hdf5.h"
+#include "h5trav.h"
+
+#define H5FOPENERROR "unable to open file"
+#define PFORMAT "%-7s %-7s %-7s\n" /* chunk info, compression info, name*/
+#define PFORMAT1 "%-7s %-7s %-7s" /* chunk info, compression info, name*/
+#define MAX_NC_NAME 256 /* max length of a name */
+#define MAX_VAR_DIMS 32 /* max per variable dimensions */
+#define FORMAT_OBJ " %-27s %s\n" /* obj type, name */
+#define FORMAT_OBJ_ATTR " %-27s %s\n" /* obj type, name */
+#define MAX_COMPACT_DSIZE 64512 /* max data size for compact layout. -1k for header size */
+
+/*-------------------------------------------------------------------------
+ * data structures for command line options
+ *-------------------------------------------------------------------------
+ */
+
+/* a list of names */
+typedef struct {
+ char obj[MAX_NC_NAME];
+} obj_list_t;
+
+/*
+ the type of filter and additional parameter
+ type can be one of the filters
+ H5Z_FILTER_NONE 0, uncompress if compressed
+ H5Z_FILTER_DEFLATE 1 , deflation like gzip
+ H5Z_FILTER_SHUFFLE 2 , shuffle the data
+ H5Z_FILTER_FLETCHER32 3 , letcher32 checksum of EDC
+ H5Z_FILTER_SZIP 4 , szip compression
+ H5Z_FILTER_NBIT 5 , nbit compression
+ H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression
+*/
+
+#define CD_VALUES 20
+
+typedef struct {
+ H5Z_filter_t filtn; /* filter identification number */
+ unsigned cd_values[CD_VALUES]; /* filter client data values */
+ size_t cd_nelmts; /* filter client number of values */
+} filter_info_t;
+
+/* chunk lengths along each dimension and rank */
+typedef struct {
+ hsize_t chunk_lengths[MAX_VAR_DIMS];
+ int rank;
+} chunk_info_t;
+
+/* we currently define a maximum value for the filters array,
+ that corresponds to the current library filters */
+#define H5_REPACK_MAX_NFILTERS 6
+
+/* information for one object, contains PATH, CHUNK info and FILTER info */
+typedef struct {
+ char path[MAX_NC_NAME]; /* name of object */
+ filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */
+ int nfilters; /* current number of filters */
+ H5D_layout_t layout; /* layout information */
+ chunk_info_t chunk; /* chunk information */
+ hid_t refobj_id; /* object ID, references */
+} pack_info_t;
+
+/* store a table of all objects */
+typedef struct {
+ unsigned int size;
+ unsigned int nelems;
+ pack_info_t *objs;
+} pack_opttbl_t;
+
+
+/*-------------------------------------------------------------------------
+ * command line options
+ *-------------------------------------------------------------------------
+ */
+
+/* all the above, ready to go to the hrepack call */
+typedef struct {
+ pack_opttbl_t *op_tbl; /*table with all -c and -f options */
+ int all_layout; /*apply the layout to all objects */
+ int all_filter; /*apply the filter to all objects */
+ filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */
+ int n_filter_g; /*number of global filters */
+ chunk_info_t chunk_g; /*global chunk INFO for the ALL case */
+ H5D_layout_t layout_g; /*global layout information for the ALL case */
+ int verbose; /*verbose mode */
+ hsize_t min_comp; /*minimum size to compress, in bytes */
+ int use_native; /*use a native type in write */
+ hbool_t latest; /*pack file with the latest file format */
+ int grp_compact; /* Set the maximum number of links to store as header messages in the group */
+ int grp_indexed; /* Set the minimum number of links to store in the indexed format */
+ int msg_size[8]; /* Minimum size of shared messages: dataspace,
+ datatype, fill value, filter pipleline, attribute */
+ const char *ublock_filename; /* user block file name */
+ hsize_t ublock_size; /* user block size */
+ hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */
+ hsize_t threshold; /* alignment threshold for H5Pset_alignment */
+ hsize_t alignment; /* alignment for H5Pset_alignment */
+ H5F_file_space_type_t fs_strategy; /* File space handling strategy */
+ hsize_t fs_threshold; /* Free space section threshold */
+} pack_opt_t;
+
+
+typedef struct named_dt_t {
+ haddr_t addr_in; /* Address of the named dtype in the in file */
+ hid_t id_out; /* Open identifier for the dtype in the out file */
+ struct named_dt_t *next; /* Next dtype */
+} named_dt_t;
+
+/*-------------------------------------------------------------------------
+ * public functions
+ *-------------------------------------------------------------------------
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int h5repack(const char* infile, const char* outfile, pack_opt_t *options);
+int h5repack_addfilter(const char* str, pack_opt_t *options);
+int h5repack_addlayout(const char* str, pack_opt_t *options);
+int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest,
+ H5F_file_space_type_t strategy, hsize_t threshold);
+int h5repack_end(pack_opt_t *options);
+int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options);
+int h5repack_cmp_pl(const char *fname1, const char *fname2);
+
+/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
+ * and struct named_dt_t were located in h5repack_copy.c as static prior to
+ * bugfix1726.
+ * Made shared functions as copy_attr() was needed in h5repack_refs.c.
+ * However copy_attr() may be obsoleted when H5Acopy is available and put back
+ * others to static in h5repack_copy.c.
+ */
+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);
+int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err);
+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);
+
+#ifdef __cplusplus
+}
+#endif
+
+
+
+/*-------------------------------------------------------------------------
+ * private functions
+ *-------------------------------------------------------------------------
+ */
+
+
+/*-------------------------------------------------------------------------
+ * copy module
+ *-------------------------------------------------------------------------
+ */
+
+int copy_objects (const char* fnamein,
+ const char* fnameout,
+ pack_opt_t *options);
+
+int do_copy_refobjs(hid_t fidin,
+ hid_t fidout,
+ trav_table_t *travt,
+ pack_opt_t *options);
+
+/*-------------------------------------------------------------------------
+ * filters and verify module
+ *-------------------------------------------------------------------------
+ */
+void init_packobject(pack_info_t *obj);
+
+
+/*-------------------------------------------------------------------------
+ * filters and copy module
+ *-------------------------------------------------------------------------
+ */
+
+int apply_filters(const char* name, /* object name from traverse list */
+ int rank, /* rank of dataset */
+ hsize_t *dims, /* dimensions of dataset */
+ size_t msize, /* size of type */
+ hid_t dcpl_id, /* dataset creation property list */
+ pack_opt_t *options, /* repack options */
+ int *has_filter); /* (OUT) object NAME has a filter */
+
+
+/*-------------------------------------------------------------------------
+ * options table
+ *-------------------------------------------------------------------------
+ */
+int options_table_init( pack_opttbl_t **tbl );
+int options_table_free( pack_opttbl_t *table );
+int options_add_layout( obj_list_t *obj_list,
+ unsigned n_objs,
+ pack_info_t *pack,
+ pack_opttbl_t *table );
+int options_add_filter ( obj_list_t *obj_list,
+ unsigned n_objs,
+ filter_info_t filt,
+ pack_opttbl_t *table );
+pack_info_t* options_get_object( const char *path,
+ pack_opttbl_t *table);
+
+/*-------------------------------------------------------------------------
+ * parse functions
+ *-------------------------------------------------------------------------
+ */
+
+obj_list_t* parse_filter(const char *str,
+ unsigned *n_objs,
+ filter_info_t *filt,
+ pack_opt_t *options,
+ int *is_glb);
+
+obj_list_t* parse_layout(const char *str,
+ unsigned *n_objs,
+ pack_info_t *pack, /* info about object */
+ pack_opt_t *options);
+
+
+
+
+#endif /* H5REPACK_H__ */
+
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
new file mode 100644
index 0000000..547f61a
--- /dev/null
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -0,0 +1,1581 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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
+ *-------------------------------------------------------------------------
+ */
+
+/*-------------------------------------------------------------------------
+ * globals
+ *-------------------------------------------------------------------------
+ */
+
+/*-------------------------------------------------------------------------
+ * macros
+ *-------------------------------------------------------------------------
+ */
+
+/* size of buffer/# of bytes to xfer at a time when copying userblock */
+#define USERBLOCK_XFER_SIZE 512
+
+/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
+#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf) { \
+ H5E_BEGIN_TRY { \
+ if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) { \
+ hid_t _err_num = 0; \
+ char _msg[80]; \
+ H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
+ H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
+ error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \
+ HGOTO_DONE(_fail) \
+ } \
+ } 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);
+#if defined (H5REPACK_DEBUG_USER_BLOCK)
+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(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
+ if (err_desc)
+ *((hid_t *) 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)
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ 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);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ /* 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ if (!options->fs_strategy) {
+ if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
+ error_msg("failed to retrieve file space strategy\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ if (!options->fs_threshold) {
+ if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
+ error_msg("failed to retrieve file space threshold\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ if (H5Pclose(fcpl_in) < 0) {
+ error_msg("failed to close property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /* 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ if (ub_size > 0) {
+ if (H5Pset_userblock(fcpl, ub_size) < 0) {
+ error_msg("failed to set non-default userblock size\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ /* 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ } /* 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ } /* 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ } /* end if */
+ } /* end if */
+ } /* end if */
+#if defined (H5REPACK_DEBUG_USER_BLOCK)
+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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /* set user block size */
+ if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
+ error_msg("failed to set userblock size\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
+ error_msg("failed to set alignment\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
+ error_msg("failed to set metadata block size\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /* 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ /*-------------------------------------------------------------------------
+ * 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);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ /*-------------------------------------------------------------------------
+ * 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * get list of objects
+ *-------------------------------------------------------------------------
+ */
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fidin, travt) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_objects(fidin, fidout, travt, options) < 0) {
+ error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ } /* 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);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ /*-------------------------------------------------------------------------
+ * 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");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ return 0;
+
+ /*-------------------------------------------------------------------------
+ * out
+ *-------------------------------------------------------------------------
+ */
+
+done:
+ H5E_BEGIN_TRY {
+ H5Pclose(fapl);
+ H5Pclose(fcpl);
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ } H5E_END_TRY;
+ if (travt)
+ trav_table_free(travt);
+
+ return ret_value;
+}
+
+/*-------------------------------------------------------------------------
+ * 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 ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+ }
+ /* 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
+
+ /* pass out the hyperslab size*/
+ *hslab_nbytes_p = hslab_nbytes;
+
+done:
+ return ret_value;
+}
+
+/*-------------------------------------------------------------------------
+ * 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 */
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+
+ /* get input group creation property list */
+ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+
+ /* query and set the group creation properties */
+ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
+
+ /* set up group creation property list */
+ if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+
+ if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
+
+ /*-------------------------------------------------------------------------
+ * 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+ }
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");
+
+ if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gcreate2 failed");
+ }
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+
+ if (H5Pclose(gcpl_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pclose(gcpl_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Gclose(grp_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+ if (H5Gclose(grp_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
