aboutsummaryrefslogtreecommitdiff
path: root/src/process_hkl.c
blob: 77d5056accf983f8031391bb990e069881a17756 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
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
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
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
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
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
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
/*
 * process_hkl.c
 *
 * Assemble and process FEL Bragg intensities
 *
 * (c) 2006-2010 Thomas White <taw@physics.org>
 *
 * 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"
#include "statistics.h"
#include "sfac.h"
#include "reflections.h"
#include "likelihood.h"


/* Number of divisions for R vs |q| graphs */
#define RVQDV (20)


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Assemble and process FEL Bragg intensities.\n"
"\n"
"  -h, --help                Display this help message.\n"
"  -i, --input=<filename>    Specify input filename (\"-\" for stdin).\n"
"  -o, --output=<filename>   Specify output filename for merged intensities\n"
"                             (don't specify for no output).\n"
"  -p, --pdb=<filename>      PDB file to use (default: molecule.pdb).\n"
"\n"
"      --max-only            Take the integrated intensity to be equal to the\n"
"                             maximum intensity measured for that reflection.\n"
"                             The default is to use the mean value from all\n"
"                             measurements.\n"
"      --sum                 Sum (rather than average) the intensities for the\n"
"                             final output list.  This is useful for comparing\n"
"                             results to radially summed powder patterns, but\n"
"                             will break R-factor analysis.\n"
"      --stop-after=<n>      Stop after processing n patterns.  Zero means\n"
"                             keep going until the end of the input, and is\n"
"                             the default.\n"
"  -c, --compare-with=<file> Compare with reflection intensities in this file\n"
"\n"
"  -e, --output-every=<n>    Analyse figures of merit after every n patterns\n"
"                             Default: 1000.  A value of zero means to do the\n"
"                             analysis only after reading all the patterns.\n"
"  -r, --rvsq                Output lists of R vs |q| (\"Luzzatti plots\")\n"
"                             when analysing figures of merit.\n"
"      --zone-axis           Output an [001] zone axis pattern each time the\n"
"                             figures of merit are analysed.\n"
"      --detwin              Correlate each new pattern with the current\n"
"                             model and choose the best fitting out of the\n"
"                             allowable twins.\n"
"      --scale               Scale each pattern for best fit with the current\n"
"                             model.\n"
);
}


static void write_RvsQ(const char *name, double *ref, double *trueref,
                       unsigned int *counts, double scale, UnitCell *cell)
{
	FILE *fh;
	double smax, sbracket;
	signed int h, k, l;

	fh = fopen(name, "w");

	smax = 0.0;
	for ( h=-INDMAX; h<INDMAX; h++ ) {
	for ( k=-INDMAX; k<INDMAX; k++ ) {
	for ( l=-INDMAX; l<INDMAX; l++ ) {
		double s = 2.0*resolution(cell, h, k, l);
		if ( (lookup_count(counts, h, k, l) > 0) && (s > smax) ) {
			smax = s;
		}
	}
	}
	}

	for ( sbracket=0.0; sbracket<smax; sbracket+=smax/RVQDV ) {

		double top = 0.0;
		double bot = 0.0;
		int nhits = 0;
		int nrefl = 0;
		double R;
		double hits_per_refl;

		for ( h=-INDMAX; h<INDMAX; h++ ) {
		for ( k=-INDMAX; k<INDMAX; k++ ) {
		for ( l=-INDMAX; l<INDMAX; l++ ) {

			double s;
			int c;

			if ( (h==0) && (k==0) && (l==0) ) continue;

			c = lookup_count(counts, h, k, l);
			s = 2.0*resolution(cell, h, k, l);
			if ((s>=sbracket) && (s<sbracket+smax/RVQDV) && (c>0)) {

				double obs, calc, obsi;

				obs = lookup_intensity(ref, h, k, l);
				calc = lookup_intensity(trueref, h, k, l);

				obsi = obs / (double)c;
				top += pow(obsi - scale*calc, 2.0);
				bot += pow(obsi, 2.0);
				nhits += c;
				nrefl++;

			}

		}
		}
		}

		R = sqrt(top/bot);
		hits_per_refl = nrefl ? (double)nhits/nrefl : 0;

		fprintf(fh, "%8.5f %8.5f %5.2f\n", sbracket+smax/(2.0*RVQDV),
		                                R, hits_per_refl);

