indexamajig.c 24.5 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) 2006-2011 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>
26
27

#ifdef HAVE_CLOCK_GETTIME
28
#include <time.h>
29
30
31
#else
#include <sys/time.h>
#endif
Thomas White's avatar
Thomas White committed
32
33
34

#include "utils.h"
#include "hdf5-file.h"
Thomas White's avatar
Thomas White committed
35
#include "index.h"
36
#include "peaks.h"
37
#include "detector.h"
Thomas White's avatar
Thomas White committed
38
#include "filters.h"
39
#include "thread-pool.h"
40
#include "beam-parameters.h"
41
#include "geometry.h"
Thomas White's avatar
Thomas White committed
42
#include "stream.h"
Thomas White's avatar
Thomas White committed
43
#include "reflist-utils.h"
44

45

Thomas White's avatar
Thomas White committed
46
/* Write statistics at APPROXIMATELY this interval */
47
48
49
#define STATS_EVERY_N_SECONDS (5)


50
51
52
53
54
55
enum {
	PEAK_ZAEF,
	PEAK_HDF5,
};


56
57
/* Information about the indexing process which is common to all patterns */
struct static_index_args
58
59
60
61
62
{
	UnitCell *cell;
	int config_cmfilter;
	int config_noisefilter;
	int config_verbose;
Thomas White's avatar
Thomas White committed
63
	int stream_flags;         /* What goes into the output? */
Thomas White's avatar
Thomas White committed
64
	int config_polar;
65
	int config_satcorr;
66
	int config_closer;
67
	int config_insane;
68
	int config_bgsub;
69
	float threshold;
70
	float min_gradient;
Thomas White's avatar
Thomas White committed
71
	struct detector *det;
Thomas White's avatar
Thomas White committed
72
73
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
Thomas White's avatar
Thomas White committed
74
	int peaks;                /* Peak detection method */
75
	int cellr;
76
	struct beam_params *beam;
Thomas White's avatar
Thomas White committed
77
	const char *element;
78
	const char *hdf5_peak_path;
79

80
81
82
	/* Output stream */
	pthread_mutex_t *output_mutex;  /* Protects the output stream */
	FILE *ofh;
83
84
85
};


86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
/* 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;
103
	int config_basename;
104
105
	struct static_index_args static_args;

106
	char *use_this_one_instead;
107
108
109
110
111
112

	int n_indexable;
	int n_processed;
	int n_indexable_last_stats;
	int n_processed_last_stats;
	int t_last_stats;
113
114
115
};