+ if (H5T_REFERENCE == H5Tget_class(ftype_id))
+ is_ref = 1;
+
+ /* Check if the datatype is committed */
+ if ((is_named = H5Tcommitted(ftype_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
+ if (is_named)
+ if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
+
+ if (H5Tclose(ftype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Dclose(dset_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+
+ /*-------------------------------------------------------------------------
+ * 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if ((f_space_id = H5Dget_space(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
+ if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
+ if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
+ HDmemset(dims, 0, sizeof dims);
+ if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+ if (H5Dget_space_status(dset_in, &space_status) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed");
+
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+
+ /* 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed");
+
+ /* 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
+ *-------------------------------------------------------------------------
+ */
+ dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
+ if (dset_out == FAIL) {
+ H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ 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, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, FAIL, 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
+ }
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed");
+
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
+ if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
+ }
+ 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, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, FAIL, 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+
+ /*close */
+ if (H5Dclose(dset_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ }/*!H5T_REFERENCE*/
+ }/*h5tools_canreadf*/
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Tclose(ftype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Tclose(wtype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Pclose(dcpl_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pclose(dcpl_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Sclose(f_space_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if (H5Dclose(dset_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ }
+ /*-------------------------------------------------------------------------
+ * 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+
+ /* set options for object copy */
+ if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed");
+
+ /*-------------------------------------------------------------------------
+ * 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 */
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed");
+
+ /* close property */
+ if (H5Pclose(pid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+
+ /*-------------------------------------------------------------------------
+ * copy attrs manually
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+ if (H5Dclose(dset_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ if (H5Dclose(dset_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
+
+ /* Copy the datatype anonymously */
+ if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
+
+ /* Link in to group structure */
+ if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcreate_hard failed");
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+
+ if (H5Tclose(type_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Tclose(type_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+
+ 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed");
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "link", travt->objs[i].name);
+ break;
+
+ default:
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
+ } /* 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 ret_value;
+
+done:
+ 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 ret_value;
+}
+
+/*-------------------------------------------------------------------------
+ * 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];
+#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;
+
+ HDstrcpy(strfilter, "\0");
+
+ /* get information about input filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
+ return;
+
+ 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);
+
+ switch (filtn) {
+ case H5Z_FILTER_NONE:
+ HDstrcat(strfilter, "NONE ");
+ break;
+
+ case H5Z_FILTER_DEFLATE:
+ HDstrcat(strfilter, "GZIP ");
+
+#if defined (PRINT_DEBUG)
+ {
+ unsigned level = cd_values[0];
+
+ sprintf(temp,"(%d)", level);
+ HDstrcat(strfilter, temp);
+ }
+#endif
+ break;
+
+ 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);
+#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;
+
+ 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 ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ int infid = -1, outfid = -1; /* File descriptors */
+
+ /* 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+ if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+
+ /* 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed");
+
+ /* 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 */
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDwrite failed");
+ 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);
+
+ return ret_value;
+}
+
+/*-------------------------------------------------------------------------
+ * 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 ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ 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");
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
+ }
+
+ if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed");
+ }
+
+ if(H5Pclose(fcpl) < 0) {
+ error_msg("failed to close property list\n");
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+
+ /* open file */
+ if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
+ }
+
+ 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) {
+ HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
+ }
+
+ /* update size of userblock left to transfer */
+ size -= nread;
+ }
+
+done:
+ if(fh > 0)
+ HDclose(fh);
+
+ return;
+}
+#endif
+
diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c
new file mode 100644
index 0000000..e21b829
--- /dev/null
+++ b/tools/src/h5repack/h5repack_filters.c
@@ -0,0 +1,493 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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"
+
+/* number of members in an array */
+#ifndef NELMTS
+# define NELMTS(X) (sizeof(X)/sizeof(X[0]))
+#endif
+
+/* minimum of two values */
+#undef MIN
+#define MIN(a,b) (((a)<(b)) ? (a) : (b))
+
+/*-------------------------------------------------------------------------
+ * Function: aux_find_obj
+ *
+ * Purpose: find the object name NAME (got from the traverse list)
+ * in the repack options list
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+aux_find_obj(const char* name, /* object name from traverse list */
+ pack_opt_t *options, /* repack options */
+ pack_info_t *obj /*OUT*/) /* info about object to filter */
+{
+ char *pdest;
+ int result;
+ unsigned int i;
+
+ for ( i=0; i<options->op_tbl->nelems; i++)
+ {
+ if (HDstrcmp(options->op_tbl->objs[i].path,name)==0)
+ {
+ *obj = options->op_tbl->objs[i];
+ return (int)i;
+ }
+
+ pdest = HDstrstr(name,options->op_tbl->objs[i].path);
+ result = (int)(pdest - name);
+
+ /* found at position 1, meaning without '/' */
+ if( pdest != NULL && result==1 )
+ {
+ *obj = options->op_tbl->objs[i];
+ return (int)i;
+ }
+ }/*i*/
+
+ return -1;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: aux_assign_obj
+ *
+ * Purpose: find the object name NAME (got from the traverse list)
+ * in the repack options list; assign the filter information OBJ
+ *
+ * Return: 0 not found, 1 found
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+aux_assign_obj(const char* name, /* object name from traverse list */
+ pack_opt_t *options, /* repack options */
+ pack_info_t *obj /*OUT*/) /* info about object to filter */
+{
+
+ int idx, i;
+ pack_info_t tmp;
+
+ init_packobject(&tmp);
+
+ idx = aux_find_obj(name,options,&tmp);
+
+ /* name was on input */
+ if (idx>=0)
+ {
+
+
+ /* applying to all objects */
+ if (options->all_layout)
+ {
+ /* assign the global layout info to the OBJ info */
+ tmp.layout=options->layout_g;
+ switch (options->layout_g)
+ {
+ case H5D_CHUNKED:
+ tmp.chunk.rank=options->chunk_g.rank;
+ for ( i=0; i<tmp.chunk.rank; i++)
+ tmp.chunk.chunk_lengths[i]=options->chunk_g.chunk_lengths[i];
+ break;
+ case H5D_LAYOUT_ERROR:
+ case H5D_COMPACT:
+ case H5D_CONTIGUOUS:
+ case H5D_VIRTUAL:
+ case H5D_NLAYOUTS:
+ break;
+ default:
+ break;
+ }/*switch*/
+ }
+ else
+ {
+ tmp.layout = options->op_tbl->objs[idx].layout;
+ switch (tmp.layout)
+ {
+ case H5D_CHUNKED:
+ tmp.chunk.rank = options->op_tbl->objs[idx].chunk.rank;
+ for ( i=0; i<tmp.chunk.rank; i++)
+ tmp.chunk.chunk_lengths[i]=options->op_tbl->objs[idx].chunk.chunk_lengths[i];
+ break;
+ case H5D_LAYOUT_ERROR:
+ case H5D_COMPACT:
+ case H5D_CONTIGUOUS:
+ case H5D_VIRTUAL:
+ case H5D_NLAYOUTS:
+ break;
+ default:
+ break;
+ }/*switch*/
+
+ }
+
+ /* applying to all objects */
+ if (options->all_filter)
+ {
+ /* assign the global filter */
+ tmp.nfilters=1;
+ tmp.filter[0]=options->filter_g[0];
+ } /* if all */
+ else
+ {
+ tmp.nfilters=options->op_tbl->objs[idx].nfilters;
+ for ( i=0; i<tmp.nfilters; i++)
+ {
+ tmp.filter[i] = options->op_tbl->objs[idx].filter[i];
+ }
+ }
+
+
+ } /* if idx */
+
+
+ /* no input name */
+
+ else
+ {
+
+ if (options->all_filter)
+ {
+ int k;
+
+ /* assign the global filters */
+ tmp.nfilters=options->n_filter_g;
+ for ( k = 0; k < options->n_filter_g; k++)
+ tmp.filter[k]=options->filter_g[k];
+ }
+ if (options->all_layout)
+ {
+ /* assign the global layout info to the OBJ info */
+ tmp.layout=options->layout_g;
+ switch (options->layout_g)
+ {
+ case H5D_CHUNKED:
+ tmp.chunk.rank=options->chunk_g.rank;
+ for ( i=0; i<tmp.chunk.rank; i++)
+ tmp.chunk.chunk_lengths[i]=options->chunk_g.chunk_lengths[i];
+ break;
+ case H5D_LAYOUT_ERROR:
+ case H5D_COMPACT:
+ case H5D_CONTIGUOUS:
+ case H5D_VIRTUAL:
+ case H5D_NLAYOUTS:
+ break;
+ default:
+ break;
+ }/*switch*/
+ }
+ }
+
+ *obj = tmp;
+ return 1;
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: apply_filters
+ *
+ * Purpose: apply the filters in the object to the property list;
+ * do extra checking in the case of SZIP; delete all filters in the case
+ * of H5Z_FILTER_NONE present in the PACK_INFO_T filter array
+ *
+ * Return: 0 success, -1 an error occured
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 19, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int apply_filters(const char* name, /* object name from traverse list */
+ int rank, /* rank of dataset */
+ hsize_t *dims, /* dimensions of dataset */
+ size_t msize, /* size of type */
+ hid_t dcpl_id, /* dataset creation property list */
+ pack_opt_t *options, /* repack options */
+ int *has_filter) /* (OUT) object NAME has a filter */
+
+
+{
+ int nfilters; /* number of filters in DCPL */
+ hsize_t chsize[64]; /* chunk size in elements */
+ H5D_layout_t layout;
+ int i;
+ pack_info_t obj;
+
+ *has_filter = 0;
+
+ if (rank==0) /* scalar dataset, do not apply */
+ return 0;
+
+ /*-------------------------------------------------------------------------
+ * initialize the assigment object
+ *-------------------------------------------------------------------------
+ */
+ init_packobject(&obj);
+
+ /*-------------------------------------------------------------------------
+ * find options
+ *-------------------------------------------------------------------------
+ */
+ if (aux_assign_obj(name,options,&obj)==0)
+ return 0;
+
+ /* get information about input filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
+ return -1;
+
+ /*-------------------------------------------------------------------------
+ * check if we have filters in the pipeline
+ * we want to replace them with the input filters
+ * only remove if we are inserting new ones
+ *-------------------------------------------------------------------------
+ */
+ if (nfilters && obj.nfilters )
+ {
+ *has_filter = 1;
+ if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
+ return -1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * check if there is an existent chunk
+ * read it only if there is not a requested layout
+ *-------------------------------------------------------------------------
+ */
+ if (obj.layout == -1 )
+ {
+ if ((layout = H5Pget_layout(dcpl_id))<0)
+ return -1;
+
+ if (layout == H5D_CHUNKED)
+ {
+ if ((rank = H5Pget_chunk(dcpl_id,NELMTS(chsize),chsize/*out*/))<0)
+ return -1;
+ obj.layout = H5D_CHUNKED;
+ obj.chunk.rank = rank;
+ for ( i = 0; i < rank; i++)
+ obj.chunk.chunk_lengths[i] = chsize[i];
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * the type of filter and additional parameter
+ * type can be one of the filters
+ * H5Z_FILTER_NONE 0 , uncompress if compressed
+ * H5Z_FILTER_DEFLATE 1 , deflation like gzip
+ * H5Z_FILTER_SHUFFLE 2 , shuffle the data
+ * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
+ * H5Z_FILTER_SZIP 4 , szip compression
+ * H5Z_FILTER_NBIT 5 , nbit compression
+ * H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression
+ *-------------------------------------------------------------------------
+ */
+
+ if (obj.nfilters)
+ {
+
+ /*-------------------------------------------------------------------------
+ * filters require CHUNK layout; if we do not have one define a default
+ *-------------------------------------------------------------------------
+ */
+ if (obj.layout==-1)
+ {
+
+ /* stripmine info */
+ hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
+ hsize_t sm_nbytes; /*bytes per stripmine */
+
+ obj.chunk.rank = rank;
+
+ /*
+ * determine the strip mine size. The strip mine is
+ * a hyperslab whose size is manageable.
