aboutsummaryrefslogtreecommitdiff
path: root/src/indexamajig.c
blob: 27ea8fa5823acceccda394e3ebb9b2199b2a883e (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
/*
 * indexamajig.c
 *
 * Index patterns, output hkl+intensity etc.
 *
 * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 * Copyright © 2012 Richard Kirian
 * Copyright © 2012 Lorenzo Galli
 *
 * Authors:
 *   2010-2013 Thomas White <taw@physics.org>
 *   2011      Richard Kirian
 *   2012      Lorenzo Galli
 *   2012      Chunhong Yoon
 *
 * This file is part of CrystFEL.
 *
 * CrystFEL is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * CrystFEL is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
 *
 */


#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include <hdf5.h>
#include <gsl/gsl_errno.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>

#ifdef HAVE_CLOCK_GETTIME
#include <time.h>
#else
#include <sys/time.h>
#endif

#include "utils.h"
#include "hdf5-file.h"
#include "index.h"
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "thread-pool.h"
#include "beam-parameters.h"
#include "geometry.h"
#include "stream.h"
#include "reflist-utils.h"
#include "cell-utils.h"
#include "integration.h"

#include "im-sandbox.h"


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index FEL diffraction images.\n"
"\n"
" -h, --help               Display this help message.\n"
"\n"
" -i, --input=<filename>   Specify file containing list of images to process.\n"
"                           '-' means stdin, which is the default.\n"
" -o, --output=<filename>  Write output stream to this file. '-' for stdout.\n"
"                           Default: indexamajig.stream\n"
"\n"
"     --indexing=<methods> Use 'methods' for indexing.  Provide one or more\n"
"                           methods separated by commas.\n"
"                           See 'man indexamajig' for details.\n"
" -g. --geometry=<file>    Get detector geometry from file.\n"
" -b, --beam=<file>        Get beam parameters from file (provides nominal\n"
"                           wavelength value if no per-shot value is found in\n"
"                           the HDF5 files.\n"
" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
"                           Default: 'molecule.pdb'.\n"
"     --basename           Remove the directory parts of the filenames.\n"
" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
"     --peaks=<method>     Use 'method' for finding peaks.  Choose from:\n"
"                           zaef  : Use Zaefferer (2000) gradient detection.\n"
"                                    This is the default method.\n"
"                           hdf5  : Get from a table in HDF5 file.\n"
"     --hdf5-peaks=<p>     Find peaks table in HDF5 file here.\n"
"                           Default: /processing/hitfinder/peakinfo\n"
"     --integration=<meth> Perform final pattern integration using <meth>.\n"
"\n\n"
"For more control over the process, you might need:\n\n"
"    --tolerance=<tol>   Set the tolerances for cell comparison.\n"
"                          Default: 5,5,5,1.5.\n"
"    --filter-noise      Apply an aggressive noise filter which sets all\n"
"                         pixels in each 3x3 region to zero if any of them\n"
"                         have negative values.  Intensity measurement will\n"
"                         be performed on the image as it was before this.\n"
"    --median-filter=<n> Apply a median filter to the image data.  Intensity\n"
"                         measurement will be performed on the image as it\n"
"                         was before this.  The side length of the median\n"
"                         filter box will be 2<n>+1.  Default: 0 (no filter).\n"
"    --no-sat-corr       Don't correct values of saturated peaks using a\n"
"                         table included in the HDF5 file.\n"
"    --threshold=<n>     Only accept peaks above <n> ADU.  Default: 800.\n"
"    --min-gradient=<n>  Minimum squared gradient for Zaefferer peak search.\n"
"                         Default: 100,000.\n"
"    --min-snr=<n>       Minimum signal-to-noise ratio for peaks.\n"
"                         Default: 5.\n"
"    --int-radius=<r>    Set the integration radii.  Default: 4,5,7.\n"
"-e, --image=<element>   Use this image from the HDF5 file.\n"
"                          Example: /data/data0.\n"
"                          Default: The first one found.\n"
"\n"
"\nFor time-resolved stuff, you might want to use:\n\n"
"     --copy-hdf5-field <f>  Copy the value of field <f> into the stream. You\n"
"                             can use this option as many times as you need.\n"
"\n"
"\nOptions for greater performance:\n\n"
" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
"\n"
"\nOptions you probably won't need:\n\n"
"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
"     --closer-peak        Don't integrate from the location of a nearby peak\n"
"                           instead of the predicted spot.  Don't use.\n"
"     --no-use-saturated   During the initial peak search, reject\n"
"                           peaks which contain pixels above max_adu.\n"
"     --no-revalidate      Don't re-integrate and check HDF5 peaks for\n"
"                           validity.\n"
"     --no-peaks-in-stream Do not record peak search results in the stream.\n"
"     --no-refls-in-stream Do not record integrated reflections in the stream.\n"
);
}


