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
|
/*
* image.c
*
* Handle images and image features
*
* Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
* 2011-2017 Thomas White <taw@physics.org>
*
* 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 <assert.h>
#include <math.h>
#include <stdio.h>
#include "image.h"
#include "utils.h"
#include "detgeom.h"
#include "image-hdf5.h"
#include "image-cbf.h"
#include "datatemplate.h"
#include "datatemplate_priv.h"
/** \file image.h */
struct _imagefeaturelist
{
struct imagefeature *features;
int max_features;
int n_features;
};
void image_add_feature(ImageFeatureList *flist, double fs, double ss,
int pn,
struct image *parent, double intensity, const char *name)
{
if ( flist->n_features == flist->max_features ) {
struct imagefeature *nf;
int nmf = flist->max_features + 128;
nf = realloc(flist->features, nmf*sizeof(struct imagefeature));
if ( nf == NULL ) return;
flist->features = nf;
flist->max_features = nmf;
}
flist->features[flist->n_features].fs = fs;
flist->features[flist->n_features].ss = ss;
flist->features[flist->n_features].pn = pn;
flist->features[flist->n_features].intensity = intensity;
flist->features[flist->n_features].name = name;
flist->n_features++;
}
ImageFeatureList *image_feature_list_new()
{
ImageFeatureList *flist;
flist = malloc(sizeof(ImageFeatureList));
flist->n_features = 0;
flist->max_features = 0;
flist->features = NULL;
return flist;
}
static int comp(const void *a, const void *b)
{
const struct imagefeature *ap = a;
const struct imagefeature *bp = b;
return ap->intensity < bp->intensity;
}
ImageFeatureList *image_feature_list_copy(const ImageFeatureList *flist)
{
ImageFeatureList *n;
int nf, i;
if ( flist == NULL ) return NULL;
n = image_feature_list_new();
if ( n == NULL ) return NULL;
n->features = malloc(flist->n_features*sizeof(struct imagefeature));
if ( n->features == NULL ) {
free(n);
return NULL;
}
nf = 0;
for ( i=0; i<flist->n_features; i++ ) {
const struct imagefeature *f;
f = image_get_feature_const(flist, i);
if ( f == NULL ) continue;
n->features[nf++] = flist->features[i];
}
n->n_features = nf;
return n;
}
/**
* Strongest first.
*/
ImageFeatureList *sort_peaks(ImageFeatureList *flist)
{
ImageFeatureList *n = image_feature_list_copy(flist);
qsort(n->features, image_feature_count(n),
sizeof(struct imagefeature), comp);
return n;
}
void image_feature_list_free(ImageFeatureList *flist)
{
if ( flist == NULL ) return;
free(flist->features);
free(flist);
}
struct imagefeature *image_feature_closest(ImageFeatureList *flist,
double fs, double ss,
int pn, double *d, int *idx)
{
int i;
double dmin = +HUGE_VAL;
int closest = 0;
for ( i=0; i<flist->n_features; i++ ) {
double ds;
if ( pn != flist->features[i].pn ) continue;
ds = distance(flist->features[i].fs, flist->features[i].ss,
fs, ss);
if ( ds < dmin ) {
dmin = ds;
closest = i;
}
}
if ( dmin < +HUGE_VAL ) {
*d = dmin;
*idx = closest;
return &flist->features[closest];
}
*d = +INFINITY;
return NULL;
}
int image_feature_count(ImageFeatureList *flist)
{
if ( flist == NULL ) return 0;