+ */
+
+
+
+ sm_nbytes = msize;
+ for ( i = rank; i > 0; --i)
+ {
+ hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
+ if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
+ size = 1;
+ sm_size[i - 1] = MIN(dims[i - 1], size);
+ sm_nbytes *= sm_size[i - 1];
+ HDassert(sm_nbytes > 0);
+
+ }
+
+ for ( i = 0; i < rank; i++)
+ {
+ obj.chunk.chunk_lengths[i] = sm_size[i];
+ }
+
+ }
+
+ for ( i=0; i<obj.nfilters; i++)
+ {
+ switch (obj.filter[i].filtn)
+ {
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_NONE 0 , uncompress if compressed
+ *-------------------------------------------------------------------------
+ */
+ case H5Z_FILTER_NONE:
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_DEFLATE 1 , deflation like gzip
+ *-------------------------------------------------------------------------
+ */
+ case H5Z_FILTER_DEFLATE:
+ {
+ unsigned aggression; /* the deflate level */
+
+ aggression = obj.filter[i].cd_values[0];
+ /* set up for deflated data */
+ if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+ return -1;
+ if(H5Pset_deflate(dcpl_id,aggression)<0)
+ return -1;
+ }
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SZIP 4 , szip compression
+ *-------------------------------------------------------------------------
+ */
+ case H5Z_FILTER_SZIP:
+ {
+ unsigned options_mask;
+ unsigned pixels_per_block;
+
+ options_mask = obj.filter[i].cd_values[0];
+ pixels_per_block = obj.filter[i].cd_values[1];
+
+ /* set up for szip data */
+ if(H5Pset_chunk(dcpl_id,obj.chunk.rank,obj.chunk.chunk_lengths)<0)
+ return -1;
+ if (H5Pset_szip(dcpl_id,options_mask,pixels_per_block)<0)
+ return -1;
+
+ }
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_SHUFFLE 2 , shuffle the data
+ *-------------------------------------------------------------------------
+ */
+ case H5Z_FILTER_SHUFFLE:
+ if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+ return -1;
+ if (H5Pset_shuffle(dcpl_id)<0)
+ return -1;
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC
+ *-------------------------------------------------------------------------
+ */
+ case H5Z_FILTER_FLETCHER32:
+ if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+ return -1;
+ if (H5Pset_fletcher32(dcpl_id)<0)
+ return -1;
+ break;
+ /*----------- -------------------------------------------------------------
+ * H5Z_FILTER_NBIT , NBIT compression
+ *-------------------------------------------------------------------------
+ */
+ case H5Z_FILTER_NBIT:
+ if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+ return -1;
+ if (H5Pset_nbit(dcpl_id)<0)
+ return -1;
+ break;
+ /*----------- -------------------------------------------------------------
+ * H5Z_FILTER_SCALEOFFSET , scale+offset compression
+ *-------------------------------------------------------------------------
+ */
+
+ case H5Z_FILTER_SCALEOFFSET:
+ {
+ H5Z_SO_scale_type_t scale_type;
+ int scale_factor;
+
+ scale_type = (H5Z_SO_scale_type_t)obj.filter[i].cd_values[0];
+ scale_factor = (int)obj.filter[i].cd_values[1];
+
+ if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+ return -1;
+ if (H5Pset_scaleoffset(dcpl_id,scale_type,scale_factor)<0)
+ 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*/
+
+ }
+ /*obj.nfilters*/
+
+ /*-------------------------------------------------------------------------
+ * layout
+ *-------------------------------------------------------------------------
+ */
+
+ if (obj.layout>=0)
+ {
+ /* a layout was defined */
+ if (H5Pset_layout(dcpl_id, obj.layout)<0)
+ return -1;
+
+ if (H5D_CHUNKED == obj.layout)
+ {
+ if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+ return -1;
+ }
+ else if (H5D_COMPACT == obj.layout)
+ {
+ if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY)<0)
+ return -1;
+ }
+ /* remove filters for the H5D_CONTIGUOUS case */
+ else if (H5D_CONTIGUOUS == obj.layout)
+ {
+ if (H5Premove_filter(dcpl_id,H5Z_FILTER_ALL)<0)
+ return -1;
+ }
+
+ }
+
+ return 0;
+}
+
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
new file mode 100644
index 0000000..2d48a04
--- /dev/null
+++ b/tools/src/h5repack/h5repack_main.c
@@ -0,0 +1,664 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 "h5tools.h"
+#include "h5tools_utils.h"
+#include "h5repack.h"
+
+/* Name of tool */
+#define PROGRAMNAME "h5repack"
+
+static int parse_command_line(int argc, const char **argv, pack_opt_t* options);
+static void leave(int ret) H5_ATTR_NORETURN;
+
+
+/* module-scoped variables */
+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:E";
+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' },
+ { "enable-error-stack", no_arg, 'E' },
+ { NULL, 0, '\0' }
+};
+
+/*-------------------------------------------------------------------------
+ * Function: usage
+ *
+ * Purpose: print usage
+ *
+ * Return: void
+ *
+ *-------------------------------------------------------------------------
+ */
+static void usage(const char *prog) {
+ FLUSHSTREAM(rawoutstream);
+ PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] file1 file2\n", prog);
+ PRINTVALSTREAM(rawoutstream, " file1 Input HDF5 File\n");
+ PRINTVALSTREAM(rawoutstream, " file2 Output HDF5 File\n");
+ PRINTVALSTREAM(rawoutstream, " OPTIONS\n");
+ PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n");
+ PRINTVALSTREAM(rawoutstream, " -v, --verbose Verbose mode, print object information\n");
+ PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n");
+ PRINTVALSTREAM(rawoutstream, " -n, --native Use a native HDF5 type when repacking\n");
+ PRINTVALSTREAM(rawoutstream, " -L, --latest Use latest version of file format\n");
+ PRINTVALSTREAM(rawoutstream, " -c L1, --compact=L1 Maximum number of links in header messages\n");
+ PRINTVALSTREAM(rawoutstream, " -d L2, --indexed=L2 Minimum number of links in the indexed format\n");
+ PRINTVALSTREAM(rawoutstream, " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
+ PRINTVALSTREAM(rawoutstream, " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n");
+ PRINTVALSTREAM(rawoutstream, " -e E, --file=E Name of file E with the -f and -l options\n");
+ PRINTVALSTREAM(rawoutstream, " -u U, --ublock=U Name of file U with user block data to be added\n");
+ PRINTVALSTREAM(rawoutstream, " -b B, --block=B Size of user block to be added\n");
+ PRINTVALSTREAM(rawoutstream, " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n");
+ PRINTVALSTREAM(rawoutstream, " -t T, --threshold=T Threshold value for H5Pset_alignment\n");
+ PRINTVALSTREAM(rawoutstream, " -a A, --alignment=A Alignment value for H5Pset_alignment\n");
+ PRINTVALSTREAM(rawoutstream, " -f FILT, --filter=FILT Filter type\n");
+ PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\n");
+ PRINTVALSTREAM(rawoutstream, " -S FS_STRGY, --fs_strategy=FS_STRGY File space management strategy\n");
+ PRINTVALSTREAM(rawoutstream, " -T FS_THRD, --fs_threshold=FS_THRD Free-space section threshold\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
+ PRINTVALSTREAM(rawoutstream, " E - is a filename.\n");
+ PRINTVALSTREAM(rawoutstream, " S - is an integer\n");
+ PRINTVALSTREAM(rawoutstream, " U - is a filename.\n");
+ PRINTVALSTREAM(rawoutstream, " T - is an integer\n");
+ PRINTVALSTREAM(rawoutstream, " A - is an integer greater than zero\n");
+ PRINTVALSTREAM(rawoutstream, " B - is the user block size, any value that is 512 or greater and is\n");
+ PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n");
+ PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n");
+ PRINTVALSTREAM(rawoutstream, " pline|attr>. If F is not specified, S applies to all messages\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they\n");
+ PRINTVALSTREAM(rawoutstream, " occur.\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " FS_STRGY is the file space management strategy to use for the output file.\n");
+ PRINTVALSTREAM(rawoutstream, " It is a string as listed below:\n");
+ PRINTVALSTREAM(rawoutstream, " ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n");
+ PRINTVALSTREAM(rawoutstream, " for file space allocation\n");
+ PRINTVALSTREAM(rawoutstream, " ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n");
+ PRINTVALSTREAM(rawoutstream, " for file space allocation\n");
+ PRINTVALSTREAM(rawoutstream, " AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n");
+ PRINTVALSTREAM(rawoutstream, " VFD - Use virtual file driver for file space allocation\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " FS_THRD is the free-space section threshold to use for the output file.\n");
+ PRINTVALSTREAM(rawoutstream, " It is the minimum size (in bytes) of free-space sections to be tracked\n");
+ PRINTVALSTREAM(rawoutstream, " by the the library's free-space managers.\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " FILT - is a string with the format:\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " <list of objects>:<name of filter>=<filter parameters>\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning apply\n");
+ PRINTVALSTREAM(rawoutstream, " compression only to those objects. If no names are specified, the filter\n");
+ PRINTVALSTREAM(rawoutstream, " is applied to all objects\n");
+ PRINTVALSTREAM(rawoutstream, " <name of filter> can be:\n");
+ PRINTVALSTREAM(rawoutstream, " GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
+ PRINTVALSTREAM(rawoutstream, " SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
+ PRINTVALSTREAM(rawoutstream, " SHUF, to apply the HDF5 shuffle filter\n");
+ PRINTVALSTREAM(rawoutstream, " FLET, to apply the HDF5 checksum filter\n");
+ PRINTVALSTREAM(rawoutstream, " NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
+ PRINTVALSTREAM(rawoutstream, " SOFF, to apply the HDF5 Scale/Offset filter\n");
+ PRINTVALSTREAM(rawoutstream, " UD, to apply a user defined filter\n");
+ PRINTVALSTREAM(rawoutstream, " NONE, to remove all filters\n");
+ PRINTVALSTREAM(rawoutstream, " <filter parameters> is optional filter parameter information\n");
+ PRINTVALSTREAM(rawoutstream, " GZIP=<deflation level> from 1-9\n");
+ PRINTVALSTREAM(rawoutstream, " SZIP=<pixels per block,coding> pixels per block is a even number in\n");
+ PRINTVALSTREAM(rawoutstream, " 2-32 and coding method is either EC or NN\n");
+ PRINTVALSTREAM(rawoutstream, " SHUF (no parameter)\n");
+ PRINTVALSTREAM(rawoutstream, " FLET (no parameter)\n");
+ PRINTVALSTREAM(rawoutstream, " NBIT (no parameter)\n");
+ PRINTVALSTREAM(rawoutstream, " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
+ PRINTVALSTREAM(rawoutstream, " is either IN or DS\n");
+ PRINTVALSTREAM(rawoutstream, " UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
+ PRINTVALSTREAM(rawoutstream, " required values for filter_number,cd_value_count,value_1\n");
+ PRINTVALSTREAM(rawoutstream, " optional values for value_2 to value_N\n");
+ PRINTVALSTREAM(rawoutstream, " NONE (no parameter)\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " LAYT - is a string with the format:\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " <list of objects>:<layout type>=<layout parameters>\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning that\n");
+ PRINTVALSTREAM(rawoutstream, " layout information is supplied for those objects. If no names are\n");
+ PRINTVALSTREAM(rawoutstream, " specified, the layout type is applied to all objects\n");
