indexamajig.c 20.2 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;
Thomas White's avatar
Thomas White committed
68
	const char *element;
69

70
71
72
	/* Output stream */
	pthread_mutex_t *output_mutex;  /* Protects the output stream */
	FILE *ofh;
73
74
75
};


76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
/* 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;
96
97

	char *use_this_one_instead;
98
99
100
};


Thomas White's avatar
Thomas White committed
101
102
103
104
105
106
static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index FEL diffraction images.\n"
"\n"
107
" -h, --help               Display this help message.\n"
Thomas White's avatar
Thomas White committed
108
"\n"
109
" -i, --input=<filename>   Specify file containing list of images to process.\n"
Thomas White's avatar
Thomas White committed
110
"                           '-' means stdin, which is the default.\n"
111
" -o, --output=<filename>  Write indexed stream to this file. '-' for stdout.\n"
Thomas White's avatar
Thomas White committed
112
"\n"
Thomas White's avatar
Thomas White committed
113
114
115
116
117
118
"     --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"
119
" -g. --geometry=<file>    Get detector geometry from file.\n"
120
121
122
" -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"
123
" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
Thomas White's avatar
Thomas White committed
124
"                           Default: 'molecule.pdb'.\n"
125
" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
126
127
128
129
130
"     --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
131
132
133
"\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"
134
"     --near-bragg         Output a list of reflection intensities to stdout.\n"
Thomas White's avatar
Thomas White committed
135
136
137
138
139
140
141
142
143
144
"                           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"
145
"     --dump-peaks         Write the results of the peak search to stdout.\n"
146
147
"                           The intensities in this list are from the\n"
"                           centroid/integration procedure.\n"
Thomas White's avatar
Thomas White committed
148
149
"\n"
"\nFor more control over the process, you might need:\n\n"
Thomas White's avatar
Thomas White committed
150
151
152
153
154
"     --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"
155
"     --filter-cm          Perform common-mode noise subtraction on images\n"
Thomas White's avatar
Thomas White committed
156
157
"                           before proceeding.  Intensities will be extracted\n"
"                           from the image as it is after this processing.\n"
158
"     --filter-noise       Apply an aggressive noise filter which sets all\n"
Thomas White's avatar
Thomas White committed
159
160
161
"                           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"
162
"     --unpolarized        Don't correct for the polarisation of the X-rays.\n"
163
164
"     --no-sat-corr        Don't correct values of saturated peaks using a\n"
"                           table included in the HDF5 file.\n"
165
"     --threshold=<n>      Only accept peaks above <n> ADU.  Default: 800.\n"
166
167
"     --min-gradient=<n>   Minimum gradient for Zaefferer peak search.\n"
"                           Default: 100,000.\n"
Thomas White's avatar
Thomas White committed
168
169
170
" -e, --image=<element>    Use this image from the HDF5 file.\n"
"                           Example: /data/data0."
"                           Default: The first one found.\n"
Thomas White's avatar
Thomas White committed
171
"\n"
172
173
174
"\nOptions for greater performance or verbosity:\n\n"
"     --verbose            Be verbose about indexing.\n"
" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
175
176
177
"\n"
"\nOptions you probably won't need:\n\n"
"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
178
179
180
"     --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"
181
182
"     --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
183
);
Thomas White's avatar
Thomas White committed
184
185
186
}


187
static void process_image(void *pp, int cookie)
188
{
189
	struct index_args *pargs = pp;
190
191
192
193
	struct hdfile *hdfile;
	struct image image;
	float *data_for_measurement;
	size_t data_size;
194
	char *filename = pargs->filename;
195
196
197
198
199
200
201
	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
202
	IndexingMethod *indm = pargs->static_args.indm;
203
	const struct beam_params *beam = pargs->static_args.beam;
204
205
206
207

	image.features = NULL;
	image.data = NULL;
	image.indexed_cell = NULL;
208
	image.id = cookie;
209
	image.filename = filename;
210
	image.det = pargs->static_args.det;
211

212
	STATUS("Processing '%s'\n", image.filename);
213

Thomas White's avatar
Thomas White committed
214
	pargs->indexable = 0;
215

216
	hdfile = hdfile_open(filename);
Thomas White's avatar
Thomas White committed
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
	if ( hdfile == NULL ) return;

	if ( pargs->static_args.element != NULL ) {

		int r;
		r = hdfile_set_image(hdfile, pargs->static_args.element);
		if ( r ) {
			ERROR("Couldn't select path '%s'\n",
			      pargs->static_args.element);
			hdfile_close(hdfile);
			return;
		}

	} else {

		int r;
		r = hdfile_set_first_image(hdfile, "/");
		if ( r ) {
			ERROR("Couldn't select first path\n");
			hdfile_close(hdfile);
			return;
		}

