indexamajig.c 35.2 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
 *
6
7
 * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
 *                  a research centre of the Helmholtz Association.
8
9
 * Copyright © 2012 Richard Kirian
 * Copyright © 2012 Lorenzo Galli
10
11
 *
 * Authors:
12
13
14
 *   2010-2012 Thomas White <taw@physics.org>
 *   2011      Richard Kirian
 *   2012      Lorenzo Galli
Chuck's avatar
Chuck committed
15
 *   2012      Chunhong Yoon
Thomas White's avatar
Thomas White committed
16
 *
Thomas White's avatar
Thomas White committed
17
18
19
20
21
22
23
24
25
26
27
28
29
30
 * This file is part of CrystFEL.
 *
 * CrystFEL is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * CrystFEL is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
Thomas White's avatar
Thomas White committed
31
32
33
34
35
36
37
38
39
40
41
42
43
44
 *
 */


#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
45
#include <hdf5.h>
Thomas White's avatar
Thomas White committed
46
#include <gsl/gsl_errno.h>
47
#include <pthread.h>
Chuck's avatar
Chuck committed
48
49
#include <sys/wait.h>
#include <fcntl.h>
Thomas White's avatar
Thomas White committed
50
#include <signal.h>
51
52

#ifdef HAVE_CLOCK_GETTIME
53
#include <time.h>
54
55
56
#else
#include <sys/time.h>
#endif
Thomas White's avatar
Thomas White committed
57

Thomas White's avatar
Thomas White committed
58
59
60
61
62
63
64
65
66
67
68
#include "utils.h"
#include "hdf5-file.h"
#include "index.h"
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "thread-pool.h"
#include "beam-parameters.h"
#include "geometry.h"
#include "stream.h"
#include "reflist-utils.h"
69

70

Thomas White's avatar
Thomas White committed
71
/* Write statistics at APPROXIMATELY this interval */
72
73
#define STATS_EVERY_N_SECONDS (5)

74
75
76
77
78
79
enum {
	PEAK_ZAEF,
	PEAK_HDF5,
};


80
/* Information about the indexing process which is common to all patterns */
Thomas White's avatar
Thomas White committed
81
struct index_args
82
83
84
85
86
{
	UnitCell *cell;
	int config_cmfilter;
	int config_noisefilter;
	int config_verbose;
Thomas White's avatar
Thomas White committed
87
	int stream_flags;         /* What goes into the output? */
88
	int config_satcorr;
89
	int config_closer;
90
	int config_insane;
91
	int config_bgsub;
92
	float threshold;
93
	float min_gradient;
94
	float min_snr;
95
	double min_int_snr;
Thomas White's avatar
Thomas White committed
96
	struct detector *det;
Thomas White's avatar
Thomas White committed
97
98
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
Thomas White's avatar
Thomas White committed
99
	int peaks;                /* Peak detection method */
100
	int cellr;
101
	float tols[4];
102
	struct beam_params *beam;
Thomas White's avatar
Thomas White committed
103
104
	char *element;
	char *hdf5_peak_path;
105
106
107
	double ir_inn;
	double ir_mid;
	double ir_out;
Thomas White's avatar
Thomas White committed
108
	struct copy_hdf5_field *copyme;
109
110
111
};


112
/* Information about the indexing process for one pattern */
Thomas White's avatar
Thomas White committed
113
struct pattern_args
114
115
116
117
118
119
120
121
122
{
	/* "Input" */
	char *filename;

