aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/peaks.c
blob: 768b9ce901f5430dda0c110713546eb183fc1a20 (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
/*
 * peaks.c
 *
 * Peak search and other image analysis
 *
 * (c) 2006-2012 Thomas White <taw@physics.org>
 *	    2011 Andrew Martin
 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */


#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"


/* How close a peak must be to an indexed position to be considered "close"
 * for the purposes of double hit detection and sanity checking. */
#define PEAK_CLOSE (30.0)

/* How close a peak must be to an indexed position to be considered "close"
 * for the purposes of integration. */
#define PEAK_REALLY_CLOSE (10.0)

/* 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. */
int integrate_peak(struct image *image, int cfs, int css,
                   double *pfs, double *pss, double *intensity,
                   double *pbg, double *pmax, double *sigma,
                   int do_polar, int centroid, int bgsub)
{
	signed int fs, ss;
	double lim, out_lim, mid_lim;
	double lim_sq, out_lim_sq, mid_lim_sq;
	double total = 0.0;
	double fsct = 0.0;
	double ssct = 0.0;
	double noise = 0.0;
	int noise_counts = 0;
	double max = 0.0;
	struct panel *p = NULL;
        int pixel_counts = 0;
        double noise_mean = 0.0;
	double noise_meansq = 0.0;
	struct beam_params *beam;
	double aduph;

	beam = image->beam;
	if ( beam != NULL ) {
		aduph = image->beam->adu_per_photon;
	} else {
		aduph = 1.0;
	}

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

	lim = p->integr_radius;
	mid_lim = 3.0 + lim;
	out_lim = 6.0 + lim;
	lim_sq = pow(lim, 2.0);
	mid_lim_sq = pow(mid_lim, 2.0);
	out_lim_sq = pow(out_lim, 2.0);

	for ( fs=-out_lim; fs<+out_lim; fs++ ) {
	for ( ss=-out_lim; ss<+out_lim; ss++ ) {

		double val;
		double tt = 0.0;
		double phi, pa, pb, pol;
		uint16_t flags;
		struct panel *p2;
		int idx;

		/* Outer mask radius */
		if ( fs*fs + ss*ss > out_lim_sq ) continue;

		if ( ((fs+cfs)>=image->width) || ((fs+cfs)<0) ) continue;
		if ( ((ss+css)>=image->height) || ((ss+css)<0) ) 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];

		if ( do_polar ) {

			tt = get_tt(image, fs+cfs, ss+css);

			phi = atan2(ss+css, fs+cfs);
			pa = pow(sin(phi)*sin(tt), 2.0);
			pb = pow(cos(tt), 2.0);
			pol = 1.0 - 2.0*POL*(1-pa) + POL*(1.0+pb);

			val /= pol;

		}

		if ( val > max ) max = val;

		/* If outside inner mask, estimate noise from this region */
		if ( fs*fs + ss*ss > mid_lim_sq ) {

			/* Noise
			 * noise and noise_meansq are both in photons (^2) */
			noise += val / image->beam->adu_per_photon;
			noise_counts++;
			noise_meansq += pow(val, 2.0);

		} else if ( fs*fs + ss*ss < lim_sq ) {

			/* Peak */
			pixel_counts++;
			total += val;
			fsct += val*(cfs+fs);
			ssct += val*(css+ss);

		}

	}
	}

	noise_mean = noise / noise_counts;  /* photons */

	/* The centroid is excitingly undefined if there is no intensity */
	if ( centroid && (total != 0) ) {
		*pfs = ((double)fsct / total) + 0.5;
		*pss = ((double)ssct / total) + 0.5;
	} else {
		*pfs = (double)cfs + 0.5;
		*pss = (double)css + 0.5;
	}
	if ( bgsub ) {
		*intensity = total - aduph * pixel_counts*noise_mean; /* ADU */
	} else {
		*intensity = total;  /* ADU */
	}

	if ( in_bad_region(image->det, *pfs, *pss) ) return 1;

	if ( sigma != NULL ) {

		/* First term is standard deviation of background per pixel
		 * sqrt(pixel_counts) - increase of error for integrated value
		 * sqrt(2) - increase of error for background subtraction  */
		*sigma = sqrt(noise_meansq/noise_counts-(noise_mean*noise_mean))
		          * sqrt(2.0*pixel_counts) * aduph;

	}

	if ( pbg != NULL ) {
		*pbg = aduph * (noise / noise_counts);
	}
	if ( pmax != NULL ) {
		*pmax = max;
	}

	return 0;
}


static void search_peaks_in_panel(struct image *image, float threshold,
                                  float min_gradient, float min_snr,
                                  struct panel *p)
{
	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;
	double pbg = 0.0;
	double pmax = 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.
		 * Don't bother doing polarisation/SA correction, because the
		 * intensity of this peak is only an estimate at this stage. */
		r = integrate_peak(image, mask_fs, mask_ss,
		                   &f_fs, &f_ss, &intensity,
		                   &pbg, &pmax, &sigma, 0, 1, 1);

		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)
{
	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);

	}
}


int peak_sanity_check(struct image *image)
{

	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;

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

	/* Cell basis vectors for this image */
	cell_get_cartesian(image->indexed_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) )
		{
			n_sane++;
			continue;
		}

	}

	/* return 0 means fail test, return 1 means pass test */
	// printf("%d out of %d peaks are \"sane\"\n",n_sane,n_feat);
	if ( (float)n_sane / (float)n_feat < 0.5 ) return 0;

	return 1;
}


struct integr_ind
{
	signed int h;
	signed int k;
	signed int l;
	double res;
	Reflection *refl;
};


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

	*n = num_reflections(list);

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


	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].h = h;
		il[i].k = k;
		il[i].l = l;
		il[i].res = res;
		il[i].refl = refl;

		i++;
	}

	return il;
}


/* Integrate the list of predicted reflections in "image" */
void integrate_reflections(struct image *image, int polar, int use_closer,
                           int bgsub, double min_snr)
{
	struct integr_ind *il;
	int n, i;

	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 bg, max;
		double sigma;
		double pfs, pss;
		int r;
		Reflection *refl;

		refl = il[i].refl;

		get_detector_pos(refl, &pfs, &pss);

		/* 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;
			}
			if ( (f != NULL) && (d < PEAK_REALLY_CLOSE) ) {

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

			}
		}

		r = integrate_peak(image, pfs, pss, &fs, &ss,
		                   &intensity, &bg, &max, &sigma, polar, 0,
		                   bgsub);

		/* I/sigma(I) cutoff */
		if ( !r && (intensity/sigma < min_snr) ) r = 1;

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

	}
}