indexamajig.c 18.9 KB
Newer Older
Thomas White's avatar
Thomas White committed
1
/*
2
 * indexamajig.c
Thomas White's avatar
Thomas White committed
3
4
5
 *
 * Find hits, index patterns, output hkl+intensity etc.
 *
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
 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */


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

17
#define _GNU_SOURCE 1
Thomas White's avatar
Thomas White committed
18
19
20
21
22
23
#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
24
#include <hdf5.h>
Thomas White's avatar
Thomas White committed
25
#include <gsl/gsl_errno.h>
26
#include <pthread.h>
Thomas White's avatar
Thomas White committed
27
#include <sys/time.h>
Thomas White's avatar
Thomas White committed
28
29
30

#include "utils.h"
#include "hdf5-file.h"
Thomas White's avatar
Thomas White committed
31
#include "index.h"
32
#include "peaks.h"
33
#include "diffraction.h"
Thomas White's avatar
Thomas White committed
34
#include "diffraction-gpu.h"
35
#include "detector.h"
36
#include "sfac.h"
Thomas White's avatar
Thomas White committed
37
#include "filters.h"
38
#include "reflections.h"
Thomas White's avatar
Thomas White committed
39
40


41
42
43
44
45
#define MAX_THREADS (96)

struct process_args
{
	char *filename;
Thomas White's avatar
Thomas White committed
46
	int id;
47
48
	pthread_mutex_t *output_mutex;  /* Protects stdout */
	pthread_mutex_t *gpu_mutex;     /* Protects "gctx" */
49
50
51
52
53
54
55
56
57
58
59
	UnitCell *cell;
	int config_cmfilter;
	int config_noisefilter;
	int config_writedrx;
	int config_dumpfound;
	int config_verbose;
	int config_alternate;
	int config_nearbragg;
	int config_gpu;
	int config_simulate;
	int config_nomatch;
60
	int config_unpolar;
61
	int config_sanity;
Thomas White's avatar
Thomas White committed
62
	struct detector *det;
63
64
65
66
67
68
69
70
71
	IndexingMethod indm;
	const double *intensities;
	const unsigned int *counts;
	struct gpu_context *gctx;
};

struct process_result
{
	int hit;
Thomas White's avatar
Thomas White committed
72
	int peaks_sane;
73
74
75
};


Thomas White's avatar
Thomas White committed
76
77
78
79
80
81
82
83
84
85
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"
Thomas White's avatar
Thomas White committed
86
"\n"
Thomas White's avatar
Thomas White committed
87
88
89
"      --indexing=<method> Use 'method' for indexing.  Choose from:\n"
"                           none     : no indexing\n"
"                           dirax    : invoke DirAx\n"
Thomas White's avatar
Thomas White committed
90
"  -g. --geometry=<file>   Get detector geometry from file.\n"
Thomas White's avatar
Thomas White committed
91
92
"\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"
93
"      --near-bragg        Output a list of reflection intensities to stdout.\n"
Thomas White's avatar
Thomas White committed
94
95
96
97
98
99
100
101
102
103
"                           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"
104
"      --simulate          Simulate the diffraction pattern using the indexed\n"
Thomas White's avatar
Thomas White committed
105
106
107
108
"                           unit cell.  The simulated pattern will be saved\n"
"                           as \"simulated.h5\".  You can TRY to combine this\n"
"                           with \"-j <n>\" with n greater than 1, but it's\n"
"                           not a good idea.\n"
109
110
111
112
113
114
115
"      --filter-cm         Perform common-mode noise subtraction on images\n"
"                           before proceeding.  Intensities will be extracted\n"
"                           from the image as it is after this processing.\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"
116
117
118
119
120
"      --write-drx         Write 'xfel.drx' for visualisation of reciprocal\n"
"                           space.  Implied by any indexing method other than\n"
"                           'none'.  Beware: the units in this file are\n"
"                           reciprocal Angstroms.\n"
"      --dump-peaks        Write the results of the peak search to stdout.\n"
121
122
"                           The intensities in this list are from the\n"
"                           centroid/integration procedure.\n"
123
124
125
"      --no-match          Don't attempt to match the indexed cell to the\n"
"                           model, just proceed with the one generated by the\n"
"                           auto-indexing procedure.\n"
126
"      --unpolarized       Don't correct for the polarisation of the X-rays.\n"
127
128
"      --check-sanity      Check that indexed locations approximately correspond\n"
"                           with detected peaks.\n"
Thomas White's avatar
Thomas White committed
129
130
131
132
133
"\n\nOptions for greater performance or verbosity:\n\n"
"      --verbose           Be verbose about indexing.\n"
"      --gpu               Use the GPU to speed up the simulation.\n"
"  -j <n>                  Run <n> analyses in parallel.  Default 1.\n"
"\n\nControl of model and data input:\n\n"
Thomas White's avatar
Thomas White committed
134
135
136
"     --intensities=<file> Specify file containing reflection intensities\n"
"                           to use when simulating.\n"
" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
137
" -x, --prefix=<p>         Prefix filenames from input file with 'p'.\n"
Thomas White's avatar
Thomas White committed
138
);
Thomas White's avatar
Thomas White committed
139
140
141
}