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


Thomas White's avatar
Thomas White committed
123
124
125
126
127
128
static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index FEL diffraction images.\n"
"\n"
129
" -h, --help               Display this help message.\n"
Thomas White's avatar
Thomas White committed
130
"\n"
131
" -i, --input=<filename>   Specify file containing list of images to process.\n"
Thomas White's avatar
Thomas White committed
132
"                           '-' means stdin, which is the default.\n"
Thomas White's avatar
Thomas White committed
133
134
" -o, --output=<filename>  Write output stream to this file. '-' for stdout.\n"
"                           Default: indexamajig.stream\n"
Thomas White's avatar
Thomas White committed
135
"\n"
Thomas White's avatar
Thomas White committed
136
137
138
139
140
"     --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
141
"                            reax     : DPS algorithm with known unit cell\n"
142
" -g. --geometry=<file>    Get detector geometry from file.\n"
143
144
145
" -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"
146
" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
Thomas White's avatar
Thomas White committed
147
"                           Default: 'molecule.pdb'.\n"
148
"     --basename           Remove the directory parts of the filenames.\n"
149
" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
150
151
152
"     --peaks=<method>     Use 'method' for finding peaks.  Choose from:\n"
"                           zaef  : Use Zaefferer (2000) gradient detection.\n"
"                                    This is the default method.\n"
153
154
155
"                           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
156
157
"\n\n"
"You can control what information is included in the output stream using\n"
Thomas White's avatar
Thomas White committed
158
"' --record=<flag1>,<flag2>,<flag3>' and so on.  Possible flags are:\n\n"
159
160
" integrated        Include a list of reflection intensities, produced by\n"
"                    integrating around predicted peak locations.\n"
Thomas White's avatar
Thomas White committed
161
"\n"
162
163
" peaks             Include peak locations and intensities from the peak\n"
"                    search.\n"
Thomas White's avatar
Thomas White committed
164
"\n"
165
" peaksifindexed    As 'peaks', but only if the pattern could be indexed.\n"
Thomas White's avatar
Thomas White committed
166
"\n"
167
168
" peaksifnotindexed As 'peaks', but only if the pattern could NOT be indexed.\n"
"\n\n"
Thomas White's avatar
Thomas White committed
169
"The default is '--record=integrated'.\n"
Thomas White's avatar
Thomas White committed
170
171
"\n\n"
"For more control over the process, you might need:\n\n"
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
"  --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"
"                         compare_ab : compare 'a' and 'b' lengths only.\n"
"    --tolerance=<tol>   Set the tolerances for cell reduction.\n"
"                          Default: 5,5,5,1.5.\n"
"    --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"
"    --no-sat-corr       Don't correct values of saturated peaks using a\n"
"                         table included in the HDF5 file.\n"
"    --threshold=<n>     Only accept peaks above <n> ADU.  Default: 800.\n"
"    --min-gradient=<n>  Minimum gradient for Zaefferer peak search.\n"
"                         Default: 100,000.\n"
"    --min-snr=<n>       Minimum signal-to-noise ratio for peaks.\n"
"                         Default: 5.\n"
"    --min-integration-snr=<n> Minimum signal-to-noise ratio for peaks\n"
"                         during integration. Default: -infinity.\n"
"    --int-radius=<r>    Set the integration radii.  Default: 4,5,7.\n"
"-e, --image=<element>   Use this image from the HDF5 file.\n"
"                          Example: /data/data0.\n"
"                          Default: The first one found.\n"
Thomas White's avatar
Thomas White committed
200
"\n"
201
202
203
204
"\nFor time-resolved stuff, you might want to use:\n\n"
"     --copy-hdf5-field <f>  Copy the value of field <f> into the stream. You\n"
"                             can use this option as many times as you need.\n"
"\n"
205
206
207
"\nOptions for greater performance or verbosity:\n\n"
"     --verbose            Be verbose about indexing.\n"
" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
208
209
210
"\n"
"\nOptions you probably won't need:\n\n"
"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
Chuck's avatar
Chuck committed
211
212
"     --closer-peak        Don't integrate from the location of a nearby peak\n"
"                           instead of the predicted spot.  Don't use.\n"
213
214
"     --insane             Don't check that the reduced cell accounts for at\n"
"                           least 10%% of the located peaks.\n"
215
216
"     --no-bg-sub          Don't subtract local background estimates from\n"
"                           integrated intensities.\n"
Thomas White's avatar
Thomas White committed
217
);
Thomas White's avatar
Thomas White committed
218
219
220
}


Thomas White's avatar
WIP    
Thomas White committed
221
222
static char *get_pattern(FILE *fh, char **use_this_one_instead,
                         int config_basename, const char *prefix)
Thomas White's avatar
Thomas White committed
223
{
Thomas White's avatar
Thomas White committed
224
	char *line;
Thomas White's avatar
WIP    
Thomas White committed
225
226
	char *filename;

227
	do {
Thomas White's avatar
WIP    
Thomas White committed
228

229
230
		/* Get the next filename */
		if ( *use_this_one_instead != NULL ) {
Thomas White's avatar
WIP    
Thomas White committed
231

232
233
			line = *use_this_one_instead;
			*use_this_one_instead = NULL;
Thomas White's avatar
WIP    
Thomas White committed
234

