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
|
/*
* index.c
*
* Perform indexing (somehow)
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <assert.h>
#include "image.h"
#include "utils.h"
#include "peaks.h"
#include "dirax.h"
#include "sfac.h"
#include "detector.h"
#include "index.h"
#include "index-priv.h"
#include "templates.h"
/* Base class constructor for unspecialised indexing private data */
static IndexingPrivate *indexing_private(IndexingMethod indm)
{
struct _indexingprivate *priv;
priv = calloc(1, sizeof(struct _indexingprivate));
priv->indm = indm;
return priv;
}
IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
const char *filename, struct detector *det)
{
switch ( indm ) {
case INDEXING_NONE :
return indexing_private(indm);
case INDEXING_DIRAX :
return indexing_private(indm);
case INDEXING_TEMPLATE :
return generate_templates(cell, filename, det);
}
return 0;
}
static void write_drx(struct image *image)
{
FILE *fh;
int i;
char filename[1024];
snprintf(filename, 1023, "xfel-%i.drx", image->id);
fh = fopen(filename, "w");
if ( !fh ) {
ERROR("Couldn't open temporary file xfel.drx\n");
return;
}
fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
fprintf(fh, "%10f %10f %10f %8f\n",
f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
}
fclose(fh);
}
void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
int no_match, int verbose, IndexingPrivate *ipriv)
{
int i;
int nc = 0;
/* Map positions to 3D */
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
int c;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
c = map_position(image, f->x, f->y, &f->rx, &f->ry, &f->rz);
if ( c != 0 ) nc++;
}
if ( nc ) {
ERROR("Failed to map %i reflections\n", nc);
}
write_drx(image);
image->ncells = 0;
/* Index (or not) as appropriate */
switch ( indm ) {
case INDEXING_NONE :
return;
case INDEXING_DIRAX :
run_dirax(image);
break;
case INDEXING_TEMPLATE :
match_templates(image, ipriv);
break;
}
if ( image->ncells == 0 ) {
STATUS("No candidate cells found.\n");
return;
}
if ( no_match || (indm == INDEXING_TEMPLATE) ) {
image->indexed_cell = image->candidate_cells[0];
if ( verbose ) {
STATUS("--------------------\n");
STATUS("The indexed cell (matching not performed):\n");
cell_print(image->indexed_cell);
STATUS("--------------------\n");
}
return;
}
for ( i=0; i<image->ncells; i++ ) {
UnitCell *new_cell = NULL;
if ( verbose ) {
STATUS("--------------------\n");
STATUS("Candidate cell %i (before matching):\n", i);
cell_print(image->candidate_cells[i]);
STATUS("--------------------\n");
}
new_cell = match_cell(image->candidate_cells[i], cell, verbose);
image->indexed_cell = new_cell;
if ( new_cell != NULL ) {
STATUS("Matched on attempt %i.\n", i);
goto done;
}
}
done:
for ( i=0; i<image->ncells; i++ ) {
free(image->candidate_cells[i]);
}
}
|