+ PRINTVALSTREAM(rawoutstream, " <layout type> can be:\n");
+ PRINTVALSTREAM(rawoutstream, " CHUNK, to apply chunking layout\n");
+ PRINTVALSTREAM(rawoutstream, " COMPA, to apply compact layout\n");
+ PRINTVALSTREAM(rawoutstream, " CONTI, to apply contiguous layout\n");
+ PRINTVALSTREAM(rawoutstream, " <layout parameters> is optional layout information\n");
+ PRINTVALSTREAM(rawoutstream, " CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
+ PRINTVALSTREAM(rawoutstream, " COMPA (no parameter)\n");
+ PRINTVALSTREAM(rawoutstream, " CONTI (no parameter)\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "Examples of use:\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "1) h5repack -v -f GZIP=1 file1 file2\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " GZIP compression with level 1 to all objects\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " SZIP compression with 8 pixels per block and NN coding method to object dset1\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n");
+ PRINTVALSTREAM(rawoutstream, " and remove filters to objects dset3, dset4, dset5\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " Using latest file format with maximum compact group size of 10 and\n");
+ PRINTVALSTREAM(rawoutstream, " and minimum shared datatype size of 20\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " Add both filters SHUF and GZIP in this order to all datasets\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "6) h5repack -f UD=307,1,9 file1 file2 \n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " Add bzip2 filter to all datasets\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+}
+
+/*-------------------------------------------------------------------------
+ * Function: leave
+ *
+ * Purpose: Shutdown MPI & HDF5 and call exit()
+ *
+ * Return: Does not return
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, 31. January 2004
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void leave(int ret) {
+ h5tools_close();
+
+ HDexit(ret);
+}
+
+/*-------------------------------------------------------------------------
+ * Function: read_info
+ *
+ * Purpose: read comp and chunk options from a file
+ *
+ * Return: void, exit on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+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 != ' ') {
+ if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ } /* end if */
+ if (HDfeof(fp))
+ break;
+ }
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ } /* end if */
+ 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 != ' ') {
+ if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ } /* end if */
+ if (HDfeof(fp))
+ break;
+ }
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ } /* end if */
+ 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
+ *
+ * Purpose: parse command line input
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static
+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 = HDstrtoull(opt_arg , NULL, 0);
+ 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 = HDstrtoull(opt_arg , NULL, 0);
+ 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;
+
+ case 'E':
+ enable_error_stack = TRUE;
+ 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: main
+ *
+ * Purpose: h5repack main program
+ *
+ * Return: Success: EXIT_SUCCESS(0)
+ *
+ * Failure: EXIT_FAILURE(1)
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
+ *
+ *-------------------------------------------------------------------------
+ */
+int main(int argc, const char **argv) {
+ H5E_auto2_t func;
+ H5E_auto2_t tools_func;
+ void *edata;
+ void *tools_edata;
+
+ pack_opt_t options; /*the global options */
+
+ h5tools_setprogname(PROGRAMNAME);
+ h5tools_setstatus(EXIT_SUCCESS);
+
+ /* Disable error reporting */
+ H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+ H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+ /* Initialize h5tools lib */
+ h5tools_init();
+
+ /* Disable tools error reporting */
+ H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata);
+ H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL);
+
+ /* 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;
+ }
+ }
+
+ if (enable_error_stack) {
+ H5Eset_auto2(H5E_DEFAULT, func, edata);
+ H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
+ }
+
+ /* pack it */
+ h5tools_setstatus(h5repack(infile, outfile, &options));
+
+done:
+ /* free tables */
+ h5repack_end(&options);
+
+ leave(h5tools_getstatus());
+}
+
diff --git a/tools/src/h5repack/h5repack_opttable.c b/tools/src/h5repack/h5repack_opttable.c
new file mode 100644
index 0000000..8c98b76
--- /dev/null
+++ b/tools/src/h5repack/h5repack_opttable.c
@@ -0,0 +1,367 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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"
+
+/*-------------------------------------------------------------------------
+ * Function: init_packobject
+ *
+ * Purpose: initialize a pack_info_t structure
+ *
+ * Return: void
+ *
+ *-------------------------------------------------------------------------
+ */
+
+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;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: aux_tblinsert_filter
+ *
+ * Purpose: auxiliary function, inserts the filter in object OBJS[ I ]
+ *
+ * Return: void
+ *
+ *-------------------------------------------------------------------------
+ */
+
+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");
+ }
+}
+
+/*-------------------------------------------------------------------------
+ * Function: aux_tblinsert_layout
+ *
+ * Purpose: auxiliary function, inserts the layout in object OBJS[ I ]
+ *
+ * Return: void
+ *
+ *-------------------------------------------------------------------------
+ */
+
+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
+ *
+ * Purpose: auxiliary function, increases the size of the collection by N_OBJS
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+aux_inctable(pack_opttbl_t *table, unsigned n_objs)
+{
+ unsigned u;
+
+ 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 (u = table->nelems; u < table->size; u++)
+ init_packobject(&table->objs[u]);
+
+ return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: options_table_init
+ *
+ * Purpose: init options table
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+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;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: options_table_free
+ *
+ * Purpose: free table memory
+ *
+ * Return: 0
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int options_table_free(pack_opttbl_t *table) {
+ HDfree(table->objs);
+ HDfree(table);
+ return 0;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: options_add_layout
+ *
+ * Purpose: add a layout option to the option list
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack,
+ pack_opttbl_t *table)
+{
+ unsigned i, j, I;
+ unsigned added = 0;
+ hbool_t found = FALSE;
+
+ /* 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 = TRUE;
+ break;
+ }
+ } /* if */
+ } /* i */
+
+ if (!found) {
+ /* 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 && 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
+ *
+ * Purpose: add a compression -f option to the option list
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt,
+ pack_opttbl_t *table)
+{
+ unsigned int i, j, I;
+ unsigned added = 0;
+ hbool_t found = FALSE;
+
+ /* 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 = TRUE;
+ break;
+ } /* if */
+ } /* i */
+
+ if (!found) {
+ /* 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 && 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;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: options_get_object
+ *
+ * Purpose: get object from table; "path" is the key
+ *
+ * Return: pack_info_t* OBJECT or NULL if not found; PATH is the key
+ *
+ *-------------------------------------------------------------------------
+ */
+
+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/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c
new file mode 100644
index 0000000..004b9e4
--- /dev/null
+++ b/tools/src/h5repack/h5repack_parse.c
@@ -0,0 +1,616 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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"
+
+/*-------------------------------------------------------------------------
+ * Function: parse_filter
+ *
+ * Purpose: read filter information
+ *
+ * Return: a list of names, the number of names and its compression type
+ *
+ * <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 (compression)
+ * UD, to apply a User Defined filter k,m,n1[,…,nm]
+ * NONE, to remove the filter
+ *
+ * Examples:
+ * "GZIP=6"
+ * "A,B:NONE"
+ *-------------------------------------------------------------------------
+ */
+obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
+ pack_opt_t *options, int *is_glb) {
+ size_t i, m, u;
+ char c;
+ size_t len = HDstrlen(str);
+ int k, l, p, q, end_obj = -1, no_param = 0;
+ unsigned j, n;
+ char sobj[MAX_NC_NAME];
+ char scomp[10];
+ char stype[6];
+ 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 = (int) i;
+ if (c == ',')
+ n++;
+ }
+
+ /* Check for missing : */
+ if (end_obj == -1) {
+ /* 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 */
+ if (end_obj > 0)
+ for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) {
+ c = str[j];
+ sobj[k] = c;
+ if (c == ',' || j == (unsigned) (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 = (size_t)(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 (!HDisdigit(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 (!HDisdigit(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 */
+ 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 = HDatoi(stype);
+ l = 0;
+ }
+ else if (p == -1) {
+ filt->cd_nelmts = HDstrtoull(stype, NULL, 0);
+ p = 0;
+ }
+ else
+ filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0);
+ q = 0;
+ u++; /* skip ',' */
+ }
+ c = str[u];
+ if (!HDisdigit(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;
+ } /* for 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 (!HDisdigit(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++] = (unsigned) HDstrtoul(stype, NULL, 0);
+ if(filt->cd_nelmts == 0)
+ j = 0;
+ 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) {
+ /* parameters does not match count */
+ if (filt->cd_nelmts != j) {
+ 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;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: parse_layout
+ *
+ * Purpose: read layout info
+ *
+ * Return: a list of names, the number of names and its chunking info for
+ * chunked. NULL, on error
+ * the layout type can be:
+ * CHUNK, to apply chunking layout
+ * CONTI, to apply contiguous layout
+ * COMPA, to apply compact layout
+ *
+ * Example:
+ * "AA,B,CDE:CHUNK=10X10"
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 30, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+obj_list_t* parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */
+pack_opt_t *options) {
+ obj_list_t* obj_list = NULL;
+ unsigned i, j, n;
+ char c;
+ size_t len = HDstrlen(str);
+ int k, end_obj = -1, c_index;
+ char sobj[MAX_NC_NAME];
+ char sdim[10];
+ char slayout[10];
+
+ HDmemset(sdim, '\0', sizeof(sdim));
