aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/peaks.c
blob: cd65a0c7c7f3a35e378952c26894220af95ed482 (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
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
/*
 * peaks.c
 *
 * Peak search and other image analysis
 *
 * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 * Copyright © 2012 Richard Kirian
 *
 * Authors:
 *   2010-2016 Thomas White <taw@physics.org>
 *   2012      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
 *   2011      Andrew Martin <andrew.martin@desy.de>
 *   2011      Richard Kirian
 *   2017      Valerio Mariani <valerio.mariani@desy.de>
 *   2017-2018 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de>
 *
 * 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>

#ifdef HAVE_FDIP
#include "fastDiffractionImageProcessing/adaptions/crystfel/peakFinder9.h"
#include "fastDiffractionImageProcessing/adaptions/crystfel/mask.h"
#include "fastDiffractionImageProcessing/peakList.h"
#endif

#include "image.h"
#include "utils.h"
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "reflist-utils.h"
#include "cell-utils.h"
#include "geometry.h"
#include "peakfinder8.h"

/** \file peaks.h */

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->p != p ) 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... */
		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;
}


static void add_crystal_to_mask(struct image *image, struct panel *p,
                                double ir_inn, int *mask, Crystal *cr)
{
	Reflection *refl;
	RefListIterator *iter;

	/* Loop over all reflections */
	for ( refl = first_refl(crystal_get_reflections(cr), &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		double pk2_fs, pk2_ss;
		signed int dfs, dss;

		get_detector_pos(refl, &pk2_fs, &pk2_ss);

		/* Determine if reflection is in the same panel */
		if ( get_panel(refl) != p ) continue;

		for ( dfs=-ir_inn; dfs<=ir_inn; dfs++ ) {
		for ( dss=-ir_inn; dss<=ir_inn; dss++ ) {

			signed int fs, ss;

			/* In peak region for this peak? */
			if ( dfs*dfs + dss*dss > ir_inn*ir_inn ) continue;

			fs = pk2_fs + dfs;
			ss = pk2_ss + dss;

			/* On panel? */
			if ( fs >= p->w ) continue;
			if ( ss >= p->h ) continue;
			if ( fs < 0 ) continue;
			if ( ss < 0 ) continue;

			mask[fs + ss*p->w]++;

		}
		}

	}
}


/* cfs, css relative to panel origin */
int *make_BgMask(struct image *image, struct panel *p, double ir_inn)
{
	int *mask;
	int i;

	mask = calloc(p->w*p->h, sizeof(int));
	if ( mask == NULL ) return NULL;

	if ( image->crystals == NULL ) return mask;

	for ( i=0; i<image->n_crystals; i++ ) {
		add_crystal_to_mask(image, p, ir_inn,
		                    mask, image->crystals[i]);
	}

	return mask;
}


/* 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 p_cfs, int p_css, struct panel *p,
                          double *pfs, double *pss,
                          double *intensity, double *sigma,
                          double ir_inn, double ir_mid, double ir_out,
                          int *saturated)
{
	signed int dfs, dss;
	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;
	double bg_mean, bg_var;
	double bg_tot_sq = 0.0;
	double var;
	double aduph;
	int pn;

	if ( saturated != NULL ) *saturated = 0;

	aduph = p->adu_per_photon;

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

	pn = panel_number(image->det, p);
	if ( pn == image->det->n_panels ) {
		ERROR("Couldn't find panel %p\n", p);
		return 20;
	}

	/* Estimate the background */
	for ( dss=-ir_out; dss<=+ir_out; dss++ ) {
	for ( dfs=-ir_out; dfs<=+ir_out; dfs++ ) {

		double val;
		int idx;

		/* Restrict to annulus */
		if ( dfs*dfs + dss*dss > out_lim_sq ) continue;
		if ( dfs*dfs + dss*dss < mid_lim_sq ) continue;

		/* Strayed off one panel? */
		if ( (p_cfs+dfs >= p->w) || (p_css+dss >= p->h)
		  || (p_cfs+dfs < 0 ) || (p_css+dss < 0) ) return 4;

		/* Wandered into a bad region? */
		if ( image->bad[pn][p_cfs+dfs + p->w*(p_css+dss)] ) {
			return 14;
		}

		idx = dfs+p_cfs+p->w*(dss+p_css);
		val = image->dp[pn][idx];

		/* Check if peak contains saturation in bg region */
		if ( (saturated != NULL) && (val > p->max_adu) ) *saturated = 1;