Thomas White's avatar
Thomas White committed
116
117
118
119
120
121
static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index FEL diffraction images.\n"
"\n"
122
" -h, --help               Display this help message.\n"
Thomas White's avatar
Thomas White committed
123
"\n"
124
" -i, --input=<filename>   Specify file containing list of images to process.\n"
Thomas White's avatar
Thomas White committed
125
"                           '-' means stdin, which is the default.\n"
Thomas White's avatar
Thomas White committed
126
127
" -o, --output=<filename>  Write output stream to this file. '-' for stdout.\n"
"                           Default: indexamajig.stream\n"
Thomas White's avatar
Thomas White committed
128
"\n"
Thomas White's avatar
Thomas White committed
129
130
131
132
133
"     --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"
Thomas White's avatar
Thomas White committed
134
"                            reax     : DPS algorithm with known unit cell\n"
135
" -g. --geometry=<file>    Get detector geometry from file.\n"
136
137
138
" -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"
139
" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
Thomas White's avatar
Thomas White committed
140
"                           Default: 'molecule.pdb'.\n"
141
"     --basename           Remove the directory parts of the filenames.\n"
142
" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
143
144
145
"     --peaks=<method>     Use 'method' for finding peaks.  Choose from:\n"
"                           zaef  : Use Zaefferer (2000) gradient detection.\n"
"                                    This is the default method.\n"
146
147
148
"                           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"
Thomas White's avatar
Thomas White committed
149
150
"\n\n"
"You can control what information is included in the output stream using\n"
Thomas White's avatar
Thomas White committed
151
"' --record=<flag1>,<flag2>,<flag3>' and so on.  Possible flags are:\n\n"
152
153
" integrated        Include a list of reflection intensities, produced by\n"
"                    integrating around predicted peak locations.\n"
Thomas White's avatar
Thomas White committed
154
"\n"
155
156
" peaks             Include peak locations and intensities from the peak\n"
"                    search.\n"
Thomas White's avatar
Thomas White committed
157
"\n"
158
" peaksifindexed    As 'peaks', but only if the pattern could be indexed.\n"
Thomas White's avatar
Thomas White committed
159
"\n"
160
161
" peaksifnotindexed As 'peaks', but only if the pattern could NOT be indexed.\n"
"\n\n"
Thomas White's avatar
Thomas White committed
162
"The default is '--record=integrated'.\n"
Thomas White's avatar
Thomas White committed
163
164
"\n\n"
"For more control over the process, you might need:\n\n"
Thomas White's avatar
Thomas White committed
165
166
167
168
169
"     --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"
170
"                           compare_ab : compare 'a' and 'b' lengths only.\n"
171
"     --filter-cm          Perform common-mode noise subtraction on images\n"
Thomas White's avatar
Thomas White committed
172
173
"                           before proceeding.  Intensities will be extracted\n"
"                           from the image as it is after this processing.\n"
174
"     --filter-noise       Apply an aggressive noise filter which sets all\n"
Thomas White's avatar
Thomas White committed
175
176
177
"                           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"
178
"     --unpolarized        Don't correct for the polarisation of the X-rays.\n"
179
180
"     --no-sat-corr        Don't correct values of saturated peaks using a\n"
"                           table included in the HDF5 file.\n"
181
"     --threshold=<n>      Only accept peaks above <n> ADU.  Default: 800.\n"
182
183
"     --min-gradient=<n>   Minimum gradient for Zaefferer peak search.\n"
"                           Default: 100,000.\n"
Thomas White's avatar
Thomas White committed
184
" -e, --image=<element>    Use this image from the HDF5 file.\n"
Thomas White's avatar
Thomas White committed
185
"                           Example: /data/data0.\n"
Thomas White's avatar
Thomas White committed
186
"                           Default: The first one found.\n"
Thomas White's avatar
Thomas White committed
187
"\n"
188
189
190
"\nOptions for greater performance or verbosity:\n\n"
"     --verbose            Be verbose about indexing.\n"
" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
191
192
193
"\n"
"\nOptions you probably won't need:\n\n"
"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
194
195
196
"     --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"
197
198
"     --insane             Don't check that the reduced cell accounts for at\n"
"                           least 10%% of the located peaks.\n"
199
200
"     --no-bg-sub          Don't subtract local background estimates from\n"
"                           integrated intensities.\n"
201
"\n"
Thomas White's avatar
Thomas White committed
202
203
"\nYou can tune the CPU affinities for enhanced performance on NUMA machines:\n"
"\n"
Thomas White's avatar
Thomas White committed
204
205
"     --cpus=<n>           Specify number of CPUs.  This is NOT the same as\n"
"                           giving the number of analyses to run in parallel.\n"
206
207
"     --cpugroup=<n>       Batch threads in groups of this size.\n"
"     --cpuoffset=<n>      Start using CPUs at this group number.\n"
Thomas White's avatar
Thomas White committed
208
);
Thomas White's avatar
Thomas White committed
209
210
211
}


212
static void process_image(void *pp, int cookie)
213
{
214
	struct index_args *pargs = pp;
215
216
217
218
	struct hdfile *hdfile;
	struct image image;
	float *data_for_measurement;
	size_t data_size;
219
	char *filename = pargs->filename;
220
221
222
223
224
	UnitCell *cell = pargs->static_args.cell;
	int config_cmfilter = pargs->static_args.config_cmfilter;
	int config_noisefilter = pargs->static_args.config_noisefilter;
	int config_verbose = pargs->static_args.config_verbose;
	int config_polar = pargs->static_args.config_polar;
Thomas White's avatar
Thomas White committed
225
	IndexingMethod *indm = pargs->static_args.indm;
226
	const struct beam_params *beam = pargs->static_args.beam;
227
228
229

	image.features = NULL;
	image.data = NULL;
Thomas White's avatar
Thomas White committed
230
	image.flags = NULL;
231
	image.indexed_cell = NULL;
232
	image.id = cookie;
233
	image.filename = filename;
234
	image.det = copy_geom(pargs->static_args.det);
235

Thomas White's avatar
Thomas White committed
236
	pargs->indexable = 0;
237

238
	hdfile = hdfile_open(filename);
Thomas White's avatar
Thomas White committed
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
	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;
		}

