get_hkl.c 13.3 KB
Newer Older
1
2
3
/*
 * get_hkl.c
 *
4
 * Small program to manipulate reflection lists
5
 *
Thomas White's avatar
Thomas White committed
6
 * Copyright © 2012 Thomas White <taw@physics.org>
7
 *
Thomas White's avatar
Thomas White committed
8
9
10
11
12
13
14
15
16
17
18
19
20
21
 * 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/>.
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
 *
 */


#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>

#include "utils.h"
Thomas White's avatar
Thomas White committed
38
#include "reflist-utils.h"
39
#include "symmetry.h"
40
#include "beam-parameters.h"
41
42
43
44
45
46


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
47
"Manipulate reflection lists.\n"
48
"\n"
Thomas White's avatar
Thomas White committed
49
50
"  -h, --help                 Display this help message.\n"
"\n"
51
52
53
54
"  -i, --input=<file>         Read reflections from <file>.\n"
"  -y, --symmetry=<sym>       The symmetry of the input reflection list.\n"
"\n"
"You can add noise to the reflections with either of:\n"
Thomas White's avatar
Thomas White committed
55
"      --poisson              Simulate Poisson samples.\n"
56
"      --noise                Add 10%% random noise.\n"
57
58
59
60
"\n"
"To calculate Poisson samples accurately, you must also give:\n"
"  -b, --beam=<file>          Get beam parameters from file.\n"
"\n"
61
"You can artificially 'twin' the reflections, or expand them out.\n"
62
63
"  -w, --twin=<sym>           Generate twinned data according to the given\n"
"                              point group.\n"
Thomas White's avatar
Thomas White committed
64
"  -e, --expand=<sym>         Expand reflections to this point group.\n"
65
"\n"
66
67
68
69
70
"Use this option with care, and only if you understand why it might sometimes\n"
" be necessary:\n"
"  --trim-centrics            Remove reflections which are duplicated in the\n"
"                              point group specified with the '-y' option.\n"
"\n"
71
72
73
74
"You can restrict which reflections are written out:\n"
"  -t, --template=<filename>  Only include reflections mentioned in file.\n"
"\n"
"You might sometimes need to do this:\n"
75
76
"      --multiplicity         Multiply intensities by the number of\n"
"                              equivalent reflections.\n"
77
78
79
"\n"
"Don't forget to specify the output filename:\n"
"  -o, --output=<filename>    Output filename (default: stdout).\n"
Thomas White's avatar
Thomas White committed
80
81
"  -p, --pdb=<filename>       Use unit cell parameters from this PDB file to\n"
"                              generate resolution values in the output file.\n"
Thomas White's avatar
Thomas White committed
82
);
Thomas White's avatar
Thomas White committed
83
84
85
86
}


/* Apply Poisson noise to all reflections */
Thomas White's avatar
Thomas White committed
87
static void poisson_reflections(RefList *list, double adu_per_photon)
Thomas White's avatar
Thomas White committed
88
{
Thomas White's avatar
Thomas White committed
89
90
	Reflection *refl;
	RefListIterator *iter;
Thomas White's avatar
Thomas White committed
91

Thomas White's avatar
Thomas White committed
92
93
94
	for ( refl = first_refl(list, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
Thomas White's avatar
Thomas White committed
95

Thomas White's avatar
Thomas White committed
96
		double val, c;
Thomas White's avatar
Thomas White committed
97

Thomas White's avatar
Thomas White committed
98
		val = get_intensity(refl);
99

100
		c = adu_per_photon * poisson_noise(val/adu_per_photon);
101
		set_intensity(refl, c);
Thomas White's avatar
Thomas White committed
102
103

	}
104
105
106
107
}


/* Apply 10% uniform noise to all reflections */
Thomas White's avatar
Thomas White committed
108
static void noise_reflections(RefList *list)
109
{
Thomas White's avatar
Thomas White committed
110
111
	Reflection *refl;
	RefListIterator *iter;
112

Thomas White's avatar
Thomas White committed
113
114
115
	for ( refl = first_refl(list, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
116

Thomas White's avatar
Thomas White committed
117
		double val, r;
118

Thomas White's avatar
Thomas White committed
119
		val = get_intensity(refl);
120
121
122
123

		r = (double)random()/RAND_MAX;
		val += 0.1 * val * r;