235
236
237
238
239
240
241
242
243
244
		} else {

			char *rval;

			line = malloc(1024*sizeof(char));
			rval = fgets(line, 1023, fh);
			if ( rval == NULL ) {
				free(line);
				return NULL;
			}
Thomas White's avatar
WIP    
Thomas White committed
245
246

		}
Thomas White's avatar
Thomas White committed
247

248
		chomp(line);
Thomas White's avatar
Thomas White committed
249

250
	} while ( strlen(line) == 0 );
Thomas White's avatar
WIP    
Thomas White committed
251
252
253
254
255
256

	if ( config_basename ) {
		char *tmp;
		tmp = safe_basename(line);
		free(line);
		line = tmp;
Thomas White's avatar
Thomas White committed
257
	}
Thomas White's avatar
Thomas White committed
258

Thomas White's avatar
WIP    
Thomas White committed
259
260
261
262
263
264
265
	filename = malloc(strlen(prefix)+strlen(line)+1);

	snprintf(filename, 1023, "%s%s", prefix, line);

	free(line);

	return filename;
Chuck's avatar
Chuck committed
266
267
268
}


Thomas White's avatar
Thomas White committed
269
static void process_image(const struct index_args *iargs,
270
271
                          struct pattern_args *pargs, FILE *ofh,
                          int cookie)
272
273
274
{
	float *data_for_measurement;
	size_t data_size;
Thomas White's avatar
Thomas White committed
275
276
277
278
279
280
	UnitCell *cell = iargs->cell;
	int config_cmfilter = iargs->config_cmfilter;
	int config_noisefilter = iargs->config_noisefilter;
	int config_verbose = iargs->config_verbose;
	IndexingMethod *indm = iargs->indm;
	struct beam_params *beam = iargs->beam;
Chuck's avatar
Chuck committed
281
282
283
	int r, check;
	struct hdfile *hdfile;
	struct image image;
Thomas White's avatar
Thomas White committed
284

285
286
	image.features = NULL;
	image.data = NULL;
Thomas White's avatar
Thomas White committed
287
	image.flags = NULL;
288
	image.indexed_cell = NULL;
Thomas White's avatar
Thomas White committed
289
290
	image.det = copy_geom(iargs->det);
	image.copyme = iargs->copyme;
Thomas White's avatar
Thomas White committed
291
	image.reflections = NULL;
Thomas White's avatar
Thomas White committed
292
293
	image.id = cookie;
	image.filename = pargs->filename;
294
295
	image.beam = beam;

Thomas White's avatar
Thomas White committed
296
297
	hdfile = hdfile_open(image.filename);
	if ( hdfile == NULL ) return;
298

Thomas White's avatar
Thomas White committed
299
300
	r = hdfile_set_first_image(hdfile, "/");
	if ( r ) {
Chuck's avatar
Chuck committed
301
302
303
		ERROR("Couldn't select first path\n");
		hdfile_close(hdfile);
		return;
304
305
	}

Chuck's avatar
Chuck committed
306
	check = hdf5_read(hdfile, &image, 1);
Thomas White's avatar
Thomas White committed
307
	if ( check ) {
Chuck's avatar
Chuck committed
308
309
310
		hdfile_close(hdfile);
		return;
	}
311

Thomas White's avatar
Thomas White committed
312
313
314
	if ( (image.width != image.det->max_fs + 1 )
	  || (image.height != image.det->max_ss + 1))
	{
315
		ERROR("Image size doesn't match geometry size"
Chuck's avatar
Chuck committed
316
			" - rejecting image.\n");
317
		ERROR("Image size: %i,%i.  Geometry size: %i,%i\n",
Chuck's avatar
Chuck committed
318
319
		image.width, image.height,
		image.det->max_fs + 1, image.det->max_ss + 1);
320
321
322
323
324
		hdfile_close(hdfile);
		free_detector_geometry(image.det);
		return;
	}

Thomas White's avatar
Thomas White committed
325
326
	if ( image.lambda < 0.0 ) {
		if ( beam != NULL ) {
Thomas White's avatar
Thomas White committed
327
			ERROR("Using nominal photon energy of %.2f eV\n",
Chuck's avatar
Chuck committed
328
			beam->photon_energy);
Thomas White's avatar
Thomas White committed
329
			image.lambda = ph_en_to_lambda(
Chuck's avatar
Chuck committed
330
			eV_to_J(beam->photon_energy));
331
332
		} else {
			ERROR("No wavelength in file, so you need to give "
Chuck's avatar
Chuck committed
333
				"a beam parameters file with -b.\n");
334
			hdfile_close(hdfile);
Thomas White's avatar
Thomas White committed
335
			free_detector_geometry(image.det);
336
337
338
			return;
		}
	}
339
	fill_in_values(image.det, hdfile);
340

