aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/peaks.c
blob: 91a8c9491ec39da89940a81f3d220931febaab9f (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
485
486
487
488
489
490
491
492
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
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
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
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
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
/*
 * peaks.c
 *
 * Peak search and other image analysis
 *
 * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
 *                  a research centre of the Helmholtz Association.
 * Copyright © 2012 Richard Kirian
 *
 * Authors:
 *   2010-2012 Thomas White <taw@physics.org>
 *   2011      Andrew Martin <andrew.martin@desy.de>
 *   2011      Richard Kirian
 *
 * 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/>.
 *
 */


#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <assert.h>
#include <gsl/gsl_statistics_int.h>
#include <pthread.h>
#include <fenv.h>

#include "image.h"
#include "utils.h"
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "reflist-utils.h"
#include "beam-parameters.h"


/* Degree of polarisation of X-ray beam */
#define POL (1.0)

static int cull_peaks_in_panel(struct image *image, struct panel *p)
{
	int i, n;
	int nelim = 0;

	n = image_feature_count(image->features);

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

		struct imagefeature *f;
		int j, ncol;

		f = image_get_feature(image->features, i);
		if ( f == NULL ) continue;

		if ( f->fs < p->min_fs ) continue;
		if ( f->fs > p->max_fs ) continue;
		if ( f->ss < p->min_ss ) continue;
		if ( f->ss > p->max_ss ) continue;

		/* How many peaks are in the same column? */
		ncol = 0;
		for ( j=0; j<n; j++ ) {

			struct imagefeature *g;

			if ( i==j ) continue;

			g = image_get_feature(image->features, j);
			if ( g == NULL ) continue;

			if ( p->badrow == 'f' ) {
				if ( fabs(f->ss - g->ss) < 2.0 ) ncol++;
			} else if ( p->badrow == 's' ) {
				if ( fabs(f->fs - g->fs) < 2.0 ) ncol++;
			} /* else do nothing */

		}

		/* More than three? */
		if ( ncol <= 3 ) continue;

		/* Yes?  Delete them all... */
		nelim = 0;
		for ( j=0; j<n; j++ ) {
			struct imagefeature *g;
			g = image_get_feature(image->features, j);
			if ( g == NULL ) continue;
			if ( p->badrow == 'f' ) {
				if ( fabs(f->ss - g->ss) < 2.0 ) {
					image_remove_feature(image->features,
					                     j);
					nelim++;
				}
			} else if ( p->badrow == 's' ) {
				if ( fabs(f->fs - g->ss) < 2.0 ) {
					image_remove_feature(image->features,
					                     j);
					nelim++;
				}
			} else {
				ERROR("Invalid badrow direction.\n");
				abort();
			}

		}

	}

	return nelim;
}


/* Post-processing of the peak list to remove noise */
static int cull_peaks(struct image *image)
{
	int nelim = 0;
	struct panel *p;
	int i;

	for ( i=0; i<image->det->n_panels; i++ ) {
		p = &image->det->panels[i];
		if ( p->badrow != '-' ) {
			nelim += cull_peaks_in_panel(image, p);
		}
	}

	return nelim;
}


/* Returns non-zero if peak has been vetoed.
 * i.e. don't use result if return value is not zero. */
static int integrate_peak(struct image *image, int cfs, int css,
                          double *pfs, double *pss,
                          double *intensity, double *sigma,
                          double ir_inn, double ir_mid, double ir_out)
{
	signed int fs, ss;
	double lim_sq, out_lim_sq, mid_lim_sq;
	double pk_total;
	int pk_counts;
	double fsct, ssct;
	double bg_tot = 0.0;
	int bg_counts = 0;
	struct panel *p;
	double bg_mean, bg_var;
	double bg_tot_sq = 0.0;
	double var;
	double aduph;

	p = find_panel(image->det, cfs, css);
	if ( p == NULL ) return 1;
	if ( p->no_index ) return 1;

	aduph = p->adu_per_eV * ph_lambda_to_eV(image->lambda);

	lim_sq = pow(ir_inn, 2.0);
	mid_lim_sq = pow(ir_mid, 2.0);
	out_lim_sq = pow(ir_out, 2.0);

	/* Estimate the background */
	for ( fs=-ir_out; fs<=+ir_out; fs++ ) {
	for ( ss=-ir_out; ss<=+ir_out; ss++ ) {

		double val;
		uint16_t flags;
		struct panel *p2;
		int idx;

