indexamajig.c 19.5 KB
Newer Older
Thomas White's avatar
Thomas White committed
1
/*
2
 * indexamajig.c
Thomas White's avatar
Thomas White committed
3
 *
Thomas White's avatar
Thomas White committed
4
 * Index patterns, output hkl+intensity etc.
Thomas White's avatar
Thomas White committed
5
 *
Thomas White's avatar
Thomas White committed
6
 * (c) 2006-2010 Thomas White <taw@physics.org>
Thomas White's avatar
Thomas White committed
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */


#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>
Thomas White's avatar
Thomas White committed
23
#include <hdf5.h>
Thomas White's avatar
Thomas White committed
24
#include <gsl/gsl_errno.h>
25
#include <pthread.h>
Thomas White's avatar
Thomas White committed
26
#include <sys/time.h>
Thomas White's avatar
Thomas White committed
27
28
29

#include "utils.h"
#include "hdf5-file.h"
Thomas White's avatar
Thomas White committed
30
#include "index.h"
31
#include "peaks.h"
32
#include "detector.h"
33
#include "sfac.h"
Thomas White's avatar
Thomas White committed
34
#include "filters.h"
35
#include "reflections.h"
36
#include "thread-pool.h"
37
#include "beam-parameters.h"
38
#include "geometry.h"
39

40
41
42
43
44
45
46

enum {
	PEAK_ZAEF,
	PEAK_HDF5,
};


47
48
/* Information about the indexing process which is common to all patterns */
struct static_index_args
49
50
51
52
53
54
55
{
	UnitCell *cell;
	int config_cmfilter;
	int config_noisefilter;
	int config_dumpfound;
	int config_verbose;
	int config_nearbragg;
Thomas White's avatar
Thomas White committed
56
	int config_polar;
57
	int config_satcorr;
58
	int config_closer;
59
	int config_insane;
60
	float threshold;
61
	float min_gradient;
Thomas White's avatar
Thomas White committed
62
	struct detector *det;
Thomas White's avatar
Thomas White committed
63
64
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
65
	int peaks;
66
	int cellr;
67
	struct beam_params *beam;
68

69
70
71
	/* Output stream */
	pthread_mutex_t *output_mutex;  /* Protects the output stream */
	FILE *ofh;
72
73
74
};


75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
/* Information about the indexing process for one pattern */
struct index_args
{
	/* "Input" */
	char *filename;
	struct static_index_args static_args;

	/* "Output" */
	int indexable;
};


/* Information needed to choose the next task and dispatch it */
struct queue_args
{
	FILE *fh;
	char *prefix;
	struct static_index_args static_args;

	int n_indexable;
95
96

	char *use_this_one_instead;
97
98
99
};