Thomas White's avatar
Thomas White committed
341
	if ( config_cmfilter ) {
342
343
344
		filter_cm(&image);
	}

Thomas White's avatar
Thomas White committed
345
346
347
	/* Take snapshot of image after CM subtraction but before
	 * the aggressive noise filter. */
	data_size = image.width * image.height * sizeof(float);
348
349
	data_for_measurement = malloc(data_size);

Thomas White's avatar
Thomas White committed
350
	if ( config_noisefilter ) {
351
352
		filter_noise(&image, data_for_measurement);
	} else {
353
		memcpy(data_for_measurement, image.data, data_size);
354
355
	}

Thomas White's avatar
Thomas White committed
356
357
	switch ( iargs->peaks ) {

Chuck's avatar
Chuck committed
358
359
		case PEAK_HDF5:
		// Get peaks from HDF5
Thomas White's avatar
Thomas White committed
360
361
362
363
364
365
		if (get_peaks(&image, hdfile,
			iargs->hdf5_peak_path)) {
			ERROR("Failed to get peaks from HDF5 file.\n");
		}
		break;

Chuck's avatar
Chuck committed
366
		case PEAK_ZAEF:
Thomas White's avatar
Thomas White committed
367
		search_peaks(&image, iargs->threshold,
Thomas White's avatar
Thomas White committed
368
369
		             iargs->min_gradient, iargs->min_snr,
		             iargs->ir_inn, iargs->ir_mid, iargs->ir_out);
Thomas White's avatar
Thomas White committed
370
371
		break;

372
	}
Thomas White's avatar
Thomas White committed
373
374
375
376
377
378

	/* 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;

379
	/* Calculate orientation matrix (by magic) */
380
381
382
	image.div = beam->divergence;
	image.bw = beam->bandwidth;
	image.profile_radius = 0.0001e9;
383

Thomas White's avatar
Thomas White committed
384
385
386
	index_pattern(&image, cell, indm, iargs->cellr,
	              config_verbose, iargs->ipriv,
	              iargs->config_insane, iargs->tols);
Thomas White's avatar
Thomas White committed
387

Thomas White's avatar
Thomas White committed
388
	if ( image.indexed_cell != NULL ) {
389
		pargs->indexable = 1;
390
		image.reflections = find_intersections(&image,
Chuck's avatar
Chuck committed
391
392
				image.indexed_cell);
		if (image.reflections != NULL) {
393
			integrate_reflections(&image,
Thomas White's avatar
Thomas White committed
394
395
396
397
398
399
			                      iargs->config_closer,
			                      iargs->config_bgsub,
			                      iargs->min_int_snr,
			                      iargs->ir_inn,
			                      iargs->ir_mid,
			                      iargs->ir_out);
400
		}
401
402
	} else {
		image.reflections = NULL;
Chuck's avatar
Chuck committed
403
	}
404

405
406
407
	write_chunk(ofh, &image, hdfile, iargs->stream_flags);
	fprintf(ofh, "END\n");
	fflush(ofh);
Thomas White's avatar
Thomas White committed
408

409
	/* Only free cell if found */
410
	cell_free(image.indexed_cell);
411

Thomas White's avatar
Thomas White committed
412
	reflist_free(image.reflections);
413
	free(image.data);
Thomas White's avatar
Thomas White committed
414
	if ( image.flags != NULL ) free(image.flags);
415
416
	image_feature_list_free(image.features);
	hdfile_close(hdfile);
Thomas White's avatar
Thomas White committed
417
	free_detector_geometry(image.det);
418
419
420
}