262
263
	}

264
265
266
	hdf5_read(hdfile, &image, pargs->static_args.config_satcorr);
	if ( image.lambda < 0.0 ) {
		if ( beam != NULL ) {
267
268
			ERROR("Using nominal photon enery of %.2f eV\n",
                              beam->photon_energy);
Thomas White's avatar
Thomas White committed
269
270
			image.lambda = ph_en_to_lambda(
			                          eV_to_J(beam->photon_energy));
271
272
273
274
275
276
277
		} else {
			ERROR("No wavelength in file, so you need to give "
			      "a beam parameters file with -b.\n");
			hdfile_close(hdfile);
			return;
		}
	}
278
	fill_in_values(image.det, hdfile);
279
280
281
282
283
284
285
286
287
288
289
290
291

	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 {
292
		memcpy(data_for_measurement, image.data, data_size);
293
294
	}

295
	switch ( pargs->static_args.peaks )
296
297
298
	{
	case PEAK_HDF5 :
		/* Get peaks from HDF5 */
299
300
301
		if ( get_peaks(&image, hdfile,
		               pargs->static_args.hdf5_peak_path) )
		{
302
303
304
305
			ERROR("Failed to get peaks from HDF5 file.\n");
		}
		break;
	case PEAK_ZAEF :
306
307
		search_peaks(&image, pargs->static_args.threshold,
		             pargs->static_args.min_gradient);
308
309
		break;
	}
Thomas White's avatar
Thomas White committed
310
311
312
313
314
315

	/* 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;

316
	/* Calculate orientation matrix (by magic) */
317
318
319
	image.div = beam->divergence;
	image.bw = beam->bandwidth;
	image.profile_radius = 0.0001e9;
320
	index_pattern(&image, cell, indm, pargs->static_args.cellr,
321
322
		      config_verbose, pargs->static_args.ipriv,
		      pargs->static_args.config_insane);
323

324
	if ( image.indexed_cell != NULL ) {
Thomas White's avatar
Thomas White committed
325

326
		pargs->indexable = 1;
327

328
329
330
331
332
		if ( image.reflections != NULL ) {
			integrate_reflections(&image, config_polar,
					      pargs->static_args.config_closer,
					      pargs->static_args.config_bgsub);
		}
333

334
335
336
337
338
	} else {

		image.reflections = NULL;

	}
Thomas White's avatar
Thomas White committed
339
340
341
342
343

	pthread_mutex_lock(pargs->static_args.output_mutex);
	write_chunk(pargs->static_args.ofh, &image,
	            pargs->static_args.stream_flags);
	pthread_mutex_unlock(pargs->static_args.output_mutex);
344
345

	/* Only free cell if found */
346
	cell_free(image.indexed_cell);
347

Thomas White's avatar
Thomas White committed
348
	reflist_free(image.reflections);
349
	free(image.data);
Thomas White's avatar
Thomas White committed
350
	if ( image.flags != NULL ) free(image.flags);
351
352
	image_feature_list_free(image.features);
	hdfile_close(hdfile);
Thomas White's avatar
Thomas White committed
353
	free_detector_geometry(image.det);
354
355
356
}


357
static void *get_image(void *qp)
358
{
359
	char *line;
360
361
362
	struct index_args *pargs;
	char *rval;
	struct queue_args *qargs = qp;
363

364
	/* Initialise new task arguments */
365
366
367
	pargs = malloc(sizeof(struct index_args));
	memcpy(&pargs->static_args, &qargs->static_args,
	       sizeof(struct static_index_args));
368

369
370
371
	/* Get the next filename */
	if ( qargs->use_this_one_instead != NULL ) {

372
		line = qargs->use_this_one_instead;
373
374
375
376
		qargs->use_this_one_instead = NULL;

	} else {

377
		line = malloc(1024*sizeof(char));
378
		rval = fgets(line, 1023, qargs->fh);
Thomas White's avatar
Thomas White committed
379
380
		if ( rval == NULL ) {
			free(pargs);
Thomas White's avatar
Thomas White committed
381
			free(line);
Thomas White's avatar
Thomas White committed
382
383
			return NULL;
		}
384
385
386
		chomp(line);