return flist->n_features;
}
const struct imagefeature *image_get_feature_const(const ImageFeatureList *flist,
int idx)
{
/* Sanity check */
if ( flist == NULL ) return NULL;
if ( idx >= flist->n_features ) return NULL;
return &flist->features[idx];
}
struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx)
{
/* Sanity check */
if ( flist == NULL ) return NULL;
if ( idx >= flist->n_features ) return NULL;
return &flist->features[idx];
}
void image_remove_feature(ImageFeatureList *flist, int idx)
{
memmove(&flist->features[idx], &flist->features[idx+1],
(flist->n_features-idx-1)*sizeof(struct imagefeature));
flist->n_features--;
}
void image_add_crystal(struct image *image, Crystal *cryst)
{
Crystal **crs;
int n;
n = image->n_crystals;
crs = realloc(image->crystals, (n+1)*sizeof(Crystal *));
if ( crs == NULL ) {
ERROR("Failed to allocate memory for crystals.\n");
return;
}
crs[n] = cryst;
image->crystals = crs;
image->n_crystals = n+1;
}
int remove_flagged_crystals(struct image *image)
{
int i;
int n_bad = 0;
for ( i=0; i<image->n_crystals; i++ ) {
if ( crystal_get_user_flag(image->crystals[i]) ) {
int j;
Crystal *deleteme = image->crystals[i];
cell_free(crystal_get_cell(deleteme));
crystal_free(deleteme);
for ( j=i; j<image->n_crystals-1; j++ ) {
image->crystals[j] = image->crystals[j+1];
}
image->n_crystals--;
n_bad++;
i--;
}
}
return n_bad;
}
/* Free all crystals, including their RefLists and UnitCells */
void free_all_crystals(struct image *image)
{
int i;
if ( image->crystals == NULL ) return;
for ( i=0; i<image->n_crystals; i++ ) {
Crystal *cr = image->crystals[i];
reflist_free(crystal_get_reflections(cr));
cell_free(crystal_get_cell(cr));
crystal_free(image->crystals[i]);
}
free(image->crystals);
image->n_crystals = 0;
}
static double get_value(struct image *image, const char *from)
{
double val;
char *rval;
if ( from == NULL ) return NAN;
val = strtod(from, &rval);
if ( (*rval == '\0') && (rval != from) ) return val;
if ( is_hdf5_file(image->filename) ) {
return image_hdf5_get_value(from,
image->filename,
image->ev);
} else if ( is_cbf_file(image->filename) ) {
/* FIXME: From headers */
return NAN;
} else if ( is_cbfgz_file(image->filename) ) {
/* FIXME: From headers */
return NAN;
} else {
ERROR("Unrecognised file type: %s\n", image->filename);
return NAN;
}
}
static char *get_value_and_units(struct image *image, const char *from,
double *pvalue)
{
char *sp;
char *fromcpy;
char *unitscpy;
if ( from == NULL ) {
*pvalue = NAN;
return NULL;
}
fromcpy = strdup(from);
if ( fromcpy == NULL ) {
*pvalue = NAN;
return NULL;
}
sp = strchr(fromcpy, ' ');
if ( sp == NULL ) {
unitscpy = NULL;
} else {
unitscpy = strdup(sp+1);
sp[0] = '\0';
}
*pvalue = get_value(image, fromcpy);
free(fromcpy);
return unitscpy;
}
static double im_get_length(struct image *image, const char *from,
double default_scale)
{
char *units;
double value;
double scale;
units = get_value_and_units(image, from, &value);
if ( units == NULL ) {
scale = default_scale;
} else {
if ( strcmp(units, "mm") == 0 ) {
scale = 1e-3;
} else if ( strcmp(units, "m") == 0 ) {
