get_hkl.c 9.95 KB
Newer Older
1
2
3
/*
 * get_hkl.c
 *
4
 * Small program to manipulate reflection lists
5
 *
6
 * (c) 2006-2011 Thomas White <taw@physics.org>
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
 *
 * 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>

#include "utils.h"
Thomas White's avatar
Thomas White committed
25
#include "reflist-utils.h"
26
#include "symmetry.h"
27
#include "beam-parameters.h"
28
29
30
31
32
33


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
34
"Manipulate reflection lists.\n"
35
"\n"
Thomas White's avatar
Thomas White committed
36
37
"  -h, --help                 Display this help message.\n"
"\n"
38
39
40
41
"  -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
42
"      --poisson              Simulate Poisson samples.\n"
43
"      --noise                Add 10%% random noise.\n"
44
45
46
47
"\n"
"To calculate Poisson samples accurately, you must also give:\n"
"  -b, --beam=<file>          Get beam parameters from file.\n"
"\n"
Thomas White's avatar
Thomas White committed
48
49
"You can artificially 'twin' the reflections, or expand them out.  You can also"
" do both, in which case the 'twinning' will be done first:\n"
50
51
"  -w, --twin=<sym>           Generate twinned data according to the given\n"
"                              point group.\n"
Thomas White's avatar
Thomas White committed
52
"  -e, --expand=<sym>         Expand reflections to this point group.\n"
53
54
55
56
57
"\n"
"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"
58
59
"      --multiplicity         Multiply intensities by the number of\n"
"                              equivalent reflections.\n"
60
61
62
"\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
63
64
"  -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
65
);
Thomas White's avatar
Thomas White committed
66
67
68
69
}


/* Apply Poisson noise to all reflections */
Thomas White's avatar
Thomas White committed
70
static void poisson_reflections(RefList *list, double adu_per_photon)
Thomas White's avatar
Thomas White committed
71
{
Thomas White's avatar
Thomas White committed
72
73
	Reflection *refl;
	RefListIterator *iter;
Thomas White's avatar
Thomas White committed
74

Thomas White's avatar
Thomas White committed
75
76
77
	for ( refl = first_refl(list, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
Thomas White's avatar
Thomas White committed
78

Thomas White's avatar
Thomas White committed
79
		double val, c;
Thomas White's avatar
Thomas White committed
80

Thomas White's avatar
Thomas White committed
81
		val = get_intensity(refl);
82

83
		c = adu_per_photon * poisson_noise(val/adu_per_photon);
Thomas White's avatar
Thomas White committed
84
		set_int(refl, c);
Thomas White's avatar
Thomas White committed
85
86

	}
87
88
89
90
}


/* Apply 10% uniform noise to all reflections */
Thomas White's avatar
Thomas White committed
91
static void noise_reflections(RefList *list)
92
{
Thomas White's avatar
Thomas White committed
93
94
	Reflection *refl;
	RefListIterator *iter;
95

Thomas White's avatar
Thomas White committed
96
97
98
	for ( refl = first_refl(list, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
99

Thomas White's avatar
Thomas White committed
100
		double val, r;
101

Thomas White's avatar
Thomas White committed
102
		val = get_intensity(refl);
103
104
105
106

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

Thomas White's avatar
Thomas White committed
107
		set_int(refl, val);
108

Thomas White's avatar
Thomas White committed
109
	}
110
111
112
}


Thomas White's avatar
Thomas White committed
113
static RefList *template_reflections(RefList *list, RefList *template)
114
{
Thomas White's avatar
Thomas White committed
115
116
117
	Reflection *refl;
	RefListIterator *iter;
	RefList *out;
118

Thomas White's avatar
Thomas White committed
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
	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,
                                 const char *holo, const char *mero)
{
	Reflection *refl;
	RefListIterator *iter;
	RefList *out;
149

150
151
152
153
154
	if ( num_general_equivs(holo) < num_general_equivs(mero) ) {
		ERROR("%s is not a subgroup of %s!\n", mero, holo);
		return NULL;
	}

Thomas White's avatar
Thomas White committed
155
156
157
158
159
	out = reflist_new();

	for ( refl = first_refl(in, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
160

161
		double total, sigma;
162
163
164
165
		signed int h, k, l;
		int n, j;
		int skip;

Thomas White's avatar
Thomas White committed
166
		get_indices(refl, &h, &k, &l);
167

168
		/* There is a many-to-one correspondence between reflections
Thomas White's avatar
Thomas White committed
169
170
171
		 * in the merohedral and holohedral groups.  Do the calculation
		 * only once for each reflection in the holohedral group, which
		 * contains fewer reflections.
172
		 */
Thomas White's avatar
Thomas White committed
173
174
		get_asymm(h, k, l, &h, &k, &l, holo);
		if ( find_refl(out, h, k, l) != NULL ) continue;
175