240
241
	}

242
	hdf5_read(hdfile, &image, pargs->static_args.config_satcorr,
243
	          beam->photon_energy);
244
245
246
247
248
249
250
251
252
253
254
255
256

	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 {
257
		memcpy(data_for_measurement, image.data, data_size);
258
259
	}

260
	switch ( pargs->static_args.peaks )
261
262
263
264
265
266
267
268
269
	{
	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 :
270
271
		search_peaks(&image, pargs->static_args.threshold,
		             pargs->static_args.min_gradient);
272
273
		break;
	}
Thomas White's avatar
Thomas White committed
274
275
276
277
278
279

	/* 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;

280
	if ( config_dumpfound ) {
281
282
		dump_peaks(&image, pargs->static_args.ofh,
		           pargs->static_args.output_mutex);
283
	}
284

285
286
	/* Not indexing? Then there's nothing left to do. */
	if ( indm == NULL ) goto done;
287
288

	/* Calculate orientation matrix (by magic) */
289
	index_pattern(&image, cell, indm, pargs->static_args.cellr,
290
291
		      config_verbose, pargs->static_args.ipriv,
		      pargs->static_args.config_insane);
292
293
294

	/* No cell at this point?  Then we're done. */
	if ( image.indexed_cell == NULL ) goto done;
Thomas White's avatar
Thomas White committed
295
	pargs->indexable = 1;
296
297
298

	/* Measure intensities if requested */
	if ( config_nearbragg ) {
299
300
301

		RefList *reflections;

302
303
		image.div = beam->divergence;
		image.bw = beam->bandwidth;
Thomas White's avatar
Thomas White committed
304
		image.profile_radius = 0.0001e9;
305

Thomas White's avatar
Thomas White committed
306
307
308
309
		//reflections = find_intersections(&image, image.indexed_cell,
		//                                 0);
		reflections = find_projected_peaks(&image, image.indexed_cell,
		                                   0, 0.1);
310
311

		output_intensities(&image, image.indexed_cell, reflections,
312
		                   pargs->static_args.output_mutex,
Thomas White's avatar
Thomas White committed
313
		                   config_polar,
314
		                   pargs->static_args.config_closer,
315
316
317
318
		                   pargs->static_args.ofh);

		reflist_free(reflections);

319
320
321
	}

	/* Only free cell if found */
322
	cell_free(image.indexed_cell);
323
324
325

done:
	free(image.data);
Thomas White's avatar
Thomas White committed
326
	free(image.flags);
327
328
329
330
331
	image_feature_list_free(image.features);
	hdfile_close(hdfile);
}


332
static void *get_image(void *qp)
333
{
334
335
336
337
	char line[1024];
	struct index_args *pargs;
	char *rval;
	struct queue_args *qargs = qp;
338

339
	/* Initialise new task arguments */
340
341
342
	pargs = malloc(sizeof(struct index_args));
	memcpy(&pargs->static_args, &qargs->static_args,
	       sizeof(struct static_index_args));
343

344
345
346
347
348
349
350
351
352
353
354
355
356
357
	/* 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
358
359
360
361
		if ( rval == NULL ) {
			free(pargs);
			return NULL;
		}
362
363
364
365
366
		chomp(line);
		pargs->filename = malloc(strlen(qargs->prefix)+strlen(line)+1);
		snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);

	}
367

368
369
	return pargs;
}
370
371


372
373
374
375
static void finalise_image(void *qp, void *pp)
{
	struct queue_args *qargs = qp;
	struct index_args *pargs = pp;
376

377
	qargs->n_indexable += pargs->indexable;
378

379
380
	free(pargs->filename);
	free(pargs);
381
382
383
}


Thomas White's avatar
Thomas White committed
384
385
386
387
int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
388
	char *outfile = NULL;
Thomas White's avatar
Thomas White committed
389
	FILE *fh;
390
	FILE *ofh;
391
	char *rval = NULL;
Thomas White's avatar
Thomas White committed
392
	int n_images;
393
	int config_noindex = 0;
Thomas White's avatar
Thomas White committed
394
	int config_dumpfound = 0;
395
	int config_nearbragg = 0;
396
397
	int config_cmfilter = 0;
	int config_noisefilter = 0;
398
	int config_verbose = 0;
Thomas White's avatar
Thomas White committed
399
	int config_polar = 1;
400
	int config_satcorr = 1;
401
	int config_checkprefix = 1;
402
	int config_closer = 1;
403
	int config_insane = 0;
404
	float threshold = 800.0;
405
	float min_gradient = 100000.0;
Thomas White's avatar
Thomas White committed
406
407
	struct detector *det;
	char *geometry = NULL;
Thomas White's avatar
Thomas White committed
408
409
410
411
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	int indexer_needs_cell;
	int reduction_needs_cell;
Thomas White's avatar
Thomas White committed
412
	char *indm_str = NULL;
413
	UnitCell *cell;
Thomas White's avatar
Thomas White committed
414
	char *pdb = NULL;
415
	char *prefix = NULL;
416
	char *speaks = NULL;
417
418
	char *scellr = NULL;
	int cellr;
419
	int peaks;
420
421
	int nthreads = 1;
	int i;
422
	pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
423
424
	char prepare_line[1024];
	char prepare_filename[1024];
425
	struct queue_args qargs;
426
	struct beam_params *beam = NULL;
Thomas White's avatar
Thomas White committed
427
	char *element = NULL;
428
	double nominal_photon_energy;
Thomas White's avatar
Thomas White committed
429
430
431
432
433