		/* Restrict to annulus */
		if ( fs*fs + ss*ss > out_lim_sq ) continue;
		if ( fs*fs + ss*ss < mid_lim_sq ) continue;

		/* Strayed off one panel? */
		p2 = find_panel(image->det, fs+cfs, ss+css);
		if ( p2 != p ) return 1;

		idx = fs+cfs+image->width*(ss+css);

		/* Veto this peak if we tried to integrate in a bad region */
		if ( image->flags != NULL ) {

			flags = image->flags[idx];

			/* It must have all the "good" bits to be valid */
			if ( !((flags & image->det->mask_good)
			                   == image->det->mask_good) ) return 1;

			/* If it has any of the "bad" bits, reject */
			if ( flags & image->det->mask_bad ) return 1;

		}

		val = image->data[idx];

		/* Veto peak if it contains saturation in bg region */
		if ( val > p->max_adu ) return 1;

		bg_tot += val;
		bg_tot_sq += pow(val, 2.0);
		bg_counts++;

	}
	}

	if ( bg_counts == 0 ) return 1;
	bg_mean = bg_tot / bg_counts;
	bg_var = (bg_tot_sq/bg_counts) - pow(bg_mean, 2.0);

	/* Measure the peak */
	pk_total = 0.0;
	pk_counts = 0;
	fsct = 0.0;  ssct = 0.0;
	for ( fs=-ir_inn; fs<=+ir_inn; fs++ ) {
	for ( ss=-ir_inn; ss<=+ir_inn; ss++ ) {

		double val;
		uint16_t flags;
		struct panel *p2;
		int idx;

		/* Inner mask radius */
		if ( fs*fs + ss*ss > lim_sq ) continue;

		/* Strayed off one panel? */
		p2 = find_panel(image->det, fs+cfs, ss+css);
		if ( p2 != p ) return 1;

		idx = fs+cfs+image->width*(ss+css);

		/* Veto this peak if we tried to integrate in a bad region */
		if ( image->flags != NULL ) {

			flags = image->flags[idx];

			/* It must have all the "good" bits to be valid */
			if ( !((flags & image->det->mask_good)
			                   == image->det->mask_good) ) return 1;

			/* If it has any of the "bad" bits, reject */
			if ( flags & image->det->mask_bad ) return 1;

		}

		val = image->data[idx] - bg_mean;

		/* Veto peak if it contains saturation */
		if ( val > p->max_adu ) return 1;

		pk_counts++;
		pk_total += val;

		fsct += val*(cfs+fs);
		ssct += val*(css+ss);

	}
	}

	if ( pk_counts == 0 ) return 1;

	*pfs = ((double)fsct / pk_total) + 0.5;
	*pss = ((double)ssct / pk_total) + 0.5;

	var = pk_counts * bg_var;
	var += aduph * pk_total;
	if ( var < 0.0 ) return 1;

	if ( intensity != NULL ) *intensity = pk_total;
	if ( sigma != NULL ) *sigma = sqrt(var);

	return 0;
}


static void search_peaks_in_panel(struct image *image, float threshold,
                                  float min_gradient, float min_snr,
                                  struct panel *p,
                                  double ir_inn, double ir_mid, double ir_out)
{
	int fs, ss, stride;
	float *data;
	double d;
	int idx;
	double f_fs = 0.0;
	double f_ss = 0.0;
	double intensity = 0.0;
	double sigma = 0.0;
	int nrej_dis = 0;
	int nrej_pro = 0;
	int nrej_fra = 0;
	int nrej_bad = 0;
	int nrej_snr = 0;
	int nacc = 0;
	int ncull;
	const int pws = p->peak_sep/2;

	data = image->data;
	stride = image->width;

	for ( fs = p->min_fs+1; fs <= p->max_fs-1; fs++ ) {
	for ( ss = p->min_ss+1; ss <= p->max_ss-1; ss++ ) {

		double dx1, dx2, dy1, dy2;
		double dxs, dys;
		double grad;
		int mask_fs, mask_ss;
		int s_fs, s_ss;
		double max;
		unsigned int did_something;
		int r;

		/* Overall threshold */
		if ( data[fs+stride*ss] < threshold ) continue;

		/* Get gradients */
		dx1 = data[fs+stride*ss] - data[(fs+1)+stride*ss];
		dx2 = data[(fs-1)+stride*ss] - data[fs+stride*ss];
		dy1 = data[fs+stride*ss] - data[(fs+1)+stride*(ss+1)];
		dy2 = data[fs+stride*(ss-1)] - data[fs+stride*ss];