Thomas White's avatar
Thomas White committed
100
101
102
103
104
105
static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index FEL diffraction images.\n"
"\n"
106
" -h, --help               Display this help message.\n"
Thomas White's avatar
Thomas White committed
107
"\n"
108
" -i, --input=<filename>   Specify file containing list of images to process.\n"
Thomas White's avatar
Thomas White committed
109
"                           '-' means stdin, which is the default.\n"
110
" -o, --output=<filename>  Write indexed stream to this file. '-' for stdout.\n"
Thomas White's avatar
Thomas White committed
111
"\n"
Thomas White's avatar
Thomas White committed
112
113
114
115
116
117
"     --indexing=<methods> Use 'methods' for indexing.  Provide one or more\n"
"                           methods separated by commas.  Choose from:\n"
"                            none     : no indexing (default)\n"
"                            dirax    : invoke DirAx\n"
"                            mosflm   : invoke MOSFLM (DPS)\n"
"                            template : index by template matching\n"
118
" -g. --geometry=<file>    Get detector geometry from file.\n"
119
120
121
" -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"
122
" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
Thomas White's avatar
Thomas White committed
123
"                           Default: 'molecule.pdb'.\n"
124
" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
125
126
127
128
129
"     --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 /processing/hitfinder/peakinfo\n"
"                                    in the HDF5 file.\n"
Thomas White's avatar
Thomas White committed
130
131
132
"\n"
"\nWith just the above options, this program does not do much of practical use."
"\nYou should also enable some of the following:\n\n"
133
"     --near-bragg         Output a list of reflection intensities to stdout.\n"
Thomas White's avatar
Thomas White committed
134
135
136
137
138
139
140
141
142
143
"                           When pixels with fractional indices within 0.1 of\n"
"                           integer values (the Bragg condition) are found,\n"
"                           the integral of pixels within a ten pixel radius\n"
"                           of the nearest-to-Bragg pixel will be reported as\n"
"                           the intensity.  The centroid of the pixels will\n"
"                           be given as the coordinates, as well as the h,k,l\n"
"                           (integer) indices of the reflection.  If a peak\n"
"                           was located by the initial peak search close to\n"
"                           the \"near Bragg\" location, its coordinates will\n"
"                           be taken as the centre instead.\n"
144
"     --dump-peaks         Write the results of the peak search to stdout.\n"
145
146
"                           The intensities in this list are from the\n"
"                           centroid/integration procedure.\n"
Thomas White's avatar
Thomas White committed
147
148
"\n"
"\nFor more control over the process, you might need:\n\n"
Thomas White's avatar
Thomas White committed
149
150
151
152
153
"     --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n"
"                           none    : no matching, just use the raw cell.\n"
"                           reduce  : full cell reduction.\n"
"                           compare : match by at most changing the order of\n"
"                                     the indices.\n"
154
"     --filter-cm          Perform common-mode noise subtraction on images\n"
Thomas White's avatar
Thomas White committed
155
156
"                           before proceeding.  Intensities will be extracted\n"
"                           from the image as it is after this processing.\n"
157
"     --filter-noise       Apply an aggressive noise filter which sets all\n"
Thomas White's avatar
Thomas White committed
158
159
160
"                           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"
161
"     --unpolarized        Don't correct for the polarisation of the X-rays.\n"
162
163
"     --no-sat-corr        Don't correct values of saturated peaks using a\n"
"                           table included in the HDF5 file.\n"
164
"     --threshold=<n>      Only accept peaks above <n> ADU.  Default: 800.\n"
165
166
"     --min-gradient=<n>   Minimum gradient for Zaefferer peak search.\n"
"                           Default: 100,000.\n"
Thomas White's avatar
Thomas White committed
167
"\n"
168
169
170
"\nOptions for greater performance or verbosity:\n\n"
"     --verbose            Be verbose about indexing.\n"
" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
171
172
173
"\n"
"\nOptions you probably won't need:\n\n"
"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
174
175
176
"     --no-closer-peak     Don't integrate from the location of a nearby peak\n"
"                           instead of the position closest to the reciprocal\n"
"                           lattice point.\n"
177
178
"     --insane             Don't check that the reduced cell accounts for at\n"
"                           least 10%% of the located peaks.\n"
Thomas White's avatar
Thomas White committed
179
);
Thomas White's avatar
Thomas White committed
180
181
182
}


183
static void process_image(void *pp, int cookie)
184
{
185
	struct index_args *pargs = pp;
186
187
188
189
	struct hdfile *hdfile;
	struct image image;
	float *data_for_measurement;
	size_t data_size;
190
	char *filename = pargs->filename;
191
192
193
194
195
196
197
	UnitCell *cell = pargs->static_args.cell;
	int config_cmfilter = pargs->static_args.config_cmfilter;
	int config_noisefilter = pargs->static_args.config_noisefilter;
	int config_dumpfound = pargs->static_args.config_dumpfound;
	int config_verbose = pargs->static_args.config_verbose;
	int config_nearbragg = pargs->static_args.config_nearbragg;
	int config_polar = pargs->static_args.config_polar;
Thomas White's avatar
Thomas White committed
198
	IndexingMethod *indm = pargs->static_args.indm;
199
	const struct beam_params *beam = pargs->static_args.beam;
200
201
202
203

	image.features = NULL;
	image.data = NULL;
	image.indexed_cell = NULL;
204
	image.id = cookie;
205
	image.filename = filename;
206
	image.det = pargs->static_args.det;
207