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
434
		{"output",             1, NULL,               'o'},
435
		{"no-index",           0, &config_noindex,     1},
Thomas White's avatar
Thomas White committed
436
		{"dump-peaks",         0, &config_dumpfound,   1},
437
		{"peaks",              1, NULL,                2},
438
		{"cell-reduction",     1, NULL,                3},
439
		{"near-bragg",         0, &config_nearbragg,   1},
Thomas White's avatar
Thomas White committed
440
		{"indexing",           1, NULL,               'z'},
Thomas White's avatar
Thomas White committed
441
		{"geometry",           1, NULL,               'g'},
442
		{"beam",               1, NULL,               'b'},
443
444
		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
445
		{"verbose",            0, &config_verbose,     1},
Thomas White's avatar
Thomas White committed
446
		{"pdb",                1, NULL,               'p'},
447
		{"prefix",             1, NULL,               'x'},
Thomas White's avatar
Thomas White committed
448
		{"unpolarized",        0, &config_polar,       0},
449
450
		{"no-sat-corr",        0, &config_satcorr,     0},
		{"sat-corr",           0, &config_satcorr,     1}, /* Compat */
451
		{"threshold",          1, NULL,               't'},
452
		{"min-gradient",       1, NULL,                4},
453
		{"no-check-prefix",    0, &config_checkprefix, 0},
454
		{"no-closer-peak",     0, &config_closer,      0},
455
		{"insane",             0, &config_insane,      1},
Thomas White's avatar
Thomas White committed
456
		{"image",              1, NULL,               'e'},
Thomas White's avatar
Thomas White committed
457
458
459
460
		{0, 0, NULL, 0}
	};

	/* Short options */
Thomas White's avatar
Thomas White committed
461
	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:e:",
Thomas White's avatar
Thomas White committed
462
	                        longopts, NULL)) != -1) {
Thomas White's avatar
Thomas White committed
463
464

		switch (c) {
Thomas White's avatar
Thomas White committed
465
		case 'h' :
Thomas White's avatar
Thomas White committed
466
467
468
			show_help(argv[0]);
			return 0;

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

473
474
475
476
		case 'o' :
			outfile = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
477
		case 'z' :
Thomas White's avatar
Thomas White committed
478
479
480
			indm_str = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
481
		case 'p' :
Thomas White's avatar
Thomas White committed
482
483
484
			pdb = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
485
		case 'x' :
486
487
488
			prefix = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
489
		case 'j' :
490
491
492
			nthreads = atoi(optarg);
			break;

Thomas White's avatar
Thomas White committed
493
		case 'g' :
Thomas White's avatar
Thomas White committed
494
495
496
			geometry = strdup(optarg);
			break;

497
498
499
500
		case 't' :
			threshold = strtof(optarg, NULL);
			break;

501
502
503
504
505
506
507
508
509
		case 'b' :
			beam = get_beam_parameters(optarg);
			if ( beam == NULL ) {
				ERROR("Failed to load beam parameters"
				      " from '%s'\n", optarg);
				return 1;
			}
			break;

510
511
512
513
		case 2 :
			speaks = strdup(optarg);
			break;

514
515
516
517
		case 3 :
			scellr = strdup(optarg);
			break;

518
519
520
521
		case 4 :
			min_gradient = strtof(optarg, NULL);
			break;

Thomas White's avatar
Thomas White committed
522
523
524
525
		case 'e' :
			element = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
526
		case 0 :
Thomas White's avatar
Thomas White committed
527
528
			break;

Thomas White's avatar
Thomas White committed
529
		default :
Thomas White's avatar
Thomas White committed
530
531
532
533
534
535
536
537
538
539
540
541
542
543
			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
544
		ERROR("Failed to open input file '%s'\n", filename);
Thomas White's avatar
Thomas White committed
545
546
		return 1;
	}
Thomas White's avatar
Thomas White committed
547
	free(filename);
Thomas White's avatar
Thomas White committed
548

