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
|
/*
* image.h
*
* Handle images and image features
*
* Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2009-2013 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;
#include "utils.h"
#include "cell.h"
#include "detector.h"
#include "reflist.h"
#include "crystal.h"
#include "index.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;
/* Structure describing a feature in an image */
struct imagefeature {
struct image *parent;
double fs;
double ss;
char *pn;
double intensity;
/* Reciprocal space coordinates (m^-1 of course) of this feature */
double rx;
double ry;
double rz;
/* Internal use only */
int valid;
const char *name;
};
/* 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;
};
struct beam_params
{
double photon_energy; /* eV per photon */
char *photon_energy_from; /* HDF5 dataset name */
double photon_energy_scale; /* Scale factor for photon energy, if the
* energy is to be from the HDF5 file */
};
/**
* image:
*
* <programlisting>
* struct image
* {
* float *data;
* uint16_t *flags;
* double *twotheta;
*
* Crystal **crystals;
* int n_crystals;
* IndexingMethod indexed_by;
*
* struct detector *det;
* struct beam_params *beam;
* char *filename;
* const struct copy_hdf5_field *copyme;
*
* int id;
*
* double lambda;
* double div;
* double bw;
*
* int width;
* int height;
*
* long long int num_peaks;
* long long int num_saturated_peaks;
* ImageFeatureList *features;
* };
* </programlisting>
*
* 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. Similarly,
* <structfield>flags</structfield> contains an array of the same dimensions
* as <structfield>data</structfield> to contain the bad pixel flags.
* <structfield>twotheta</structfield> likewise contains an array of 2*theta
* (scattering angle) values in radians, since these values are generated as a
* by-product of the scattering vector calculation and can be used later for
* calculating intensities from differential scattering cross sections.
*
* <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 HDF5 fields to copy
* to the output stream.
**/
struct image;
struct image {
/* The following three fields will be going away in the future */
float *data;
uint16_t *flags;
double *twotheta;
float **dp; /* Data in panel */
int **bad; /* Bad pixels by panel */
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 copy_hdf5_field *copyme;
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; /* Bandwidth as a fraction */
int width;
int height;
/* Detected peaks */
long long int num_peaks;
long long int 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 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,
double *d, int *idx,
struct detector *det);
extern Reflection *image_reflection_closest(RefList *rlist,
double fs, double ss,
struct detector *det,
double *d);
extern int image_feature_count(ImageFeatureList *flist);
extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
extern void image_add_crystal(struct image *image, Crystal *cryst);
extern void free_all_crystals(struct image *image);
#ifdef __cplusplus
}
#endif
#endif /* IMAGE_H */
|
