summaryrefslogtreecommitdiffstats
path: root/tools/h5repack/h5repack_main.c
blob: f3fd469f251f39a04b824f502757697550794443 (plain)
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
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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:";
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 */
	{ NULL, 0, '\0' }
};

/*-------------------------------------------------------------------------
 * Function: usage
 *
 * Purpose: print usage
 *
 * Return: void
 *
 *-------------------------------------------------------------------------
 */
static void usage(const char *prog) {
	printf("usage: %s [OPTIONS] file1 file2\n", prog);
	printf("  file1                    Input HDF5 File\n");
	printf("  file2                    Output HDF5 File\n");
	printf("  OPTIONS\n");
	printf("   -h, --help              Print a usage message and exit\n");
	printf("   -v, --verbose           Verbose mode, print object information\n");
	printf("   -V, --version           Print version number and exit\n");
	printf("   -n, --native            Use a native HDF5 type when repacking\n");
	printf("   -L, --latest            Use latest version of file format\n");
	printf("   -c L1, --compact=L1     Maximum number of links in header messages\n");
	printf("   -d L2, --indexed=L2     Minimum number of links in the indexed format\n");
	printf("   -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
	printf("   -m M, --minimum=M       Do not apply the filter to datasets smaller than M\n");
	printf("   -e E, --file=E          Name of file E with the -f and -l options\n");
	printf("   -u U, --ublock=U        Name of file U with user block data to be added\n");
	printf("   -b B, --block=B         Size of user block to be added\n");
	printf("   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
	printf("   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
	printf("   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
	printf("   -f FILT, --filter=FILT  Filter type\n");
	printf("   -l LAYT, --layout=LAYT  Layout type\n");
	printf("\n");
	printf("    M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
	printf("    E - is a filename.\n");
	printf("    S - is an integer\n");
	printf("    U - is a filename.\n");
	printf("    T - is an integer\n");
	printf("    A - is an integer greater than zero\n");
	printf("    B - is the user block size, any value that is 512 or greater and is\n");
	printf("        a power of 2 (1024 default)\n");
	printf("    F - is the shared object header message type, any of <dspace|dtype|fill|\n");
	printf("        pline|attr>. If F is not specified, S applies to all messages\n");
	printf("\n");
	printf("    FILT - is a string with the format:\n");
	printf("\n");
	printf("      <list of objects>:<name of filter>=<filter parameters>\n");
	printf("\n");
	printf("      <list of objects> is a comma separated list of object names, meaning apply\n");
	printf("        compression only to those objects. If no names are specified, the filter\n");
	printf("        is applied to all objects\n");
	printf("      <name of filter> can be:\n");
	printf("        GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
	printf("        SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
	printf("        SHUF, to apply the HDF5 shuffle filter\n");
	printf("        FLET, to apply the HDF5 checksum filter\n");
	printf("        NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
	printf("        SOFF, to apply the HDF5 Scale/Offset filter\n");
	printf("        UD,   to apply a user defined filter\n");
	printf("        NONE, to remove all filters\n");
	printf("      <filter parameters> is optional filter parameter information\n");
	printf("        GZIP=<deflation level> from 1-9\n");
	printf("        SZIP=<pixels per block,coding> pixels per block is a even number in\n");
	printf("            2-32 and coding method is either EC or NN\n");
	printf("        SHUF (no parameter)\n");
	printf("        FLET (no parameter)\n");
	printf("        NBIT (no parameter)\n");
	printf("        SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
	printf("            is either IN or DS\n");
	printf("        UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
	printf("            required values for filter_number,cd_value_count,value_1\n");
	printf("            optional values for value_2 to value_N\n");
	printf("        NONE (no parameter)\n");
	printf("\n");
	printf("    LAYT - is a string with the format:\n");
	printf("\n");
	printf("      <list of objects>:<layout type>=<layout parameters>\n");
	printf("\n");
	printf("      <list of objects> is a comma separated list of object names, meaning that\n");
	printf("        layout information is supplied for those objects. If no names are\n");
	printf("        specified, the layout type is applied to all objects\n");
	printf("      <layout type> can be:\n");
	printf("        CHUNK, to apply chunking layout\n");
	printf("        COMPA, to apply compact layout\n");
	printf("        CONTI, to apply contiguous layout\n");
	printf("      <layout parameters> is optional layout information\n");
	printf("        CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
	printf("        COMPA (no parameter)\n");
	printf("        CONTI (no parameter)\n");
	printf("\n");
	printf("Examples of use:\n");
	printf("\n");
	printf("1) h5repack -v -f GZIP=1 file1 file2\n");
	printf("\n");
	printf("   GZIP compression with level 1 to all objects\n");
	printf("\n");
	printf("2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n");
	printf("\n");
	printf("   SZIP compression with 8 pixels per block and NN coding method to object dset1\n");
	printf("\n");
	printf("3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n");
	printf("\n");
	printf("   Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n");
	printf("   and remove filters to objects dset3, dset4, dset5\n");
	printf("\n");
	printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
	printf("\n");
	printf("   Using latest file format with maximum compact group size of 10 and\n");
	printf("   and minimum shared datatype size of 20\n");
	printf("\n");
	printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
	printf("\n");
	printf("   Add both filters SHUF and GZIP in this order to all datasets\n");
	printf("\n");
	printf("6) h5repack -f UD=307,1,9 file1 file2 \n");
	printf("\n");
	printf("   Add bzip2 filter to all datasets\n");
	printf("\n");
}