549
550
551
552
553
554
555
556
557
558
559
560
561
562
	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);

563
564
565
566
567
568
569
570
571
572
573
574
575
	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
576
	free(speaks);
577

Thomas White's avatar
Thomas White committed
578
579
580
581
	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

582
	if ( prefix == NULL ) {
Thomas White's avatar
Thomas White committed
583
		prefix = strdup("");
584
	} else {
585
586
587
		if ( config_checkprefix ) {
			prefix = check_prefix(prefix);
		}
588
589
	}

590
	if ( nthreads == 0 ) {
591
592
593
594
		ERROR("Invalid number of threads.\n");
		return 1;
	}

Thomas White's avatar
Thomas White committed
595
596
	if ( indm_str == NULL ) {
		STATUS("You didn't specify an indexing method, so I won't"
597
598
599
		       " 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
600
		indm = NULL;
601
		indexer_needs_cell = 0;
Thomas White's avatar
Thomas White committed
602
	} else {
Thomas White's avatar
Thomas White committed
603
604
605
606
607
608
		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
609
610
	}

Thomas White's avatar
Thomas White committed
611
	reduction_needs_cell = 0;
612
613
614
615
	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
616
		reduction_needs_cell = 1;
617
618
619
620
	} 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
621
		reduction_needs_cell = 1;
622
623
	} else if ( strcmp(scellr, "compare") == 0) {
		cellr = CELLR_COMPARE;
Thomas White's avatar
Thomas White committed
624
		reduction_needs_cell = 1;
625
626
627
628
629
630
	} else {
		ERROR("Unrecognised cell reduction method '%s'\n", scellr);
		return 1;
	}
	free(scellr);  /* free(NULL) is OK. */

631
632
633
	/* No indexing -> no reduction */
	if ( indm == NULL ) reduction_needs_cell = 0;

Thomas White's avatar
Thomas White committed
634
635
636
637
638
639
640
641
642
643
644
645
	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
646
	if ( reduction_needs_cell || indexer_needs_cell ) {
647
648
		cell = load_cell_from_pdb(pdb);
		if ( cell == NULL ) {
649
650
651
			ERROR("Couldn't read unit cell (from %s)\n", pdb);
			return 1;
		}
652
	} else {
Thomas White's avatar
Thomas White committed
653
654
		STATUS("No cell needed for these choices of indexing"
		       " and reduction.\n");
655
		cell = NULL;
656
	}
657
	free(pdb);
658

659
660
661
662
663
	/* Start by writing the entire command line to stdout */
	fprintf(ofh, "Command line:");
	for ( i=0; i<argc; i++ ) {
		fprintf(ofh, " %s", argv[i]);
	}
664
665
	fprintf(ofh, "\n");
	fflush(ofh);
666

667
668
669
670
671
672
673
674
	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;
	}

675
	/* Get first filename and use it to set up the indexing */
676
677
678
679
	rval = fgets(prepare_line, 1023, fh);
	if ( rval == NULL ) {
		ERROR("Failed to get filename to prepare indexing.\n");
		return 1;
680
	}
681
682
683
684
685
	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
686
687
688
689
690
691
692
693
694
	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;
695
696
	}

Thomas White's avatar
Thomas White committed
697
	gsl_set_error_handler_off();
Thomas White's avatar
Thomas White committed
698

699
700
701
702
703
704
705
706
707
	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;
708
	qargs.static_args.config_insane = config_insane;
709
	qargs.static_args.cellr = cellr;
710
	qargs.static_args.threshold = threshold;
711
	qargs.static_args.min_gradient = min_gradient;
712
713
714
715
716
717
	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;
718
	qargs.static_args.beam = beam;
Thomas White's avatar
Thomas White committed
719
	qargs.static_args.element = element;
720
721
722
723
724
725
726

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

	n_images = run_threads(nthreads, process_image, get_image,
	                       finalise_image, &qargs, 0);
727

728
729
	cleanup_indexing(ipriv);

Thomas White's avatar
Thomas White committed
730
731
	free(indm);
	free(ipriv);
732
	free(prefix);
Thomas White's avatar
Thomas White committed
733
734
	free(det->panels);
	free(det);
Thomas White's avatar
Thomas White committed
735
	free(element);
736
	cell_free(cell);
Thomas White's avatar
Thomas White committed
737
738
	if ( fh != stdin ) fclose(fh);
	if ( ofh != stdout ) fclose(ofh);
Thomas White's avatar
Thomas White committed
739

740
741
	STATUS("There were %i images, of which %i could be indexed.\n",
	        n_images, qargs.n_indexable);
Thomas White's avatar
Thomas White committed
742
743
744

	return 0;
}