partialator.c 11.2 KB
Newer Older
1
/*
2
 * partialator.c
3
 *
4
 * Scaling and post refinement for coherent nanocrystallography
5
 *
Thomas White's avatar
Thomas White committed
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
 *
 * 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>
Thomas White's avatar
Thomas White committed
23
#include <assert.h>
Thomas White's avatar
Tidy up    
Thomas White committed
24
#include <pthread.h>
25
#include <gsl/gsl_errno.h>
26

Thomas White's avatar
Thomas White committed
27
#include "utils.h"
28
#include "hdf5-file.h"
Thomas White's avatar
Thomas White committed
29
#include "symmetry.h"
Thomas White's avatar
Thomas White committed
30
#include "stream.h"
31
#include "geometry.h"
32
#include "peaks.h"
Thomas White's avatar
Thomas White committed
33
#include "thread-pool.h"
Thomas White's avatar
Thomas White committed
34
#include "beam-parameters.h"
35
#include "post-refinement.h"
36
#include "hrs-scaling.h"
Thomas White's avatar
Thomas White committed
37
#include "reflist.h"
Thomas White's avatar
Thomas White committed
38
#include "reflist-utils.h"
39
40
41
42
43
44


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
45
"Scaling and post refinement for coherent nanocrystallography.\n"
46
47
48
"\n"
"  -h, --help                 Display this help message.\n"
"\n"
Thomas White's avatar
Thomas White committed
49
50
"  -i, --input=<filename>     Specify the name of the input 'stream'.\n"
"                              (must be a file, not e.g. stdin)\n"
Thomas White's avatar
Thomas White committed
51
"  -o, --output=<filename>    Output filename.  Default: facetron.hkl.\n"
Thomas White's avatar
Thomas White committed
52
"  -g. --geometry=<file>      Get detector geometry from file.\n"
53
54
55
56
"  -b, --beam=<file>          Get beam parameters from file, which provides\n"
"                              initial values for parameters, and nominal\n"
"                              wavelengths if no per-shot value is found in \n"
"                              an HDF5 file.\n"
57
"  -y, --symmetry=<sym>       Merge according to symmetry <sym>.\n"
58
"  -n, --iterations=<n>       Run <n> cycles of scaling and post-refinement.\n"
59
60
61
"      --reference=<file>     Refine images against reflections in <file>,\n"
"                              instead of taking the mean of the intensity\n"
"                              estimates.\n"
62
"\n"
Thomas White's avatar
Thomas White committed
63
64
65
66
"  -j <n>                     Run <n> analyses in parallel.\n");
}


Thomas White's avatar
Thomas White committed
67
struct refine_args
Thomas White's avatar
Thomas White committed
68
{
Thomas White's avatar
Thomas White committed
69
70
	const char *sym;
	ReflItemList *obs;
71
	RefList *full;
Thomas White's avatar
Thomas White committed
72
	struct image *image;
73
	FILE *graph;
74
	FILE *pgraph;
Thomas White's avatar
Thomas White committed
75
76
77
};


Thomas White's avatar
Thomas White committed
78
struct queue_args
Thomas White's avatar
Thomas White committed
79
{
Thomas White's avatar
Thomas White committed
80
81
82
83
84
85
86
87
88
89
90
	int n;
	int n_done;
	int n_total_patterns;
	struct image *images;
	struct refine_args task_defaults;
};


static void refine_image(void *task, int id)
{
	struct refine_args *pargs = task;
91
	struct image *image = pargs->image;
Thomas White's avatar
Thomas White committed
92
	image->id = id;
93

94
	pr_refine(image, pargs->full, pargs->sym);
95
96
97
}


Thomas White's avatar
Thomas White committed
98
static void *get_image(void *vqargs)
99
{
Thomas White's avatar
Thomas White committed
100
101
	struct refine_args *task;
	struct queue_args *qargs = vqargs;
Thomas White's avatar
Thomas White committed
102

Thomas White's avatar
Thomas White committed
103
104
	task = malloc(sizeof(struct refine_args));
	memcpy(task, &qargs->task_defaults, sizeof(struct refine_args));
105

Thomas White's avatar
Thomas White committed
106
	task->image = &qargs->images[qargs->n];
107

Thomas White's avatar
Thomas White committed
108
109
110
111
	qargs->n++;

	return task;
}
Thomas White's avatar
Thomas White committed
112

113

Thomas White's avatar
Thomas White committed
114
115
116
117
118
119
static void done_image(void *vqargs, void *task)
{
	struct queue_args *qargs = vqargs;

	qargs->n_done++;

