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
|
/*
* detector.h
*
* Detector properties
*
* Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
*
* Authors:
* 2009-2017 Thomas White <taw@physics.org>
* 2011-2012 Richard Kirian <rkirian@asu.edu>
* 2014 Valerio Mariani
* 2011 Andrew Aquila
*
* 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 DETECTOR_H
#define DETECTOR_H
struct rigid_group;
struct rg_collection;
struct detector;
struct panel;
struct badregion;
struct beam_params;
struct hdfile;
struct event;
#include "hdf5-file.h"
#include "image.h"
#ifdef __cplusplus
extern "C" {
#endif
struct rigid_group
{
char *name;
struct panel **panels;
int n_panels;
/* Updates to panel position calculated during integration */
double d_fsx;
double d_ssx;
double d_cnx;
double d_fsy;
double d_ssy;
double d_cny;
int have_deltas;
};
struct rg_collection
{
char *name;
struct rigid_group **rigid_groups;
int n_rigid_groups;
};
/**
* panel:
* @name: Text name for the panel (fixed length array)
* @cnx: Location of corner, in pixels, x coordinate
* @cny: Location of corner, in pixels, y coordinate
* @coffset: The offset to be applied from @clen (which may come from elsewhere)
* @clen: The distance from the interaction point to the corner of the first pixel
* @clen_from: Location to get @clen from, e.g. from HDF5 file
* @mask: Location of mask data
* @mask_file: Filename for mask data
* @satmap: Location of per-pixel saturation map
* @satmap_file: Filename for saturation map
* @res: Resolution of panel in pixels per metre
* @badrow: Readout direction (for filtering out clusters of peaks)
* @no_index: Non-zero if panel is entirely "bad"
* @adu_per_photon: Number of detector intensity units per photon
* @adu_per_eV: Number of detector intensity units per eV of photon energy
* @max_adu: Saturation value
* @dim_structure: Dimension structure
* @fsx: Real-space x-direction of data fast-scan direction
* @fsy: Real-space y-direction of data fast-scan direction
* @fsz: Real-space z-direction of data fast-scan direction
* @ssx: Real-space x-direction of data slow-scan direction
* @ssy: Real-space y-direction of data slow-scan direction
* @ssz: Real-space z-direction of data slow-scan direction
* @rail_x: x direction of camera length "rail"
* @rail_y: y direction of camera length "rail"
* @rail_z: z direction of camera length "rail"
* @clen_for_centering: Value of clen (without coffset) at which beam is centered
* @xfs: Data fast-scan direction of real-space x-direction
* @yfs: Data fast-scan direction of real-space y-direction
* @xss: Data slow-scan direction of real-space x-direction
* @yss: Data slow-scan direction of real-space y-direction
* @orig_min_fs: Minimum fs coordinate of data in file
* @orig_max_fs: Maximum fs coordinate of data in file
* @orig_min_ss: Minimum ss coordinate of data in file (inclusive)
* @orig_max_ss: Maximum ss coordinate of data in file (inclusive)
* @data: Location of data in file
* @w: Width of panel
* @h: Height of panel
*/
struct panel
{
char name[1024]; /* Name for this panel */
double cnx; /* Location of corner (min_fs,min_ss) in pixels */
double cny;
double coffset;
double clen; /* Camera length in metres */
char *clen_from;
char *mask;
char *mask_file;
char *satmap;
char *satmap_file;
double res; /* Resolution in pixels per metre */
char badrow; /* 'x' or 'y' */
int no_index; /* Don't index peaks in this panel if non-zero */
double adu_per_photon; /* Number of ADU per photon */
double max_adu; /* Treat pixel as unreliable if higher than this */
char *data;
double adu_per_eV; /* Number of ADU per eV */
struct dim_structure *dim_structure;
double fsx;
double fsy;
double fsz;
double ssx;
double ssy;
double ssz;
double rail_x;
double rail_y;
double rail_z;
double clen_for_centering;
double xfs;
double yfs;
double xss;
double yss;
/* Position of the panel in the data block in the file. The panels may
* get moved around when the file is loaded (see hdf5_read2()),
* especially if the panels come from different HDF5 elements. */
int orig_min_fs;
int orig_max_fs;
int orig_min_ss;
int orig_max_ss;
int w; /* Width, calculated as max_fs-min_fs+1 */
int h; /* Height, calculated as max_ss-min_ss+1 */
};
struct badregion
{
char name[1024];
int is_fsss;
char *panel;
double min_x;
double max_x;
double min_y;
double max_y;
/* Specified INCLUSIVELY */
int min_fs;
int max_fs;
int min_ss;
int max_ss;
};
struct detector
{
struct panel *panels;
int n_panels;
struct badregion *bad;
int n_bad;
unsigned int mask_bad;
unsigned int mask_good;
struct rigid_group **rigid_groups;
int n_rigid_groups;
struct rg_collection **rigid_group_collections;
int n_rg_collections;
/* Location of the pixel furthest away from the beam position, which
* will have the largest value of 2theta regardless of camera length
* and wavelength */
struct panel *furthest_out_panel;
double furthest_out_fs;
double furthest_out_ss;
/* As above, but for the smallest 2theta */
struct panel *furthest_in_panel;
double furthest_in_fs;
double furthest_in_ss;
int path_dim;
int dim_dim;
struct panel defaults;
};
extern struct rvec get_q_for_panel(struct panel *p, double fs, double ss,
double *ttp, double k);
extern double get_tt(struct image *image, double xs, double ys, int *err);
extern int in_bad_region(struct detector *det, struct panel *p,
double fs, double ss);
extern void record_image(struct image *image, int do_poisson, double background,
gsl_rng *rng, double beam_radius, double nphotons);
extern struct panel *find_orig_panel(struct detector *det,
double fs, double ss);
extern signed int find_orig_panel_number(struct detector *det,
double fs, double ss);
extern int panel_number(struct detector *det, struct panel *p);
extern struct detector *get_detector_geometry(const char *filename,
struct beam_params *beam);
extern struct detector *get_detector_geometry_2(const char *filename,
struct beam_params *beam,
char **hdf5_peak_path);
extern void free_detector_geometry(struct detector *det);
extern struct detector *simple_geometry(const struct image *image, int w, int h);
extern void get_pixel_extents(struct detector *det,
double *min_x, double *min_y,
double *max_x, double *max_y);
extern void fill_in_adu(struct image *image);
extern void adjust_centering_for_rail(struct panel *p);
extern int panel_is_in_rigid_group(const struct rigid_group *rg,
struct panel *p);
extern int rigid_group_is_in_collection(struct rg_collection *c,
struct rigid_group *rg);
extern struct detector *copy_geom(const struct detector *in);
extern int reverse_2d_mapping(double x, double y, struct detector *det,
struct panel **pp, double *pfs, double *pss);
extern double largest_q(struct image *image);
extern double smallest_q(struct image *image);
extern struct panel *find_panel_by_name(struct detector *det, const char *name);
extern int write_detector_geometry_2(const char *geometry_filename,
const char *output_filename,
struct detector *det,
const char *additional_comment,
int write_panel_coffset);
extern int write_detector_geometry(const char *geometry_filename,
const char *output_filename,
struct detector *det);
extern void mark_resolution_range_as_bad(struct image *image,
double min, double max);
extern int single_panel_data_source(struct detector *det, const char *element);
struct rg_collection *find_rigid_group_collection_by_name(struct detector *det,
const char *name);
extern int detector_has_clen_references(struct detector *det);
extern int multi_event_geometry(struct detector *det);
#ifdef __cplusplus
}
#endif
#endif /* DETECTOR_H */
|
