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
|
/*
* image.h
*
* Handle images and image features
*
* Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2009-2017 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/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifndef IMAGE_H
#define IMAGE_H
struct detector;
#include <stdint.h>
#include <complex.h>
#include <sys/types.h>
struct imagefeature;
struct sample;
struct image;
struct imagefile;
struct imagefile_field_list;
#include "utils.h"
#include "cell.h"
#include "detector.h"
#include "reflist.h"
#include "crystal.h"
#include "index.h"
#include "events.h"
/**
* SpectrumType:
* @SPECTRUM_TOPHAT: A top hat distribution of wavelengths
* @SPECTRUM_SASE: A simulated SASE spectrum
* @SPECTRUM_TWOCOLOUR: A spectrum containing two peaks
*
* A %SpectrumType represents a type of X-ray energy spectrum to use for
* generating simulated data.
**/
typedef enum {
SPECTRUM_TOPHAT,
SPECTRUM_SASE,
SPECTRUM_TWOCOLOUR
} SpectrumType;
/**
* imagefeature:
* @parent: Image this feature belongs to
* @fs: Fast scan coordinate
* @ss: Slow scan coordinate
* @p: Pointer to panel
* @intensity: Intensity of peak
* @rx: Reciprocal x coordinate in m^-1
* @ry: Reciprocal y coordinate in m^-1
* @rz: Reciprocal z coordinate in m^-1
* @name: Text name for feature
*
* Represents a peak in an image.
*
* Note carefully that the @fs and @ss coordinates 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.
*/
struct imagefeature {
struct image *parent;
double fs;
double ss;
struct panel *p;
double intensity;
/* Reciprocal space coordinates (m^-1 of course) of this feature */
double rx;
double ry;
double rz;
const char *name;
/*< private >*/
int valid;
};
/* An enum representing the image file formats we can handle */
enum imagefile_type
{
IMAGEFILE_HDF5,
IMAGEFILE_CBF
};
/* An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;
/* Structure describing a wavelength sample from a spectrum */
struct sample
{
double k;
double weight;
};
/**
* beam_params:
* @photon_energy: eV per photon
* @photon_energy_from: HDF5 dataset name
* @photon_energy_scale: Scale factor for photon energy, if it comes from HDF5
*/
struct beam_params
{
double photon_energy;
char *photon_energy_from;
double photon_energy_scale;
};
/**
* image:
* @crystals: Array of crystals in the image
* @n_crystals: The number of crystals in the image
* @indexed_by: Indexing method which indexed this pattern
* @det: Detector structure
* @beam: Beam parameters structure
* @filename: Filename for the image file
* @copyme: Fields to copy from the image file to the stream
* @id: ID number of the thread handling this image
* @serial: Serial number for this image
* @lambda: Wavelength
* @div: Divergence
* @bw: Bandwidth
* @num_peaks: The number of peaks
* @num_saturated_peaks: The number of saturated peaks
* @features: The peaks found in the image
* @dp: The image data, by panel
* @bad: The bad pixel mask, array by panel
* @sat: The per-pixel saturation mask, array by panel
* @event: Event ID for the image
* @stuff_from_stream: Items read back from the stream
* @avg_clen: Mean of camera length values for all panels
* @spectrum: Spectrum information
* @nsamples: Number of spectrum samples
* @spectrum_size: SIze of spectrum array
*
* The field <structfield>data</structfield> contains the raw image data, if it
* is currently available. The data might be available throughout the
* processing of an experimental pattern, but it might not be available when
* simulating, scaling or merging patterns.
*
* <structfield>crystals</structfield> is an array of %Crystal directly
* returned by the low-level indexing system. <structfield>n_crystals</structfield>
* is the number of crystals which were found in the image.
*
* <structfield>copyme</structfield> represents a list of fields in the image
* file (e.g. HDF5 fields or CBF headers) to copy to the output stream.
**/
struct image;
struct image {
float **dp; /* Data in panel */
int **bad; /* Bad pixels by panel */
float **sat; /* Per-pixel saturation values */
Crystal **crystals;
int n_crystals;
IndexingMethod indexed_by;
struct detector *det;
struct beam_params *beam; /* The nominal beam parameters */
char *filename;
struct event *event;
const struct imagefile_field_list *copyme;
struct stuff_from_stream *stuff_from_stream;
double avg_clen; /* Average camera length extracted
* from stuff_from_stream */
int id; /* ID number of the thread
* handling this image */
int serial; /* Monotonically ascending serial
* number for this image */
struct sample *spectrum;
int nsamples; /* Number of wavelengths */
int spectrum_size; /* Size of "spectrum" */
/* Per-shot radiation values */
double lambda; /* Wavelength in m */
double div; /* Divergence in radians */
double bw; /* FWHM bandwidth as a fraction */
/* Detected peaks */
long long num_peaks;
long long num_saturated_peaks;
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,
struct panel *p,
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,
struct panel *p,
double *d, int *idx);
extern Reflection *image_reflection_closest(RefList *rlist,
double fs, double ss,
struct panel *p,
struct detector *det,
double *d);
extern int image_feature_count(ImageFeatureList *flist);
extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
extern ImageFeatureList *sort_peaks(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);
/* Image files */
extern struct imagefile *imagefile_open(const char *filename);
extern int imagefile_read(struct imagefile *f, struct image *image,
struct event *event);
extern int imagefile_read_simple(struct imagefile *f, struct image *image);
extern struct hdfile *imagefile_get_hdfile(struct imagefile *f);
extern enum imagefile_type imagefile_get_type(struct imagefile *f);
extern void imagefile_copy_fields(struct imagefile *f,
const struct imagefile_field_list *copyme,
FILE *fh, struct event *ev);
extern void imagefile_close(struct imagefile *f);
extern signed int is_cbf_file(const char *filename);
/* Field lists */
extern struct imagefile_field_list *new_imagefile_field_list(void);
extern void free_imagefile_field_list(struct imagefile_field_list *f);
extern void add_imagefile_field(struct imagefile_field_list *copyme,
const char *name);
#ifdef __cplusplus
}
#endif
#endif /* IMAGE_H */
|