	}
387

388
389
390
391
392
393
394
395
396
397
398
399
400
	if ( qargs->config_basename ) {
		char *tmp;
		tmp = safe_basename(line);
		free(line);
		line = tmp;
	}

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

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

	free(line);

401
402
	return pargs;
}
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
#ifdef HAVE_CLOCK_GETTIME

static time_t get_monotonic_seconds()
{
	struct timespec tp;
	clock_gettime(CLOCK_MONOTONIC, &tp);
	return tp.tv_sec;
}

#else

/* Fallback version of the above.  The time according to gettimeofday() is not
 * monotonic, so measuring intervals based on it will screw up if there's a
 * timezone change (e.g. daylight savings) while the program is running. */
static time_t get_monotonic_seconds()
{
	struct timeval tp;
	gettimeofday(&tp, NULL);
	return tp.tv_sec;
}

#endif

428
429
430
431
static void finalise_image(void *qp, void *pp)
{
	struct queue_args *qargs = qp;
	struct index_args *pargs = pp;
432
	time_t monotonic_seconds;
433

434
	qargs->n_indexable += pargs->indexable;
435
436
	qargs->n_processed++;

437
438
	monotonic_seconds = get_monotonic_seconds();
	if ( monotonic_seconds >= qargs->t_last_stats+STATS_EVERY_N_SECONDS ) {
439
440

		STATUS("%i out of %i indexed so far,"
Thomas White's avatar
Thomas White committed
441
		       " %i out of %i since the last message.\n",
442
443
		       qargs->n_indexable, qargs->n_processed,
		       qargs->n_indexable - qargs->n_indexable_last_stats,
Thomas White's avatar
Thomas White committed
444
		       qargs->n_processed - qargs->n_processed_last_stats);
445
446
447

		qargs->n_processed_last_stats = qargs->n_processed;
		qargs->n_indexable_last_stats = qargs->n_indexable;
448
		qargs->t_last_stats = monotonic_seconds;
449
450

	}
451

452
453
	free(pargs->filename);
	free(pargs);
454
455
456
}


457
458
459
static int parse_cell_reduction(const char *scellr, int *err,
                                int *reduction_needs_cell)
{
Thomas White's avatar
Thomas White committed
460
	*err = 0;
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
	if ( strcmp(scellr, "none") == 0 ) {
		*reduction_needs_cell = 0;
		return CELLR_NONE;
	} else if ( strcmp(scellr, "reduce") == 0) {
		*reduction_needs_cell = 1;
		return CELLR_REDUCE;
	} else if ( strcmp(scellr, "compare") == 0) {
		*reduction_needs_cell = 1;
		return CELLR_COMPARE;
	} else if ( strcmp(scellr, "compare_ab") == 0) {
		*reduction_needs_cell = 1;
		return CELLR_COMPARE_AB;
	} else {
		*err = 1;
		*reduction_needs_cell = 0;
		return CELLR_NONE;
	}
}


Thomas White's avatar
Thomas White committed
481
482
483
484
int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
485
	char *outfile = NULL;
Thomas White's avatar
Thomas White committed
486
	FILE *fh;
487
	FILE *ofh;
488
	char *rval = NULL;
Thomas White's avatar
Thomas White committed
489
	int n_images;
490
	int config_noindex = 0;
491
492
	int config_cmfilter = 0;
	int config_noisefilter = 0;
493
	int config_verbose = 0;
Thomas White's avatar
Thomas White committed
494
	int config_polar = 1;
495
	int config_satcorr = 1;
496
	int config_checkprefix = 1;
497
	int config_closer = 1;
498
	int config_insane = 0;
499
	int config_bgsub = 1;
500
	int config_basename = 0;
501
	float threshold = 800.0;
502
	float min_gradient = 100000.0;
Thomas White's avatar
Thomas White committed
503
504
	struct detector *det;
	char *geometry = NULL;
Thomas White's avatar
Thomas White committed
505
506
507
508
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	int indexer_needs_cell;
	int reduction_needs_cell;
Thomas White's avatar
Thomas White committed
509
	char *indm_str = NULL;
510
	UnitCell *cell;
Thomas White's avatar
Thomas White committed
511
	char *pdb = NULL;
512
	char *prefix = NULL;
513
	char *speaks = NULL;
514
515
	char *scellr = NULL;
	int cellr;
516
	int peaks;
517
	int nthreads = 1;
518
	pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
519
	char *prepare_line;
520
	char prepare_filename[1024];
521
	struct queue_args qargs;
522
	struct beam_params *beam = NULL;
Thomas White's avatar
Thomas White committed
523
	char *element = NULL;
524
	double nominal_photon_energy;
Thomas White's avatar
Thomas White committed
525
	int stream_flags = STREAM_INTEGRATED;
526
527
528
529
	int cpu_num = 0;
	int cpu_groupsize = 1;
	int cpu_offset = 0;
	char *endptr;
530
	char *hdf5_peak_path = NULL;
Thomas White's avatar
Thomas White committed
531
532
533
534
535