176
177
		total = 0.0;
		sigma = 0.0;
178
		skip = 0;
Thomas White's avatar
Thomas White committed
179
		n = num_equivs(h, k, l, holo);
180
181
182
183
184
185
186
187
188
189
190
191
		for ( j=0; j<n; j++ ) {

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

			get_equiv(h, k, l, &he, &ke, &le, holo, j);

			/* 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
192
193
			if ( !find_equiv_in_list(in, he, ke, le, mero,
			                         &hu, &ku, &lu) ) {
194
195
196
197
198
199
200
201
202
203
				/* 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",
				      h, k, l, he, ke, le, mero, h, k, l);
				skip = 1;
				break;
			}

Thomas White's avatar
Thomas White committed
204
205
			total += get_intensity(refl);
			sigma += pow(get_esd_intensity(refl), 2.0);
206
207
208
209
210

		}

		if ( !skip ) {

Thomas White's avatar
Thomas White committed
211
212
213
			Reflection *new = add_refl(out, h, k, l);
			set_int(new, total);
			set_esd_intensity(new, sqrt(sigma));
214
215
216
217
218

		}

	}

Thomas White's avatar
Thomas White committed
219
	return out;
220
221
222
}


Thomas White's avatar
Thomas White committed
223
224
static RefList *expand_reflections(RefList *in,
                                   const char *target, const char *initial)
Thomas White's avatar
Thomas White committed
225
{
Thomas White's avatar
Thomas White committed
226
227
228
	Reflection *refl;
	RefListIterator *iter;
	RefList *out;
Thomas White's avatar
Thomas White committed
229

230
231
232
233
234
	if ( num_general_equivs(target) > num_general_equivs(initial) ) {
		ERROR("%s is not a subgroup of %s!\n", initial, target);
		return NULL;
	}

Thomas White's avatar
Thomas White committed
235
236
237
238
239
	out = reflist_new();

	for ( refl = first_refl(in, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {
Thomas White's avatar
Thomas White committed
240
241
242
243
244

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

Thomas White's avatar
Thomas White committed
245
246
		get_indices(refl, &h, &k, &l);
		intensity = get_intensity(refl);
Thomas White's avatar
Thomas White committed
247
248
249

		n = num_equivs(h, k, l, initial);

Thomas White's avatar
Thomas White committed
250
		/* For each equivalent in the higher symmetry group */
Thomas White's avatar
Thomas White committed
251
252
253
		for ( j=0; j<n; j++ ) {

			signed int he, ke, le;
Thomas White's avatar
Thomas White committed
254
			Reflection *new;
Thomas White's avatar
Thomas White committed
255
256
257
258
259
260
261
262

			/* Get the equivalent */
			get_equiv(h, k, l, &he, &ke, &le, initial, j);

			/* Put it into the asymmetric unit for the target */
			get_asymm(he, ke, le, &he, &ke, &le, target);

			/* Make sure the intensity is in the right place */
Thomas White's avatar
Thomas White committed
263
264
			new = add_refl(out, he, ke, le);
			copy_data(new, refl);
Thomas White's avatar
Thomas White committed
265
266
267
268
269

		}

	}

Thomas White's avatar
Thomas White committed
270
	return out;
Thomas White's avatar
Thomas White committed
271
272
273
}


274
275
276
int main(int argc, char *argv[])
{
	int c;
277
278
	int config_noise = 0;
	int config_poisson = 0;
279
	int config_multi = 0;
280
281
	char *holo = NULL;
	char *mero = NULL;
Thomas White's avatar
Thomas White committed
282
	char *expand = NULL;
Thomas White's avatar
Thomas White committed
283
284
	char *input_file = NULL;
	char *template = NULL;
Thomas White's avatar
Thomas White committed
285
	char *output = NULL;
286
	char *beamfile = NULL;
287
	struct beam_params *beam = NULL;
Thomas White's avatar
Thomas White committed
288
289
	RefList *input;
	UnitCell *cell = NULL;
290
291
292
293

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
Thomas White's avatar
Thomas White committed
294
		{"template",           1, NULL,               't'},
295
296
		{"poisson",            0, &config_poisson,     1},
		{"noise",              0, &config_noise,       1},
Thomas White's avatar
Thomas White committed
297
		{"output",             1, NULL,               'o'},
298
		{"symmetry",           1, NULL,               'y'},
Thomas White's avatar
Thomas White committed
299
300
		{"twin",               1, NULL,               'w'},
		{"expand",             1, NULL,               'e'},
301
		{"intensities",        1, NULL,               'i'},
302
		{"multiplicity",       0, &config_multi,       1},
303
		{"beam",               1, NULL,               'b'},
Thomas White's avatar
Thomas White committed
304
		{"pdb",                1, NULL,               'p'},
305
306
307
308
		{0, 0, NULL, 0}
	};