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

	}
	}

	if ( bg_counts == 0 ) return 7;
	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 ( dss=-ir_inn; dss<=+ir_inn; dss++ ) {
	for ( dfs=-ir_inn; dfs<=+ir_inn; dfs++ ) {

		double val;
		int idx;

		/* Inner mask radius */
		if ( dfs*dfs + dss*dss > lim_sq ) continue;

		/* Strayed off one panel? */
		if ( (p_cfs+dfs >= p->w) || (p_css+dss >= p->h)
		  || (p_cfs+dfs < 0 ) || (p_css+dss < 0) ) return 8;

		/* Wandered into a bad region? */
		if ( image->bad[pn][p_cfs+dfs + p->w*(p_css+dss)] ) {
			return 15;
		}

		idx = dfs+p_cfs+p->w*(dss+p_css);
		val = image->dp[pn][idx];

		/* Check if peak contains saturation */
		if ( (saturated != NULL) && (val > p->max_adu) ) *saturated = 1;

		val -= bg_mean;

		pk_counts++;
		pk_total += val;

		fsct += val*(p_cfs+dfs);
		ssct += val*(p_css+dss);

	}
	}

	if ( pk_counts == 0 ) return 11;
	if ( pk_total == 0 ) return 13;

	*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 12;

	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_sq_gradient, float min_snr, int pn,
                                  double ir_inn, double ir_mid, double ir_out,
                                  int use_saturated)
{
	int fs, ss, stride;
	float *data;
	struct panel *p;
	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_fail = 0;
	int nrej_snr = 0;
	int nrej_sat = 0;
	int nacc = 0;
	int ncull;

	p = &image->det->panels[pn];
	data = image->dp[pn];
	stride = p->w;

	for ( ss=1; ss<p->h-1; ss++ ) {
	for ( fs=1; fs<p->w-1; fs++ ) {

		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;
		int saturated;

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

		/* Immediate rejection of pixels above max_adu */
		if ( !use_saturated && (data[fs+stride*ss] > p->max_adu) ) {
			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 (squared) gradient */
		grad = dxs + dys;

		if ( grad < min_sq_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-ir_inn, 0);
			      s_ss<=smallest(mask_ss+ir_inn, p->h-1);
			      s_ss++ )
			{
			for ( s_fs=biggest(mask_fs-ir_inn, 0);
			      s_fs<=smallest(mask_fs+ir_inn, p->w-1);
			      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) > ir_inn )
			{
				break;
			}

		} while ( did_something );

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

		/* Should be enforced by bounds used above.  Muppet check. */
		assert(mask_fs <= p->w);
		assert(mask_ss <= p->h);
		assert(mask_fs >= 0);
		assert(mask_ss >= 0);

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

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

		/* It is possible for the centroid to fall outside the image */
		if ( (f_fs < 0) || (f_fs > p->w)
		  || (f_ss < 0) || (f_ss > p->h) ) {
			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, p, &d, &idx);
		if ( d < 2.0*ir_inn ) {
			nrej_pro++;
			continue;
		}

		if ( saturated && !use_saturated ) {
			nrej_sat++;
			continue;
		}

		/* Add using "better" coordinates */
		image_add_feature(image->features, f_fs, f_ss, p,
		                  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 failed integration, %i with SNR < %g, %i badrow culled, "
	//        "%i saturated.\n",
	//       nacc, nrej_dis, nrej_pro, nrej_fra, nrej_fail,
	//       nrej_snr, min_snr, ncull, nrej_sat);

	if ( ncull != 0 ) {
		STATUS("WARNING: %i peaks were badrow culled.  This feature"
		       " should not usually be used.\nConsider setting"
		       " badrow=- in the geometry file.\n", ncull);
	}
}


void search_peaks(struct image *image, float threshold, float min_sq_gradient,
                  float min_snr, double ir_inn, double ir_mid,
                  double ir_out, int use_saturated)
{
	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++ ) {

		if ( image->det->panels[i].no_index ) continue;

		search_peaks_in_panel(image, threshold, min_sq_gradient,
		                      min_snr, i, ir_inn, ir_mid, ir_out,
		                      use_saturated);

