1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 */
int 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 */
} 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);
int h5repack_end(pack_opt_t *options);
int h5repack_verify(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__ */
|