+ HDmemset(sobj, '\0', sizeof(sobj));
+ HDmemset(slayout, '\0', sizeof(slayout));
+
+ /* 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 = (int) i;
+ if (c == ',')
+ n++;
+ }
+
+ if (end_obj == -1) { /* missing : chunk all */
+ options->all_layout = 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 */
+ if (end_obj > 0)
+ for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) {
+ c = str[j];
+ sobj[k] = c;
+ if (c == ',' || j == (unsigned) (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("in parse layout, no characters after : in <%s>\n", str);
+ HDexit(EXIT_FAILURE);
+ }
+
+ /* get layout info */
+ for (j = (unsigned) (end_obj + 1), n = 0; n <= 5; j++, n++) {
+ if (n == 5) {
+ slayout[n] = '\0'; /*cut string */
+ if (HDstrcmp(slayout, "COMPA") == 0)
+ pack->layout = H5D_COMPACT;
+ else if (HDstrcmp(slayout, "CONTI") == 0)
+ pack->layout = H5D_CONTIGUOUS;
+ else if (HDstrcmp(slayout, "CHUNK") == 0)
+ pack->layout = H5D_CHUNKED;
+ else {
+ error_msg("in parse layout, not a valid layout in <%s>\n", str);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+ else {
+ c = str[j];
+ slayout[n] = c;
+ }
+ } /* j */
+
+ if (pack->layout == H5D_CHUNKED) {
+ /*-------------------------------------------------------------------------
+ * get chunk info
+ *-------------------------------------------------------------------------
+ */
+ k = 0;
+ if (j > len) {
+ if (obj_list)
+ HDfree(obj_list);
+ error_msg("in parse layout, <%s> Chunk dimensions missing\n", str);
+ HDexit(EXIT_FAILURE);
+ }
+
+ for (i = j, c_index = 0; i < len; i++) {
+ c = str[i];
+ sdim[k] = c;
+ k++; /*increment sdim index */
+
+ if (!HDisdigit(c) && c != 'x' && c != 'N' && c != 'O' && c != 'N' && c != 'E') {
+ if (obj_list)
+ HDfree(obj_list);
+ error_msg("in parse layout, <%s> Not a valid character in <%s>\n", sdim, str);
+ HDexit(EXIT_FAILURE);
+ }
+
+ if (c == 'x' || i == len - 1) {
+ if (c == 'x') {
+ sdim[k - 1] = '\0';
+ k = 0;
+ pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
+ if (pack->chunk.chunk_lengths[c_index] == 0) {
+ if (obj_list)
+ HDfree(obj_list);
+ error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
+ HDexit(EXIT_FAILURE);
+ }
+ c_index++;
+ }
+ else if (i == len - 1) { /*no more parameters */
+ sdim[k] = '\0';
+ k = 0;
+ if (HDstrcmp(sdim,"NONE") == 0) {
+ pack->chunk.rank = -2;
+ }
+ else {
+ pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
+ if (pack->chunk.chunk_lengths[c_index] == 0) {
+ if (obj_list)
+ HDfree(obj_list);
+ error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
+ HDexit(EXIT_FAILURE);
+ }
+ pack->chunk.rank = c_index + 1;
+ }
+ } /*if */
+ } /*if c=='x' || i==len-1 */
+ } /*i*/
+ } /*H5D_CHUNKED*/
+
+ return obj_list;
+}
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c
new file mode 100644
index 0000000..f0f32c3
--- /dev/null
+++ b/tools/src/h5repack/h5repack_refs.c
@@ -0,0 +1,877 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 "h5diff.h"
+#include "h5tools.h"
+
+
+/*-------------------------------------------------------------------------
+ * local functions
+ *-------------------------------------------------------------------------
+ */
+
+static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
+static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
+ trav_table_t *travt, hid_t fidout);
+static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
+ hid_t fid_out, void *ref_out, trav_table_t *travt);
+
+/*-------------------------------------------------------------------------
+ * Function: do_copy_refobjs
+ *
+ * Purpose: duplicate all referenced HDF5 objects in the file
+ * and create hard links
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December, 10, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int do_copy_refobjs(hid_t fidin,
+ hid_t fidout,
+ trav_table_t *travt,
+ pack_opt_t *options) /* repack options */
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ hid_t grp_in = (-1); /* read group ID */
+ hid_t grp_out = (-1); /* write group ID */
+ hid_t dset_in = (-1); /* read dataset ID */
+ hid_t dset_out = (-1); /* write dataset ID */
+ hid_t type_in = (-1); /* named type ID */
+ hid_t dcpl_id = (-1); /* dataset creation property list ID */
+ hid_t space_id = (-1); /* space ID */
+ hid_t ftype_id = (-1); /* file data type ID */
+ hid_t mtype_id = (-1); /* memory data type ID */
+ size_t msize; /* memory size of memory type */
+ hsize_t nelmts; /* number of elements in dataset */
+ int rank; /* rank of dataset */
+ hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
+ unsigned int i, j;
+ int k;
+ named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes
+ copied */
+
+ /*-------------------------------------------------------------------------
+ * browse
+ *-------------------------------------------------------------------------
+ */
+ for(i = 0; i < travt->nobjs; i++) {
+ switch(travt->objs[i].type)
+ {
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_GROUP
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_GROUP:
+ /*-------------------------------------------------------------------------
+ * copy referenced objects in attributes
+ *-------------------------------------------------------------------------
+ */
+ if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+
+ if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+
+ if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
+
+ if(H5Gclose(grp_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+ if(H5Gclose(grp_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+
+ /*-------------------------------------------------------------------------
+ * check for hard links
+ *-------------------------------------------------------------------------
+ */
+ if(travt->objs[i].nlinks)
+ for(j = 0; j < travt->objs[i].nlinks; j++)
+ H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_DATASET
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_DATASET:
+ if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if((space_id = H5Dget_space(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
+ if((ftype_id = H5Dget_type(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
+ if((dcpl_id = H5Dget_create_plist(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ if((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
+ if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+ nelmts = 1;
+ for(k = 0; k < rank; k++)
+ nelmts *= dims[k];
+
+ if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+
+ if((msize = H5Tget_size(mtype_id)) == 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+
+ /*-------------------------------------------------------------------------
+ * 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(NULL, dcpl_id) == 1) {
+ /*-------------------------------------------------------------------------
+ * test for a valid output dataset
+ *-------------------------------------------------------------------------
+ */
+ dset_out = FAIL;
+
+ /*-------------------------------------------------------------------------
+ * object references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ *-------------------------------------------------------------------------
+ */
+ if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
+ hid_t refobj_id;
+ hobj_ref_t *refbuf = NULL; /* buffer for object references */
+ hobj_ref_t *buf = NULL;
+ const char* refname;
+ unsigned u;
+
+ /*-------------------------------------------------------------------------
+ * read to memory
+ *-------------------------------------------------------------------------
+ */
+ if(nelmts) {
+ buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+ if(buf==NULL) {
+ printf("cannot read into memory\n" );
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
+ } /* end if */
+ if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+
+ refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize);
+ if(refbuf == NULL){
+ printf("cannot allocate memory\n" );
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
+ } /* end if */
+ for(u = 0; u < nelmts; u++) {
+ H5E_BEGIN_TRY {
+ if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0)
+ continue;
+ } H5E_END_TRY;
+
+ /* get the name. a valid name could only occur
+ * in the second traversal of the file
+ */
+ if((refname = MapIdToName(refobj_id, travt)) != NULL) {
+ /* create the reference, -1 parameter for objects */
+ if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
+ if(options->verbose)
+ {
+ printf(FORMAT_OBJ,"dset",travt->objs[i].name );
+ printf("object <%s> object reference created to <%s>\n",
+ travt->objs[i].name,
+ refname);
+ }
+ } /*refname*/
+ H5Oclose(refobj_id);
+ } /* u */
+ } /*nelmts*/
+
+ /*-------------------------------------------------------------------------
+ * create/write dataset/close
+ *-------------------------------------------------------------------------
+ */
+ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ if(nelmts)
+ if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
+
+ if(buf)
+ HDfree(buf);
+ if(refbuf)
+ HDfree(refbuf);
+
+ /*------------------------------------------------------
+ * copy attrs
+ *----------------------------------------------------*/
+ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+ } /*H5T_STD_REF_OBJ*/
+
+ /*-------------------------------------------------------------------------
+ * dataset region references
+ *-------------------------------------------------------------------------
+ */
+ else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
+ {
+ hid_t refobj_id;
+ hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
+ hdset_reg_ref_t *buf = NULL; /* output buffer */
+ const char* refname;
+ unsigned u;
+
+ /*-------------------------------------------------------------------------
+ * read input to memory
+ *-------------------------------------------------------------------------
+ */
+ if(nelmts) {
+ buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+ if(buf == NULL) {
+ printf("cannot read into memory\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
+ } /* end if */
+ if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+
+ /*-------------------------------------------------------------------------
+ * create output
+ *-------------------------------------------------------------------------
+ */
+ refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
+ if(refbuf == NULL) {
+ printf("cannot allocate memory\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
+ } /* end if */
+
+ for(u = 0; u < nelmts; u++) {
+ H5E_BEGIN_TRY {
+ if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, &buf[u])) < 0)
+ continue;
+ } H5E_END_TRY;
+
+ /* get the name. a valid name could only occur
+ * in the second traversal of the file
+ */
+ if((refname = MapIdToName(refobj_id, travt)) != NULL) {
+ hid_t region_id; /* region id of the referenced dataset */
+
+ if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed");
+
+ /* create the reference, we need the space_id */
+ if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
+ if(H5Sclose(region_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if(options->verbose)
+ {
+ printf(FORMAT_OBJ,"dset",travt->objs[i].name );
+ printf("object <%s> region reference created to <%s>\n",
