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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#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 */
/* timing formats */
#define FORMAT_OBJ_TIME " %-27s %e/%e %s\n" /* obj type, name */
#define FORMAT_OBJ_ATTR_TIME " %-27s %e/%e %s\n" /* obj type, name */
#define FORMAT_OBJ_NOTIME " %-27s %s\n" /* obj type, name */
#define FORMAT_OBJ_ATTR_NOTIME " %-27s %s\n" /* obj type, name */
/* File space default information */
#define FS_PAGESIZE_DEF 4096
#define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR
#define FS_PERSIST_DEF FALSE
#define FS_THRESHOLD_DEF 1
/*-------------------------------------------------------------------------
* 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 filt_flag; /* filter definition flag */
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 */
hbool_t merge; /* Merge external file. */
hbool_t prune; /* Don't follow external file. */
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 */
H5F_libver_t low_bound; /* The file's low bound as in H5Fset_libver_bounds() */
H5F_libver_t high_bound; /* The file's high bound as in H5Fset_libver_bounds() */
hid_t fin_fapl; /* FAPL to use for opening the input file */
hid_t fout_fapl; /* FAPL to use for opening/creating the output file */
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 pipeline, 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_fspace_strategy_t fs_strategy; /* File space handling strategy */
int fs_persist; /* Free space section threshold */
long fs_threshold; /* Free space section threshold */
long long fs_pagesize; /* File space page size */
} pack_opt_t;
typedef struct named_dt_t {
H5O_token_t obj_token; /* Object token for 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);
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, hid_t fname1_fapl, const char *fname2, hid_t fname2_fapl);
/* 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 */
const 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 */
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