208
	STATUS("Processing '%s'\n", image.filename);
209

Thomas White's avatar
Thomas White committed
210
	pargs->indexable = 0;
211

212
213
	hdfile = hdfile_open(filename);
	if ( hdfile == NULL ) {
Thomas White's avatar
Thomas White committed
214
		return;
215
216
	} else if ( hdfile_set_first_image(hdfile, "/") ) {
		ERROR("Couldn't select path\n");
Thomas White's avatar
Thomas White committed
217
		return;
218
219
	}

220
	hdf5_read(hdfile, &image, pargs->static_args.config_satcorr,
221
	          beam->photon_energy);
222
223
224
225
226
227
228
229
230
231
232
233
234

	if ( config_cmfilter ) {
		filter_cm(&image);
	}

	/* Take snapshot of image after CM subtraction but before
	 * the aggressive noise filter. */
	data_size = image.width*image.height*sizeof(float);
	data_for_measurement = malloc(data_size);

	if ( config_noisefilter ) {
		filter_noise(&image, data_for_measurement);
	} else {
235
		memcpy(data_for_measurement, image.data, data_size);
236
237
	}

238
	switch ( pargs->static_args.peaks )
239
240
241
242
243
244
245
246
247
	{
	case PEAK_HDF5 :
		/* Get peaks from HDF5 */
		if ( get_peaks(&image, hdfile) ) {
			ERROR("Failed to get peaks from HDF5 file.\n");
			return;
		}
		break;
	case PEAK_ZAEF :
248
249
		search_peaks(&image, pargs->static_args.threshold,
		             pargs->static_args.min_gradient);
250
251
		break;
	}
Thomas White's avatar
Thomas White committed
252
253
254
255
256
257

	/* Get rid of noise-filtered version at this point
	 * - it was strictly for the purposes of peak detection. */
	free(image.data);
	image.data = data_for_measurement;

258
	if ( config_dumpfound ) {
259
260
		dump_peaks(&image, pargs->static_args.ofh,
		           pargs->static_args.output_mutex);
261
	}
262

263
264
	/* Not indexing? Then there's nothing left to do. */
	if ( indm == NULL ) goto done;
265
266

	/* Calculate orientation matrix (by magic) */
267
	index_pattern(&image, cell, indm, pargs->static_args.cellr,
268
269
		      config_verbose, pargs->static_args.ipriv,
		      pargs->static_args.config_insane);
270
271
272

	/* No cell at this point?  Then we're done. */
	if ( image.indexed_cell == NULL ) goto done;
Thomas White's avatar
Thomas White committed
273
	pargs->indexable = 1;
274
275
276

	/* Measure intensities if requested */
	if ( config_nearbragg ) {
277
278
279

		RefList *reflections;

280
281
		image.div = beam->divergence;
		image.bw = beam->bandwidth;
Thomas White's avatar
Thomas White committed
282
		image.profile_radius = 0.0001e9;
283

Thomas White's avatar
Thomas White committed
284
285
286
287
		//reflections = find_intersections(&image, image.indexed_cell,
		//                                 0);
		reflections = find_projected_peaks(&image, image.indexed_cell,
		                                   0, 0.1);
288
289

		output_intensities(&image, image.indexed_cell, reflections,
290
		                   pargs->static_args.output_mutex,
Thomas White's avatar
Thomas White committed
291
		                   config_polar,
292
		                   pargs->static_args.config_closer,
293
294
295
296
		                   pargs->static_args.ofh);

		reflist_free(reflections);