	}
	fclose(fh);
}


static void process_reflections(double *ref, unsigned int *counts,
                                double *trueref, unsigned int *truecounts,
                                unsigned int n_patterns,
                                UnitCell *cell, int do_rvsq, int do_zoneaxis)
{
	int j;
	double mean_counts;
	int ctot = 0;
	int nmeas = 0;
	double R, scale;
	FILE *fh;

	for ( j=0; j<LIST_SIZE; j++ ) {
		ctot += counts[j];
		if ( counts[j] > 0 ) nmeas++;
	}
	mean_counts = (double)ctot/nmeas;

	R = stat_r2(ref, counts, trueref, truecounts, &scale);
	STATUS("%8u: R=%5.2f%% (sf=%7.4e)  mean meas/refl=%5.2f,"
	       " %i reflections measured\n",
	       n_patterns, R*100.0, scale, mean_counts, nmeas);

	if ( do_rvsq ) {
		/* Record graph of R against q for this N */
		char name[64];
		snprintf(name, 63, "R_vs_q-%u.dat", n_patterns);
		write_RvsQ(name, ref, trueref, counts, scale, cell);
	}

	if ( do_zoneaxis ) {
		char name[64];
		snprintf(name, 63, "ZA-%u.dat", n_patterns);
		write_reflections(name, counts, ref, NULL, 1, cell, 1);
	}

	fh = fopen("results/convergence.dat", "a");
	fprintf(fh, "%u %5.2f %5.2f\n", n_patterns, R*100.0, mean_counts);
	fclose(fh);
}


static void merge_pattern(double *model, const double *new,
                          unsigned int *model_counts,
                          const unsigned int *counts, int mo, int sum)
{
	signed int h, k, l;

	for ( l=-INDMAX; l<INDMAX; l++ ) {
	for ( k=-INDMAX; k<INDMAX; k++ ) {
	for ( h=-INDMAX; h<INDMAX; h++ ) {

		double intensity;

		if ( lookup_count(counts, h, k, l) == 0 ) continue;

		intensity = lookup_intensity(new, h, k, l);

		if ( !mo ) {
			integrate_intensity(model, h, k, l, intensity);
			if ( sum ) {
				set_count(model_counts, h, k, l, 1);
			} else {
				integrate_count(model_counts, h, k, l, 1);
			}
		} else {
			if ( intensity > lookup_intensity(model, h, k, l) ) {
				set_intensity(model, h, k, l, intensity);
			}
			set_count(model_counts, h, k, l, 1);
		}

	}
	}
	}
}


int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
	char *output = NULL;
	FILE *fh;
	unsigned int n_patterns;
	double *model, *trueref = NULL;
	unsigned int *model_counts;
	char *rval;
	UnitCell *cell;
	int config_maxonly = 0;
	int config_every = 1000;
	int config_rvsq = 0;
	int config_stopafter = 0;
	int config_zoneaxis = 0;
	int config_sum = 0;
	int config_detwin = 0;
	int config_scale = 0;
	char *intfile = NULL;
	double *new_pattern = NULL;
	unsigned int *new_counts = NULL;
	unsigned int n_total_patterns;
	unsigned int *truecounts = NULL;
	char *sym = NULL;
	char *pdb = NULL;
	float f0;
	int f0_valid;
	int n_nof0 = 0;

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
		{"output",             1, NULL,               'o'},
		{"max-only",           0, &config_maxonly,     1},
		{"output-every",       1, NULL,               'e'},
		{"rvsq",               0, NULL,               'r'},
		{"stop-after",         1, NULL,               's'},
		{"zone-axis",          0, &config_zoneaxis,    1},
		{"compare-with",       0, NULL,               'c'},
		{"sum",                0, &config_sum,         1},
		{"detwin",             0, &config_detwin,      1},
		{"scale",              0, &config_scale,       1},
		{"symmetry",           0, NULL,               'y'},
		{"pdb",                1, NULL,               'p'},
		{0, 0, NULL, 0}
	};

	/* Short options */
	while ((c = getopt_long(argc, argv, "hi:e:ro:p:y:",
	                        longopts, NULL)) != -1) {

		switch (c) {
		case 'h' :
			show_help(argv[0]);
			return 0;

		case 'i' :
			filename = strdup(optarg);
			break;

		case 'o' :
			output = strdup(optarg);
			break;


		case 'r' :
			config_rvsq = 1;
			break;

		case 'e' :
			config_every = atoi(optarg);
			break;

		case 's' :
			config_stopafter = atoi(optarg);
			break;

		case 'c' :
			intfile = strdup(optarg);
			break;

		case 'p' :
			pdb = strdup(optarg);
			break;

		case 'y' :
			sym = strdup(optarg);
			break;

		case 0 :
			break;

		default :
			return 1;
		}

	}

	if ( filename == NULL ) {
		ERROR("Please specify filename using the -i option\n");
		return 1;
	}

	if ( intfile != NULL ) {
		truecounts = new_list_count();
		STATUS("Comparing against '%s'\n", intfile);
		trueref = read_reflections(intfile, truecounts, NULL);
		free(intfile);
	} else {
		trueref = NULL;
	}