scale = 1.0;
} else {
ERROR("Invalid length unit '%s'\n", units);
free(units);
return NAN;
}
}
free(units);
return value * scale;
}
static double convert_to_m(double val, int units)
{
switch ( units ) {
case WAVELENGTH_M :
return val;
case WAVELENGTH_A :
return val * 1e-10;
case WAVELENGTH_PHOTON_EV :
return ph_eV_to_lambda(val);
case WAVELENGTH_PHOTON_KEV :
return ph_eV_to_lambda(val*1e3);
case WAVELENGTH_ELECTRON_V :
return el_V_to_lambda(val);
case WAVELENGTH_ELECTRON_KV :
return el_V_to_lambda(val*1e3);
}
return NAN;
}
void create_detgeom(struct image *image, const DataTemplate *dtempl)
{
struct detgeom *detgeom;
int i;
if ( dtempl == NULL ) {
ERROR("NULL data template!\n");
return;
}
detgeom = malloc(sizeof(struct detgeom));
if ( detgeom == NULL ) return;
detgeom->panels = malloc(dtempl->n_panels*sizeof(struct detgeom_panel));
if ( detgeom->panels == NULL ) return;
detgeom->n_panels = dtempl->n_panels;
for ( i=0; i<dtempl->n_panels; i++ ) {
double shift_x, shift_y;
detgeom->panels[i].name = safe_strdup(dtempl->panels[i].name);
detgeom->panels[i].pixel_pitch = dtempl->panels[i].pixel_pitch;
/* NB cnx,cny are in pixels, cnz is in m */
detgeom->panels[i].cnx = dtempl->panels[i].cnx;
detgeom->panels[i].cny = dtempl->panels[i].cny;
detgeom->panels[i].cnz = im_get_length(image,
dtempl->panels[i].cnz_from,
1e-3);
/* Apply offset (in m) and then convert cnz from
* m to pixels */
detgeom->panels[i].cnz += dtempl->panels[i].cnz_offset;
detgeom->panels[i].cnz /= detgeom->panels[i].pixel_pitch;
/* Apply overall shift (already in m) */
shift_x = im_get_length(image, dtempl->shift_x_from, 1.0);
shift_y = im_get_length(image, dtempl->shift_y_from, 1.0);
if ( !isnan(shift_x) ) {
detgeom->panels[i].cnx += shift_x;
}
if ( !isnan(shift_y) ) {
detgeom->panels[i].cny += shift_y;
}
detgeom->panels[i].max_adu = dtempl->panels[i].max_adu;
switch ( dtempl->panels[i].adu_scale_unit ) {
case ADU_PER_PHOTON:
detgeom->panels[i].adu_per_photon = dtempl->panels[i].adu_scale;
break;
case ADU_PER_EV:
detgeom->panels[i].adu_per_photon = dtempl->panels[i].adu_scale
* ph_lambda_to_eV(image->lambda);
break;
default:
detgeom->panels[i].adu_per_photon = 1.0;
ERROR("Invalid ADU/ph scale unit (%i)\n",
dtempl->panels[i].adu_scale_unit);
break;
}
detgeom->panels[i].w = dtempl->panels[i].orig_max_fs
- dtempl->panels[i].orig_min_fs + 1;
detgeom->panels[i].h = dtempl->panels[i].orig_max_ss
- dtempl->panels[i].orig_min_ss + 1;
detgeom->panels[i].fsx = dtempl->panels[i].fsx;
detgeom->panels[i].fsy = dtempl->panels[i].fsy;
detgeom->panels[i].fsz = dtempl->panels[i].fsz;
detgeom->panels[i].ssx = dtempl->panels[i].ssx;
detgeom->panels[i].ssy = dtempl->panels[i].ssy;
detgeom->panels[i].ssz = dtempl->panels[i].ssz;
}
image->detgeom = detgeom;
/* FIXME: spectrum */
}
int image_set_zero_data(struct image *image,
const DataTemplate *dtempl)
{
int pi;
image->dp = malloc(dtempl->n_panels*sizeof(float *));
if ( image->dp == NULL ) return 1;
for ( pi=0; pi<dtempl->n_panels; pi++ ) {
struct panel_template *p;
int p_w, p_h;
long int i;
p = &dtempl->panels[pi];
p_w = p->orig_max_fs - p->orig_min_fs + 1;