124
		set_intensity(refl, val);
125

Thomas White's avatar
Thomas White committed
126
	}
127
128
129
}


Thomas White's avatar
Thomas White committed
130
static RefList *template_reflections(RefList *list, RefList *template)
131
{
Thomas White's avatar
Thomas White committed
132
133
134
	Reflection *refl;
	RefListIterator *iter;
	RefList *out;
135

Thomas White's avatar
Thomas White committed
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
	out = reflist_new();

	for ( refl = first_refl(template, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {

		signed int h, k, l;
		Reflection *new;
		Reflection *old;

		get_indices(refl, &h, &k, &l);

		old = find_refl(list, h, k, l);
		if ( old == NULL ) continue;

		new = add_refl(out, h, k, l);
		copy_data(new, old);

	}

	return out;
}


static RefList *twin_reflections(RefList *in,
Thomas White's avatar
Thomas White committed
161
                                 const SymOpList *holo, const SymOpList *mero)
Thomas White's avatar
Thomas White committed
162
163
164
165
{
	Reflection *refl;
	RefListIterator *iter;
	RefList *out;
Thomas White's avatar
Thomas White committed
166
	SymOpMask *m;
167

Thomas White's avatar
Thomas White committed
168
	/* FIXME: Check properly by coset decomposition */
Thomas White's avatar
Thomas White committed
169
	if ( num_equivs(holo, NULL) < num_equivs(mero, NULL) ) {
Thomas White's avatar
Thomas White committed
170
171
		ERROR("%s is not a subgroup of %s!\n", symmetry_name(mero),
		                                       symmetry_name(holo));
172
173
174
		return NULL;
	}

Thomas White's avatar
Thomas White committed
175
	out = reflist_new();
Thomas White's avatar
Thomas White committed
176
	m = new_symopmask(holo);
Thomas White's avatar
Thomas White committed
177
178
179
180

	for ( refl = first_refl(in, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
181

182
		double total, sigma;
183
184
185
186
		signed int h, k, l;
		int n, j;
		int skip;

Thomas White's avatar
Thomas White committed
187
		get_indices(refl, &h, &k, &l);
188

189
		/* There is a many-to-one correspondence between reflections
Thomas White's avatar
Thomas White committed
190
191
192
		 * in the merohedral and holohedral groups.  Do the calculation
		 * only once for each reflection in the holohedral group, which
		 * contains fewer reflections.
193
		 */
Thomas White's avatar
Thomas White committed
194
		get_asymm(holo, h, k, l, &h, &k, &l);
Thomas White's avatar
Thomas White committed
195
		if ( find_refl(out, h, k, l) != NULL ) continue;
196

197
198
		total = 0.0;
		sigma = 0.0;
199
		skip = 0;
Thomas White's avatar
Thomas White committed
200
201
202
		special_position(holo, m, h, k, l);
		n = num_equivs(holo, m);

203
204
205
206
207
		for ( j=0; j<n; j++ ) {

			signed int he, ke, le;
			signed int hu, ku, lu;

Thomas White's avatar
Thomas White committed
208
			get_equiv(holo, m, j, h, k, l, &he, &ke, &le);
209
210
211
212
213
214

			/* Do we have this reflection?
			 * We might not have the particular (merohedral)
			 * equivalent which belongs to our definition of the
			 * asymmetric unit cell, so check them all.
			 */
Thomas White's avatar
Thomas White committed
215
216
			if ( !find_equiv_in_list(in, he, ke, le, mero,
			                         &hu, &ku, &lu) ) {
217
218
219
220
221
				/* Don't have this reflection, so bail out */
				ERROR("Twinning %i %i %i requires the %i %i %i "
				      "reflection (or an equivalent in %s), "
				      "which I don't have. %i %i %i won't "
				      "appear in the output\n",
Thomas White's avatar
Thomas White committed
222
223
				      h, k, l, he, ke, le, symmetry_name(mero),
				      h, k, l);
224
225
226
227
				skip = 1;
				break;
			}

Thomas White's avatar
Thomas White committed
228
229
			total += get_intensity(refl);
			sigma += pow(get_esd_intensity(refl), 2.0);
230
231
232
233
234

		}

		if ( !skip ) {

Thomas White's avatar
Thomas White committed
235
			Reflection *new = add_refl(out, h, k, l);
236
			set_intensity(new, total);
Thomas White's avatar
Thomas White committed
237
			set_esd_intensity(new, sqrt(sigma));
238
239
240
241
242