	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

	model = new_list_intensity();
	model_counts = new_list_count();
	cell = load_cell_from_pdb(pdb);
	new_pattern = new_list_intensity();
	new_counts = new_list_count();

	if ( strcmp(filename, "-") == 0 ) {
		fh = stdin;
	} else {
		fh = fopen(filename, "r");
	}
	free(filename);
	if ( fh == NULL ) {
		ERROR("Failed to open input file\n");
		return 1;
	}

	/* Count the number of patterns in the file */
	n_total_patterns = 0;
	do {
		char line[1024];

		rval = fgets(line, 1023, fh);
		if ( (strncmp(line, "Reflections from indexing", 25) == 0)
		    || (strncmp(line, "New pattern", 11) == 0) ) {
		    n_total_patterns++;
		}
	} while ( rval != NULL );
	rewind(fh);
	STATUS("There are %i patterns to process\n", n_total_patterns);

	n_patterns = 0;
	f0_valid = 0;
	do {

		char line[1024];
		signed int h, k, l;
		float intensity;
		int r;

		rval = fgets(line, 1023, fh);
		if ( (strncmp(line, "Reflections from indexing", 25) == 0)
		    || (strncmp(line, "New pattern", 11) == 0) ) {

			/* Start of first pattern? */
			if ( n_patterns == 0 ) {
				n_patterns++;
				continue;
			}

			/* Detwin before scaling */
			if ( config_detwin ) {
				detwin_intensities(model, new_pattern,
				                   model_counts, new_counts);
			}

			/* Assume a default I0 if we don't have one by now */
			if ( config_scale && !f0_valid ) {
				n_nof0++;
				f0 = 1.0;
			}

			/* Scale if requested */
			if ( config_scale ) {
				scale_intensities(model, new_pattern,
				                  model_counts, new_counts, f0,
				                  f0_valid);
			}

			/* Start of second or later pattern */
			merge_pattern(model, new_pattern, model_counts,
			              new_counts, config_maxonly, config_sum);

			if ( (trueref != NULL) && config_every
			    && (n_patterns % config_every == 0) ) {
				process_reflections(model, model_counts,
				                    trueref, truecounts,
				                    n_patterns, cell,
				                    config_rvsq,
				                    config_zoneaxis);
			}

			if ( n_patterns == config_stopafter ) break;

			zero_list_count(new_counts);

			n_patterns++;

			progress_bar(n_patterns, n_total_patterns, "Merging");

			f0_valid = 0;

		}

		if ( strncmp(line, "f0 = ", 5) == 0 ) {
			r = sscanf(line, "f0 = %f", &f0);
			if ( r != 1 ) {
				f0 = 1.0;
				f0_valid = 0;
				continue;
			}
			f0_valid = 1;
		}

		r = sscanf(line, "%i %i %i %f", &h, &k, &l, &intensity);
		if ( r != 4 ) continue;

		if ( (h==0) && (k==0) && (l==0) ) continue;

		if ( lookup_count(new_counts, h, k, l) != 0 ) {
			ERROR("More than one measurement for %i %i %i in"
			      " pattern number %i\n", h, k, l, n_patterns);
		}
		set_intensity(new_pattern, h, k, l, intensity);
		set_count(new_counts, h, k, l, 1);

	} while ( rval != NULL );

	fclose(fh);

	if ( trueref != NULL ) {
		process_reflections(model, model_counts, trueref, truecounts,
		                    n_patterns, cell, config_rvsq,
		                    config_zoneaxis);
	}

	if ( output != NULL ) {
		write_reflections(output, model_counts, model, NULL,
		                  0, cell, 1);
	}

	if ( config_zoneaxis ) {
		char name[64];
		snprintf(name, 63, "ZA-%u.dat", n_patterns);
		write_reflections(name, model_counts, model, NULL, 1, cell, 10);
	}

	STATUS("There were %u patterns.\n", n_patterns);
	STATUS("%i had no f0 valid value.\n", n_nof0);

	return 0;
}