p_h = p->orig_max_ss - p->orig_min_ss + 1;
image->dp[pi] = malloc(p_w*p_h*sizeof(float));
if ( image->dp[pi] == NULL ) return 1;
for ( i=0; i<p_w*p_h; i++ ) {
image->dp[pi][i] = 0.0;
}
}
return 0;
}
int image_set_zero_mask(struct image *image,
const DataTemplate *dtempl)
{
int pi;
image->bad = malloc(dtempl->n_panels*sizeof(int *));
image->sat = malloc(dtempl->n_panels*sizeof(float *));
if ( (image->bad == NULL) || (image->sat == NULL) ) return 1;
for ( pi=0; pi<dtempl->n_panels; pi++ ) {
struct panel_template *p;
int p_w, p_h;
long int i;
p = &dtempl->panels[pi];
p_w = p->orig_max_fs - p->orig_min_fs + 1;
p_h = p->orig_max_ss - p->orig_min_ss + 1;
image->bad[pi] = malloc(p_w*p_h*sizeof(int));
image->sat[pi] = malloc(p_w*p_h*sizeof(float));
if ( image->bad[pi] == NULL ) return 1;
if ( image->sat[pi] == NULL ) return 1;
for ( i=0; i<p_w*p_h; i++ ) {
image->bad[pi][i] = 0;
image->sat[pi][i] = INFINITY;
}
}
return 0;
}
int image_read_image_data(struct image *image,
const DataTemplate *dtempl,
const char *filename,
const char *event)
{
if ( is_hdf5_file(filename) ) {
return image_hdf5_read(image, dtempl, filename, event);
} else if ( is_cbf_file(filename) ) {
return image_cbf_read(image, dtempl, filename, event, 0);
} else if ( is_cbfgz_file(filename) ) {
return image_cbf_read(image, dtempl, filename, event, 1);
}
ERROR("Unrecognised file type: %s\n", filename);
return 1;
}
struct image *image_read(DataTemplate *dtempl,
const char *filename,
const char *event,
int no_image_data,
int no_mask_data)
{
struct image *image;
int i;
int r;
if ( dtempl == NULL ) {
ERROR("NULL data template!\n");
return NULL;
}
image = image_new();
if ( image == NULL ) {
ERROR("Couldn't allocate image structure.\n");
return NULL;
}
if ( !no_image_data ) {
r = image_read_image_data(image, dtempl,
filename, event);
} else {
r = image_set_zero_data(image, dtempl);
}
if ( r ) {
image_free(image);
return NULL;
}
/* Wavelength might be needed to create detgeom (adu_per_eV) */
image->lambda = convert_to_m(get_value(image,
dtempl->wavelength_from),
dtempl->wavelength_unit);
create_detgeom(image, dtempl);
image->bad = malloc(dtempl->n_panels * sizeof(int *));
if ( image->bad == NULL ) {
ERROR("Failed to allocate bad pixel mask\n");
return NULL;
}
for ( i=0; i<dtempl->n_panels; i++ ) {
const char *mask_fn;
int p_w, p_h;
struct panel_template *p = &dtempl->panels[i];
p_w = p->orig_max_fs - p->orig_min_fs + 1;
p_h = p->orig_max_ss - p->orig_min_ss + 1;
image->bad[i] = calloc(p_w*p_h, sizeof(int));
if ( image->bad[i] == NULL ) {
ERROR("Failed to allocate bad pixel mask\n");
return NULL;
}
/* Panel marked as bad? */
if ( p->bad ) {
/* NB this sets every element to 0x1111,
* but that's OK - value is still 'true'. */
memset(image->bad[i], 1, p_w*p_h);
}
/* Add bad regions (skip if panel is bad anyway) */
if ( !p->bad ) {
int fs, ss;
for ( fs=0; fs<p_w; fs++ ) {
for ( ss=0; ss<p_h; ss++ ) {
if ( data_template_in_bad_region(dtempl, i, fs, ss)
|| isnan(image->dp[i][fs+ss*p_w])
|| isinf(image->dp[i][fs+ss*p_w]) )
{
image->bad[i][fs+ss*p_w] = 1;
}
}
}
}