int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
	char *outfile = NULL;
	FILE *fh;
	int ofd;
	char *rval = NULL;
	int config_checkprefix = 1;
	int config_basename = 0;
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	char *indm_str = NULL;
	char *pdb = NULL;
	char *prefix = NULL;
	char *speaks = NULL;
	char *toler = NULL;
	int n_proc = 1;
	char *prepare_line;
	char prepare_filename[1024];
	char *use_this_one_instead;
	struct index_args iargs;
	char *intrad = NULL;
	char *int_str = NULL;

	/* Defaults */
	iargs.cell = NULL;
	iargs.noisefilter = 0;
	iargs.median_filter = 0;
	iargs.satcorr = 1;
	iargs.closer = 0;
	iargs.tols[0] = 5.0;
	iargs.tols[1] = 5.0;
	iargs.tols[2] = 5.0;
	iargs.tols[3] = 1.5;
	iargs.threshold = 800.0;
	iargs.min_gradient = 100000.0;
	iargs.min_snr = 5.0;
	iargs.det = NULL;
	iargs.peaks = PEAK_ZAEF;
	iargs.beam = NULL;
	iargs.element = NULL;
	iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
	iargs.copyme = NULL;
	iargs.ir_inn = 4.0;
	iargs.ir_mid = 5.0;
	iargs.ir_out = 7.0;
	iargs.use_saturated = 1;
	iargs.integrate_saturated = 0;
	iargs.no_revalidate = 0;
	iargs.stream_peaks = 1;
	iargs.stream_refls = 1;
	iargs.copyme = new_copy_hdf5_field_list();
	if ( iargs.copyme == NULL ) {
		ERROR("Couldn't allocate HDF5 field list.\n");
		return 1;
	}
	iargs.indm = NULL;  /* No default */
	iargs.ipriv = NULL;  /* No default */
	iargs.int_meth = integration_method("rings", NULL);

	/* Long options */
	const struct option longopts[] = {

		/* Options with long and short versions */
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
		{"output",             1, NULL,               'o'},
		{"indexing",           1, NULL,               'z'},
		{"geometry",           1, NULL,               'g'},
		{"beam",               1, NULL,               'b'},
		{"pdb",                1, NULL,               'p'},
		{"prefix",             1, NULL,               'x'},
		{"threshold",          1, NULL,               't'},
		{"image",              1, NULL,               'e'},

		/* Long-only options with no arguments */
		{"filter-noise",       0, &iargs.noisefilter,        1},
		{"no-sat-corr",        0, &iargs.satcorr,            0},
		{"sat-corr",           0, &iargs.satcorr,            1},
		{"no-check-prefix",    0, &config_checkprefix,       0},
		{"no-closer-peak",     0, &iargs.closer,             0},
		{"closer-peak",        0, &iargs.closer,             1},
		{"basename",           0, &config_basename,          1},
		{"no-peaks-in-stream", 0, &iargs.stream_peaks,       0},
		{"no-refls-in-stream", 0, &iargs.stream_refls,       0},
		{"integrate-saturated",0, &iargs.integrate_saturated,1},
		{"use-saturated",      0, &iargs.use_saturated,      1},
		{"no-use-saturated",   0, &iargs.use_saturated,      0},
		{"no-revalidate",      0, &iargs.no_revalidate,      1},