142
static struct image *get_simage(struct image *template, int alternate)
143
{
144
	struct image *image;
145
	struct panel panels[2];
146

147
148
	image = malloc(sizeof(*image));

149
	/* Simulate a diffraction pattern */
150
151
152
	image->twotheta = NULL;
	image->data = NULL;
	image->det = template->det;
153
154

	/* View head-on (unit cell is tilted) */
155
156
157
158
	image->orientation.w = 1.0;
	image->orientation.x = 0.0;
	image->orientation.y = 0.0;
	image->orientation.z = 0.0;
159
160
161

	/* Detector geometry for the simulation
	 * - not necessarily the same as the original. */
162
163
	image->width = 1024;
	image->height = 1024;
Thomas White's avatar
Thomas White committed
164
	image->det->n_panels = 2;
165

166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
	if ( alternate ) {

		/* Upper */
		panels[0].min_x = 0;
		panels[0].max_x = 1023;
		panels[0].min_y = 512;
		panels[0].max_y = 1023;
		panels[0].cx = 523.6;
		panels[0].cy = 502.5;
		panels[0].clen = 56.4e-2;  /* 56.4 cm */
		panels[0].res = 13333.3;   /* 75 microns/pixel */

		/* Lower */
		panels[1].min_x = 0;
		panels[1].max_x = 1023;
		panels[1].min_y = 0;
		panels[1].max_y = 511;
		panels[1].cx = 520.8;
184
		panels[1].cy = 525.0;
185
186
187
		panels[1].clen = 56.7e-2;  /* 56.7 cm */
		panels[1].res = 13333.3;   /* 75 microns/pixel */

Thomas White's avatar
Thomas White committed
188
		image->det->panels = panels;
189

190
191
192
	} else {

		/* Copy pointer to old geometry */
Thomas White's avatar
Thomas White committed
193
		image->det->panels = template->det->panels;
194
195

	}
196

197
	image->lambda = ph_en_to_lambda(eV_to_J(1.8e3));
198
	image->features = template->features;
199
	image->filename = template->filename;
200
	image->indexed_cell = template->indexed_cell;
Thomas White's avatar
Thomas White committed
201
	image->f0 = template->f0;
202

Thomas White's avatar
Thomas White committed
203
204
205
206
	/* Prevent muppetry */
	image->hits = NULL;
	image->n_hits = 0;

207
208
	return image;
}
209
210


211
static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
212
213
                               const double *intensities,
                               const unsigned int *counts, UnitCell *cell)
214
{
215
	/* Set up GPU if necessary */
Thomas White's avatar
Thomas White committed
216
	if ( (gctx != NULL) && (*gctx == NULL) ) {
217
		*gctx = setup_gpu(0, simage, intensities, counts);
218
219
	}

Thomas White's avatar
Thomas White committed
220
	if ( (gctx != NULL) && (*gctx != NULL) ) {
221
		get_diffraction_gpu(*gctx, simage, 24, 24, 40, cell);
222
	} else {
223
		get_diffraction(simage, 24, 24, 40,
224
225
		                intensities, counts, NULL, cell, 0,
		                GRADIENT_MOSAIC);
226
	}
227
	record_image(simage, 0);
228

229
	hdf5_write("simulated.h5", simage->data, simage->width, simage->height,
230
231
232
233
		   H5T_NATIVE_FLOAT);
}


