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
|
/*
* index.h
*
* Perform indexing (somehow)
*
* Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
* Copyright © 2012 Lorenzo Galli
*
* Authors:
* 2010-2017 Thomas White <taw@physics.org>
* 2010 Richard Kirian
* 2012 Lorenzo Galli
* 2015 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
*
* 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 INDEX_H
#define INDEX_H
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS \
| INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX \
| INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_TAKETWO (INDEXING_TAKETWO | INDEXING_CHECK_PEAKS \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_USE_LATTICE_TYPE \
| INDEXING_RETRY | INDEXING_REFINE)
/* Axis check is needed for XDS, because it likes to permute the axes */
#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_CHECK_CELL_AXES \
| INDEXING_CHECK_PEAKS \
| INDEXING_RETRY | INDEXING_REFINE)
/**
* IndexingMethod:
* @INDEXING_NONE: No indexing to be performed
* @INDEXING_DIRAX: Invoke DirAx
* @INDEXING_MOSFLM: Invoke MOSFLM
* @INDEXING_FELIX: Invoke Felix
* @INDEXING_XDS: Invoke XDS
* @INDEXING_SIMULATION: Dummy value
* @INDEXING_DEBUG: Results injector for debugging
* @INDEXING_ASDF: Use in-built "asdf" indexer
* @INDEXING_TAKETWO: Use in-built "taketwo" indexer
* @INDEXING_ERROR: Special value for unrecognised indexing engine name
* @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell
* axes for agreement with given cell.
* @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given
* cell, and permute them if necessary.
* @INDEXING_CHECK_PEAKS: Check that the peaks can be explained by the indexing
* result.
* @INDEXING_USE_LATTICE_TYPE: Use lattice type and centering information to
* guide the indexing process.
* @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
* indexing process.
* @INDEXING_RETRY: If the indexer doesn't succeed, delete the weakest peaks
* and try again.
* @INDEXING_MULTI: If the indexer succeeds, delete the peaks explained by the
* lattice and try again in the hope of finding another crystal.
* @INDEXING_REFINE: Perform "prediction refinement" after indexing.
*
* An enumeration of all the available indexing methods. The dummy value
* @INDEXING_SIMULATION is used by partial_sim to indicate that no indexing was
* performed, and that the indexing results are just from simulation.
**/
typedef enum {
INDEXING_NONE = 0,
/* The core indexing methods themselves */
INDEXING_DIRAX = 1,
INDEXING_MOSFLM = 2,
INDEXING_FELIX = 4,
INDEXING_XDS = 5,
INDEXING_SIMULATION = 6,
INDEXING_DEBUG = 7,
INDEXING_ASDF = 8,
INDEXING_TAKETWO = 9,
INDEXING_ERROR = 255, /* Unrecognised indexing engine */
/* Bits at the top of the IndexingMethod are flags which modify the
* behaviour of the indexer. */
INDEXING_CHECK_CELL_COMBINATIONS = 256,
INDEXING_CHECK_CELL_AXES = 512,
INDEXING_CHECK_PEAKS = 1024,
INDEXING_USE_LATTICE_TYPE = 2048,
INDEXING_USE_CELL_PARAMETERS = 4096,
INDEXING_RETRY = 8192,
INDEXING_MULTI = 16384,
INDEXING_REFINE = 32768,
} IndexingMethod;
/* This defines the bits in "IndexingMethod" which are used to represent the
* core of the indexing method */
#define INDEXING_METHOD_MASK (0xff)
/* Indexing flags which the indexing method does not need to know about */
#define INDEXING_CONTROL_FLAGS (INDEXING_RETRY | INDEXING_MULTI | INDEXING_REFINE)
#ifdef __cplusplus
extern "C" {
#endif
/**
* IndexingPrivate:
*
* This is an opaque data structure containing information needed by the
* indexing system.
**/
typedef struct _indexingprivate IndexingPrivate;
/* Convert indexing methods to/from text */
extern char *indexer_str(IndexingMethod indm);
extern IndexingMethod get_indm_from_string(const char *method);
#include "detector.h"
#include "cell.h"
#include "image.h"
extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
struct detector *det, float *ltl,
int no_refine, const char *options);
extern void index_pattern(struct image *image, IndexingPrivate *ipriv);
extern void index_pattern_2(struct image *image, IndexingPrivate *ipriv,
int *ping);
extern void cleanup_indexing(IndexingPrivate *ipriv);
#ifdef __cplusplus
}
#endif
#endif /* INDEX_H */
|