297
298
299
	}

	/* Only free cell if found */
300
	cell_free(image.indexed_cell);
301
302
303

done:
	free(image.data);
Thomas White's avatar
Thomas White committed
304
	free(image.flags);
305
306
307
308
309
	image_feature_list_free(image.features);
	hdfile_close(hdfile);
}


310
static void *get_image(void *qp)
311
{
312
313
314
315
	char line[1024];
	struct index_args *pargs;
	char *rval;
	struct queue_args *qargs = qp;
316

317
	/* Initialise new task arguments */
318
319
320
	pargs = malloc(sizeof(struct index_args));
	memcpy(&pargs->static_args, &qargs->static_args,
	       sizeof(struct static_index_args));
321

322
323
324
325
326
327
328
329
330
331
332
333
334
335
	/* Get the next filename */
	if ( qargs->use_this_one_instead != NULL ) {

		pargs->filename = malloc(strlen(qargs->prefix) +
		                       strlen(qargs->use_this_one_instead) + 1);

		snprintf(pargs->filename, 1023, "%s%s", qargs->prefix,
		         qargs->use_this_one_instead);

		qargs->use_this_one_instead = NULL;

	} else {

		rval = fgets(line, 1023, qargs->fh);
Thomas White's avatar
Thomas White committed
336
337
338
339
		if ( rval == NULL ) {
			free(pargs);
			return NULL;
		}
340
341
342
343
344
		chomp(line);
		pargs->filename = malloc(strlen(qargs->prefix)+strlen(line)+1);
		snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);

	}
345

346
347
	return pargs;
}
348
349


350
351
352
353
static void finalise_image(void *qp, void *pp)
{
	struct queue_args *qargs = qp;
	struct index_args *pargs = pp;
354

355
	qargs->n_indexable += pargs->indexable;
356

357
358
	free(pargs->filename);
	free(pargs);
359
360
361
}


Thomas White's avatar
Thomas White committed
362
363
364
365
int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
366
	char *outfile = NULL;
Thomas White's avatar
Thomas White committed
367
	FILE *fh;
368
	FILE *ofh;
369
	char *rval = NULL;
Thomas White's avatar
Thomas White committed
370
	int n_images;
371
	int config_noindex = 0;
Thomas White's avatar
Thomas White committed
372
	int config_dumpfound = 0;
373
	int config_nearbragg = 0;
374
375
	int config_cmfilter = 0;
	int config_noisefilter = 0;
376
	int config_verbose = 0;
Thomas White's avatar
Thomas White committed
377
	int config_polar = 1;
378
	int config_satcorr = 1;
379
	int config_checkprefix = 1;
380
	int config_closer = 1;
381
	int config_insane = 0;
382
	float threshold = 800.0;
383
	float min_gradient = 100000.0;
Thomas White's avatar
Thomas White committed
384
385
	struct detector *det;
	char *geometry = NULL;
Thomas White's avatar
Thomas White committed
386
387
388
389
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	int indexer_needs_cell;
	int reduction_needs_cell;
Thomas White's avatar
Thomas White committed
390
	char *indm_str = NULL;
391
	UnitCell *cell;
Thomas White's avatar
Thomas White committed
392
	char *pdb = NULL;
393
	char *prefix = NULL;
394
	char *speaks = NULL;
395
396
	char *scellr = NULL;
	int cellr;
397
	int peaks;
398
399
	int nthreads = 1;
	int i;
400
	pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
401
402
	char prepare_line[1024];
	char prepare_filename[1024];
403
	struct queue_args qargs;
404
405
	struct beam_params *beam = NULL;
	double nominal_photon_energy;
Thomas White's avatar
Thomas White committed
406
407
408
409
410