	}
}


/**
 * \param image An \ref image structure
 * \param max_n_peaks The maximum number of peaks to be searched for
 * \param threshold The image threshold value, in detector units
 * \param min_snr The minimum signal to noise ratio for a peak
 * \param min_pix_count The minimum number of pixels in a peak
 * \param max_pix_count The maximum number of pixels in a peak
 * \param local_bg_radius The averaging radius for background calculation
 * \param min_res The minimum number of pixels out from the center
 * \param max_res The maximum number of pixels out from the center
 * \param use_saturated Whether saturated peaks should be considered
 *
 * Runs the peakfinder8 peak search algorithm.  This is a thin wrapper which
 * creates an empty \ref ImageFeatureList for \p image, then calls
 * the actual \ref peakfinder8 function, found in \ref peakfinder8.h.
 */
int search_peaks_peakfinder8(struct image *image, int max_n_peaks,
                              float threshold, float min_snr,
                              int min_pix_count, int max_pix_count,
                              int local_bg_radius, int min_res,
                              int max_res, int use_saturated)
{
	if ( image->features != NULL ) {
		image_feature_list_free(image->features);
	}
	image->features = image_feature_list_new();

	return peakfinder8(image, max_n_peaks, threshold, min_snr,
	                   min_pix_count, max_pix_count,
	                   local_bg_radius, min_res,
	                   max_res, use_saturated);
}


#ifdef HAVE_FDIP

int search_peaks_peakfinder9(struct image *image, float min_snr_biggest_pix,
                             float min_snr_peak_pix, float min_snr_whole_peak,
                             float min_sig, float min_peak_over_neighbour,
                             int window_radius)
{
	peakFinder9_accuracyConstants_t accuracy_consts;
	peakList_t peakList;
	long NpeaksMax = 10000; //more peaks per panel should not appear
	float *data_copy = NULL;
	float *data_copy_new;
	int panel_number;

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

	accuracy_consts.minSNR_biggestPixel = min_snr_biggest_pix;
	accuracy_consts.minSNR_peakPixel = min_snr_peak_pix;
	accuracy_consts.minSNR_wholePeak = min_snr_whole_peak;
	accuracy_consts.minimumSigma = min_sig;
	accuracy_consts.minimumPeakOversizeOverNeighbours = min_peak_over_neighbour;
	accuracy_consts.windowRadius = window_radius;

	if ( allocatePeakList(&peakList, NpeaksMax) ) return 1;

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

		int w, h;
		int peak_number;
		detectorRawFormat_t det_size_one_panel;

		if ( image->det->panels[panel_number].no_index ) continue;

		w = image->det->panels[panel_number].w;
		h = image->det->panels[panel_number].h;

		det_size_one_panel.asic_nx = w;
		det_size_one_panel.asic_ny = h;
		det_size_one_panel.nasics_x = 1;
		det_size_one_panel.nasics_y = 1;
		det_size_one_panel.pix_nx = w;
		det_size_one_panel.pix_ny = h;
		det_size_one_panel.pix_nn = w * h;

		data_copy_new = realloc(data_copy, w*h*sizeof(*data_copy));
		if ( data_copy_new == NULL ) {
			if ( data_copy != NULL ) {
				free(data_copy);
			}
			freePeakList(peakList);
			return 1;
		} else {
			data_copy = data_copy_new;
		}

		mergeMaskAndDataIntoDataCopy(image->dp[panel_number], data_copy,
		                             image->bad[panel_number],
		                             &det_size_one_panel);

		peakList.peakCount = 0;
		peakFinder9_onePanel_noSlab(data_copy, &accuracy_consts,
		                            &det_size_one_panel, &peakList);

		for ( peak_number=0; peak_number<peakList.peakCount; peak_number++) {
			image_add_feature(image->features,
			                  peakList.centerOfMass_rawX[peak_number],
			                  peakList.centerOfMass_rawY[peak_number],
			                  &image->det->panels[panel_number],
			                  image,
			                  peakList.totalIntensity[peak_number],
			                  NULL);
		}

	}

	freePeakList(peakList);
	free(data_copy);
	return 0;
}

#else

int search_peaks_peakfinder9(struct image *image, float min_snr_biggest_pix,
                             float min_snr_peak_pix, float min_snr_whole_peak,
                             float min_sig, float min_peak_over_neighbour,
                             int window_radius)
{
	ERROR("This copy of CrystFEL was compiled without peakfinder9 support.\n");
	return 1;
}