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
536
		{"output",             1, NULL,               'o'},
537
		{"no-index",           0, &config_noindex,     1},
538
		{"peaks",              1, NULL,                2},
539
		{"cell-reduction",     1, NULL,                3},
Thomas White's avatar
Thomas White committed
540
		{"indexing",           1, NULL,               'z'},
Thomas White's avatar
Thomas White committed
541
		{"geometry",           1, NULL,               'g'},
542
		{"beam",               1, NULL,               'b'},
543
544
		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
545
		{"verbose",            0, &config_verbose,     1},
Thomas White's avatar
Thomas White committed
546
		{"pdb",                1, NULL,               'p'},
547
		{"prefix",             1, NULL,               'x'},
Thomas White's avatar
Thomas White committed
548
		{"unpolarized",        0, &config_polar,       0},
549
550
		{"no-sat-corr",        0, &config_satcorr,     0},
		{"sat-corr",           0, &config_satcorr,     1}, /* Compat */
551
		{"threshold",          1, NULL,               't'},
552
		{"min-gradient",       1, NULL,                4},
553
		{"no-check-prefix",    0, &config_checkprefix, 0},
554
		{"no-closer-peak",     0, &config_closer,      0},
555
		{"insane",             0, &config_insane,      1},
Thomas White's avatar
Thomas White committed
556
		{"image",              1, NULL,               'e'},
557
		{"basename",           0, &config_basename,    1},
Thomas White's avatar
Thomas White committed
558
		{"record",             1, NULL,                5},
559
560
		{"cpus",               1, NULL,                6},
		{"cpugroup",           1, NULL,                7},
561
		{"cpuoffset",          1, NULL,                8},
Thomas White's avatar
Thomas White committed
562
		{"bg-sub",             0, &config_bgsub,       1}, /* Compat */
563
		{"no-bg-sub",          0, &config_bgsub,       0},
564
		{"hdf5-peaks",         1, NULL,                9},
Thomas White's avatar
Thomas White committed
565
566
567
568
		{0, 0, NULL, 0}
	};

	/* Short options */
Thomas White's avatar
Thomas White committed
569
	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:e:",
Thomas White's avatar
Thomas White committed
570
	                        longopts, NULL)) != -1) {
Thomas White's avatar
Thomas White committed
571
572

		switch (c) {
Thomas White's avatar
Thomas White committed
573
		case 'h' :
Thomas White's avatar
Thomas White committed
574
575
576
			show_help(argv[0]);
			return 0;

Thomas White's avatar
Thomas White committed
577
		case 'i' :
Thomas White's avatar
Thomas White committed
578
579
580
			filename = strdup(optarg);
			break;

581
582
583
584
		case 'o' :
			outfile = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
585
		case 'z' :
Thomas White's avatar
Thomas White committed
586
587
588
			indm_str = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
589
		case 'p' :
Thomas White's avatar
Thomas White committed
590
591
592
			pdb = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
593
		case 'x' :
594
595
596
			prefix = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
597
		case 'j' :
598
599
600
			nthreads = atoi(optarg);
			break;

Thomas White's avatar
Thomas White committed
601
		case 'g' :
Thomas White's avatar
Thomas White committed
602
603
604
			geometry = strdup(optarg);
			break;

605
606
607
608
		case 't' :
			threshold = strtof(optarg, NULL);
			break;

609
610
611
612
613
614
615
616
617
		case 'b' :
			beam = get_beam_parameters(optarg);
			if ( beam == NULL ) {
				ERROR("Failed to load beam parameters"
				      " from '%s'\n", optarg);
				return 1;
			}
			break;

618
619
620
621
		case 2 :
			speaks = strdup(optarg);
			break;

