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
|
/*
* index.h
*
* Perform indexing (somehow)
*
* Copyright © 2012-2020 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
/**
* \file index.h
* The indexing subsystem
*/
#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX)
#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_USE_CELL_PARAMETERS)
#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS)
#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX | INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS)
#define INDEXING_DEFAULTS_TAKETWO (INDEXING_TAKETWO \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_USE_LATTICE_TYPE)
#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS)
#define INDEXING_DEFAULTS_XGANDALF (INDEXING_XGANDALF | INDEXING_USE_CELL_PARAMETERS)
#define INDEXING_DEFAULTS_PINKINDEXER (INDEXING_PINKINDEXER | INDEXING_USE_CELL_PARAMETERS)
/**
* An enumeration of all the available indexing methods.
**/
typedef enum {
INDEXING_NONE = 0, /**< No indexing to be performed */
INDEXING_DIRAX = 1, /**< Invoke DirAx program */
INDEXING_MOSFLM = 2, /**< Invoke MOSFLM program */
INDEXING_FELIX = 4, /**< Invoke Felix program */
INDEXING_XDS = 5, /**< Invoke XDS program (NB not nXDS) */
INDEXING_SIMULATION = 6, /**< Dummy value for simulated data */
INDEXING_FILE = 7, /**< Results injector for debugging */
INDEXING_ASDF = 8, /**< Use built-in ASDF algorithm */
INDEXING_TAKETWO = 9, /**< Use built-in TakeTwo algorithm */
INDEXING_XGANDALF = 10, /**< Use XGANDALF (via optional library) */
INDEXING_PINKINDEXER = 11,/**< Use PinkIndexer (via optional library) */
INDEXING_ERROR = 255, /**< Special value for unrecognised indexing
* engine */
/** \name Bits which can be set to modify the behaviour of the above
* indexing methods */
/**@{*/
/** Use lattice type and centering information */
INDEXING_USE_LATTICE_TYPE = 2048,
/** Use the cell parameters themselves */
INDEXING_USE_CELL_PARAMETERS = 4096,
/**@}*/
} IndexingMethod;
/** This defines the bits in "IndexingMethod" which are used to represent the
* core of the indexing method */
#define INDEXING_METHOD_MASK (0xff)
/**
* Flags affecting how the indexing system processes the results from the
* indexing engine
*/
typedef enum {
/** Retry indexing if it doesn't work */
INDEXING_RETRY = 1,
/** Attempt to index remaining peaks to find more lattices */
INDEXING_MULTI = 2,
/** Refine the indexing solution */
INDEXING_REFINE = 4,
/* 8, 16 reserved (formerly INDEXING_CHECK_CELL_COMBINATIONS and
* INDEXING_CHECK_CELL_AXES respectively) */
/** Check that the peaks agree with the indexing solution */
INDEXING_CHECK_PEAKS = 32,
/** Check that the unit cell agrees with the target cell */
INDEXING_CHECK_CELL = 64,
} IndexingFlags;
#ifdef __cplusplus
extern "C" {
#endif
/**
* 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);
extern IndexingMethod get_indm_from_string_2(const char *method, int *err);
#include "detector.h"
#include "cell.h"
#include "image.h"
#include "taketwo.h"
#include "xgandalf.h"
#include "pinkindexer.h"
#include "felix.h"
extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
struct detector *det,
struct beam_params *beam, float *ltl,
IndexingFlags flags,
struct taketwo_options *ttopts,
struct xgandalf_options *xgandalf_opts,
struct pinkIndexer_options *pinkIndexer_opts,
struct felix_options *felix_opts,
char *filename);
extern const IndexingMethod *indexing_methods(IndexingPrivate *p, int *n);
extern char *detect_indexing_methods(UnitCell *cell);
extern void index_pattern(struct image *image, IndexingPrivate *ipriv);
extern void index_pattern_2(struct image *image, IndexingPrivate *ipriv,
int *ping);
extern void index_pattern_3(struct image *image, IndexingPrivate *ipriv,
int *ping, char *last_task);
extern void cleanup_indexing(IndexingPrivate *ipriv);
#ifdef __cplusplus
}
#endif
#endif /* INDEX_H */
|