234
static void *process_image(void *pargsv)
235
{
236
	struct process_args *pargs = pargsv;
237
238
239
240
241
	struct hdfile *hdfile;
	struct image image;
	struct image *simage;
	float *data_for_measurement;
	size_t data_size;
242
243
244
245
246
247
248
249
250
251
252
253
	const char *filename = pargs->filename;
	UnitCell *cell = pargs->cell;
	int config_cmfilter = pargs->config_cmfilter;
	int config_noisefilter = pargs->config_noisefilter;
	int config_writedrx = pargs->config_writedrx;
	int config_dumpfound = pargs->config_dumpfound;
	int config_verbose = pargs->config_verbose;
	int config_alternate  = pargs->config_alternate;
	int config_nearbragg = pargs->config_nearbragg;
	int config_gpu = pargs->config_gpu;
	int config_simulate = pargs->config_simulate;
	int config_nomatch = pargs->config_nomatch;
254
	int config_unpolar = pargs->config_unpolar;
255
256
257
258
259
	IndexingMethod indm = pargs->indm;
	const double *intensities = pargs->intensities;
	const unsigned int *counts = pargs->counts;
	struct gpu_context *gctx = pargs->gctx;
	struct process_result *result;
260
261
262
263

	image.features = NULL;
	image.data = NULL;
	image.indexed_cell = NULL;
Thomas White's avatar
Thomas White committed
264
	image.id = pargs->id;
265
	image.filename = filename;
Thomas White's avatar
Thomas White committed
266
267
	image.hits = NULL;
	image.n_hits = 0;
Thomas White's avatar
Thomas White committed
268
	image.det = pargs->det;
269

270
271
272
273
274
275
	/* View head-on (unit cell is tilted) */
	image.orientation.w = 1.0;
	image.orientation.x = 0.0;
	image.orientation.y = 0.0;
	image.orientation.z = 0.0;

276
	STATUS("Processing '%s'\n", image.filename);
277

278
279
	result = malloc(sizeof(*result));
	if ( result == NULL ) return NULL;
280
281
	result->peaks_sane = 0;
	result->hit = 0;
282

283
284
	hdfile = hdfile_open(filename);
	if ( hdfile == NULL ) {
285
		return result;
286
287
	} else if ( hdfile_set_first_image(hdfile, "/") ) {
		ERROR("Couldn't select path\n");
288
		return result;
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
	}

	hdf5_read(hdfile, &image);

	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 {
305
		memcpy(data_for_measurement, image.data, data_size);
306
307
308
309
	}

	/* Perform 'fine' peak search */
	search_peaks(&image);
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
317
	if ( image_feature_count(image.features) < 5 ) goto done;

318
	if ( config_dumpfound ) dump_peaks(&image, pargs->output_mutex);
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334

	/* Not indexing nor writing xfel.drx?
	 * Then there's nothing left to do. */
	if ( (!config_writedrx) && (indm == INDEXING_NONE) ) {
		goto done;
	}

	/* Calculate orientation matrix (by magic) */
	if ( config_writedrx || (indm != INDEXING_NONE) ) {
		index_pattern(&image, cell, indm, config_nomatch,
		              config_verbose);
	}

	/* No cell at this point?  Then we're done. */
	if ( image.indexed_cell == NULL ) goto done;

Thomas White's avatar
Thomas White committed
335
	/* Sanity check */
336
337
	if ( pargs->config_sanity
	  && !peak_sanity_check(&image, image.indexed_cell) ) {
Thomas White's avatar
Thomas White committed
338
339
340
341
342
343
		STATUS("Failed peak sanity check.\n");
		goto done;
	} else {
		result->peaks_sane = 1;
	}

344
345
	/* Measure intensities if requested */
	if ( config_nearbragg ) {
346
		output_intensities(&image, image.indexed_cell,
347
		                   pargs->output_mutex, config_unpolar);
348
349
	}

350
351
	simage = get_simage(&image, config_alternate);

352
353
354
	/* Simulate if requested */
	if ( config_simulate ) {
		if ( config_gpu ) {
355
			pthread_mutex_lock(pargs->gpu_mutex);
356
			simulate_and_write(simage, &gctx, intensities,
357
			                   counts, image.indexed_cell);
358
			pthread_mutex_unlock(pargs->gpu_mutex);
359
360
		} else {
			simulate_and_write(simage, NULL, intensities,
361
			                   counts, image.indexed_cell);
362
363
364
365
366
367
368
369
370
371
372
373
374
		}
	}

	/* Finished with alternate image */
	if ( simage->twotheta != NULL ) free(simage->twotheta);
	if ( simage->data != NULL ) free(simage->data);
	free(simage);