		/* Average gradient measurements from both sides */
		dxs = ((dx1*dx1) + (dx2*dx2)) / 2;
		dys = ((dy1*dy1) + (dy2*dy2)) / 2;

		/* Calculate overall gradient */
		grad = dxs + dys;

		if ( grad < min_gradient ) continue;

		mask_fs = fs;
		mask_ss = ss;

		do {

			max = data[mask_fs+stride*mask_ss];
			did_something = 0;

			for ( s_ss=biggest(mask_ss-pws/2,
			                   p->min_ss);
			      s_ss<=smallest(mask_ss+pws/2,
			                     p->max_ss);
			      s_ss++ ) {
			for ( s_fs=biggest(mask_fs-pws/2,
			                   p->min_fs);
			      s_fs<=smallest(mask_fs+pws/2,
			                     p->max_fs);
			      s_fs++ ) {

				if ( data[s_fs+stride*s_ss] > max ) {
					max = data[s_fs+stride*s_ss];
					mask_fs = s_fs;
					mask_ss = s_ss;
					did_something = 1;
				}

			}
			}

			/* Abort if drifted too far from the foot point */
			if ( distance(mask_fs, mask_ss, fs, ss) >
			     p->peak_sep/2.0 )
			{
				break;
			}

		} while ( did_something );

		/* Too far from foot point? */
		if ( distance(mask_fs, mask_ss, fs, ss) > p->peak_sep/2.0 ) {
			nrej_dis++;
			continue;
		}

		/* Should be enforced by bounds used above.  Muppet check. */
		assert(mask_fs <= p->max_fs);
		assert(mask_ss <= p->max_ss);
		assert(mask_fs >= p->min_fs);
		assert(mask_ss >= p->min_ss);

		/* Centroid peak and get better coordinates. */
		r = integrate_peak(image, mask_fs, mask_ss,
		                   &f_fs, &f_ss, &intensity, &sigma,
		                   ir_inn, ir_mid, ir_out);

		if ( r ) {
			/* Bad region - don't detect peak */
			nrej_bad++;
			continue;
		}

		/* It is possible for the centroid to fall outside the image */
		if ( (f_fs < p->min_fs) || (f_fs > p->max_fs)
		  || (f_ss < p->min_ss) || (f_ss > p->max_ss) ) {
			nrej_fra++;
			continue;
		}

		if ( fabs(intensity)/sigma < min_snr ) {
			nrej_snr++;
			continue;
		}

		/* Check for a nearby feature */
		image_feature_closest(image->features, f_fs, f_ss, &d, &idx);
		if ( d < p->peak_sep/2.0 ) {
			nrej_pro++;
			continue;
		}

		/* Add using "better" coordinates */
		image_add_feature(image->features, f_fs, f_ss, image, intensity,
		                  NULL);
		nacc++;

	}
	}

	if ( image->det != NULL ) {
		ncull = cull_peaks(image);
		nacc -= ncull;
	} else {
		STATUS("Not culling peaks because I don't have a "
		       "detector geometry file.\n");
		ncull = 0;
	}

//	STATUS("%i accepted, %i box, %i proximity, %i outside panel, "
//	       "%i in bad regions, %i with SNR < %g, %i badrow culled.\n",
//	       nacc, nrej_dis, nrej_pro, nrej_fra, nrej_bad,
//	       nrej_snr, min_snr, ncull);
}


void search_peaks(struct image *image, float threshold, float min_gradient,
                  float min_snr, double ir_inn, double ir_mid, double ir_out)
{
	int i;

	if ( image->features != NULL ) {
		image_feature_list_free(image->features);
	}
	image->features = image_feature_list_new();

	for ( i=0; i<image->det->n_panels; i++ ) {

		struct panel *p = &image->det->panels[i];

		if ( p->no_index ) continue;
		search_peaks_in_panel(image, threshold, min_gradient,
		                      min_snr, p, ir_inn, ir_mid, ir_out);

	}
}


double peak_lattice_agreement(struct image *image, UnitCell *cell, double *pst)
{
	int i;
	int n_feat = 0;
	int n_sane = 0;
	double ax, ay, az;
	double bx, by, bz;
	double cx, cy, cz;
	double min_dist = 0.25;
	double stot = 0.0;

	/* Round towards nearest */
	fesetround(1);

	/* Cell basis vectors for this image */
	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);

	/* Loop over peaks, checking proximity to nearest reflection */
	for ( i=0; i<image_feature_count(image->features); i++ ) {

		struct imagefeature *f;
		struct rvec q;
		double h,k,l,hd,kd,ld;

