mirror of
https://github.com/HDFGroup/hdf5.git
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20fd1f47b7
Fix for the bug1726 - NPOESS: h5repack loses attributes for datasets of
type H5T_REFERENCE.
Description:
include test cases.
also test cases for attribute with object and region reference.
Tested:
jam, amani, linew
242 lines
9.9 KiB
C
242 lines
9.9 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#ifndef H5REPACK_H__
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#define H5REPACK_H__
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#include <assert.h>
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#include <string.h>
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#include "hdf5.h"
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#include "h5trav.h"
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#define H5FOPENERROR "unable to open file"
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#define PFORMAT "%-7s %-7s %-7s\n" /* chunk info, compression info, name*/
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#define PFORMAT1 "%-7s %-7s %-7s" /* chunk info, compression info, name*/
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#define MAX_NC_NAME 256 /* max length of a name */
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#define MAX_VAR_DIMS 32 /* max per variable dimensions */
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#define FORMAT_OBJ " %-27s %s\n" /* obj type, name */
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#define FORMAT_OBJ_ATTR " %-27s %s\n" /* obj type, name */
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/*-------------------------------------------------------------------------
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* data structures for command line options
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*-------------------------------------------------------------------------
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*/
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/* a list of names */
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typedef struct {
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char obj[MAX_NC_NAME];
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} obj_list_t;
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/*
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the type of filter and additional parameter
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type can be one of the filters
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H5Z_FILTER_NONE 0, uncompress if compressed
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H5Z_FILTER_DEFLATE 1 , deflation like gzip
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H5Z_FILTER_SHUFFLE 2 , shuffle the data
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H5Z_FILTER_FLETCHER32 3 , letcher32 checksum of EDC
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H5Z_FILTER_SZIP 4 , szip compression
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H5Z_FILTER_NBIT 5 , nbit compression
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H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression
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*/
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#define CD_VALUES 20
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typedef struct {
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H5Z_filter_t filtn; /* filter identification number */
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unsigned cd_values[CD_VALUES]; /* filter client data values */
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size_t cd_nelmts; /* filter client number of values */
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} filter_info_t;
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/* chunk lengths along each dimension and rank */
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typedef struct {
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hsize_t chunk_lengths[MAX_VAR_DIMS];
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int rank;
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} chunk_info_t;
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/* we currently define a maximum value for the filters array,
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that corresponds to the current library filters */
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#define H5_REPACK_MAX_NFILTERS 6
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/* information for one object, contains PATH, CHUNK info and FILTER info */
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typedef struct {
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char path[MAX_NC_NAME]; /* name of object */
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filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */
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int nfilters; /* current number of filters */
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H5D_layout_t layout; /* layout information */
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chunk_info_t chunk; /* chunk information */
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hid_t refobj_id; /* object ID, references */
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} pack_info_t;
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/* store a table of all objects */
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typedef struct {
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unsigned int size;
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unsigned int nelems;
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pack_info_t *objs;
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} pack_opttbl_t;
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/*-------------------------------------------------------------------------
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* command line options
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*-------------------------------------------------------------------------
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*/
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/* all the above, ready to go to the hrepack call */
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typedef struct {
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pack_opttbl_t *op_tbl; /*table with all -c and -f options */
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int all_layout; /*apply the layout to all objects */
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int all_filter; /*apply the filter to all objects */
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filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */
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int n_filter_g; /*number of global filters */
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chunk_info_t chunk_g; /*global chunk INFO for the ALL case */
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H5D_layout_t layout_g; /*global layout information for the ALL case */
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int verbose; /*verbose mode */
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hsize_t min_comp; /*minimum size to compress, in bytes */
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int use_native; /*use a native type in write */
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int latest; /*pack file with the latest file format */
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int grp_compact; /* Set the maximum number of links to store as header messages in the group */
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int grp_indexed; /* Set the minimum number of links to store in the indexed format */
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int msg_size[8]; /* Minimum size of shared messages: dataspace,
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datatype, fill value, filter pipleline, attribute */
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const char *ublock_filename; /* user block file name */
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hsize_t ublock_size; /* user block size */
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hsize_t threshold; /* alignment threshold for H5Pset_alignment */
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hsize_t alignment ; /* alignment for H5Pset_alignment */
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H5F_file_space_type_t fs_strategy; /* File space handling strategy */
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hsize_t fs_threshold; /* Free space section threshold */