		}

	}

Thomas White's avatar
Thomas White committed
243
	return out;
244
245
246
}


Thomas White's avatar
Thomas White committed
247
248
static RefList *expand_reflections(RefList *in, const SymOpList *target,
                                                const SymOpList *initial)
Thomas White's avatar
Thomas White committed
249
{
Thomas White's avatar
Thomas White committed
250
251
252
	Reflection *refl;
	RefListIterator *iter;
	RefList *out;
Thomas White's avatar
Thomas White committed
253
	SymOpMask *m;
Thomas White's avatar
Thomas White committed
254

Thomas White's avatar
Thomas White committed
255
	/* FIXME: Check properly */
Thomas White's avatar
Thomas White committed
256
	if ( num_equivs(target, NULL) > num_equivs(initial, NULL) ) {
Thomas White's avatar
Thomas White committed
257
258
		ERROR("%s is not a subgroup of %s!\n", symmetry_name(initial),
		                                       symmetry_name(target));
259
260
261
		return NULL;
	}

Thomas White's avatar
Thomas White committed
262
	out = reflist_new();
Thomas White's avatar
Thomas White committed
263
	m = new_symopmask(initial);
Thomas White's avatar
Thomas White committed
264
265
266
267

	for ( refl = first_refl(in, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
Thomas White's avatar
Thomas White committed
268
269
270
271
272

		signed int h, k, l;
		int n, j;
		double intensity;

Thomas White's avatar
Thomas White committed
273
274
		get_indices(refl, &h, &k, &l);
		intensity = get_intensity(refl);
Thomas White's avatar
Thomas White committed
275

Thomas White's avatar
Thomas White committed
276
277
		special_position(initial, m, h, k, l);
		n = num_equivs(initial, m);
Thomas White's avatar
Thomas White committed
278

Thomas White's avatar
Thomas White committed
279
		/* For each equivalent in the higher symmetry group */
Thomas White's avatar
Thomas White committed
280
281
282
		for ( j=0; j<n; j++ ) {

			signed int he, ke, le;
Thomas White's avatar
Thomas White committed
283
			Reflection *new;
284
285
			int have_phase;
			double ph;
Thomas White's avatar
Thomas White committed
286
287

			/* Get the equivalent */
Thomas White's avatar
Thomas White committed
288
			get_equiv(initial, m, j, h, k, l, &he, &ke, &le);
Thomas White's avatar
Thomas White committed
289
290

			/* Put it into the asymmetric unit for the target */
Thomas White's avatar
Thomas White committed
291
			get_asymm(target, he, ke, le, &he, &ke, &le);
Thomas White's avatar
Thomas White committed
292
293

			/* Make sure the intensity is in the right place */
Thomas White's avatar
Thomas White committed
294
295
			new = add_refl(out, he, ke, le);
			copy_data(new, refl);
Thomas White's avatar
Thomas White committed
296

Thomas White's avatar
Thomas White committed
297
298
			/* FIXME: Make phase negative if the reflection is
			 * separated from the original via an inversion */
299
			get_phase(refl, &have_phase);
300
			if ( have_phase ) set_phase(new, -ph);
Thomas White's avatar
Thomas White committed
301

Thomas White's avatar
Thomas White committed
302
303
304
305
		}

	}

Thomas White's avatar
Thomas White committed
306
307
	free_symopmask(m);

Thomas White's avatar
Thomas White committed
308
	return out;
Thomas White's avatar
Thomas White committed
309
310
311
}


312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
static RefList *trim_centrics(RefList *in, const SymOpList *sym)
{
	Reflection *refl;
	RefListIterator *iter;
	RefList *out;

	out = reflist_new();

	for ( refl = first_refl(in, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		signed int h, k, l;
		signed int ha, ka, la;
		Reflection *new;

		get_indices(refl, &h, &k, &l);

		/* Put it into the asymmetric unit */
		get_asymm(sym, h, k, l, &ha, &ka, &la);

		new = find_refl(out, ha, ka, la);
		if ( new != NULL ) {
			STATUS("Trimmed %i %i %i\n", h, k, l);
			continue;
		}

		/* Add new reflection under asymmetric (unique) indices */
		new = add_refl(out, ha, ka, la);
		copy_data(new, refl);
	}

	return out;
}


348
349
350
int main(int argc, char *argv[])
{
	int c;
351
352
	int config_noise = 0;
	int config_poisson = 0;
353
	int config_multi = 0;
354
	int config_trimc = 0;
Thomas White's avatar
Thomas White committed
355
356
357
358
359
360
	char *holo_str = NULL;
	char *mero_str = NULL;
	char *expand_str = NULL;
	SymOpList *holo;
	SymOpList *mero;
	SymOpList *expand;
Thomas White's avatar
Thomas White committed
361
362
	char *input_file = NULL;
	char *template = NULL;
Thomas White's avatar
Thomas White committed
363
	char *output = NULL;
364
	char *beamfile = NULL;
365
	struct beam_params *beam = NULL;
Thomas White's avatar
Thomas White committed
366
367
	RefList *input;
	UnitCell *cell = NULL;
368
369
370
371