120
	progress_bar(qargs->n_done+1, qargs->n_total_patterns, "Refining");
Thomas White's avatar
Thomas White committed
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
	free(task);
}


static void refine_all(struct image *images, int n_total_patterns,
                       struct detector *det, const char *sym,
                       ReflItemList *obs, RefList *full, int nthreads,
                       FILE *graph, FILE *pgraph)
{
	struct refine_args task_defaults;
	struct queue_args qargs;

	task_defaults.sym = sym;
	task_defaults.obs = obs;
	task_defaults.full = full;
	task_defaults.image = NULL;
	task_defaults.graph = graph;
	task_defaults.pgraph = pgraph;

	qargs.task_defaults = task_defaults;
	qargs.n = 0;
	qargs.n_done = 0;
Thomas White's avatar
Thomas White committed
143
144
	qargs.n_total_patterns = n_total_patterns;
	qargs.images = images;
Thomas White's avatar
Thomas White committed
145
146

	run_threads(nthreads, refine_image, get_image, done_image,
147
	            &qargs, n_total_patterns-1, 0, 0, 0);
148
149
150
}


Thomas White's avatar
Thomas White committed
151
152
153
154
int main(int argc, char *argv[])
{
	int c;
	char *infile = NULL;
Thomas White's avatar
Thomas White committed
155
	char *outfile = NULL;
Thomas White's avatar
Thomas White committed
156
	char *geomfile = NULL;
Thomas White's avatar
Thomas White committed
157
158
	char *sym = NULL;
	FILE *fh;
Thomas White's avatar
Thomas White committed
159
160
	int nthreads = 1;
	struct detector *det;
161
	ReflItemList *scalable;
Thomas White's avatar
Thomas White committed
162
163
	int i;
	int n_total_patterns;
164
165
	struct image *images;
	int n_iter = 10;
Thomas White's avatar
Thomas White committed
166
	struct beam_params *beam = NULL;
167
	RefList *full;
168
169
170
	int n_found = 0;
	int n_expected = 0;
	int n_notfound = 0;
171
	char *cref;
Thomas White's avatar
Thomas White committed
172
	int n_usable_patterns = 0;
173
	char *reference_file = NULL;
174
	double *reference = NULL;
Thomas White's avatar
Thomas White committed
175
176
177
178
179

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
Thomas White's avatar
Thomas White committed
180
		{"output",             1, NULL,               'o'},
Thomas White's avatar
Thomas White committed
181
		{"geometry",           1, NULL,               'g'},
Thomas White's avatar
Thomas White committed
182
		{"beam",               1, NULL,               'b'},
183
		{"symmetry",           1, NULL,               'y'},
184
		{"iterations",         1, NULL,               'n'},
185
		{"reference",          1, NULL,                1},
Thomas White's avatar
Thomas White committed
186
187
188
189
		{0, 0, NULL, 0}
	};

	/* Short options */
Thomas White's avatar
Thomas White committed
190
	while ((c = getopt_long(argc, argv, "hi:g:x:j:y:o:b:",
191
192
	                        longopts, NULL)) != -1)
	{
Thomas White's avatar
Thomas White committed
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210

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

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

		case 'g' :
			geomfile = strdup(optarg);
			break;

		case 'j' :
			nthreads = atoi(optarg);
			break;

211
212
213
214
		case 'y' :
			sym = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
215
216
217
218
		case 'o' :
			outfile = strdup(optarg);
			break;

219
220
221
222
		case 'n' :
			n_iter = atoi(optarg);
			break;

Thomas White's avatar
Thomas White committed
223
224
225
226
227
228
229
230
231
		case 'b' :
			beam = get_beam_parameters(optarg);
			if ( beam == NULL ) {
				ERROR("Failed to load beam parameters"
				      " from '%s'\n", optarg);
				return 1;
			}
			break;

232
		case 1 :
233
			reference_file = strdup(optarg);
234
235
			break;

Thomas White's avatar
Thomas White committed
236
237
238
239
240
241
242
243
244
		case 0 :
			break;

		default :
			return 1;
		}

	}

Thomas White's avatar
Thomas White committed
245
	/* Sanitise input filename and open */
Thomas White's avatar
Thomas White committed
246
247
248
249
250
251
252
253
254
255
256
257
258
259
	if ( infile == NULL ) {
		infile = strdup("-");
	}
	if ( strcmp(infile, "-") == 0 ) {
		fh = stdin;
	} else {
		fh = fopen(infile, "r");
	}
	if ( fh == NULL ) {
		ERROR("Failed to open input file '%s'\n", infile);
		return 1;
	}
	free(infile);

Thomas White's avatar
Thomas White committed
260
261
	/* Sanitise output filename */
	if ( outfile == NULL ) {
Thomas White's avatar
Whoops    
Thomas White committed
262
		outfile = strdup("partialator.hkl");
Thomas White's avatar
Thomas White committed
263
264
	}