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
411
		{"output",             1, NULL,               'o'},
412
		{"no-index",           0, &config_noindex,     1},
Thomas White's avatar
Thomas White committed
413
		{"dump-peaks",         0, &config_dumpfound,   1},
414
		{"peaks",              1, NULL,                2},
415
		{"cell-reduction",     1, NULL,                3},
416
		{"near-bragg",         0, &config_nearbragg,   1},
Thomas White's avatar
Thomas White committed
417
		{"indexing",           1, NULL,               'z'},
Thomas White's avatar
Thomas White committed
418
		{"geometry",           1, NULL,               'g'},
419
		{"beam",               1, NULL,               'b'},
420
421
		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
422
		{"verbose",            0, &config_verbose,     1},
Thomas White's avatar
Thomas White committed
423
		{"pdb",                1, NULL,               'p'},
424
		{"prefix",             1, NULL,               'x'},
Thomas White's avatar
Thomas White committed
425
		{"unpolarized",        0, &config_polar,       0},
426
427
		{"no-sat-corr",        0, &config_satcorr,     0},
		{"sat-corr",           0, &config_satcorr,     1}, /* Compat */
428
		{"threshold",          1, NULL,               't'},
429
		{"min-gradient",       1, NULL,                4},
430
		{"no-check-prefix",    0, &config_checkprefix, 0},
431
		{"no-closer-peak",     0, &config_closer,      0},
432
		{"insane",             0, &config_insane,      1},
Thomas White's avatar
Thomas White committed
433
434
435
436
		{0, 0, NULL, 0}
	};

	/* Short options */
437
	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:",
Thomas White's avatar
Thomas White committed
438
	                        longopts, NULL)) != -1) {
Thomas White's avatar
Thomas White committed
439
440

		switch (c) {
Thomas White's avatar
Thomas White committed
441
		case 'h' :
Thomas White's avatar
Thomas White committed
442
443
444
			show_help(argv[0]);
			return 0;

Thomas White's avatar
Thomas White committed
445
		case 'i' :
Thomas White's avatar
Thomas White committed
446
447
448
			filename = strdup(optarg);
			break;

449
450
451
452
		case 'o' :
			outfile = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
453
		case 'z' :
Thomas White's avatar
Thomas White committed
454
455
456
			indm_str = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
457
		case 'p' :
Thomas White's avatar
Thomas White committed
458
459
460
			pdb = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
461
		case 'x' :
462
463
464
			prefix = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
465
		case 'j' :
466
467
468
			nthreads = atoi(optarg);
			break;

Thomas White's avatar
Thomas White committed
469
		case 'g' :
Thomas White's avatar
Thomas White committed
470
471
472
			geometry = strdup(optarg);
			break;

473
474
475
476
		case 't' :
			threshold = strtof(optarg, NULL);
			break;

477
478
479
480
481
482
483
484
485
		case 'b' :
			beam = get_beam_parameters(optarg);
			if ( beam == NULL ) {
				ERROR("Failed to load beam parameters"
				      " from '%s'\n", optarg);
				return 1;
			}
			break;

486
487
488
489
		case 2 :
			speaks = strdup(optarg);
			break;

490
491
492
493
		case 3 :
			scellr = strdup(optarg);
			break;

494
495
496
497
		case 4 :
			min_gradient = strtof(optarg, NULL);
			break;

Thomas White's avatar
Thomas White committed
498
		case 0 :
Thomas White's avatar
Thomas White committed
499
500
			break;

Thomas White's avatar
Thomas White committed
501
		default :
Thomas White's avatar
Thomas White committed
502
503
504
505
506
507
508
509
510
511
512
513
514
515
			return 1;
		}

	}

	if ( filename == NULL ) {
		filename = strdup("-");
	}
	if ( strcmp(filename, "-") == 0 ) {
		fh = stdin;
	} else {
		fh = fopen(filename, "r");
	}
	if ( fh == NULL ) {
Thomas White's avatar
Thomas White committed
516
		ERROR("Failed to open input file '%s'\n", filename);
Thomas White's avatar
Thomas White committed
517
518
		return 1;
	}
Thomas White's avatar
Thomas White committed
519
	free(filename);
Thomas White's avatar
Thomas White committed
520

