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
|
/*
* reax.c
*
* A new auto-indexer
*
* (c) 2011 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 <assert.h>
#include <fftw3.h>
#include "image.h"
#include "utils.h"
#include "peaks.h"
#include "cell.h"
#include "index.h"
#include "index-priv.h"
struct dvec
{
double x;
double y;
double z;
};
struct reax_private
{
IndexingPrivate base;
struct dvec *directions;
int n_dir;
};
static double check_dir(struct dvec *dir, ImageFeatureList *flist, double modv,
double pmax, double *fft_in, fftw_complex *fft_out,
fftw_plan plan)
{
int n, i, v;
double *vals;
n = image_feature_count(flist);
vals = malloc(n*sizeof(double));
v = 0;
for ( i=0; i<n; i++ ) {
struct imagefeature *f;
f = image_get_feature(flist, i);
if ( f == NULL ) continue;
vals[v] = f->rx*dir->x + f->ry*dir->y + f->rz*dir->z;
v++; /* Yuk, yuk, yuk */
}
free(vals);
return 0.0;
}
void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
{
int i;
struct reax_private *p;
double fom;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double mod_as;
double dx, dy, dz;
int nel, n;
double pmax;
double *fft_in;
fftw_complex *fft_out;
fftw_plan plan;
const double cellmax = 50.0e9; /* 50 nm max cell size */
assert(pp->indm == INDEXING_REAX);
p = (struct reax_private *)pp;
cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
mod_as = modulus(asx, asy, asz);
n = image_feature_count(image->features);
pmax = 0.0;
for ( i=0; i<n; i++ ) {
struct imagefeature *f;
double val;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
val = modulus(f->rx, f->ry, f->rz);
if ( val > pmax ) pmax = val;
}
nel = 2.0*pmax*5.0*cellmax;
fft_in = fftw_malloc(nel*sizeof(double));
fft_out = fftw_malloc((nel/2 + 1)*sizeof(fftw_complex));
plan = fftw_plan_dft_r2c_1d(nel, fft_in, fft_out, FFTW_ESTIMATE);
/* Search for a* */
fom = 0.0; dx = 0.0; dy = 0.0; dz = 0.0;
for ( i=0; i<p->n_dir; i++ ) {
double new_fom;
new_fom = check_dir(&p->directions[i], image->features, mod_as,
pmax, fft_in, fft_out, plan);
if ( new_fom > fom ) {
fom = new_fom;
dx = p->directions[i].x;
dy = p->directions[i].x;
dz = p->directions[i].x;
}
}
fftw_destroy_plan(plan);
fftw_free(fft_in);
fftw_free(fft_out);
/* No improvement from zero? */
if ( fom == 0.0 ) return;
}
IndexingPrivate *reax_prepare()
{
struct reax_private *priv;
int ui, vi;
int samp;
double angular_inc;
priv = calloc(1, sizeof(*priv));
if ( priv == NULL ) return NULL;
priv->base.indm = INDEXING_REAX;
/* Decide on sampling interval */
angular_inc = 0.03; /* From Steller (1997) */
samp = (2.0 * M_PI) / angular_inc;
priv->n_dir = samp*samp;
priv->directions = malloc(priv->n_dir*sizeof(struct dvec));
if ( priv == NULL) {
free(priv);
return NULL;
}
/* Generate vectors for 1D Fourier transforms */
for ( ui=0; ui<samp; ui++ ) {
for ( vi=0; vi<samp; vi++ ) {
double u, v;
double th, ph;
struct dvec *dir;
u = (double)ui/samp;
v = (double)vi/samp;
/* Uniform sampling of a hemisphere */
th = 2.0 * M_PI * u;
ph = acos(v);
dir = &priv->directions[ui + vi*samp];
dir->x = cos(th) * sin(ph);
dir->y = sin(th) * sin(th);
dir->z = cos(ph);
}
}
return (IndexingPrivate *)priv;
}
|