Thomas White's avatar
Thomas White committed
265
266
	if ( sym == NULL ) sym = strdup("1");

Thomas White's avatar
Thomas White committed
267
	/* Get detector geometry */
Thomas White's avatar
Thomas White committed
268
269
270
271
272
273
274
	det = get_detector_geometry(geomfile);
	if ( det == NULL ) {
		ERROR("Failed to read detector geometry from '%s'\n", geomfile);
		return 1;
	}
	free(geomfile);

Thomas White's avatar
Thomas White committed
275
276
277
278
279
	if ( beam == NULL ) {
		ERROR("You must provide a beam parameters file.\n");
		return 1;
	}

280
	if ( reference_file != NULL ) {
281
282
283
		RefList *list;
		RefList *symmed;
		list = read_reflections(reference_file);
284
		free(reference_file);
285
286
287
288
289
		if ( list == NULL ) return 1;
		symmed = asymmetric_indices(list, sym);
		reflist_free(list);
		reference = intensities_from_list(symmed);
		reflist_free(symmed);
290
291
	}

Thomas White's avatar
Thomas White committed
292
	n_total_patterns = count_patterns(fh);
Thomas White's avatar
Thomas White committed
293
294
295
296
	if ( n_total_patterns == 0 ) {
		ERROR("No patterns to process.\n");
		return 1;
	}
Thomas White's avatar
Thomas White committed
297
298
	STATUS("There are %i patterns to process\n", n_total_patterns);

299
300
	gsl_set_error_handler_off();

301
302
303
304
305
306
307
308
	images = malloc(n_total_patterns * sizeof(struct image));
	if ( images == NULL ) {
		ERROR("Couldn't allocate memory for images.\n");
		return 1;
	}

	/* Fill in what we know about the images so far */
	rewind(fh);
309
	scalable = new_items();
310
311
	for ( i=0; i<n_total_patterns; i++ ) {

312
313
		RefList *as;

Thomas White's avatar
Thomas White committed
314
		images[n_usable_patterns].det = NULL;
315

Thomas White's avatar
Thomas White committed
316
		if ( read_chunk(fh, &images[n_usable_patterns]) != 0 ) {
Thomas White's avatar
Thomas White committed
317
318
			/* Should not happen, because we counted the patterns
			 * earlier. */
Thomas White's avatar
Thomas White committed
319
			ERROR("Failed to read chunk from the input stream.\n");
320
321
322
			return 1;
		}

323
		/* Won't be needing this, if it exists */
Thomas White's avatar
Thomas White committed
324
325
		image_feature_list_free(images[n_usable_patterns].features);
		images[n_usable_patterns].features = NULL;
326

Thomas White's avatar
Thomas White committed
327
328
		/* "n_usable_patterns" will not be incremented in this case */
		if ( images[n_usable_patterns].indexed_cell == NULL ) continue;
329

Thomas White's avatar
Thomas White committed
330
331
332
333
334
335
336
337
		/* Fill in initial estimates of stuff */
		images[n_usable_patterns].div = beam->divergence;
		images[n_usable_patterns].bw = beam->bandwidth;
		images[n_usable_patterns].det = det;
		images[n_usable_patterns].width = det->max_fs;
		images[n_usable_patterns].height = det->max_ss;
		images[n_usable_patterns].osf = 1.0;
		images[n_usable_patterns].profile_radius = 0.005e9;
338

Thomas White's avatar
Thomas White committed
339
340
341
342
		/* Muppet proofing */
		images[n_usable_patterns].data = NULL;
		images[n_usable_patterns].flags = NULL;
		images[n_usable_patterns].beam = NULL;
343

Thomas White's avatar
Thomas White committed
344
		/* This is the raw list of reflections */
345
346
347
348
349
		as = asymmetric_indices(images[n_usable_patterns].reflections,
		                        sym);
		optimise_reflist(as);
		reflist_free(images[n_usable_patterns].reflections);
		images[n_usable_patterns].reflections = as;
350

351
352
		update_partialities(&images[n_usable_patterns], sym, scalable,
		                    &n_expected, &n_found, &n_notfound);
353

354
		progress_bar(i, n_total_patterns-1, "Loading pattern data");
Thomas White's avatar
Thomas White committed
355
		n_usable_patterns++;
356
357
358

	}
	fclose(fh);
Thomas White's avatar
Thomas White committed
359
360
	STATUS("Found %5.2f%% of the expected peaks (missed %i of %i).\n",
	       100.0 * (double)n_found / n_expected, n_notfound, n_expected);
361
362
	STATUS("Mean measurements per scalable unique reflection: %5.2f\n",
	       (double)n_found / num_items(scalable));
363