+ travt->objs[i].name,
+ refname);
+ }
+ } /*refname*/
+ H5Oclose(refobj_id);
+ } /* u */
+ } /*nelmts*/
+
+ /*-------------------------------------------------------------------------
+ * create/write dataset/close
+ *-------------------------------------------------------------------------
+ */
+ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ if(nelmts)
+ if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
+
+ if(buf)
+ HDfree(buf);
+ if(refbuf)
+ HDfree(refbuf);
+
+ /*-----------------------------------------------------
+ * copy attrs
+ *----------------------------------------------------*/
+ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+ } /* H5T_STD_REF_DSETREG */
+ /*-------------------------------------------------------------------------
+ * not references, open previously created object in 1st traversal
+ *-------------------------------------------------------------------------
+ */
+ else {
+ if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ } /* end else */
+
+ HDassert(dset_out != FAIL);
+
+ /*-------------------------------------------------------------------------
+ * copy referenced objects in attributes
+ *-------------------------------------------------------------------------
+ */
+ if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
+
+ /*-------------------------------------------------------------------------
+ * check for hard links
+ *-------------------------------------------------------------------------
+ */
+ if(travt->objs[i].nlinks)
+ for(j = 0; j < travt->objs[i].nlinks; j++)
+ H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
+
+ if(H5Dclose(dset_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ } /*can_read*/
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if(H5Tclose(ftype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if(H5Tclose(mtype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if(H5Pclose(dcpl_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if(H5Sclose(space_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if(H5Dclose(dset_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_NAMED_DATATYPE
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_NAMED_DATATYPE:
+ if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
+ if(H5Tclose(type_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_LINK
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_LINK:
+ /*nothing to do */
+ break;
+
+ case H5TRAV_TYPE_UNKNOWN:
+ case H5TRAV_TYPE_UDLINK:
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5TRAV invalid type");
+
+ default:
+ break;
+ } /* end switch */
+ } /* end for */
+
+ /* Finalize (link) the stack of named datatypes (if any)
+ * This function is paired with copy_named_datatype() which is called
+ * in copy_attr(), so need to free.
+ */
+ named_datatype_free(&named_dt_head, 0);
+
+ return ret_value;
+
+done:
+ H5E_BEGIN_TRY {
+ H5Gclose(grp_in);
+ H5Gclose(grp_out);
+ H5Pclose(dcpl_id);
+ H5Sclose(space_id);
+ H5Dclose(dset_in);
+ H5Dclose(dset_out);
+ H5Tclose(ftype_id);
+ H5Tclose(mtype_id);
+ H5Tclose(type_in);
+ named_datatype_free(&named_dt_head, 0);
+ } H5E_END_TRY;
+
+ return ret_value;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: copy_refs_attr
+ *
+ * Purpose: duplicate all referenced HDF5 located in attributes
+ * relative to LOC_IN, which is obtained either from
+ * loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
+ * loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
+ * loc_id = H5Topen2(fid, name, H5P_DEFAULT);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Modifier: xcao@hdfgroup.org, 9/12/2011
+ * Update values of references(object and region) for the following types:
+ * 1) References,
+ * 2) ARRAY of reference,
+ * 3) VLEN of references.
+ * 4) COMPOUND of references.
+ * This function does not handle references in other complicated structures,
+ * such as references in nested compound datatypes.
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static int copy_refs_attr(hid_t loc_in,
+ hid_t loc_out,
+ pack_opt_t *options,
+ trav_table_t *travt,
+ hid_t fidout /* for saving references */
+ )
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ 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 data type ID */
+ hid_t mtype_id = -1; /* memory data type ID */
+ size_t msize; /* memory size of type */
+ hsize_t nelmts; /* number of elements in dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ char name[255];
+ H5O_info_t oinfo; /* Object info */
+ unsigned u, i, j;
+ int rank;
+ H5T_class_t type_class = -1;
+ hbool_t is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0;
+ void *refbuf = NULL;
+ void *buf = NULL;
+ const char* refname = NULL;
+ unsigned *ref_comp_index = NULL;
+ size_t *ref_comp_size = NULL;
+ int ref_comp_field_n = 0;
+
+
+ if(H5Oget_info(loc_in, &oinfo) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
+
+ for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
+ is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
+
+ /* 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)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
+
+ /* get the file datatype */
+ if((ftype_id = H5Aget_type(attr_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
+
+ type_class = H5Tget_class(ftype_id);
+
+ if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+
+ if((msize = H5Tget_size(mtype_id)) == 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+
+ is_ref = (type_class == H5T_REFERENCE);
+
+ if(type_class == H5T_VLEN ) {
+ hid_t base_type;
+
+ base_type = H5Tget_super(ftype_id);
+ is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
+ msize = H5Tget_size(base_type);
+ H5Tclose(base_type);
+ }
+ else if(type_class == H5T_ARRAY ) {
+ hid_t base_type;
+
+ base_type = H5Tget_super(ftype_id);
+ is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
+ msize = H5Tget_size(base_type);
+ H5Tclose(base_type);
+ }
+ else if(type_class == H5T_COMPOUND) {
+ int nmembers = H5Tget_nmembers(ftype_id) ;
+
+ if (nmembers < 1)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed");
+
+ ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers*sizeof(unsigned));
+ ref_comp_size = (size_t *)HDmalloc((size_t)nmembers*sizeof(ref_comp_size));
+ ref_comp_field_n = 0;
+
+ for (i=0; i<(unsigned)nmembers; i++) {
+ hid_t mtid = H5Tget_member_type( ftype_id, i );
+
+ if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
+ ref_comp_index[ref_comp_field_n] = i;
+ ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
+ ref_comp_field_n++;
+ }
+ H5Tclose(mtid);
+ }
+
+ /* if compound don't contain reference type member, free the above
+ * mallocs. Otherwise there can be memory leaks by the 'continue'
+ * statement below. */
+ if (!ref_comp_field_n) {
+ if (ref_comp_index) {
+ HDfree(ref_comp_index);
+ ref_comp_index = NULL;
+ }
+
+ if (ref_comp_size) {
+ HDfree(ref_comp_size);
+ ref_comp_size = NULL;
+ }
+ }
+ }
+
+ is_ref_comp = (ref_comp_field_n > 0);
+
+ if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) {
+ H5Tclose(mtype_id);
+ H5Tclose(ftype_id);
+ H5Aclose(attr_id);
+ continue;
+ }
+
+ /* get name */
+ if(H5Aget_name(attr_id, 255, name) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_name failed");
+
+ /* get the dataspace handle */
+ if((space_id = H5Aget_space(attr_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed");
+
+ /* get dimensions */
+ if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+
+
+ /*-------------------------------------------------------------------------
+ * elements
+ *-------------------------------------------------------------------------
+ */
+ nelmts = 1;
+ for(j = 0; j < (unsigned)rank; j++)
+ nelmts *= dims[j];
+
+ if (is_ref_array) {
+ unsigned array_rank = 0;
+ hsize_t array_size = 1;
+ hsize_t array_dims[H5S_MAX_RANK];
+ hid_t base_type;
+
+ base_type = H5Tget_super(ftype_id);
+ msize = H5Tget_size(base_type);
+ H5Tclose(base_type);
+
+ array_rank = (unsigned)H5Tget_array_ndims(mtype_id);
+ H5Tget_array_dims2(mtype_id, array_dims);
+ for(j = 0; j <array_rank; j++)
+ array_size *= array_dims[j];
+ nelmts *= array_size;
+ }
+
+ if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed");
+
+ if (nelmts>0) {
+ /* handle object references */
+ if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) {
+ buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+ if(buf == NULL) {
+ printf("cannot read into memory\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
+ } /* end if */
+ if(H5Aread(attr_id, mtype_id, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
+
+ refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize);
+ if(refbuf == NULL) {
+ printf("cannot allocate memory\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
+ } /* end if */
+
+ for(i = 0; i < (unsigned)nelmts; i++) {
+ if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0)
+ continue;
+ if(options->verbose)
+ printf("object <%s> reference created to <%s>\n", name, refname);
+ } /* i */
+ } /* H5T_STD_REF_OBJ */
+ /* handle region references */
+ else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) {
+ buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+
+ if(buf == NULL) {
+ printf( "cannot read into memory\n" );
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
+ } /* end if */
+ if(H5Aread(attr_id, mtype_id, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
+
+ /*-------------------------------------------------------------------------
+ * create output
+ *-------------------------------------------------------------------------
+ */
+ refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
+ if(refbuf == NULL) {
+ printf( "cannot allocate memory\n" );
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
+ } /* end if */
+
+ for(i = 0; i < (unsigned)nelmts; i++) {
+ if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0)
+ continue;
+ if(options->verbose)
+ printf("object <%s> region reference created to <%s>\n", name, refname);
+ }
+ } /* H5T_STD_REF_DSETREG */
+ else if (is_ref_vlen) {
+ /* handle VLEN of references */
+
+ buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t)));
+ refbuf = buf; /* reuse the read buffer for write */
+
+ if(buf == NULL) {
+ printf( "cannot read into memory\n" );
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
+ } /* end if */
+
+ if(H5Aread(attr_id, mtype_id, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
+
+ if (H5R_OBJ_REF_BUF_SIZE==msize) {
+ hobj_ref_t ref_out;
+
+ for (i=0; i<(unsigned)nelmts; i++) {
+ hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p;
+
+ for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
+ if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0)
+ continue;
+ HDmemcpy(&(ptr[j]), &ref_out, msize);
+ }
+ } /* for (i=0; i<nelems; i++) */
+ } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
+ hdset_reg_ref_t ref_out;
+
+ for (i=0; i<(unsigned)nelmts; i++) {
+ hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p;
+
+ for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
+ if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0)
+ continue;
+ HDmemcpy(&(ptr[j]), &ref_out, msize);
+ }
+ } /* for (i=0; i<nelems; i++) */
+ }
+ } /* else if (is_ref_vlen) */
+ else if (is_ref_comp) {