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
Thomas White's avatar
Thomas White committed
372
		{"template",           1, NULL,               't'},
373
374
		{"poisson",            0, &config_poisson,     1},
		{"noise",              0, &config_noise,       1},
Thomas White's avatar
Thomas White committed
375
		{"output",             1, NULL,               'o'},
376
		{"symmetry",           1, NULL,               'y'},
Thomas White's avatar
Thomas White committed
377
378
		{"twin",               1, NULL,               'w'},
		{"expand",             1, NULL,               'e'},
379
		{"intensities",        1, NULL,               'i'},
380
		{"multiplicity",       0, &config_multi,       1},
381
		{"beam",               1, NULL,               'b'},
Thomas White's avatar
Thomas White committed
382
		{"pdb",                1, NULL,               'p'},
383
		{"trim-centrics",      0, &config_trimc,       1},
384
385
386
387
		{0, 0, NULL, 0}
	};

	/* Short options */
Thomas White's avatar
Thomas White committed
388
	while ((c = getopt_long(argc, argv, "ht:o:i:w:y:e:b:p:",
Thomas White's avatar
Thomas White committed
389
	                        longopts, NULL)) != -1) {
390
391

		switch (c) {
Thomas White's avatar
Thomas White committed
392
		case 'h' :
393
394
395
			show_help(argv[0]);
			return 0;

Thomas White's avatar
Thomas White committed
396
		case 't' :
Thomas White's avatar
Thomas White committed
397
398
399
			template = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
400
		case 'o' :
Thomas White's avatar
Thomas White committed
401
402
403
			output = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
404
		case 'i' :
Thomas White's avatar
Thomas White committed
405
			input_file = strdup(optarg);
406
407
			break;

408
		case 'y' :
Thomas White's avatar
Thomas White committed
409
			mero_str = strdup(optarg);
410
411
412
			break;

		case 'w' :
Thomas White's avatar
Thomas White committed
413
			holo_str = strdup(optarg);
414
415
			break;

Thomas White's avatar
Thomas White committed
416
		case 'e' :
Thomas White's avatar
Thomas White committed
417
			expand_str = strdup(optarg);
Thomas White's avatar
Thomas White committed
418
419
			break;

420
421
422
423
		case 'b' :
			beamfile = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
424
425
426
427
428
429
430
431
		case 'p' :
			cell = load_cell_from_pdb(optarg);
			if ( cell == NULL ) {
				ERROR("Failed to get cell from '%s'\n", optarg);
				return 1;
			}
			break;

Thomas White's avatar
Thomas White committed
432
		case 0 :
433
434
			break;

Thomas White's avatar
Thomas White committed
435
		default :
436
437
438
439
440
			return 1;
		}

	}

Thomas White's avatar
Thomas White committed
441
	if ( (holo_str != NULL) && (expand_str != NULL) ) {
Thomas White's avatar
Thomas White committed
442
443
		ERROR("You cannot 'twin' and 'expand' at the same time.\n");
		ERROR("Decide which one you want to do first.\n");
444
445
446
447
448
449
450
451
452
453
		return 1;
	}

	if ( beamfile != NULL ) {
		beam = get_beam_parameters(beamfile);
		if ( beam == NULL ) {
			ERROR("Failed to load beam parameters from '%s'\n",
			      beamfile);
			return 1;
		}
Thomas White's avatar
Thomas White committed
454
455
	}

Thomas White's avatar
Thomas White committed
456
457
458
	if ( cell == NULL ) {
		ERROR("You need to give a PDB file with the unit cell.\n");
		return 1;
459
	}
460

Thomas White's avatar
Thomas White committed
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
	if ( holo_str != NULL ) {
		holo = get_pointgroup(holo_str);
		free(holo_str);
	} else {
		holo = NULL;
	}
	if ( mero_str != NULL ) {
		mero = get_pointgroup(mero_str);
		free(mero_str);
	} else {
		mero = NULL;
	}
	if ( expand_str != NULL ) {
		expand = get_pointgroup(expand_str);
		free(expand_str);
	} else {
		expand = NULL;
	}