622
623
624
625
		case 3 :
			scellr = strdup(optarg);
			break;

626
627
628
629
		case 4 :
			min_gradient = strtof(optarg, NULL);
			break;

Thomas White's avatar
Thomas White committed
630
631
632
633
		case 'e' :
			element = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
634
635
636
637
638
		case 5 :
			stream_flags = parse_stream_flags(optarg);
			if ( stream_flags < 0 ) return 1;
			break;

639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
		case 6 :
			cpu_num = strtol(optarg, &endptr, 10);
			if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
				ERROR("Invalid number of CPUs ('%s')\n",
				      optarg);
				return 1;
			}
			break;

		case 7 :
			cpu_groupsize = strtol(optarg, &endptr, 10);
			if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
				ERROR("Invalid CPU group size ('%s')\n",
				      optarg);
				return 1;
			}
			if ( cpu_groupsize < 1 ) {
				ERROR("CPU group size cannot be"
				      " less than 1.\n");
				return 1;
			}
			break;

		case 8 :
			cpu_offset = strtol(optarg, &endptr, 10);
			if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
				ERROR("Invalid CPU offset ('%s')\n",
				      optarg);
				return 1;
			}
			if ( cpu_offset < 0 ) {
				ERROR("CPU offset must be positive.\n");
				return 1;
			}
			break;

675
676
677
678
		case 9 :
			hdf5_peak_path = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
679
		case 0 :
Thomas White's avatar
Thomas White committed
680
681
			break;

Thomas White's avatar
Thomas White committed
682
		default :
Thomas White's avatar
Thomas White committed
683
684
685
686
687
			return 1;
		}

	}

688
689
690
691
692
693
694
	if ( (cpu_num > 0) && (cpu_num % cpu_groupsize != 0) ) {
		ERROR("Number of CPUs must be divisible by"
		      " the CPU group size.\n");
		return 1;
	}


Thomas White's avatar
Thomas White committed
695
696
697
698
699
700
701
702
703
	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
704
		ERROR("Failed to open input file '%s'\n", filename);
Thomas White's avatar
Thomas White committed
705
706
		return 1;
	}
Thomas White's avatar
Thomas White committed
707
	free(filename);
Thomas White's avatar
Thomas White committed
708

709
710
711
712
713
714
715
716
717
718
719
720
721
722
	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);

723
724
725
726
	if ( hdf5_peak_path == NULL ) {
		hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
	}

727
728
729
730
731
732
733
734
735
736
737
738
739
	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
740
	free(speaks);
741

Thomas White's avatar
Thomas White committed
742
743
744
745
	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

746
	if ( prefix == NULL ) {
Thomas White's avatar
Thomas White committed
747
		prefix = strdup("");
748
	} else {
749
750
751
		if ( config_checkprefix ) {
			prefix = check_prefix(prefix);
		}
752
753
	}

754
	if ( nthreads == 0 ) {
755
756
757
758
		ERROR("Invalid number of threads.\n");
		return 1;
	}

759
760
	if ( (indm_str == NULL) ||
	     ((indm_str != NULL) && (strcmp(indm_str, "none") == 0)) ) {
761
		STATUS("Not indexing anything.\n");
762
		indexer_needs_cell = 0;
763
764
765
		reduction_needs_cell = 0;
		indm = NULL;
		cellr = CELLR_NONE;
Thomas White's avatar
Thomas White committed
766
	} else {
767
768
769
770
771
772
773
774
		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=<method>.\n");
			indm = NULL;
			indexer_needs_cell = 0;
		} else {
Thomas White's avatar
Thomas White committed
775
776
			indm = build_indexer_list(indm_str,
			                          &indexer_needs_cell);
777
778
779
780
781
			if ( indm == NULL ) {
				ERROR("Invalid indexer list '%s'\n", indm_str);
				return 1;
			}
			free(indm_str);
Thomas White's avatar
Thomas White committed
782
		}
Thomas White's avatar
Thomas White committed
783

784
785
786
787
788
789
790
		reduction_needs_cell = 0;
		if ( scellr == NULL ) {
			STATUS("You didn't specify a cell reduction method, so"
			       " I'm going to use 'reduce'.\n");
			cellr = CELLR_REDUCE;
			reduction_needs_cell = 1;
		} else {
791
792
793
794
795
796
797
798
799
			int err;
			cellr = parse_cell_reduction(scellr, &err,
			                             &reduction_needs_cell);
			if ( err ) {
				ERROR("Unrecognised cell reduction '%s'\n",
			              scellr);
				return 1;
			}
			free(scellr);
800
		}
801
802
	}