+ /* handle ref fields in a compound */
+
+ buf = HDmalloc((unsigned)(nelmts * msize));
+ refbuf = buf; /* reuse the read buffer for write */
+
+ if(buf == NULL)
+ {
+ printf( "cannot read into memory\n" );
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
+ } /* end if */
+
+ if(H5Aread(attr_id, mtype_id, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
+
+ for (i=0; i<(unsigned)nelmts; i++) {
+ for (j=0; j<(unsigned)ref_comp_field_n; j++) {
+ if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
+ size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]);
+ hobj_ref_t ref_out;
+
+ if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+ continue;
+ HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+ } /* if */
+ else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
+ size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]);
+ hdset_reg_ref_t ref_out;
+
+ if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+ continue;
+ HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+ } /* else if */
+ } /* j */
+ } /* i */
+ } /* else if (is_ref_comp) */
+
+ if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");
+
+ if (is_ref_vlen && buf)
+ H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
+ } /* if (nelmts) */
+
+ if (refbuf == buf)
+ refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
+
+ if(buf) {
+ HDfree(buf);
+ buf = NULL;
+ }
+
+ if(refbuf) {
+ HDfree(refbuf);
+ refbuf = NULL;
+ }
+
+ if (ref_comp_index) {
+ HDfree(ref_comp_index);
+ ref_comp_index = NULL;
+ }
+
+ if (ref_comp_size) {
+ HDfree(ref_comp_size);
+ ref_comp_size = NULL;
+ }
+
+ if(H5Aclose(attr_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if(H5Tclose(ftype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if(H5Tclose(mtype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if(H5Sclose(space_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if(H5Aclose(attr_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
+ } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */
+
+ return ret_value;
+
+done:
+ if(refbuf)
+ HDfree(refbuf);
+ if(buf)
+ HDfree(buf);
+
+ if (ref_comp_index)
+ HDfree(ref_comp_index);
+
+ if (ref_comp_size)
+ HDfree(ref_comp_size);
+
+ H5E_BEGIN_TRY {
+ H5Tclose(ftype_id);
+ H5Tclose(mtype_id);
+ H5Sclose(space_id);
+ H5Aclose(attr_id);
+ H5Aclose(attr_out);
+ } H5E_END_TRY;
+
+ return ret_value;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: MapIdToName
+ *
+ * Purpose: map a ID from a reference to a dataset name
+ *
+ *-------------------------------------------------------------------------
+ */
+static const char*
+MapIdToName(hid_t refobj_id, trav_table_t *travt)
+{
+ unsigned int u;
+ const char* ret = NULL;
+
+ /* linear search */
+ for(u = 0; u < travt->nobjs; u++) {
+ if(travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET ||
+ travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP ||
+ travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) {
+ H5O_info_t ref_oinfo; /* Stat for the refobj id */
+
+ /* obtain information to identify the referenced object uniquely */
+ if(H5Oget_info(refobj_id, &ref_oinfo) < 0)
+ goto out;
+
+ if(ref_oinfo.addr == travt->objs[u].objno) {
+ ret = travt->objs[u].name;
+ goto out;
+ } /* end if */
+ } /* end if */
+ } /* u */
+
+out:
+ return ret;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: Update_Ref_value
+ *
+ * Purpose: Update a reference value
+ *
+ * Programmer: xcao@hdfgroup.org 9/12/2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
+ hid_t fid_out, void *ref_out, trav_table_t *travt)
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ const char* ref_obj_name;
+ hid_t space_id=-1, ref_obj_id=-1;
+
+ ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
+ if (ref_obj_id < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rdereference2 failed");
+
+ ref_obj_name = MapIdToName(ref_obj_id, travt);
+ if (ref_obj_name == NULL)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "MapIdToName failed");
+
+ if (ref_type == H5R_DATASET_REGION) {
+ space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
+ if (space_id < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed");
+ }
+
+ if(H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
+
+done:
+ H5E_BEGIN_TRY {
+ H5Sclose(space_id);
+ H5Oclose(ref_obj_id);
+ } H5E_END_TRY;
+
+ return ret_value;
+}
+
diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c
new file mode 100644
index 0000000..6765c49
--- /dev/null
+++ b/tools/src/h5repack/h5repack_verify.c
@@ -0,0 +1,675 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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"
+
+/* number of members in an array */
+#ifndef NELMTS
+# define NELMTS(X) (sizeof(X)/sizeof(X[0]))
+#endif
+
+static int verify_layout(hid_t pid, pack_info_t *obj);
+static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter);
+
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack_verify
+ *
+ * Purpose: verify if filters and layout in the input file match the output file
+ *
+ * Return:
+ * 1 match
+ * 0 do not match
+ * -1 error
+ *
+ * Programmer: Pedro Vicente, pvn@hdfgroup.org
+ *
+ * Date: December 19, 2003
+ * Modified: December, 19, 2007 (exactly 4 years later :-) )
+ * Separate into 3 cases
+ * 1) no filter input, get all datasets and compare DCPLs. TO DO
+ * 2) filter input on selected datasets, get each one trough OBJ and match
+ * 3) filter input on all datasets, get all objects and match
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int
+h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options)
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ hid_t fidin = -1; /* file ID for input file*/
+ hid_t fidout = -1; /* file ID for output file*/
+ hid_t did = -1; /* dataset ID */
+ hid_t pid = -1; /* dataset creation property list ID */
+ hid_t sid = -1; /* space ID */
+ hid_t tid = -1; /* type ID */
+ unsigned int i;
+ trav_table_t *travt = NULL;
+ int ok = 1;
+ hid_t fcpl_in = -1; /* file creation property for input file */
+ hid_t fcpl_out = -1; /* file creation property for output file */
+ H5F_file_space_type_t in_strat, out_strat; /* file space handling strategy for in/output file */
+ hsize_t in_thresh, out_thresh; /* free space section threshold for in/output file */
+
+ /* open the output file */
+ if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
+ return -1;
+
+ for(i = 0; i < options->op_tbl->nelems; i++)
+ {
+ char* name = options->op_tbl->objs[i].path;
+ pack_info_t *obj = &options->op_tbl->objs[i];
+
+ /*-------------------------------------------------------------------------
+ * open
+ *-------------------------------------------------------------------------
+ */
+ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if((sid = H5Dget_space(did)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
+ if((pid = H5Dget_create_plist(did)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ if((tid = H5Dget_type(did)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
+
+ /*-------------------------------------------------------------------------
+ * filter check
+ *-------------------------------------------------------------------------
+ */
+ if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0)
+ ok = 0;
+
+
+ /*-------------------------------------------------------------------------
+ * layout check
+ *-------------------------------------------------------------------------
+ */
+ if((obj->layout != -1) && (verify_layout(pid, obj) == 0))
+ ok = 0;
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if(H5Pclose(pid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Sclose(sid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if (H5Dclose(did) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ if (H5Tclose(tid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+
+ }
+
+
+ /*-------------------------------------------------------------------------
+ * check for the "all" objects option
+ *-------------------------------------------------------------------------
+ */
+
+ if(options->all_filter == 1 || options->all_layout == 1)
+ {
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if(h5trav_gettable(fidout, travt) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
+
+ for(i = 0; i < travt->nobjs; i++)
+ {
+ char *name = travt->objs[i].name;
+
+ if(travt->objs[i].type == H5TRAV_TYPE_DATASET)
+ {
+
+ /*-------------------------------------------------------------------------
+ * open
+ *-------------------------------------------------------------------------
+ */
+ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if((sid = H5Dget_space(did)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
+ if((pid = H5Dget_create_plist(did)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ if((tid = H5Dget_type(did)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
+
+ /*-------------------------------------------------------------------------
+ * filter check
+ *-------------------------------------------------------------------------
+ */
+ if(options->all_filter == 1)
+ {
+ if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0)
+ ok = 0;
+ }
+
+ /*-------------------------------------------------------------------------
+ * layout check
+ *-------------------------------------------------------------------------
+ */
+ if(options->all_layout == 1)
+ {
+ pack_info_t pack;
+
+ init_packobject(&pack);
+ pack.layout = options->layout_g;
+ pack.chunk = options->chunk_g;
+ if(verify_layout(pid, &pack) == 0)
+ ok = 0;
+ }
+
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Pclose(pid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Sclose(sid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if (H5Dclose(did) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ if (H5Tclose(tid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ } /* if */
+
+ } /* i */
+
+ /* free table */
+ trav_table_free(travt);
+ }
+
+ /*-------------------------------------------------------------------------
+ * Verify that file space strategy and free space threshold
+ * are set as expected
+ *-------------------------------------------------------------------------
+ */
+
+ /* open the input file */
+ if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed");
+
+ /* Get file creation property list for input file */
+ if((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed");
+ }
+
+ /* Get file space management info for input file */
+ if(H5Pget_file_space(fcpl_in, &in_strat, &in_thresh) < 0) {
+ error_msg("failed to retrieve file space strategy & threshold\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space failed");
+ }
+
+ /* Output file is already opened */
+ /* Get file creation property list for output file */
+ if((fcpl_out = H5Fget_create_plist(fidout)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed");
+ }
+
+ /* Get file space management info for output file */
+ if(H5Pget_file_space(fcpl_out, &out_strat, &out_thresh) < 0) {
+ error_msg("failed to retrieve file space strategy & threshold\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space failed");
+ }
+
+ /*
+ * If the strategy option is not set,
+ * file space handling strategy should be the same for both
+ * input & output files.