		/* Long-only options with arguments */
		{"peaks",              1, NULL,                2},
		{"cell-reduction",     1, NULL,                3},
		{"min-gradient",       1, NULL,                4},
		{"record",             1, NULL,                5},
		{"cpus",               1, NULL,                6},
		{"cpugroup",           1, NULL,                7},
		{"cpuoffset",          1, NULL,                8},
		{"hdf5-peaks",         1, NULL,                9},
		{"copy-hdf5-field",    1, NULL,               10},
		{"min-snr",            1, NULL,               11},
		{"tolerance",          1, NULL,               13},
		{"int-radius",         1, NULL,               14},
		{"median-filter",      1, NULL,               15},
		{"integration",        1, NULL,               16},

		{0, 0, NULL, 0}
	};

	/* Short options */
	while ((c = getopt_long(argc, argv, "hi:o:z:p:x:j:g:t:b:e:",
	                        longopts, NULL)) != -1)
	{
		switch (c) {

			case 'h' :
			show_help(argv[0]);
			return 0;

			case 'i' :
			filename = strdup(optarg);
			break;

			case 'o' :
			outfile = strdup(optarg);
			break;

			case 'z' :
			indm_str = strdup(optarg);
			break;

			case 'p' :
			pdb = strdup(optarg);
			break;

			case 'x' :
			prefix = strdup(optarg);
			break;

			case 'j' :
			n_proc = atoi(optarg);
			break;

			case 'g' :
			iargs.det = get_detector_geometry(optarg);
			if ( iargs.det == NULL ) {
				ERROR("Failed to read detector geometry from "
				      "'%s'\n", optarg);
				return 1;
			}
			break;

			case 't' :
			iargs.threshold = strtof(optarg, NULL);
			break;

			case 'b' :
			iargs.beam = get_beam_parameters(optarg);
			if ( iargs.beam == NULL ) {
				ERROR("Failed to load beam parameters"
				      " from '%s'\n", optarg);
				return 1;
			}
			break;

			case 'e' :
			iargs.element = strdup(optarg);
			break;

			case 2 :
			speaks = strdup(optarg);
			break;

			case 3 :
			ERROR("The option '--cell-reduction' is no longer "
			      "used.\n"
			      "The complete indexing behaviour is now "
			      "controlled using '--indexing'.\n"
			      "See 'man indexamajig' for details of the "
			      "available methods.\n");
			return 1;

			case 4 :
			iargs.min_gradient = strtof(optarg, NULL);
			break;

			case 5 :
			ERROR("The option '--record' is no longer used.\n"
			      "Use '--no-peaks-in-stream' and"
			      "'--no-refls-in-stream' if you need to control"
			      "the contents of the stream.\n");
			return 1;

			case 6 :
			case 7 :
			case 8 :
			ERROR("The options --cpus, --cpugroup and --cpuoffset"
			      " are no longer used by indexamajig.\n");
			break;

			case 9 :
			free(iargs.hdf5_peak_path);
			iargs.hdf5_peak_path = strdup(optarg);
			break;

			case 10 :
			add_copy_hdf5_field(iargs.copyme, optarg);
			break;

			case 11 :
			iargs.min_snr = strtof(optarg, NULL);
			break;

			case 13 :
			toler = strdup(optarg);
			break;

			case 14 :
			intrad = strdup(optarg);
			break;

			case 15 :
			iargs.median_filter = atoi(optarg);
			break;

			case 16 :
			int_str = strdup(optarg);
			break;

			case 0 :
			break;

			case '?' :
			break;

			default :
			ERROR("Unhandled option '%c'\n", c);
			break;

		}

	}

	if ( filename == NULL ) {
		filename = strdup("-");
	}
	if ( strcmp(filename, "-") == 0 ) {
		fh = stdin;
	} else {
		fh = fopen(filename, "r");
	}
	if ( fh == NULL ) {
		ERROR("Failed to open input file '%s'\n", filename);
		return 1;
	}
	free(filename);

	if ( speaks == NULL ) {
		speaks = strdup("zaef");
		STATUS("You didn't specify a peak detection method.\n");
		STATUS("I'm using 'zaef' for you.\n");
	}
	if ( strcmp(speaks, "zaef") == 0 ) {
		iargs.peaks = PEAK_ZAEF;
	} else if ( strcmp(speaks, "hdf5") == 0 ) {
		iargs.peaks = PEAK_HDF5;
	} else {
		ERROR("Unrecognised peak detection method '%s'\n", speaks);
		return 1;
	}
	free(speaks);