		/* Assume all image "features" are genuine peaks */
		f = image_get_feature(image->features, i);
		if ( f == NULL ) continue;
		n_feat++;

		/* Reciprocal space position of found peak */
		q = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);

		/* Decimal and fractional Miller indices of nearest
		 * reciprocal lattice point */
		hd = q.u * ax + q.v * ay + q.w * az;
		kd = q.u * bx + q.v * by + q.w * bz;
		ld = q.u * cx + q.v * cy + q.w * cz;
		h = lrint(hd);
		k = lrint(kd);
		l = lrint(ld);

		/* Check distance */
		if ( (fabs(h - hd) < min_dist) && (fabs(k - kd) < min_dist)
		  && (fabs(l - ld) < min_dist) )
		{
			double sval;
			n_sane++;
			sval = pow(h-hd, 2.0) + pow(k-kd, 2.0) + pow(l-ld, 2.0);
			stot += 1.0 - sval;
			continue;
		}

	}

	*pst = stot;
	return (double)n_sane / (float)n_feat;
}


int peak_sanity_check(struct image *image)
{
	double stot;
	/* 0 means failed test, 1 means passed test */
	return peak_lattice_agreement(image, image->indexed_cell, &stot) >= 0.5;
}


struct integr_ind
{
	double res;
	Reflection *refl;
};


static int compare_resolution(const void *av, const void *bv)
{
	const struct integr_ind *a = av;
	const struct integr_ind *b = bv;

	return a->res > b->res;
}


static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
                                           int *np)
{
	struct integr_ind *il;
	Reflection *refl;
	RefListIterator *iter;
	int i, n;

	n = num_reflections(list);
	*np = 0;  /* For now */

	if ( n == 0 ) return NULL;

	il = calloc(n, sizeof(struct integr_ind));
	if ( il == NULL ) return NULL;

	i = 0;
	for ( refl = first_refl(list, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		signed int h, k, l;
		double res;

		get_indices(refl, &h, &k, &l);
		res = resolution(cell, h, k, l);

		il[i].res = res;
		il[i].refl = refl;

		i++;
		assert(i <= n);
	}

	qsort(il, n, sizeof(struct integr_ind), compare_resolution);

	*np = n;
	return il;
}


/* Integrate the list of predicted reflections in "image" */
void integrate_reflections(struct image *image, int use_closer, int bgsub,
                           double min_snr,
                           double ir_inn, double ir_mid, double ir_out)
{
	struct integr_ind *il;
	int n, i;
	double av = 0.0;
	int first = 1;

	il = sort_reflections(image->reflections, image->indexed_cell, &n);
	if ( il == NULL ) {
		ERROR("Couldn't sort reflections\n");
		return;
	}

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

		double fs, ss, intensity;
		double d;
		int idx;
		double sigma, snr;
		double pfs, pss;
		int r;
		Reflection *refl;
		signed int h, k, l;

		refl = il[i].refl;

		get_detector_pos(refl, &pfs, &pss);
		get_indices(refl, &h, &k, &l);

		/* Is there a really close feature which was detected? */
		if ( use_closer ) {

			struct imagefeature *f;

			if ( image->features != NULL ) {
				f = image_feature_closest(image->features,
					                  pfs, pss, &d, &idx);
			} else {
				f = NULL;
			}

			/* FIXME: Horrible hardcoded value */
			if ( (f != NULL) && (d < 10.0) ) {

				double exe;

				exe = get_excitation_error(refl);

				pfs = f->fs;
				pss = f->ss;

				set_detector_pos(refl, exe, pfs, pss);

			}

		}

		r = integrate_peak(image, pfs, pss, &fs, &ss,
		                   &intensity, &sigma, ir_inn, ir_mid, ir_out);

		/* Record intensity and set redundancy to 1 on success */
		if ( r == 0 ) {
			set_intensity(refl, intensity);
			set_esd_intensity(refl, sigma);
			set_redundancy(refl, 1);
		} else {
			set_redundancy(refl, 0);
		}

		snr = intensity / sigma;
		if ( snr > 1.0 ) {
			if ( first ) {
				av = snr;
				first = 0;
			} else {
				av = av + 0.1*(snr - av);
			}
			//STATUS("%5.2f A, %5.2f, av %5.2f\n",
			//       1e10/il[i].res, snr, av);
			//if ( av < 1.0 ) break;
		}
	}

	image->diffracting_resolution = 0.0;

	free(il);
}