+ * If the strategy option is set,
+ * the output file's file space handling strategy should be the same
+ * as what is set via the strategy option
+ */
+ if(!options->fs_strategy && out_strat != in_strat) {
+ error_msg("file space strategy not set as unexpected\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected");
+
+ }
+ else if(options->fs_strategy && out_strat!= options->fs_strategy) {
+ error_msg("file space strategy not set as unexpected\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected");
+ }
+
+ /*
+ * If the threshold option is not set,
+ * the free space section threshold should be the same for both
+ * input & output files.
+ * If the threshold option is set,
+ * the output file's free space section threshold should be the same
+ * as what is set via the threshold option.
+ */
+ if(!options->fs_threshold && out_thresh != in_thresh) {
+ error_msg("free space threshold not set as unexpected\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free space threshold not set as unexpected");
+ }
+ else if(options->fs_threshold && out_thresh != options->fs_threshold) {
+ error_msg("free space threshold not set as unexpected\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free space threshold not set as unexpected");
+ }
+
+ /* Closing */
+ if (H5Pclose(fcpl_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pclose(fcpl_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Fclose(fidin) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
+ if (H5Fclose(fidout) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
+
+ return ok;
+
+done:
+ H5E_BEGIN_TRY {
+ H5Pclose(fcpl_in);
+ H5Pclose(fcpl_out);
+ H5Pclose(pid);
+ H5Sclose(sid);
+ H5Dclose(did);
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ if (travt)
+ trav_table_free(travt);
+ } H5E_END_TRY;
+
+ return ret_value;
+} /* h5repack_verify() */
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: verify_layout
+ *
+ * Purpose: verify which layout is present in the property list DCPL_ID
+ *
+ * H5D_COMPACT = 0
+ * H5D_CONTIGUOUS = 1
+ * H5D_CHUNKED = 2
+ *
+ * Return: 1 has, 0 does not, -1 error
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 30, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int verify_layout(hid_t pid,
+ pack_info_t *obj)
+{
+ hsize_t chsize[64]; /* chunk size in elements */
+ H5D_layout_t layout; /* layout */
+ int nfilters; /* number of filters */
+ int rank; /* rank */
+ int i; /* index */
+
+ /* check if we have filters in the input object */
+ if ((nfilters = H5Pget_nfilters(pid)) < 0)
+ return -1;
+
+ /* a non chunked layout was requested on a filtered object */
+ if (nfilters && obj->layout!=H5D_CHUNKED)
+ return 0;
+
+ /* get layout */
+ if ((layout = H5Pget_layout(pid)) < 0)
+ return -1;
+
+ if (obj->layout != layout)
+ return 0;
+
+ if (layout==H5D_CHUNKED)
+ {
+ if ((rank = H5Pget_chunk(pid,NELMTS(chsize),chsize/*out*/)) < 0)
+ return -1;
+ if (obj->chunk.rank != rank)
+ return 0;
+ for ( i=0; i<rank; i++)
+ if (chsize[i] != obj->chunk.chunk_lengths[i])
+ return 0;
+ }
+
+ return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack_cmp_pl
+ *
+ * Purpose: compare 2 files for identical property lists of all objects
+ *
+ * Return: 1=identical, 0=not identical, -1=error
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 31, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_cmp_pl(const char *fname1,
+ const char *fname2)
+{
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ hid_t fid1=-1; /* file ID */
+ hid_t fid2=-1; /* file ID */
+ hid_t dset1=-1; /* dataset ID */
+ hid_t dset2=-1; /* dataset ID */
+ hid_t gid=-1; /* group ID */
+ hid_t dcpl1=-1; /* dataset creation property list ID */
+ hid_t dcpl2=-1; /* dataset creation property list ID */
+ hid_t gcplid=-1; /* group creation property list */
+ unsigned crt_order_flag1; /* group creation order flag */
+ unsigned crt_order_flag2; /* group creation order flag */
+ trav_table_t *trav=NULL;
+ int ret=1;
+ unsigned int i;
+
+ /*-------------------------------------------------------------------------
+ * open the files
+ *-------------------------------------------------------------------------
+ */
+
+ /* disable error reporting */
+ H5E_BEGIN_TRY
+ {
+
+ /* Open the files */
+ if ((fid1 = H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 )
+ {
+ error_msg("<%s>: %s\n", fname1, H5FOPENERROR );
+ return -1;
+ }
+ if ((fid2 = H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 )
+ {
+ error_msg("<%s>: %s\n", fname2, H5FOPENERROR );
+ H5Fclose(fid1);
+ return -1;
+ }
+ /* enable error reporting */
+ } H5E_END_TRY;
+
+ /*-------------------------------------------------------------------------
+ * get file table list of objects
+ *-------------------------------------------------------------------------
+ */
+ trav_table_init(&trav);
+ if(h5trav_gettable(fid1, trav) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
+
+ /*-------------------------------------------------------------------------
+ * traverse the suppplied object list
+ *-------------------------------------------------------------------------
+ */
+ for(i = 0; i < trav->nobjs; i++)
+ {
+
+ if(trav->objs[i].type == H5TRAV_TYPE_GROUP)
+ {
+
+ if ((gid = H5Gopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+ if ((gcplid = H5Gget_create_plist(gid)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+ if (H5Pget_link_creation_order(gcplid, &crt_order_flag1) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
+ if (H5Pclose(gcplid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Gclose(gid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+
+ if ((gid = H5Gopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+ if ((gcplid = H5Gget_create_plist(gid)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+ if (H5Pget_link_creation_order(gcplid, &crt_order_flag2) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
+ if (H5Pclose(gcplid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Gclose(gid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+
+ if (crt_order_flag1 != crt_order_flag2) {
+ error_msg("property lists for <%s> are different\n",trav->objs[i].name);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed");
+ }
+
+ }
+
+
+
+ else if(trav->objs[i].type == H5TRAV_TYPE_DATASET)
+ {
+ if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if((dcpl1 = H5Dget_create_plist(dset1)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ if((dcpl2 = H5Dget_create_plist(dset2)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+
+ /*-------------------------------------------------------------------------
+ * compare the property lists
+ *-------------------------------------------------------------------------
+ */
+ if((ret = H5Pequal(dcpl1, dcpl2)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pequal failed");
+
+ if(ret == 0) {
+ error_msg("property lists for <%s> are different\n",trav->objs[i].name);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed");
+ }
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if(H5Pclose(dcpl1) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if(H5Pclose(dcpl2) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if(H5Dclose(dset1) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ if(H5Dclose(dset2) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ } /*if*/
+ } /*i*/
+
+ /*-------------------------------------------------------------------------
+ * free
+ *-------------------------------------------------------------------------
+ */
+
+ trav_table_free(trav);
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ H5Fclose(fid1);
+ H5Fclose(fid2);
+
+ return ret;
+
+/*-------------------------------------------------------------------------
+* error
+*-------------------------------------------------------------------------
+*/
+done:
+ H5E_BEGIN_TRY
+ {
+ H5Pclose(dcpl1);
+ H5Pclose(dcpl2);
+ H5Dclose(dset1);
+ H5Dclose(dset2);
+ H5Fclose(fid1);
+ H5Fclose(fid2);
+ H5Pclose(gcplid);
+ H5Gclose(gid);
+ trav_table_free(trav);
+ } H5E_END_TRY;
+
+ return ret_value;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: verify_filters
+ *
+ * Purpose: verify if all requested filters in the array FILTER obtained
+ * from user input are present in the property list PID obtained from
+ * the output file
+ *
+ * Return:
+ * 1 match
+ * 0 do not match
+ * -1 error
+ *
+ * Programmer: Pedro Vicente, pvn@hdfgroup.org
+ *
+ * Date: December 21, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static
+int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
+{
+ int nfilters_dcpl; /* number of filters in DCPL*/
+ 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_name[256]; /* filter name */
+ size_t size; /* type size */
+ int i; /* index */
+ unsigned j; /* index */
+
+ /* get information about filters */
+ if((nfilters_dcpl = H5Pget_nfilters(pid)) < 0)
+ return -1;
+
+ /* if we do not have filters and the requested filter is NONE, return 1 */
+ if(!nfilters_dcpl &&
+ nfilters == 1 &&
+ filter[0].filtn == H5Z_FILTER_NONE )
+ return 1;
+
+ /* else the numbers of filters must match */
+ if (nfilters_dcpl != nfilters )
+ return 0;
+
+ /*-------------------------------------------------------------------------
+ * build a list with DCPL filters
+ *-------------------------------------------------------------------------
+ */
+
+ for( i = 0; i < nfilters_dcpl; i++)
+ {
+ cd_nelmts = NELMTS(cd_values);
+ filtn = H5Pget_filter2(pid, (unsigned)i, &filt_flags, &cd_nelmts,
+ cd_values, sizeof(f_name), f_name, NULL);
+
+ /* filter ID */
+ if (filtn != filter[i].filtn)
+ return 0;
+
+ /* compare client data values. some filters do return local values */
+ switch (filtn)
+ {
+
+ case H5Z_FILTER_NONE:
+ break;
+
+ case H5Z_FILTER_SHUFFLE:
+ /* 1 private client value is returned by DCPL */
+ if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS )
+ return 0;
+
+ /* get dataset's type size */
+ if((size = H5Tget_size(tid)) <= 0)
+ return -1;
+
+ /* the private client value holds the dataset's type size */
+ if ( size != cd_values[0] )
+ return 0;
+
+ break;
+
+ case H5Z_FILTER_SZIP:
+ /* 4 private client values are returned by DCPL */
+ if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS )
+ return 0;
+
+ /* "User" parameter for pixels-per-block (index 1) */
+ if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] )
+ return 0;
+
+ break;
+
+ case H5Z_FILTER_NBIT:
+ /* only client data values number of values checked */
+ if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts)
+ return 0;
+ break;
+
+ case H5Z_FILTER_SCALEOFFSET:
+ /* only client data values checked */
+ for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++)
+ if (cd_values[j] != filter[i].cd_values[j])
+ return 0;
+ break;
+
+ /* for these filters values must match, no local values set in DCPL */
+ case H5Z_FILTER_FLETCHER32:
+ case H5Z_FILTER_DEFLATE:
+
+ 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;
+
+ default:
+ 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 */
+ }
+
+ return 1;
+}
+