521
522
523
524
525
526
527
528
529
530
531
532
533
534
	if ( outfile == NULL ) {
		outfile = strdup("-");
	}
	if ( strcmp(outfile, "-") == 0 ) {
		ofh = stdout;
	} else {
		ofh = fopen(outfile, "w");
	}
	if ( ofh == NULL ) {
		ERROR("Failed to open output file '%s'\n", outfile);
		return 1;
	}
	free(outfile);

535
536
537
538
539
540
541
542
543
544
545
546
547
	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 ) {
		peaks = PEAK_ZAEF;
	} else if ( strcmp(speaks, "hdf5") == 0 ) {
		peaks = PEAK_HDF5;
	} else {
		ERROR("Unrecognised peak detection method '%s'\n", speaks);
		return 1;
	}
Thomas White's avatar
Thomas White committed
548
	free(speaks);
549

Thomas White's avatar
Thomas White committed
550
551
552
553
	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

554
	if ( prefix == NULL ) {
Thomas White's avatar
Thomas White committed
555
		prefix = strdup("");
556
	} else {
557
558
559
		if ( config_checkprefix ) {
			prefix = check_prefix(prefix);
		}
560
561
	}

562
	if ( nthreads == 0 ) {
563
564
565
566
		ERROR("Invalid number of threads.\n");
		return 1;
	}

Thomas White's avatar
Thomas White committed
567
568
	if ( indm_str == NULL ) {
		STATUS("You didn't specify an indexing method, so I won't"
569
570
571
		       " try to index anything.\n"
		       "If that isn't what you wanted, re-run with"
		       " --indexing=<method>.\n");
Thomas White's avatar
Thomas White committed
572
		indm = NULL;
573
		indexer_needs_cell = 0;
Thomas White's avatar
Thomas White committed
574
	} else {
Thomas White's avatar
Thomas White committed
575
576
577
578
579
580
		indm = build_indexer_list(indm_str, &indexer_needs_cell);
		if ( indm == NULL ) {
			ERROR("Invalid indexer list '%s'\n", indm_str);
			return 1;
		}
		free(indm_str);
Thomas White's avatar
Thomas White committed
581
582
	}

Thomas White's avatar
Thomas White committed
583
	reduction_needs_cell = 0;
584
585
586
587
	if ( scellr == NULL ) {
		STATUS("You didn't specify a cell reduction method, so I'm"
		       " going to use 'reduce'.\n");
		cellr = CELLR_REDUCE;
Thomas White's avatar
Thomas White committed
588
		reduction_needs_cell = 1;
589
590
591
592
	} else if ( strcmp(scellr, "none") == 0 ) {
		cellr = CELLR_NONE;
	} else if ( strcmp(scellr, "reduce") == 0) {
		cellr = CELLR_REDUCE;
Thomas White's avatar
Thomas White committed
593
		reduction_needs_cell = 1;
594
595
	} else if ( strcmp(scellr, "compare") == 0) {
		cellr = CELLR_COMPARE;
Thomas White's avatar
Thomas White committed
596
		reduction_needs_cell = 1;
597
598
599
600
601
602
	} else {
		ERROR("Unrecognised cell reduction method '%s'\n", scellr);
		return 1;
	}
	free(scellr);  /* free(NULL) is OK. */

603
604
605
	/* No indexing -> no reduction */
	if ( indm == NULL ) reduction_needs_cell = 0;

Thomas White's avatar
Thomas White committed
606
607
608
609
610
611
612
613
614
615
616
617
	if ( geometry == NULL ) {
		ERROR("You need to specify a geometry file with --geometry\n");
		return 1;
	}

	det = get_detector_geometry(geometry);
	if ( det == NULL ) {
		ERROR("Failed to read detector geometry from '%s'\n", geometry);
		return 1;
	}
	free(geometry);