Thomas White's avatar
Thomas White committed
480
	input = read_reflections(input_file);
Thomas White's avatar
Thomas White committed
481
482
483
484
	if ( input == NULL ) {
		ERROR("Problem reading input file %s\n", input_file);
		return 1;
	}
Thomas White's avatar
Thomas White committed
485
	free(input_file);
486
487
488
489

	STATUS("%i reflections in input.\n", num_reflections(input));

	if ( !config_trimc && check_list_symmetry(input, mero) ) {
490
		ERROR("The input reflection list does not appear to"
Thomas White's avatar
Thomas White committed
491
		      " have symmetry %s\n", symmetry_name(mero));
492
		return 1;
493
	}
494

495
496
	if ( config_poisson ) {
		if ( beam != NULL ) {
Thomas White's avatar
Thomas White committed
497
			poisson_reflections(input, beam->adu_per_photon);
498
499
500
501
502
503
504
		} else {
			ERROR("You must give a beam parameters file in order"
			      " to calculate Poisson noise.\n");
			return 1;
		}
	}

Thomas White's avatar
Thomas White committed
505
	if ( config_noise ) noise_reflections(input);
Thomas White's avatar
Thomas White committed
506

507
	if ( holo != NULL ) {
508

Thomas White's avatar
Thomas White committed
509
		RefList *new;
Thomas White's avatar
Thomas White committed
510
511
		STATUS("Twinning from %s into %s\n", symmetry_name(mero),
		                                     symmetry_name(holo));
Thomas White's avatar
Thomas White committed
512
513
514
515
516
517
518
519
520
		new = twin_reflections(input, holo, mero);

		/* Replace old with new */
		reflist_free(input);
		input = new;

		/* The symmetry of the list has changed */
		free(mero);
		mero = holo;
521

Thomas White's avatar
Thomas White committed
522
523
	}

Thomas White's avatar
Thomas White committed
524
	if ( expand != NULL ) {
525

Thomas White's avatar
Thomas White committed
526
		RefList *new;
Thomas White's avatar
Thomas White committed
527
528
		STATUS("Expanding from %s into %s\n", symmetry_name(mero),
		                                      symmetry_name(expand));
Thomas White's avatar
Thomas White committed
529
530
531
532
533
		new = expand_reflections(input, expand, mero);

		/* Replace old with new */
		reflist_free(input);
		input = new;
534

Thomas White's avatar
Thomas White committed
535
536
	}

537
538
539
540
541
542
543
544
545
546
547
548
549
	if ( config_trimc ) {

		RefList *new;

		STATUS("Trimming duplicate reflections in %s\n",
		       symmetry_name(mero));
		new = trim_centrics(input, mero);
		reflist_free(input);
		input = new;
		STATUS("%i output reflections\n", num_reflections(input));

	}

550
551
	if ( config_multi ) {

Thomas White's avatar
Thomas White committed
552
553
		Reflection *refl;
		RefListIterator *iter;
Thomas White's avatar
Thomas White committed
554
555
556
		SymOpMask *m;

		m = new_symopmask(mero);
557

Thomas White's avatar
Thomas White committed
558
559
560
		for ( refl = first_refl(input, &iter);
		      refl != NULL;
		      refl = next_refl(refl, iter) ) {
561
562

			double inty;
Thomas White's avatar
Thomas White committed
563
564
565
566
			signed int h, k, l;

			get_indices(refl, &h, &k, &l);
			inty = get_intensity(refl);
567

Thomas White's avatar
Thomas White committed
568
569
			special_position(mero, m, h, k, l);
			inty *= (double)num_equivs(mero, m);
570
			set_intensity(refl, inty);
571
572

		}
Thomas White's avatar
Thomas White committed
573
574

		free_symopmask(m);
575
576
	}

Thomas White's avatar
Thomas White committed
577
	if ( template ) {
578

Thomas White's avatar
Thomas White committed
579
580
581
582
		RefList *t = read_reflections(template);
		RefList *new = template_reflections(input, t);
		reflist_free(input);
		input = new;
583

Thomas White's avatar
Thomas White committed
584
585
	}

Thomas White's avatar
Thomas White committed
586
	write_reflist(output, input, cell);
Thomas White's avatar
Thomas White committed
587

Thomas White's avatar
Thomas White committed
588
	reflist_free(input);
589
590
591

	return 0;
}