aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/reflist.h
blob: 3085a2aabb1eb1be60384c72e713a00d04bc7b62 (plain)
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
/*
 * reflist.h
 *
 * Fast reflection/peak list
 *
 * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 *
 * Authors:
 *   2011-2018 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/>.
 *
 */

#ifndef REFLIST_H
#define REFLIST_H

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#define SERIAL(h, k, l) ((((h)+512)<<20) + (((k)+512)<<10) + ((l)+512))
#define GET_H(serial) ((((serial) & 0x3ff00000)>>20)-512)
#define GET_K(serial) ((((serial) & 0x000ffc00)>>10)-512)
#define GET_L(serial) (((serial) & 0x000003ff)-512)

/**
 * \file reflist.h
 * The fast reflection list stores reflections in an RB-tree indexed
 * by the Miller indices h, k and l.  Any reflection can be found in a
 * length of time which scales logarithmically with the number of reflections in
 * the list.
 *
 * A RefList can contain any number of reflections, and can store more than
 * one reflection with a given set of indices, for example when two distinct
 * reflections are to be stored according to their asymmetric indices.
 *
 * There are getters and setters which can be used to get and set values for an
 * individual reflection.  The reflection list does not calculate any values,
 * only stores what it was given earlier.  As such, you will need to carefully
 * examine which fields your prior processing steps have filled in.
 */


/**
 * A RefList represents a list of Bragg reflections.
 *
 * This data structure is opaque.  You must use the available accessor functions
 * to read and write its contents.
 *
 **/
typedef struct _reflist RefList;

/**
 * A Reflection represents a single Bragg reflection.
 *
 * This data structure is opaque.  You must use the available accessor functions
 * to read and write its contents.
 *
 **/
typedef struct _reflection Reflection;

/**
 * A RefListIterator is an opaque data type used when iterating over a
 * RefList.
 *
 **/
typedef struct _reflistiterator RefListIterator;

#include "crystal.h"

#ifdef __cplusplus
extern "C" {
#endif

/* Structure representing the contributions to a merged reflection */
struct reflection_contributions
{
	int          n_contrib;
	int          max_contrib;
	Reflection **contribs;
	Crystal    **contrib_crystals;
};

extern RefList *reflist_new(void);


extern void reflist_free(RefList *list);
extern Reflection *reflection_new(signed int h, signed int k, signed int l);
extern void reflection_free(Reflection *refl);

/* Search */
extern Reflection *find_refl(const RefList *list, signed int h, signed int k, signed int l);
extern Reflection *next_found_refl(Reflection *refl);

/* Get */
extern void get_detector_pos(const Reflection *refl, double *fs, double *ss);
extern struct panel *get_panel(const Reflection *refl);
extern double get_partiality(const Reflection *refl);
extern double get_khalf(const Reflection *refl);
extern double get_kpred(const Reflection *refl);
extern double get_exerr(const Reflection *refl);
extern double get_lorentz(const Reflection *refl);
extern void get_indices(const Reflection *refl,
                        signed int *h, signed int *k, signed int *l);
extern void get_symmetric_indices(const Reflection *refl,
                                  signed int *hs, signed int *ks,
                                  signed int *ls);
extern double get_intensity(const Reflection *refl);
extern int get_redundancy(const Reflection *refl);
extern double get_temp1(const Reflection *refl);
extern double get_temp2(const Reflection *refl);
extern double get_esd_intensity(const Reflection *refl);
extern double get_phase(const Reflection *refl, int *have_phase);
extern double get_peak(const Reflection *refl);
extern double get_mean_bg(const Reflection *refl);
extern int get_flag(const Reflection *refl);
extern struct reflection_contributions *get_contributions(const Reflection *refl);

/* Set */
extern void copy_data(Reflection *to, const Reflection *from);
extern void set_detector_pos(Reflection *refl, double fs, double ss);
extern void set_panel(Reflection *refl, struct panel *p);
extern void set_kpred(Reflection *refl, double kpred);
extern void set_khalf(Reflection *refl, double khalf);
extern void set_exerr(Reflection *refl, double exerr);
extern void set_partiality(Reflection *refl, double p);
extern void set_lorentz(Reflection *refl, double L);
extern void set_intensity(Reflection *refl, double intensity);
extern void set_redundancy(Reflection *refl, int red);
extern void set_temp1(Reflection *refl, double temp);
extern void set_temp2(Reflection *refl, double temp);
extern void set_esd_intensity(Reflection *refl, double esd);
extern void set_phase(Reflection *refl, double phase);
extern void set_peak(Reflection *refl, double peak);
extern void set_mean_bg(Reflection *refl, double mean_bg);
extern void set_symmetric_indices(Reflection *refl,
                                  signed int hs, signed int ks, signed int ls);
extern void set_flag(Reflection *refl, int flag);
extern void set_contributions(Reflection *refl,
                              struct reflection_contributions *contribs);

/* Insertion */
extern Reflection *add_refl(RefList *list,
                            signed int h, signed int k, signed int l);
extern void add_refl_to_list(Reflection *refl, RefList *list);

/* Iteration */
extern Reflection *first_refl(RefList *list, RefListIterator **piter);
extern Reflection *next_refl(Reflection *refl, RefListIterator *iter);
extern const Reflection *first_refl_const(const RefList *list, RefListIterator **piter);
extern const Reflection *next_refl_const(const Reflection *refl, RefListIterator *iter);

/* Misc */
extern int num_reflections(RefList *list);
extern int tree_depth(RefList *list);
extern void lock_reflection(Reflection *refl);
extern void unlock_reflection(Reflection *refl);
extern const char *reflist_get_notes(RefList *reflist);
extern void reflist_add_notes(RefList *reflist, const char *notes_add);

#ifdef __cplusplus
}
#endif

#endif	/* REFLIST_H */