Thomas White's avatar
Thomas White committed
421
static void run_work(const struct index_args *iargs,
422
423
                     int filename_pipe, int results_pipe, FILE *ofh,
                     int cookie)
Thomas White's avatar
Thomas White committed
424
425
{
	int allDone = 0;
Thomas White's avatar
WIP    
Thomas White committed
426
427
428
429
430
431
432
	FILE *fh;

	fh = fdopen(filename_pipe, "r");
	if ( fh == NULL ) {
		ERROR("Failed to fdopen() the filename pipe!\n");
		return;
	}
Thomas White's avatar
Thomas White committed
433
434
435

	while ( !allDone ) {

Thomas White's avatar
Thomas White committed
436
		struct pattern_args pargs;
Thomas White's avatar
WIP    
Thomas White committed
437
		int  w, c;
Thomas White's avatar
Thomas White committed
438
		char buf[1024];
Thomas White's avatar
WIP    
Thomas White committed
439
440
441
442
443
444
445
		char *line;
		char *rval;

		line = malloc(1024*sizeof(char));
		rval = fgets(line, 1023, fh);
		if ( rval == NULL ) {
			free(line);
446
447
448
449
450
			if ( feof(fh) ) {
				allDone = 1;
				continue;
			} else {
				ERROR("Read error!\n");
451
				break;
452
			}
Thomas White's avatar
WIP    
Thomas White committed
453
		}
Thomas White's avatar
Thomas White committed
454

Thomas White's avatar
WIP    
Thomas White committed
455
		chomp(line);
Thomas White's avatar
Thomas White committed
456

457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
		if ( strlen(line) == 0 ) {

			allDone = 1;

		} else {

			pargs.filename = line;
			pargs.indexable = 0;

			process_image(iargs, &pargs, ofh, cookie);

			/* Request another image */
			c = sprintf(buf, "%i\n", pargs.indexable);
			w = write(results_pipe, buf, c);
			if ( w < 0 ) {
				ERROR("write P0\n");
			}
Thomas White's avatar
Thomas White committed
474

Thomas White's avatar
Thomas White committed
475
476
		}

Thomas White's avatar
WIP    
Thomas White committed
477
478
		free(line);

Thomas White's avatar
Thomas White committed
479
	}
Thomas White's avatar
Thomas White committed
480

Thomas White's avatar
Thomas White committed
481
	/* close my pipes */
Thomas White's avatar
WIP    
Thomas White committed
482
	fclose(fh);
Thomas White's avatar
Thomas White committed
483
484
485
486
487
488
489
490
491
492

	cleanup_indexing(iargs->ipriv);
	free(iargs->indm);
	free(iargs->ipriv);
	free_detector_geometry(iargs->det);
	free(iargs->beam);
	free(iargs->element);
	free(iargs->hdf5_peak_path);
	free_copy_hdf5_field_list(iargs->copyme);
	cell_free(iargs->cell);
Thomas White's avatar
Thomas White committed
493
494
495
}


496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
#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

519

520
521
522
static int parse_cell_reduction(const char *scellr, int *err,
                                int *reduction_needs_cell)
{
Thomas White's avatar
Thomas White committed
523
	*err = 0;
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
	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
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
static void pump_chunk(FILE *fh, int *finished, FILE *ofh)
{
	int chunk_started = 0;
	int chunk_finished = 0;

	do {

		char line[1024];
		char *rval;

		rval = fgets(line, 1024, fh);
		if ( rval == NULL ) {

			if ( feof(fh) ) {
				/* Process died */
				*finished = 1;
				if ( chunk_started ) {
					ERROR("EOF during chunk!\n");
					fprintf(ofh, "Chunk is unfinished!\n");
				}
			} else {
				ERROR("fgets() failed: %s\n", strerror(errno));
			}
			chunk_finished = 1;
			continue;

		}

		if ( strcmp(line, "END\n") == 0 ) {
			chunk_finished = 1;
		} else {
			chunk_started = 1;
			fprintf(ofh, "%s", line);
		}

	} while ( !chunk_finished );
}


583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
static void run_reader(int *stream_pipe_read, int n_proc, FILE *ofh)
{
	int done = 0;
	int *finished;
	FILE **fhs;
	int i;

	finished = calloc(n_proc, sizeof(int));
	if ( finished == NULL ) {
		ERROR("Couldn't allocate memory for flags!\n");
		exit(1);
	}

	fhs = calloc(n_proc, sizeof(FILE *));
	if ( fhs == NULL ) {
		ERROR("Couldn't allocate memory for file handles!\n");
		exit(1);
	}

	for ( i=0; i<n_proc; i++ ) {
		fhs[i] = fdopen(stream_pipe_read[i], "r");
		if ( fhs[i] == NULL ) {
			ERROR("Couldn't fdopen() stream!\n");
			exit(1);
		}
	}

	while ( !done ) {

		int r, i;
		struct timeval tv;
		fd_set fds;
		int fdmax;

		tv.tv_sec = 5;
		tv.tv_usec = 0;