#endif // HAVE_FDIP


/**
 * \param image An \ref image structure
 * \param crystals Pointer to array of pointers to crystals
 * \param n_cryst The number of crystals
 * \param multi_mode Whether the thresholds should be set for multi-lattice indexing
 *
 * Checks whether the peaks in \p image appear to be explained by the crystals
 * provided.
 *
 * Returns 1 if the peaks appear to be well-explained by the crystals.
 * Otherwise, if the indexing solutions appear to be "bad", returns 0.
 */
int indexing_peak_check(struct image *image, Crystal **crystals, int n_cryst,
                        int multi_mode)
{
	int n_feat = 0;
	int n_sane = 0;
	int i;
	const double min_dist = 0.25;

	for ( i=0; i<image_feature_count(image->features); i++ ) {

		struct imagefeature *f;
		struct rvec q;
		double h,k,l,hd,kd,ld;
		int j;
		int ok = 0;

		/* 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_for_panel(f->p, f->fs, f->ss,
		                    NULL, 1.0/image->lambda);

		for ( j=0; j<n_cryst; j++ ) {

			double ax, ay, az;
			double bx, by, bz;
			double cx, cy, cz;

			cell_get_cartesian(crystal_get_cell(crystals[j]),
			                   &ax, &ay, &az,
			                   &bx, &by, &bz,
			                   &cx, &cy, &cz);

			/* 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) )
			{
				ok = 1;
				break;  /* Don't need to check other crystals */
			}

		}

		n_sane += ok;

	}

	/* 0 means failed test, 1 means passed test */

	if ( multi_mode ) {
		return (n_sane > 70)
		    || ((n_sane > 25) && (n_sane > 0.3*n_feat))
		    || (n_sane > 0.4*n_feat);
	} else {
		return ((double)n_sane / n_feat) >= 0.5;
	}
}


/**
 * Deprecated: use indexing_peak_check instead
 */
int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst)
{
	return indexing_peak_check(image, crystals, n_cryst, 1);
}


void validate_peaks(struct image *image, double min_snr,
                    int ir_inn, int ir_mid, int ir_out, int use_saturated,
                    int check_snr)
{
	int i, n;
	ImageFeatureList *flist;
	int n_wtf, n_int, n_snr, n_sat;

	flist = image_feature_list_new();
	if ( flist == NULL ) return;

	n = image_feature_count(image->features);

	/* Loop over peaks, putting each one through the integrator */
	n_wtf = 0;  n_int = 0;  n_snr = 0;  n_sat = 0;
	for ( i=0; i<n; i++ ) {

		struct imagefeature *f;
		int r;
		double f_fs, f_ss;
		double intensity, sigma;
		int saturated;

		f = image_get_feature(image->features, i);
		if ( f == NULL ) {
			n_wtf++;
			continue;
		}

		r = integrate_peak(image, f->fs, f->ss, f->p,
		                   &f_fs, &f_ss, &intensity, &sigma,
		                   ir_inn, ir_mid, ir_out, &saturated);
		if ( r ) {
			n_int++;
			continue;
		}

		if ( saturated ) {
			if ( !use_saturated ) {
				n_sat++;
				continue;
			}
		}

		if ( check_snr && (fabs(intensity)/sigma < min_snr) ) {
			n_snr++;
			continue;
		}

		/* Add using "better" coordinates */
		image_add_feature(flist, f->fs, f->ss, f->p, image, intensity,
		                  NULL);

	}

	//STATUS("HDF5: %i peaks, validated: %i.  WTF: %i, integration: %i, "
	//       "SNR: %i, saturated: %i\n",
	//       n, image_feature_count(flist), n_wtf, n_int, n_snr, n_sat);
	image_feature_list_free(image->features);
	image->features = flist;
}


static int compare_double(const void *av, const void *bv)
{
	double a = *(double *)av;
	double b = *(double *)bv;
	if ( a > b ) return 1;
	if ( a < b ) return -1;
	return 0;
}


double estimate_peak_resolution(ImageFeatureList *peaks, double lambda)
{
	int i, npk, ncut;
	double *rns;
	double max_res;

	npk = image_feature_count(peaks);

	/* No peaks -> no resolution! */
	if ( npk == 0 ) return 0.0;

	rns = malloc(npk*sizeof(double));
	if ( rns == NULL ) return -1.0;

	/* Get resolution values for all peaks */
	for ( i=0; i<npk; i++ ) {

		struct imagefeature *f;
		struct rvec r;

		f = image_get_feature(peaks, i);

		r = get_q_for_panel(f->p, f->fs, f->ss, NULL, 1.0/lambda);
		rns[i] = modulus(r.u, r.v, r.w);

	}

	/* Slightly horrible outlier removal */
	qsort(rns, npk, sizeof(double), compare_double);
	ncut = npk/50;
	if ( ncut < 2 ) ncut = 0;
	max_res = rns[(npk-1)-ncut];

	free(rns);
	return max_res;
}