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

done:
	free(image.data);
Thomas White's avatar
Thomas White committed
375
	free(image.flags);
376
	image_feature_list_free(image.features);
Thomas White's avatar
Thomas White committed
377
	free(image.hits);
378
379
	hdfile_close(hdfile);

380
381
382
383
384
385
	if ( image.indexed_cell == NULL ) {
		result->hit = 0;
	} else {
		result->hit = 1;
	}
	return result;
386
387
388
}


Thomas White's avatar
Thomas White committed
389
390
391
int main(int argc, char *argv[])
{
	int c;
Thomas White's avatar
Thomas White committed
392
	struct gpu_context *gctx = NULL;
Thomas White's avatar
Thomas White committed
393
394
	char *filename = NULL;
	FILE *fh;
395
	char *rval = NULL;
Thomas White's avatar
Thomas White committed
396
397
	int n_images;
	int n_hits;
Thomas White's avatar
Thomas White committed
398
	int n_sane;
399
	int config_noindex = 0;
Thomas White's avatar
Thomas White committed
400
	int config_dumpfound = 0;
401
	int config_nearbragg = 0;
Thomas White's avatar
Thomas White committed
402
	int config_writedrx = 0;
403
	int config_simulate = 0;
404
405
	int config_cmfilter = 0;
	int config_noisefilter = 0;
406
	int config_nomatch = 0;
Thomas White's avatar
Thomas White committed
407
	int config_gpu = 0;
408
	int config_verbose = 0;
409
	int config_alternate = 0;
410
	int config_unpolar = 0;
411
	int config_sanity = 0;
Thomas White's avatar
Thomas White committed
412
413
	struct detector *det;
	char *geometry = NULL;
Thomas White's avatar
Thomas White committed
414
415
	IndexingMethod indm;
	char *indm_str = NULL;
416
417
418
	UnitCell *cell;
	double *intensities = NULL;
	char *intfile = NULL;
419
	unsigned int *counts;
Thomas White's avatar
Thomas White committed
420
	char *pdb = NULL;
421
	char *prefix = NULL;
422
423
424
	int nthreads = 1;
	pthread_t workers[MAX_THREADS];
	struct process_args *worker_args[MAX_THREADS];
Thomas White's avatar
Thomas White committed
425
	int worker_active[MAX_THREADS];
426
	int i;
427
	pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
428
	pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER;
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'},
Thomas White's avatar
Thomas White committed
434
		{"gpu",                0, &config_gpu,         1},
435
		{"no-index",           0, &config_noindex,     1},
Thomas White's avatar
Thomas White committed
436
		{"dump-peaks",         0, &config_dumpfound,   1},
437
		{"near-bragg",         0, &config_nearbragg,   1},
Thomas White's avatar
Thomas White committed
438
439
		{"write-drx",          0, &config_writedrx,    1},
		{"indexing",           1, NULL,               'z'},
Thomas White's avatar
Thomas White committed
440
		{"geometry",           1, NULL,               'g'},
441
		{"simulate",           0, &config_simulate,    1},
442
443
		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
444
		{"no-match",           0, &config_nomatch,     1},
445
		{"verbose",            0, &config_verbose,     1},
446
		{"alternate",          0, &config_alternate,   1},
447
		{"intensities",        1, NULL,               'q'},
Thomas White's avatar
Thomas White committed
448
		{"pdb",                1, NULL,               'p'},
449
		{"prefix",             1, NULL,               'x'},
450
		{"unpolarized",        0, &config_unpolar,     1},
451
		{"check-sanity",       0, &config_sanity,      1},
Thomas White's avatar
Thomas White committed
452
453
454
455
		{0, 0, NULL, 0}
	};

	/* Short options */
Thomas White's avatar
Thomas White committed
456
457
	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:",
	                        longopts, NULL)) != -1) {
Thomas White's avatar
Thomas White committed
458
459

		switch (c) {
Thomas White's avatar
Thomas White committed
460
		case 'h' :
Thomas White's avatar
Thomas White committed
461
462
463
			show_help(argv[0]);
			return 0;

Thomas White's avatar
Thomas White committed
464
		case 'i' :
Thomas White's avatar
Thomas White committed
465
466
467
			filename = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
468
		case 'z' :
Thomas White's avatar
Thomas White committed
469
470
471
			indm_str = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
472
		case 'q' :
473
474
475
			intfile = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
476
		case 'p' :
Thomas White's avatar
Thomas White committed
477
478
479
			pdb = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
480
		case 'x' :
481
482
483
			prefix = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
484
		case 'j' :
485
486
487
			nthreads = atoi(optarg);
			break;