		FD_ZERO(&fds);
		fdmax = 0;
		for ( i=0; i<n_proc; i++ ) {

			int fd;

			if ( finished[i] ) continue;

			fd = stream_pipe_read[i];

			FD_SET(fd, &fds);
			if ( fd > fdmax ) fdmax = fd;

		}

		r = select(fdmax+1, &fds, NULL, NULL, &tv);

		if ( r == -1 ) {
			ERROR("select() failed: %s\n", strerror(errno));
			continue;
		}

		if ( r == 0 ) continue; /* Nothing this time.  Try again */

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

			if ( finished[i] ) continue;

			if ( !FD_ISSET(stream_pipe_read[i], &fds) ) continue;

Thomas White's avatar
Thomas White committed
650
			pump_chunk(fhs[i], &finished[i], ofh);
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665

		}

		done = 1;
		for ( i=0; i<n_proc; i++ ) {
			if ( !finished[i] ) done = 0;
		}

	}

	free(finished);

	for ( i=0; i<n_proc; i++ ) {
		fclose(fhs[i]);
	}
Thomas White's avatar
Thomas White committed
666
667
668
	free(fhs);

	if ( ofh != stdout ) fclose(ofh);
669
670
671
}


Thomas White's avatar
Thomas White committed
672
673
674
675
676
677
678
679
static void signal_handler(int sig, siginfo_t *si, void *uc_v)
{
	struct ucontext_t *uc = uc_v;

	STATUS("Signal!\n");
}


Thomas White's avatar
Thomas White committed
680
681
682
683
int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
684
	char *outfile = NULL;
Thomas White's avatar
Thomas White committed
685
	FILE *fh;
686
	FILE *ofh;
687
	char *rval = NULL;
688
	int config_noindex = 0;
689
690
	int config_cmfilter = 0;
	int config_noisefilter = 0;
691
	int config_verbose = 0;
692
	int config_satcorr = 1;
693
	int config_checkprefix = 1;
Chuck's avatar
Chuck committed
694
	int config_closer = 0;
695
	int config_insane = 0;
696
	int config_bgsub = 1;
697
	int config_basename = 0;
698
	float threshold = 800.0;
699
	float min_gradient = 100000.0;
Thomas White's avatar
Thomas White committed
700
	float min_snr = 5.0;
701
	double min_int_snr = -INFINITY;
Thomas White's avatar
Thomas White committed
702
703
	struct detector *det;
	char *geometry = NULL;
Thomas White's avatar
Thomas White committed
704
705
706
707
	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	int indexer_needs_cell;
	int reduction_needs_cell;
Thomas White's avatar
Thomas White committed
708
	char *indm_str = NULL;
709
	UnitCell *cell;
Thomas White's avatar
Thomas White committed
710
	char *pdb = NULL;
711
	char *prefix = NULL;
712
	char *speaks = NULL;
713
	char *scellr = NULL;
714
	char *toler = NULL;
Thomas White's avatar
Thomas White committed
715
	float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
716
	int cellr;
717
	int peaks;
Thomas White's avatar
Thomas White committed
718
	int n_proc = 1;
719
	char *prepare_line;
Thomas White's avatar
Thomas White committed
720
	char prepare_filename[1024];
Thomas White's avatar
WIP    
Thomas White committed
721
	char *use_this_one_instead;
Thomas White's avatar
Thomas White committed
722
	struct index_args iargs;
723
	struct beam_params *beam = NULL;
Thomas White's avatar
Thomas White committed
724
	char *element = NULL;
725
	double nominal_photon_energy;
Thomas White's avatar
Thomas White committed
726
	int stream_flags = STREAM_INTEGRATED;
727
	char *hdf5_peak_path = NULL;
728
	struct copy_hdf5_field *copyme;
729
730
731
732
	char *intrad = NULL;
	float ir_inn = 4.0;
	float ir_mid = 5.0;
	float ir_out = 7.0;
Thomas White's avatar
Thomas White committed
733
734
735
736
737
	int n_indexable, n_processed, n_indexable_last_stats;
	int n_processed_last_stats;
	int t_last_stats;
	pid_t *pids;
	int *filename_pipes;
738
739
	int *stream_pipe_read;
	int *stream_pipe_write;
740
	FILE **result_fhs;
Thomas White's avatar
Thomas White committed
741
	int i;
742
743
	int allDone;
	int *finished;
744
	pid_t pr;
Thomas White's avatar
Thomas White committed
745
746
	struct sigaction sa;
	int r;
747
748
749
750
751
752

	copyme = new_copy_hdf5_field_list();
	if ( copyme == NULL ) {
		ERROR("Couldn't allocate HDF5 field list.\n");
		return 1;
	}
Thomas White's avatar
Thomas White committed
753
754
755
756
757