Thomas White's avatar
Thomas White committed
618
	if ( reduction_needs_cell || indexer_needs_cell ) {
619
620
		cell = load_cell_from_pdb(pdb);
		if ( cell == NULL ) {
621
622
623
			ERROR("Couldn't read unit cell (from %s)\n", pdb);
			return 1;
		}
624
	} else {
Thomas White's avatar
Thomas White committed
625
626
		STATUS("No cell needed for these choices of indexing"
		       " and reduction.\n");
627
		cell = NULL;
628
	}
629
	free(pdb);
630

631
632
633
634
635
	/* Start by writing the entire command line to stdout */
	fprintf(ofh, "Command line:");
	for ( i=0; i<argc; i++ ) {
		fprintf(ofh, " %s", argv[i]);
	}
636
637
	fprintf(ofh, "\n");
	fflush(ofh);
638

639
640
641
642
643
644
645
646
	if ( beam != NULL ) {
		nominal_photon_energy = beam->photon_energy;
	} else {
		STATUS("No beam parameters file was given, so I'm taking the"
		       " nominal photon energy to be 2 keV.\n");
		nominal_photon_energy = 2000.0;
	}

647
	/* Get first filename and use it to set up the indexing */
648
649
650
651
	rval = fgets(prepare_line, 1023, fh);
	if ( rval == NULL ) {
		ERROR("Failed to get filename to prepare indexing.\n");
		return 1;
652
	}
653
654
655
656
657
	chomp(prepare_line);
	snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
	qargs.use_this_one_instead = prepare_line;

	/* Prepare the indexer */
Thomas White's avatar
Thomas White committed
658
659
660
661
662
663
664
665
666
	if ( indm != NULL ) {
		ipriv = prepare_indexing(indm, cell, prepare_filename, det,
		                         nominal_photon_energy);
		if ( ipriv == NULL ) {
			ERROR("Failed to prepare indexing.\n");
			return 1;
		}
	} else {
		ipriv = NULL;
667
668
	}

Thomas White's avatar
Thomas White committed
669
	gsl_set_error_handler_off();
Thomas White's avatar
Thomas White committed
670

671
672
673
674
675
676
677
678
679
	qargs.static_args.cell = cell;
	qargs.static_args.config_cmfilter = config_cmfilter;
	qargs.static_args.config_noisefilter = config_noisefilter;
	qargs.static_args.config_dumpfound = config_dumpfound;
	qargs.static_args.config_verbose = config_verbose;
	qargs.static_args.config_nearbragg = config_nearbragg;
	qargs.static_args.config_polar = config_polar;
	qargs.static_args.config_satcorr = config_satcorr;
	qargs.static_args.config_closer = config_closer;
680
	qargs.static_args.config_insane = config_insane;
681
	qargs.static_args.cellr = cellr;
682
	qargs.static_args.threshold = threshold;
683
	qargs.static_args.min_gradient = min_gradient;
684
685
686
687
688
689
	qargs.static_args.det = det;
	qargs.static_args.indm = indm;
	qargs.static_args.ipriv = ipriv;
	qargs.static_args.peaks = peaks;
	qargs.static_args.output_mutex = &output_mutex;
	qargs.static_args.ofh = ofh;
690
	qargs.static_args.beam = beam;
691
692
693
694
695
696
697

	qargs.fh = fh;
	qargs.prefix = prefix;
	qargs.n_indexable = 0;

	n_images = run_threads(nthreads, process_image, get_image,
	                       finalise_image, &qargs, 0);
698

699
700
	cleanup_indexing(ipriv);

Thomas White's avatar
Thomas White committed
701
702
	free(indm);
	free(ipriv);
703
	free(prefix);
Thomas White's avatar
Thomas White committed
704
705
	free(det->panels);
	free(det);
706
	cell_free(cell);
Thomas White's avatar
Thomas White committed
707
708
	if ( fh != stdin ) fclose(fh);
	if ( ofh != stdout ) fclose(ofh);
Thomas White's avatar
Thomas White committed
709

710
711
	STATUS("There were %i images, of which %i could be indexed.\n",
	        n_images, qargs.n_indexable);
Thomas White's avatar
Thomas White committed
712
713
714

	return 0;
}