Thomas White's avatar
Thomas White committed
488
		case 'g' :
Thomas White's avatar
Thomas White committed
489
490
491
			geometry = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
492
		case 0 :
Thomas White's avatar
Thomas White committed
493
494
			break;

Thomas White's avatar
Thomas White committed
495
		default :
Thomas White's avatar
Thomas White committed
496
497
498
499
500
501
502
503
504
505
506
507
508
509
			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
510
		ERROR("Failed to open input file '%s'\n", filename);
Thomas White's avatar
Thomas White committed
511
512
		return 1;
	}
Thomas White's avatar
Thomas White committed
513
	free(filename);
Thomas White's avatar
Thomas White committed
514

515
	if ( intfile != NULL ) {
516
		counts = new_list_count();
517
		intensities = read_reflections(intfile, counts, NULL);
518
519
	} else {
		intensities = NULL;
520
		counts = NULL;
521
522
	}

Thomas White's avatar
Thomas White committed
523
524
525
526
	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

527
	if ( prefix == NULL ) {
Thomas White's avatar
Thomas White committed
528
		prefix = strdup("");
529
530
	}

531
	if ( (nthreads == 0) || (nthreads > MAX_THREADS) ) {
532
533
534
535
		ERROR("Invalid number of threads.\n");
		return 1;
	}

Thomas White's avatar
Thomas White committed
536
537
	if ( indm_str == NULL ) {
		STATUS("You didn't specify an indexing method, so I won't"
538
539
540
		       " 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
541
542
543
544
545
546
547
548
549
		indm = INDEXING_NONE;
	} else if ( strcmp(indm_str, "none") == 0 ) {
		indm = INDEXING_NONE;
	} else if ( strcmp(indm_str, "dirax") == 0) {
		indm = INDEXING_DIRAX;
	} else {
		ERROR("Unrecognised indexing method '%s'\n", indm_str);
		return 1;
	}
550
	free(indm_str);
Thomas White's avatar
Thomas White committed
551

Thomas White's avatar
Thomas White committed
552
553
554
555
556
557
558
559
560
561
562
563
	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
564
	cell = load_cell_from_pdb(pdb);
565
	if ( cell == NULL ) {
Thomas White's avatar
Thomas White committed
566
		ERROR("Couldn't read unit cell (from %s)\n", pdb);
567
568
		return 1;
	}
569
	free(pdb);
570

Thomas White's avatar
Thomas White committed
571
	gsl_set_error_handler_off();
Thomas White's avatar
Thomas White committed
572
573
	n_images = 0;
	n_hits = 0;
Thomas White's avatar
Thomas White committed
574
	n_sane = 0;
575

576
577
578
579
580
581
	for ( i=0; i<nthreads; i++ ) {
		worker_args[i] = malloc(sizeof(struct process_args));
		worker_args[i]->filename = malloc(1024);
		worker_active[i] = 0;
	}

582
583
	/* Initially, fire off the full number of threads */
	for ( i=0; i<nthreads; i++ ) {
Thomas White's avatar
Thomas White committed
584
585

		char line[1024];
586
587
		struct process_args *pargs;
		int r;
Thomas White's avatar
Thomas White committed
588

589
		pargs = worker_args[i];
Thomas White's avatar
Thomas White committed
590

Thomas White's avatar
Thomas White committed
591
		rval = fgets(line, 1023, fh);
Thomas White's avatar
Thomas White committed
592
		if ( rval == NULL ) continue;
Thomas White's avatar
Thomas White committed
593
		chomp(line);
594
		snprintf(pargs->filename, 1023, "%s%s", prefix, line);
595

596
597
		n_images++;