803
804
805
	/* No indexing -> no reduction */
	if ( indm == NULL ) reduction_needs_cell = 0;

Thomas White's avatar
Thomas White committed
806
807
808
809
810
811
812
813
814
815
816
817
	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
818
	if ( reduction_needs_cell || indexer_needs_cell ) {
819
820
		cell = load_cell_from_pdb(pdb);
		if ( cell == NULL ) {
821
822
823
			ERROR("Couldn't read unit cell (from %s)\n", pdb);
			return 1;
		}
824
	} else {
Thomas White's avatar
Thomas White committed
825
826
		STATUS("No cell needed for these choices of indexing"
		       " and reduction.\n");
827
		cell = NULL;
828
	}
829
	free(pdb);
830

Thomas White's avatar
Thomas White committed
831
	write_stream_header(ofh, argc, argv);
832

833
834
835
836
837
838
839
840
	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;
	}

841
	/* Get first filename and use it to set up the indexing */
842
	prepare_line = malloc(1024*sizeof(char));
843
844
845
846
	rval = fgets(prepare_line, 1023, fh);
	if ( rval == NULL ) {
		ERROR("Failed to get filename to prepare indexing.\n");
		return 1;
847
	}
848
	chomp(prepare_line);
849
850
851
852
853
854
	if ( config_basename ) {
		char *tmp;
		tmp = safe_basename(prepare_line);
		free(prepare_line);
		prepare_line = tmp;
	}
855
856
857
858
	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
859
860
861
862
863
864
865
866
867
	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;
868
869
	}

Thomas White's avatar
Thomas White committed
870
	gsl_set_error_handler_off();
Thomas White's avatar
Thomas White committed
871

872
873
874
875
876
877
878
	qargs.static_args.cell = cell;
	qargs.static_args.config_cmfilter = config_cmfilter;
	qargs.static_args.config_noisefilter = config_noisefilter;
	qargs.static_args.config_verbose = config_verbose;
	qargs.static_args.config_polar = config_polar;
	qargs.static_args.config_satcorr = config_satcorr;
	qargs.static_args.config_closer = config_closer;
879
	qargs.static_args.config_insane = config_insane;
880
	qargs.static_args.config_bgsub = config_bgsub;
881
	qargs.static_args.cellr = cellr;
882
	qargs.static_args.threshold = threshold;
883
	qargs.static_args.min_gradient = min_gradient;
884
885
886
887
888
889
	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;
890
	qargs.static_args.beam = beam;
Thomas White's avatar
Thomas White committed
891
	qargs.static_args.element = element;
892
	qargs.static_args.stream_flags = stream_flags;
893
	qargs.static_args.hdf5_peak_path = hdf5_peak_path;
894
895
896

	qargs.fh = fh;
	qargs.prefix = prefix;
897
	qargs.config_basename = config_basename;
898
	qargs.n_indexable = 0;
899
900
901
	qargs.n_processed = 0;
	qargs.n_indexable_last_stats = 0;
	qargs.n_processed_last_stats = 0;
902
	qargs.t_last_stats = get_monotonic_seconds();
903

904
	n_images = run_threads(nthreads, process_image, get_image,
905
906
	                       finalise_image, &qargs, 0,
	                       cpu_num, cpu_groupsize, cpu_offset);
907

908
909
	cleanup_indexing(ipriv);

Thomas White's avatar
Thomas White committed
910
911
	free(indm);
	free(ipriv);
912
	free(prefix);
Thomas White's avatar
Thomas White committed
913
914
	free_detector_geometry(det);
	free(beam);
Thomas White's avatar
Thomas White committed
915
	free(element);
916
	free(hdf5_peak_path);
917
	cell_free(cell);
Thomas White's avatar
Thomas White committed
918
919
	if ( fh != stdin ) fclose(fh);
	if ( ofh != stdout ) fclose(ofh);
Thomas White's avatar
Thomas White committed
920

921
922
	STATUS("There were %i images, of which %i could be indexed.\n",
	        n_images, qargs.n_indexable);
Thomas White's avatar
Thomas White committed
923
924
925

	return 0;
}