/* Load mask (skip if panel is bad anyway) */
if ( (!no_mask_data) && (!p->bad) && (p->mask != NULL) )
{
if ( p->mask_file == NULL ) {
mask_fn = filename;
} else {
mask_fn = p->mask_file;
}
if ( is_hdf5_file(mask_fn) ) {
image_hdf5_read_mask(p, mask_fn, event,
image->bad[i],
dtempl->mask_good,
dtempl->mask_bad);
} else if ( is_cbf_file(filename) ) {
image_cbf_read_mask(p, mask_fn, event,
0, image->bad[i],
dtempl->mask_good,
dtempl->mask_bad);
} else if ( is_cbfgz_file(filename) ) {
image_cbf_read_mask(p, mask_fn, event,
1, image->bad[i],
dtempl->mask_good,
dtempl->mask_bad);
} else {
ERROR("Unrecognised mask file type"
" (%s)\n", filename);
return NULL;
}
}
}
/* FIXME: Load saturation map */
return image;
}
void image_free(struct image *image)
{
int i, np;
if ( image == NULL ) return;
image_feature_list_free(image->features);
free_all_crystals(image);
free(image->filename);
free(image->ev);
if ( image->detgeom != NULL ) {
np = image->detgeom->n_panels;
detgeom_free(image->detgeom);
} else {
np = 0;
}
for ( i=0; i<np; i++ ) {
if ( image->dp != NULL ) free(image->dp[i]);
if ( image->sat != NULL ) free(image->sat[i]);
if ( image->bad != NULL ) free(image->bad[i]);
}
free(image->dp);
free(image->sat);
free(image->bad);
free(image);
}
struct image *image_new()
{
struct image *image;
image = malloc(sizeof(struct image));
if ( image == NULL ) return NULL;
image->dp = NULL;
image->bad = NULL;
image->sat = NULL;
image->hit = 0;
image->crystals = NULL;
image->n_crystals = 0;
image->indexed_by = INDEXING_NONE;
image->detgeom = NULL;
image->filename = NULL;
image->ev = NULL;
image->copied_headers = NULL;
image->avg_clen = -1.0;
image->id = 0;
image->serial = 0;
image->spectrum = NULL;
image->lambda = -1.0;
image->div = -1.0;
image->bw = -1.0;
image->peak_resolution = -1.0;
image->features = NULL;
return image;
}
ImageFeatureList *image_read_peaks(const DataTemplate *dtempl,
const char *filename,
const char *event,
int half_pixel_shift)
{
if ( is_hdf5_file(filename) ) {
const char *ext;
ext = filename_extension(filename, NULL);
if ( strcmp(ext, ".cxi") == 0 ) {
return image_hdf5_read_peaks_cxi(dtempl,
filename,
event,
half_pixel_shift);
} else {
return image_hdf5_read_peaks_hdf5(dtempl,
filename,
event,
half_pixel_shift);
}
} else {
ERROR("Peak lists can only be read from HDF5 files\n");
return NULL;
}
}
char **image_expand_frames(const DataTemplate *dtempl,
const char *filename, int *n_frames)
{
if ( is_hdf5_file(filename) ) {
return image_hdf5_expand_frames(dtempl, filename,
n_frames);
} else {
ERROR("Can only expand HDF5 files\n");
return NULL;
}
}
void mark_resolution_range_as_bad(struct image *image,
double min, double max)
{
int i;
if ( isinf(min) && isinf(max) ) return; /* nothing to do */
for ( i=0; i<image->detgeom->n_panels; i++ ) {
int fs, ss;
struct detgeom_panel *p = &image->detgeom->panels[i];
for ( ss=0; ss<p->h; ss++ ) {
for ( fs=0; fs<p->w; fs++ ) {
double q[3];
double r;
detgeom_transform_coords(p, fs, ss,
image->lambda,
q);
r = modulus(q[0], q[1], q[2]);
if ( (r >= min) && (r <= max) ) {
image->bad[i][fs+p->w*ss] = 1;
}
}
}
}
}
|