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
|
/*
* crystal.c
*
* A class representing a single crystal
*
* Copyright © 2013 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2013 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/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "crystal.h"
#include "utils.h"
/**
* SECTION:crystal
* @short_description: Crystal
* @title: Crystal
* @section_id:
* @see_also:
* @include: "crystal.h"
* @Image:
*
* This structure represents a single crystal.
*/
struct _crystal
{
/* The image containing the crystal */
struct image *image;
/* Information about the crystal */
UnitCell *cell;
double m; /* Mosaicity in radians */
double osf;
double profile_radius;
int pr_dud;
double resolution_limit;
/* Integrated (or about-to-be-integrated) reflections */
RefList *reflections;
long long int n_saturated; /* Number of overloads */
/* User flag, e.g. for "this is a bad crystal". */
int user_flag;
};
/************************** Constructor / Destructor **************************/
/**
* crystal_new:
*
* Create a new %Crystal.
*
* Returns: the new unit cell, or NULL on failure.
*
*/
Crystal *crystal_new()
{
Crystal *cryst;
cryst = malloc(sizeof(Crystal));
if ( cryst == NULL ) return NULL;
cryst->cell = NULL;
cryst->reflections = NULL;
cryst->resolution_limit = 0.0;
cryst->n_saturated = 0;
return cryst;
}
/**
* crystal_free:
* @cryst: A %Crystal to free.
*
* Frees a %Crystal, and all internal resources concerning that crystal.
*
*/
void crystal_free(Crystal *cryst)
{
if ( cryst == NULL ) return;
if ( cryst->cell != NULL ) cell_free(cryst->cell);
if ( cryst->reflections != NULL ) reflist_free(cryst->reflections);
free(cryst);
}
/********************************** Getters ***********************************/
UnitCell *crystal_get_cell(Crystal *cryst)
{
return cryst->cell;
}
double crystal_get_profile_radius(Crystal *cryst)
{
return cryst->profile_radius;
}
RefList *crystal_get_reflections(Crystal *cryst)
{
return cryst->reflections;
}
double crystal_get_resolution_limit(Crystal *cryst)
{
return cryst->resolution_limit;
}
long long int crystal_get_num_saturated_reflections(Crystal *cryst)
{
return cryst->n_saturated;
}
struct image *crystal_get_image(Crystal *cryst)
{
return cryst->image;
}
double crystal_get_osf(Crystal *cryst)
{
return cryst->osf;
}
int crystal_get_user_flag(Crystal *cryst)
{
return cryst->user_flag;
}
/********************************** Setters ***********************************/
void crystal_set_cell(Crystal *cryst, UnitCell *cell)
{
if ( cryst->cell != NULL ) cell_free(cryst->cell);
cryst->cell = cell_new_from_cell(cell);
}
void crystal_set_profile_radius(Crystal *cryst, double r)
{
cryst->profile_radius = r;
}
void crystal_set_reflections(Crystal *cryst, RefList *reflist)
{
if ( cryst->reflections != NULL ) reflist_free(reflist);
cryst->reflections = reflist;
}
void crystal_set_resolution_limit(Crystal *cryst, double res)
{
cryst->resolution_limit = res;
}
void crystal_set_num_saturated_reflections(Crystal *cryst, long long int n)
{
cryst->n_saturated = n;
}
void crystal_set_image(Crystal *cryst, struct image *image)
{
cryst->image = image;
}
void crystal_set_osf(Crystal *cryst, double osf)
{
cryst->osf = osf;
}
void crystal_set_user_flag(Crystal *cryst, int user_flag)
{
cryst->user_flag = user_flag;
}
|