	/* Short options */
309
	while ((c = getopt_long(argc, argv, "ht:o:i:w:y:e:b:",
Thomas White's avatar
Thomas White committed
310
	                        longopts, NULL)) != -1) {
311
312

		switch (c) {
Thomas White's avatar
Thomas White committed
313
		case 'h' :
314
315
316
			show_help(argv[0]);
			return 0;

Thomas White's avatar
Thomas White committed
317
		case 't' :
Thomas White's avatar
Thomas White committed
318
319
320
			template = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
321
		case 'o' :
Thomas White's avatar
Thomas White committed
322
323
324
			output = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
325
		case 'i' :
Thomas White's avatar
Thomas White committed
326
			input_file = strdup(optarg);
327
328
			break;

329
330
331
332
333
334
335
336
		case 'y' :
			mero = strdup(optarg);
			break;

		case 'w' :
			holo = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
337
338
339
340
		case 'e' :
			expand = strdup(optarg);
			break;

341
342
343
344
		case 'b' :
			beamfile = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
345
346
347
348
349
350
351
352
		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
353
		case 0 :
354
355
			break;

Thomas White's avatar
Thomas White committed
356
		default :
357
358
359
360
361
			return 1;
		}

	}

Thomas White's avatar
Thomas White committed
362
363
364
	if ( (holo != NULL) && (expand != NULL) ) {
		ERROR("You cannot 'twin' and 'expand' at the same time.\n");
		ERROR("Decide which one you want to do first.\n");
365
366
367
368
369
370
371
372
373
374
		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
375
376
	}

Thomas White's avatar
Thomas White committed
377
378
379
	if ( cell == NULL ) {
		ERROR("You need to give a PDB file with the unit cell.\n");
		return 1;
380
	}
381

Thomas White's avatar
Thomas White committed
382
	input = read_reflections(input_file);
383
	free(input);
Thomas White's avatar
Thomas White committed
384
	if ( check_list_symmetry(input, mero) ) {
385
386
387
		ERROR("The input reflection list does not appear to"
		      " have symmetry %s\n", mero);
		return 1;
388
	}
389

390
391
	if ( config_poisson ) {
		if ( beam != NULL ) {
Thomas White's avatar
Thomas White committed
392
			poisson_reflections(input, beam->adu_per_photon);
393
394
395
396
397
398
399
		} 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
400
	if ( config_noise ) noise_reflections(input);
Thomas White's avatar
Thomas White committed
401

402
	if ( holo != NULL ) {
403

Thomas White's avatar
Thomas White committed
404
		RefList *new;
405
		STATUS("Twinning from %s into %s\n", mero, holo);
Thomas White's avatar
Thomas White committed
406
407
408
409
410
411
412
413
414
		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;
415

Thomas White's avatar
Thomas White committed
416
417
	}

Thomas White's avatar
Thomas White committed
418
	if ( expand != NULL ) {
419

Thomas White's avatar
Thomas White committed
420
		RefList *new;
Thomas White's avatar
Thomas White committed
421
		STATUS("Expanding from %s into %s\n", mero, expand);
Thomas White's avatar
Thomas White committed
422
423
424
425
426
		new = expand_reflections(input, expand, mero);

		/* Replace old with new */
		reflist_free(input);
		input = new;
427

Thomas White's avatar
Thomas White committed
428
429
	}

430
431
	if ( config_multi ) {

Thomas White's avatar
Thomas White committed
432
433
		Reflection *refl;
		RefListIterator *iter;
434

Thomas White's avatar
Thomas White committed
435
436
437
		for ( refl = first_refl(input, &iter);
		      refl != NULL;
		      refl = next_refl(refl, iter) ) {
438
439

			double inty;
Thomas White's avatar
Thomas White committed
440
441
442
443
			signed int h, k, l;

			get_indices(refl, &h, &k, &l);
			inty = get_intensity(refl);
444

Thomas White's avatar
Thomas White committed
445
446
			inty *= (double)num_equivs(h, k, l, mero);
			set_int(refl, inty);
447
448
449
450

		}
	}

Thomas White's avatar
Thomas White committed
451
	if ( template ) {
452

Thomas White's avatar
Thomas White committed
453
454
455
456
		RefList *t = read_reflections(template);
		RefList *new = template_reflections(input, t);
		reflist_free(input);
		input = new;
457

Thomas White's avatar
Thomas White committed
458
459
	}

Thomas White's avatar
Thomas White committed
460
	write_reflist(output, input, cell);
Thomas White's avatar
Thomas White committed
461

Thomas White's avatar
Thomas White committed
462
	reflist_free(input);
463
464
465

	return 0;
}