598
		pargs->output_mutex = &output_mutex;
599
		pargs->gpu_mutex = &gpu_mutex;
600
601
602
603
604
605
606
607
608
609
		pargs->config_cmfilter = config_cmfilter;
		pargs->config_noisefilter = config_noisefilter;
		pargs->config_writedrx = config_writedrx;
		pargs->config_dumpfound = config_dumpfound;
		pargs->config_verbose = config_verbose;
		pargs->config_alternate = config_alternate;
		pargs->config_nearbragg = config_nearbragg;
		pargs->config_gpu = config_gpu;
		pargs->config_simulate = config_simulate;
		pargs->config_nomatch = config_nomatch;
610
		pargs->config_unpolar = config_unpolar;
611
		pargs->config_sanity = config_sanity;
612
		pargs->cell = cell;
Thomas White's avatar
Thomas White committed
613
		pargs->det = det;
614
615
616
617
		pargs->indm = indm;
		pargs->intensities = intensities;
		pargs->counts = counts;
		pargs->gctx = gctx;
Thomas White's avatar
Thomas White committed
618
		pargs->id = i;
619

Thomas White's avatar
Thomas White committed
620
		worker_active[i] = 1;
621
622
		r = pthread_create(&workers[i], NULL, process_image, pargs);
		if ( r != 0 ) {
Thomas White's avatar
Thomas White committed
623
			worker_active[i] = 0;
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
			ERROR("Couldn't start thread %i\n", i);
		}

	}

	/* Start new threads as old ones finish */
	do {

		int i;

		for ( i=0; i<nthreads; i++ ) {

			char line[1024];
			int r;
			struct process_result *result = NULL;
			struct timespec t;
Thomas White's avatar
Thomas White committed
640
			struct timeval tv;
641
642
			struct process_args *pargs;

Thomas White's avatar
Thomas White committed
643
644
			if ( !worker_active[i] ) continue;

645
646
			pargs = worker_args[i];

Thomas White's avatar
Thomas White committed
647
648
649
			gettimeofday(&tv, NULL);
			t.tv_sec = tv.tv_sec;
			t.tv_nsec = tv.tv_usec * 1000 + 20000;
650
651
652
653
654

			r = pthread_timedjoin_np(workers[i], (void *)&result,
			                         &t);
			if ( r != 0 ) continue; /* Not ready yet */

Thomas White's avatar
Thomas White committed
655
656
			worker_active[i] = 0;

657
658
			if ( result != NULL ) {
				n_hits += result->hit;
Thomas White's avatar
Thomas White committed
659
				n_sane += result->peaks_sane;
660
661
662
663
664
665
				free(result);
			}

			rval = fgets(line, 1023, fh);
			if ( rval == NULL ) break;
			chomp(line);
666
			snprintf(pargs->filename, 1023, "%s%s", prefix, line);
667

Thomas White's avatar
Thomas White committed
668
			worker_active[i] = 1;
669
670
671
			r = pthread_create(&workers[i], NULL, process_image,
			                   pargs);
			if ( r != 0 ) {
Thomas White's avatar
Thomas White committed
672
				worker_active[i] = 0;
673
674
675
676
677
				ERROR("Couldn't start thread %i\n", i);
			}

			n_images++;
		}
Thomas White's avatar
Thomas White committed
678

Thomas White's avatar
Thomas White committed
679
680
	} while ( rval != NULL );

Thomas White's avatar
Thomas White committed
681
	/* Catch all remaining threads */
682
	for ( i=0; i<nthreads; i++ ) {
Thomas White's avatar
Thomas White committed
683
684
685

		struct process_result *result = NULL;

Thomas White's avatar
Thomas White committed
686
		if ( !worker_active[i] ) goto free;
Thomas White's avatar
Thomas White committed
687
688
689
690
691
692
693
694
695
696

		pthread_join(workers[i], (void *)&result);

		worker_active[i] = 0;

		if ( result != NULL ) {
			n_hits += result->hit;
			free(result);
		}

Thomas White's avatar
Thomas White committed
697
	free:
698
		if ( worker_args[i]->filename != NULL ) {
699
700
			free(worker_args[i]->filename);
		}
701
		free(worker_args[i]);
Thomas White's avatar
Thomas White committed
702

703
704
705
	}

	free(prefix);
Thomas White's avatar
Thomas White committed
706
707
	free(det->panels);
	free(det);
708
	free(cell);
Thomas White's avatar
Thomas White committed
709
710
711
	fclose(fh);

	STATUS("There were %i images.\n", n_images);
Thomas White's avatar
Thomas White committed
712
	STATUS("%i hits were found, of which %i were sane.\n", n_hits, n_sane);
Thomas White's avatar
Thomas White committed
713

Thomas White's avatar
Thomas White committed
714
715
716
717
	if ( gctx != NULL ) {
		cleanup_gpu(gctx);
	}

Thomas White's avatar
Thomas White committed
718
719
	return 0;
}