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
758
		{"output",             1, NULL,               'o'},
759
		{"no-index",           0, &config_noindex,     1},
Thomas White's avatar
Thomas White committed
760
		{"indexing",           1, NULL,               'z'},
Thomas White's avatar
Thomas White committed
761
		{"geometry",           1, NULL,               'g'},
762
		{"beam",               1, NULL,               'b'},
763
764
		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
765
		{"verbose",            0, &config_verbose,     1},
Thomas White's avatar
Thomas White committed
766
		{"pdb",                1, NULL,               'p'},
767
		{"prefix",             1, NULL,               'x'},
768
769
		{"no-sat-corr",        0, &config_satcorr,     0},
		{"sat-corr",           0, &config_satcorr,     1}, /* Compat */
770
		{"threshold",          1, NULL,               't'},
771
		{"no-check-prefix",    0, &config_checkprefix, 0},
772
		{"no-closer-peak",     0, &config_closer,      0},
Chuck's avatar
Chuck committed
773
		{"closer-peak",        0, &config_closer,      1},
774
		{"insane",             0, &config_insane,      1},
Thomas White's avatar
Thomas White committed
775
		{"image",              1, NULL,               'e'},
776
		{"basename",           0, &config_basename,    1},
Thomas White's avatar
Thomas White committed
777
778
779
780
781
782
		{"bg-sub",             0, &config_bgsub,       1}, /* Compat */
		{"no-bg-sub",          0, &config_bgsub,       0},

		{"peaks",              1, NULL,                2},
		{"cell-reduction",     1, NULL,                3},
		{"min-gradient",       1, NULL,                4},
Thomas White's avatar
Thomas White committed
783
		{"record",             1, NULL,                5},
784
785
		{"cpus",               1, NULL,                6},
		{"cpugroup",           1, NULL,                7},
786
		{"cpuoffset",          1, NULL,                8},
787
		{"hdf5-peaks",         1, NULL,                9},
788
		{"copy-hdf5-field",    1, NULL,               10},
Thomas White's avatar
Thomas White committed
789
790
791
		{"min-snr",            1, NULL,               11},
		{"min-integration-snr",1, NULL,               12},
		{"tolerance",          1, NULL,               13},
792
		{"int-radius",         1, NULL,               14},
Thomas White's avatar
Thomas White committed
793
794
795
796
		{0, 0, NULL, 0}
	};

	/* Short options */
Chuck's avatar
Chuck committed
797
	while ((c = getopt_long(argc, argv, "hi:o:z:p:x:j:g:t:b:e:",
Thomas White's avatar
Thomas White committed
798
799
	                        longopts, NULL)) != -1)
	{
Thomas White's avatar
Thomas White committed
800
		switch (c) {
Thomas White's avatar
Thomas White committed
801
802

			case 'h' :
Thomas White's avatar
Thomas White committed
803
804
805
			show_help(argv[0]);
			return 0;

Thomas White's avatar
Thomas White committed
806
			case 'i' :
Thomas White's avatar
Thomas White committed
807
808
809
			filename = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
810
			case 'o' :
811
812
813
			outfile = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
814
			case 'z' :
Thomas White's avatar
Thomas White committed
815
816
817
			indm_str = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
818
			case 'p' :
Thomas White's avatar
Thomas White committed
819
820
821
			pdb = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
822
			case 'x' :
823
824
825
			prefix = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
826
			case 'j' :
Thomas White's avatar
Thomas White committed
827
			n_proc = atoi(optarg);
828
829
			break;

Thomas White's avatar
Thomas White committed
830
			case 'g' :
Thomas White's avatar
Thomas White committed
831
832
833
			geometry = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
834
			case 't' :
835
836
837
			threshold = strtof(optarg, NULL);
			break;

Thomas White's avatar
Thomas White committed
838
			case 'b' :
839
840
841
842
843
844
845
846
			beam = get_beam_parameters(optarg);
			if ( beam == NULL ) {
				ERROR("Failed to load beam parameters"
				      " from '%s'\n", optarg);
				return 1;
			}
			break;