	if ( prefix == NULL ) {
		prefix = strdup("");
	} else {
		if ( config_checkprefix ) {
			prefix = check_prefix(prefix);
		}
	}

	if ( n_proc == 0 ) {
		ERROR("Invalid number of processes.\n");
		return 1;
	}

	if ( indm_str == NULL ) {

		STATUS("You didn't specify an indexing method, so I  won't try "
		       " to index anything.\n"
		       "If that isn't what you wanted, re-run with"
		       " --indexing=<methods>.\n");
		indm = NULL;

	} else {

		indm = build_indexer_list(indm_str);
		if ( indm == NULL ) {
			ERROR("Invalid indexer list '%s'\n", indm_str);
			return 1;
		}
		free(indm_str);
	}

	if ( int_str != NULL ) {

		int err;

		iargs.int_meth = integration_method(int_str, &err);
		if ( err ) {
			ERROR("Invalid integration method '%s'\n", int_str);
			return 1;
		}
		free(int_str);
	}

	if ( toler != NULL ) {
		int ttt;
		ttt = sscanf(toler, "%f,%f,%f,%f",
		             &iargs.tols[0], &iargs.tols[1],
		             &iargs.tols[2], &iargs.tols[3]);
		if ( ttt != 4 ) {
			ERROR("Invalid parameters for '--tolerance'\n");
			return 1;
		}
		free(toler);
	}

	if ( intrad != NULL ) {
		int r;
		r = sscanf(intrad, "%f,%f,%f",
		           &iargs.ir_inn, &iargs.ir_mid, &iargs.ir_out);
		if ( r != 3 ) {
			ERROR("Invalid parameters for '--int-radius'\n");
			return 1;
		}
		free(intrad);
	} else {
		STATUS("WARNING: You did not specify --int-radius.\n");
		STATUS("WARNING: I will use the default values, which are"
		       " probably not appropriate for your patterns.\n");
	}

	if ( iargs.det == NULL ) {
		ERROR("You need to provide a geometry file (please read the"
		      " manual for more details).\n");
		return 1;
	}

	if ( iargs.beam == NULL ) {
		ERROR("You need to provide a beam parameters file (please read"
		      " the manual for more details).\n");
		return 1;
	}

	if ( pdb != NULL ) {
		iargs.cell = load_cell_from_pdb(pdb);
		if ( iargs.cell == NULL ) {
			ERROR("Couldn't read unit cell (from %s)\n", pdb);
			return 1;
		}
		free(pdb);
		STATUS("This is what I understood your unit cell to be:\n");
		cell_print(iargs.cell);
	} else {
		STATUS("No unit cell given.\n");
		iargs.cell = NULL;
	}

	ofd = open(outfile, O_CREAT | O_TRUNC | O_WRONLY, S_IRUSR | S_IWUSR);
	if ( ofd == -1 ) {
		ERROR("Failed to open stream '%s'\n", outfile);
		return 1;
	}
	free(outfile);

	/* Get first filename and use it to set up the indexing */
	prepare_line = malloc(1024);
	rval = fgets(prepare_line, 1023, fh);
	if ( rval == NULL ) {
		ERROR("Failed to get filename to prepare indexing.\n");
		return 1;
	}
	use_this_one_instead = strdup(prepare_line);
	chomp(prepare_line);
	if ( config_basename ) {
		char *tmp;
		tmp = safe_basename(prepare_line);
		free(prepare_line);
		prepare_line = tmp;
	}
	snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
	free(prepare_line);

	/* Prepare the indexer */
	if ( indm != NULL ) {
		ipriv = prepare_indexing(indm, iargs.cell, prepare_filename,
		                         iargs.det, iargs.beam, iargs.tols);
		if ( ipriv == NULL ) {
			ERROR("Failed to prepare indexing.\n");
			return 1;
		}
	} else {
		ipriv = NULL;
	}

	gsl_set_error_handler_off();

	iargs.indm = indm;
	iargs.ipriv = ipriv;

	create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
	               use_this_one_instead, ofd, argc, argv);

	free(prefix);

	return 0;
}