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
|
/*
* image.h
*
* Handle images and image features
*
* Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2009-2021 Thomas White <taw@physics.org>
* 2014 Valerio Mariani
*
*
* 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/>.
*
*/
#ifndef IMAGE_H
#define IMAGE_H
#include <stdint.h>
#include <complex.h>
#include <sys/types.h>
struct imagefeature;
struct image;
#include "utils.h"
#include "cell.h"
#include "reflist.h"
#include "crystal.h"
#include "index.h"
#include "spectrum.h"
#include "datatemplate.h"
/**
* \file image.h
*
* Information about images
*/
/** Represents a peak in an image. */
struct imagefeature {
/** \name Coordinates on panel (fast scan, slow scan)
* Note carefully that these are the distances, measured in pixels,
* from the corner of the panel. They are NOT pixel indices.
* If the peak is in the middle of the first pixel, its coordinates would be
* 0.5,0.5. */
/**@{*/
double fs;
double ss;
/**@}*/
int pn; /**< Panel number */
double intensity; /**< Intensity */
const char *name; /**< Text name, e.g. "5,3,-1" */
};
/** An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;
#define HEADER_CACHE_SIZE (128)
typedef enum
{
HEADER_FLOAT,
HEADER_INT,
HEADER_STR
} HeaderCacheType;
struct header_cache_entry {
char *header_name;
HeaderCacheType type;
union {
int val_int;
double val_float;
char *val_str;
};
};
typedef enum
{
DST_UNKNOWN,
DST_NONE,
DST_HDF5,
DST_CBF,
DST_CBFGZ,
DST_MSGPACK
} DataSourceType;
struct image
{
/** The image data, by panel */
float **dp;
/** The bad pixel mask, by panel */
int **bad;
/** The per-pixel saturation values, by panel */
float **sat;
/** Non-zero if the frame was determined to be a "hit" */
int hit;
/**Array of crystals in the image */
Crystal **crystals;
/** The number of crystals in the image (size of \p crystals) */
int n_crystals;
/** Indexing method which indexed this pattern */
IndexingMethod indexed_by;
/** Number of times the indexer was tried before succeeding */
int n_indexing_tries;
/** The detector structure */
struct detgeom *detgeom;
DataSourceType data_source_type;
/** \name The filename and event ID for the image
* @{ */
char *filename;
char *ev;
/** @} */
/** The data block, e.g. received over ZMQ, for the image.
* filenename/ev OR this should be filled in, but not both */
void *data_block;
size_t data_block_size;
/** A list of metadata read from the stream */
struct header_cache_entry *header_cache[HEADER_CACHE_SIZE];
int n_cached_headers;
/** ID number of the worker processing handling this image */
int id;
/** Monotonically increasing serial number for this image */
int serial;
/** Spectrum information */
Spectrum *spectrum;
/** Wavelength of the incident radiation, in metres */
double lambda;
/** Convergence angle of the incident ration, in radians (full angle) */
double div;
/** Full-width half-maximum bandwidth as a fraction, applied to wavelength */
double bw;
/** Resolution estimate based on peaks */
double peak_resolution;
/** List of peaks found in the image */
ImageFeatureList *features;
};
#ifdef __cplusplus
extern "C" {
#endif
/* Feature lists */
extern ImageFeatureList *image_feature_list_new(void);
extern void image_feature_list_free(ImageFeatureList *flist);
extern void image_add_feature(ImageFeatureList *flist, double x, double y,
int pn,
struct image *parent, double intensity,
const char *name);
extern void image_remove_feature(ImageFeatureList *flist, int idx);
extern struct imagefeature *image_feature_closest(ImageFeatureList *flist,
double fs, double ss,
int pn,
double *d, int *idx);
extern int image_feature_count(ImageFeatureList *flist);
extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
extern const struct imagefeature *image_get_feature_const(const ImageFeatureList *flist,
int idx);
extern ImageFeatureList *sort_peaks(ImageFeatureList *flist);
extern ImageFeatureList *image_feature_list_copy(const ImageFeatureList *flist);
extern void image_add_crystal(struct image *image, Crystal *cryst);
extern int remove_flagged_crystals(struct image *image);
extern void free_all_crystals(struct image *image);
extern void mark_resolution_range_as_bad(struct image *image,
double min, double max);
extern struct image *image_new(void);
extern struct image *image_read(const DataTemplate *dtempl,
const char *filename,
const char *event,
int no_image_data,
int no_mask_data);
extern struct image *image_create_for_simulation(const DataTemplate *dtempl);
extern struct image *image_read_data_block(const DataTemplate *dtempl,
void *data_block,
size_t data_block_size,
DataSourceType type,
int serial,
int no_image_data,
int no_mask_data);
extern void image_free(struct image *image);
extern int image_read_header_float(struct image *image, const char *from,
double *val);
/* NB image_read_header_int and image_read_header_str should exist, but there
* is currently no use for them. Get in touch if you disagree! */
extern void image_cache_header_float(struct image *image,
const char *header_name,
double header_val);
extern void image_cache_header_int(struct image *image,
const char *header_name,
int header_val);
extern void image_cache_header_str(struct image *image,
const char *header_name,
const char *header_val);
extern ImageFeatureList *image_read_peaks(const DataTemplate *dtempl,
const char *filename,
const char *event,
int half_pixel_shift);
extern char **image_expand_frames(const DataTemplate *dtempl,
const char *filename, int *nframes);
extern int image_set_zero_data(struct image *image,
const DataTemplate *dtempl);
extern int image_set_zero_mask(struct image *image,
const DataTemplate *dtempl);
extern int image_write(const struct image *image,
const DataTemplate *dtempl,
const char *filename);
/* Use within libcrystfel only */
extern int create_detgeom(struct image *image,
const DataTemplate *dtempl);
#ifdef __cplusplus
}
#endif
#endif /* IMAGE_H */
|