Thomas White's avatar
Thomas White committed
364
	cref = find_common_reflections(images, n_usable_patterns);
Thomas White's avatar
Thomas White committed
365

366
	/* Make initial estimates */
367
	STATUS("Performing initial scaling.\n");
368
	full = scale_intensities(images, n_usable_patterns, sym,
369
	                         scalable, cref, reference);
370

Thomas White's avatar
Thomas White committed
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
	for ( i=0; i<num_items(scalable); i++ ) {
		Reflection *f;
		struct refl_item *it = get_item(scalable, i);
		f = find_refl(full, it->h, it->k, it->l);
		if ( f == NULL ) {
			ERROR("%3i %3i %3i was designated scalable, but no"
			      " full intensity was recorded.\n",
			      it->h, it->k, it->l);
		}
	}

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

		Reflection *refl;
		RefListIterator *iter;

		for ( refl = first_refl(images[i].reflections, &iter);
		      refl != NULL;
		      refl = next_refl(refl, iter) )
		{
			signed int h, k, l;

			if ( !get_scalable(refl) ) continue;
			get_indices(refl, &h, &k, &l);

			if ( find_item(scalable, h, k, l) == 0 ) {
				ERROR("%3i %3i %3i in image %i is scalable"
				      " but is not in the list of scalable"
				      " reflections.\n", h, k, l, i);
			}
		}
	}

Thomas White's avatar
Thomas White committed
404
	/* Iterate */
405
	for ( i=0; i<n_iter; i++ ) {
Thomas White's avatar
Thomas White committed
406

407
408
		FILE *fhg;
		FILE *fhp;
409
410
		char filename[1024];

411
		STATUS("Post refinement iteration %i of %i\n", i+1, n_iter);
Thomas White's avatar
Thomas White committed
412

413
414
415
416
417
418
419
420
421
422
		snprintf(filename, 1023, "p-iteration-%i.dat", i+1);
		fhg = fopen(filename, "w");
		if ( fhg == NULL ) {
			ERROR("Failed to open '%s'\n", filename);
			/* Nothing will be written later */
		}

		snprintf(filename, 1023, "g-iteration-%i.dat", i+1);
		fhp = fopen(filename, "w");
		if ( fhp == NULL ) {
423
424
425
426
			ERROR("Failed to open '%s'\n", filename);
			/* Nothing will be written later */
		}

Thomas White's avatar
Thomas White committed
427
		/* Refine the geometry of all patterns to get the best fit */
Thomas White's avatar
Thomas White committed
428
429
		/* FIXME: Refine against reference intensity if present */
		/* FIXME: Speedup by using array instead of RefList for 'full'? */
430
		refine_all(images, n_total_patterns, det, sym, scalable, full,
431
		           nthreads, fhg, fhp);
Thomas White's avatar
Thomas White committed
432
433

		/* Re-estimate all the full intensities */
434
		reflist_free(full);
Thomas White's avatar
Thomas White committed
435
		full = scale_intensities(images, n_usable_patterns,
436
		                         sym, scalable, cref, reference);
Thomas White's avatar
Thomas White committed
437

438
439
		fclose(fhg);
		fclose(fhp);
Thomas White's avatar
Thomas White committed
440
441
442
443

	}

	STATUS("Final scale factors:\n");
Thomas White's avatar
Thomas White committed
444
	for ( i=0; i<n_usable_patterns; i++ ) {
Thomas White's avatar
Thomas White committed
445
		STATUS("%4i : %5.2f\n", i, images[i].osf);
Thomas White's avatar
Thomas White committed
446
447
448
	}

	/* Output results */
449
	write_reflist(outfile, full, images[0].indexed_cell);
Thomas White's avatar
Thomas White committed
450

Thomas White's avatar
Thomas White committed
451
	/* Clean up */
Thomas White's avatar
Thomas White committed
452
	for ( i=0; i<n_usable_patterns; i++ ) {
Thomas White's avatar
Thomas White committed
453
		reflist_free(images[i].reflections);
Thomas White's avatar
Thomas White committed
454
	}
455
	reflist_free(full);
456
	delete_items(scalable);
Thomas White's avatar
Thomas White committed
457
	free(sym);
Thomas White's avatar
Thomas White committed
458
	free(outfile);
Thomas White's avatar
Thomas White committed
459
	free_detector_geometry(det);
460
	free(beam);
461
	free(cref);
462
	free(reference);
Thomas White's avatar
Thomas White committed
463
	for ( i=0; i<n_usable_patterns; i++ ) {
464
465
466
467
		cell_free(images[i].indexed_cell);
		free(images[i].filename);
	}
	free(images);
468
469
470

	return 0;
}