/*-------------------------------------------------------------------------
 * Function:    leave
 *
 * 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 != ' ') {
				fscanf(fp, "%c", &c);
				if (HDfeof(fp))
					break;
			}
			c = '0';
			/* go until end */
			while (c != ' ') {
				fscanf(fp, "%c", &c);
				comp_info[i] = c;
				i++;
				if (HDfeof(fp))
					break;
				if (c == 10 /*eol*/)
					break;
			}
			comp_info[i - 1] = '\0'; /*cut the last " */

			if (h5repack_addfilter(comp_info, options) == -1) {
				error_msg("could not add compression option\n");
				h5tools_setstatus(EXIT_FAILURE);
				ret_value = EXIT_FAILURE;
				goto done;
			}
		}
		/*-------------------------------------------------------------------------
		 * layout
		 *-------------------------------------------------------------------------
		 */
		else if (HDstrcmp(stype,"-l") == 0) {

			/* find begining of info */
			i = 0;
			c = '0';
			while (c != ' ') {
				fscanf(fp, "%c", &c);
				if (HDfeof(fp))
					break;
			}
			c = '0';
			/* go until end */
			while (c != ' ') {
				fscanf(fp, "%c", &c);
				comp_info[i] = c;
				i++;
				if (HDfeof(fp))
					break;
				if (c == 10 /*eol*/)
					break;
			}
			comp_info[i - 1] = '\0'; /*cut the last " */

			if (h5repack_addlayout(comp_info, options) == -1) {
				error_msg("could not add chunck option\n");
				h5tools_setstatus(EXIT_FAILURE);
				ret_value = EXIT_FAILURE;
				goto done;
			}
		}
		/*-------------------------------------------------------------------------
		 * not valid
		 *-------------------------------------------------------------------------
		 */
		else {
			error_msg("bad file format for %s", filename);
			h5tools_setstatus(EXIT_FAILURE);
			ret_value = EXIT_FAILURE;
			goto done;
		}
	}

done:
	if (fp)
		HDfclose(fp);

	return ret_value;
}

/*-------------------------------------------------------------------------
 * Function: parse_command_line
 *
 * 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 = HDatoi( opt_arg );
			if ((int) options->min_comp <= 0) {
				error_msg("invalid minimum compress size <%s>\n", opt_arg);
				h5tools_setstatus(EXIT_FAILURE);
				ret_value = -1;
				goto done;
			}
			break;

		case 'e':
			ret_value = read_info(opt_arg, options);
			if (ret_value < 0)
				goto done;
			break;

		case 'n':
			options->use_native = 1;
			break;

		case 'L':
			options->latest = 1;
			break;

		case 'c':
			options->grp_compact = HDatoi( opt_arg );
			if (options->grp_compact > 0)
				options->latest = 1; /* must use latest format */
			break;

		case 'd':
			options->grp_indexed = HDatoi( opt_arg );
			if (options->grp_indexed > 0)
				options->latest = 1; /* must use latest format */
			break;

		case 's':
			{
				int idx = 0;
				int ssize = 0;
				char *msgPtr = HDstrchr( opt_arg, ':');
				options->latest = 1; /* must use latest format */
				if (msgPtr == NULL) {
					ssize = HDatoi( opt_arg );
					for (idx = 0; idx < 5; idx++)
						options->msg_size[idx] = ssize;
				}
				else {
					char msgType[10];
					HDstrcpy(msgType, msgPtr + 1);
					msgPtr[0] = '\0';
					ssize = HDatoi( opt_arg );
					if (HDstrncmp(msgType, "dspace",6) == 0) {
						options->msg_size[0] = ssize;
					}
					else if (HDstrncmp(msgType, "dtype", 5) == 0) {
						options->msg_size[1] = ssize;
					}
					else if (HDstrncmp(msgType, "fill", 4) == 0) {
						options->msg_size[2] = ssize;
					}
					else if (HDstrncmp(msgType, "pline", 5) == 0) {
						options->msg_size[3] = ssize;
					}
					else if (HDstrncmp(msgType, "attr", 4) == 0) {
						options->msg_size[4] = ssize;
					}
				}
			}
			break;

		case 'u':
			options->ublock_filename = opt_arg;
			break;

		case 'b':
			options->ublock_size = (hsize_t) HDatol( opt_arg );
			break;

		case 'M':
			options->meta_block_size = (hsize_t) HDatol( opt_arg );
			break;

		case 't':
			options->threshold = (hsize_t) HDatol( opt_arg );
			break;

		case 'a':
			options->alignment = HDatol( opt_arg );
			if (options->alignment < 1) {
				error_msg("invalid alignment size\n", opt_arg);
				h5tools_setstatus(EXIT_FAILURE);
				ret_value = -1;
				goto done;
			}
			break;

		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) {

	pack_opt_t options; /*the global options */

	h5tools_setprogname(PROGRAMNAME);
	h5tools_setstatus(EXIT_SUCCESS);

	/* Initialize h5tools lib */
	h5tools_init();

	/* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
	if (h5tools_getenv_update_hyperslab_bufsize() < 0) {
		h5tools_setstatus(EXIT_FAILURE);
		goto done;
	}

	/* initialize options  */
	h5repack_init(&options, 0);

	if (parse_command_line(argc, argv, &options) < 0)
		goto done;

	/* get file names if they were not yet got */
	if (has_i_o == 0) {

		if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
			infile = argv[opt_ind];
			outfile = argv[opt_ind + 1];

			if ( HDstrcmp( infile, outfile ) == 0) {
				error_msg("file names cannot be the same\n");
				usage(h5tools_getprogname());
				h5tools_setstatus(EXIT_FAILURE);
				goto done;
			}
		}
		else {
			error_msg("file names missing\n");
			usage(h5tools_getprogname());
			h5tools_setstatus(EXIT_FAILURE);
			goto done;
		}
	}

	/* pack it */
	h5tools_setstatus(h5repack(infile, outfile, &options));

done:
	/* free tables */
	h5repack_end(&options);

	leave(h5tools_getstatus());
}