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} pack_opt_t;
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typedef struct named_dt_t {
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haddr_t addr_in; /* Address of the named dtype in the in file */
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hid_t id_out; /* Open identifier for the dtype in the out file */
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struct named_dt_t *next; /* Next dtype */
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} named_dt_t;
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/*-------------------------------------------------------------------------
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* public functions
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*-------------------------------------------------------------------------
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*/
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#ifdef __cplusplus
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extern "C" {
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#endif
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int h5repack(const char* infile, const char* outfile, pack_opt_t *options);
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int h5repack_addfilter(const char* str, pack_opt_t *options);
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int h5repack_addlayout(const char* str, pack_opt_t *options);
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int h5repack_init(pack_opt_t *options, int verbose, H5F_file_space_type_t strategy, hsize_t threshold);
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int h5repack_end(pack_opt_t *options);
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int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options);
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int h5repack_cmp_pl(const char *fname1, const char *fname2);
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/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
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* and struct named_dt_t were located in h5repack_copy.c as static prior to
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* bugfix1726.
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* Made shared functions as copy_attr() was needed in h5repack_refs.c.
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* However copy_attr() may be obsoleted when H5Acopy is available and put back
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* others to static in h5repack_copy.c.
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*/
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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);
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int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err);
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int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
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trav_table_t *travt, pack_opt_t *options);
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#ifdef __cplusplus
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}
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#endif
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/*-------------------------------------------------------------------------
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* private functions
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*-------------------------------------------------------------------------
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*/
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/*-------------------------------------------------------------------------
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* copy module
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*-------------------------------------------------------------------------
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*/
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int copy_objects (const char* fnamein,
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const char* fnameout,
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pack_opt_t *options);
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int do_copy_refobjs(hid_t fidin,
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hid_t fidout,
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trav_table_t *travt,
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pack_opt_t *options);
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/*-------------------------------------------------------------------------
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* filters and verify module
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*-------------------------------------------------------------------------
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*/
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void init_packobject(pack_info_t *obj);
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/*-------------------------------------------------------------------------
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* filters and copy module
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*-------------------------------------------------------------------------
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*/
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int apply_filters(const char* name, /* object name from traverse list */
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int rank, /* rank of dataset */
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hsize_t *dims, /* dimensions of dataset */
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size_t msize, /* size of type */
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hid_t dcpl_id, /* dataset creation property list */
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pack_opt_t *options, /* repack options */
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int *has_filter); /* (OUT) object NAME has a filter */
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/*-------------------------------------------------------------------------
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* options table
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*-------------------------------------------------------------------------
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*/
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int options_table_init( pack_opttbl_t **tbl );
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int options_table_free( pack_opttbl_t *table );
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int options_add_layout( obj_list_t *obj_list,
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int n_objs,
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pack_info_t *pack,
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pack_opttbl_t *table );
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int options_add_filter ( obj_list_t *obj_list,
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int n_objs,
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filter_info_t filt,
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pack_opttbl_t *table );
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pack_info_t* options_get_object( const char *path,
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pack_opttbl_t *table);
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/*-------------------------------------------------------------------------
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* parse functions
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*-------------------------------------------------------------------------
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*/
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obj_list_t* parse_filter(const char *str,
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int *n_objs,
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filter_info_t *filt,
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pack_opt_t *options,
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int *is_glb);
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obj_list_t* parse_layout(const char *str,
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int *n_objs,
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pack_info_t *pack, /* info about object */
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pack_opt_t *options);
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#endif /* H5REPACK_H__ */
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