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
|
/*
* 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"
static void write_drx(struct image *image)
{
FILE *fh;
int i;
fh = fopen("xfel.drx", "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)
{
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 */
if ( indm == INDEXING_NONE ) return;
if ( indm == INDEXING_DIRAX ) run_dirax(image);
if ( image->ncells == 0 ) {
STATUS("No candidate cells found.\n");
return;
}
if ( no_match ) {
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]);
}
}
|