Thomas White's avatar
Thomas White committed
847
848
			case 'e' :
			element = strdup(optarg);
849
850
			break;

Thomas White's avatar
Thomas White committed
851
852
			case 2 :
			speaks = strdup(optarg);
853
854
			break;

Thomas White's avatar
Thomas White committed
855
856
			case 3 :
			scellr = strdup(optarg);
857
858
			break;

Thomas White's avatar
Thomas White committed
859
			case 4 :
860
861
862
			min_gradient = strtof(optarg, NULL);
			break;

Thomas White's avatar
Thomas White committed
863
			case 5 :
Thomas White's avatar
Thomas White committed
864
865
866
867
			stream_flags = parse_stream_flags(optarg);
			if ( stream_flags < 0 ) return 1;
			break;

Thomas White's avatar
Thomas White committed
868
869
870
			case 6 :
			case 7 :
			case 8 :
871
872
			ERROR("The options --cpus, --cpugroup and --cpuoffset"
			      " are no longer used by indexamajig.\n");
873
874
			break;

Thomas White's avatar
Thomas White committed
875
			case 9 :
876
877
878
			hdf5_peak_path = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
879
			case 10 :
880
881
882
			add_copy_hdf5_field(copyme, optarg);
			break;

Thomas White's avatar
Thomas White committed
883
884
885
886
887
888
			case 11 :
			min_snr = strtof(optarg, NULL);
			break;

			case 12 :
			min_int_snr = strtof(optarg, NULL);
Thomas White's avatar
Thomas White committed
889
890
			break;

Thomas White's avatar
Thomas White committed
891
892
893
894
			case 13 :
			toler = strdup(optarg);
			break;

895
896
897
898
			case 14 :
			intrad = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
899
900
901
902
			case 0 :
			break;

			default :
Thomas White's avatar
Thomas White committed
903
			return 1;
Thomas White's avatar
Thomas White committed
904

Thomas White's avatar
Thomas White committed
905
906
907
908
909
910
911
912
913
914
915
916
917
		}

	}

	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
918
		ERROR("Failed to open input file '%s'\n", filename);
Thomas White's avatar
Thomas White committed
919
920
		return 1;
	}
Thomas White's avatar
Thomas White committed
921
	free(filename);
Thomas White's avatar
Thomas White committed
922

923
924
925
926
	if ( outfile == NULL ) {
		ofh = stdout;
	} else {
		ofh = fopen(outfile, "w");
Thomas White's avatar
Thomas White committed
927
928
929
930
931
		if ( ofh == NULL ) {
			ERROR("Failed to open output file '%s'\n", outfile);
			return 1;
		}
		free(outfile);
932
933
	}

934
935
936
937
	if ( hdf5_peak_path == NULL ) {
		hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
	}

938
939
940
941
942
943
944
945
946
947
948
949
950
	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
951
	free(speaks);
952

Thomas White's avatar
Thomas White committed
953
954
955
956
	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

957
	if ( prefix == NULL ) {
Thomas White's avatar
Thomas White committed
958
		prefix = strdup("");
959
	} else {
960
961
962
		if ( config_checkprefix ) {
			prefix = check_prefix(prefix);
		}
963
964
	}

Thomas White's avatar
Thomas White committed
965
	if ( n_proc == 0 ) {
Chuck's avatar
Chuck committed
966
		ERROR("Invalid number of processes.\n");
967
968
969
		return 1;
	}

970
971
	if ( (indm_str == NULL) ||
	     ((indm_str != NULL) && (strcmp(indm_str, "none") == 0)) ) {
972
		STATUS("Not indexing anything.\n");
973
		indexer_needs_cell = 0;
974
975
976
		reduction_needs_cell = 0;
		indm = NULL;
		cellr = CELLR_NONE;
Thomas White's avatar
Thomas White committed
977
	} else {
978
979
980
981
982
983
984
985
		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
986
987
			indm = build_indexer_list(indm_str,
			                          &indexer_needs_cell);
988
989
990
991
992
			if ( indm == NULL ) {
				ERROR("Invalid indexer list '%s'\n", indm_str);
				return 1;
			}
			free(indm_str);
Thomas White's avatar
Thomas White committed
993
		}
Thomas White's avatar
Thomas White committed
994

995
996
997
998
999
1000
		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;