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
|
/*
* reproject.c
*
* Synthesize diffraction patterns
*
* (c) 2007 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#include <stdlib.h>
#include <math.h>
#include "control.h"
#include "reflections.h"
#include "utils.h"
#define MAX_IMAGE_REFLECTIONS 8*1024
ImageReflection *reproject_get_reflections(ImageRecord image, size_t *n, ReflectionContext *rctx, ControlContext *ctx) {
ImageReflection *refl;
Reflection *reflection;
int i;
double smax = 0.5e9;
double tilt, omega;
tilt = 2*M_PI*(image.tilt/360);
omega = 2*M_PI*(image.omega/360); /* Convert to Radians */
refl = malloc(MAX_IMAGE_REFLECTIONS*sizeof(ImageReflection));
i = 0;
reflection = rctx->reflections;
do {
double xl, yl, zl;
double nx, ny, nz;
double xt, yt, zt;
double a, b, c;
double s1, s2, s;
/* Get the coordinates of the reciprocal lattice point */
xl = reflection->x;
yl = reflection->y;
zl = reflection->z;
/* Now calculate the (normalised) incident electron wavevector */
xt = 0;
yt = - sin(tilt);
zt = - cos(tilt);
nx = xt*cos(omega) + yt*-sin(omega);
ny = xt*sin(omega) + yt*cos(omega);
nz = zt;
/* Next, solve the relrod equation to calculate the excitation error */
a = 1.0;
b = 2.0*(xl*nx + yl*ny + zl*nz - nz/image.lambda);
c = xl*xl + yl*yl + zl*zl - 2.0*zl/image.lambda;
s1 = (-b + sqrt(b*b-4.0*a*c))/(2.0*a);
s2 = (-b - sqrt(b*b-4.0*a*c))/(2.0*a);
if ( fabs(s1) < fabs(s2) ) s = s1; else s = s2;
/* Skip this reflection if s is large */
if ( fabs(s) <= smax ) {
double xi, yi, zi;
double gx, gy, gz;
double kx, ky, kz;
double cx, cy, cz;
double ux, uy, uz;
double uxt, uyt, uzt;
double theta, psi;
double x, y;
/* Determine the intersection point */
xi = xl + s*nx; yi = yl + s*ny; zi = zl + s*nz;
reflection_add(ctx->reflectionctx, xl, yl, zl, 1, REFLECTION_CENTRAL);
reflection_add(ctx->reflectionctx, xi, yi, zi, 1, REFLECTION_MARKER);
/* Calculate Bragg angle and azimuth of point in image */
kx = nx / image.lambda;
ky = ny / image.lambda;
kz = nz / image.lambda; /* This is the centre of the Ewald sphere */
gx = xi - kx;
gy = yi - ky;
gz = zi - kz; /* This is the vector from the centre of the sphere to the intersection */
theta = angle_between(-kx, -ky, -kz, gx, gy, gz);
printf("theta=%f ", theta);
theta = deg2rad(theta);
cx = nz*gy - ny*gz;
cy = nz*gx - nx*gz;
cz = ny*gx - nx*gy;
uxt = 0;
uyt = cos(tilt);
uzt = -sin(tilt);
ux = uyt*-sin(omega);
uy = uyt*cos(omega);
uz = uzt;
psi = angle_between(cx, cy, cz, ux, uy, uz);
psi -= 90;
printf("psi=%f\n", psi);
psi = deg2rad(psi);
if ( image.fmode == FORMULATION_CLEN ) {
x = image.camera_len*sin(theta)*cos(psi);
y = image.camera_len*sin(theta)*sin(psi);
x *= image.resolution;
y *= image.resolution;
} else if ( image.fmode == FORMULATION_PIXELSIZE ) {
x = 0;
y = 0;
} else {
fprintf(stderr, "Unrecognised formulation mode in reproject_get_reflections()\n");
return NULL;
}
/* Adjust centre */
x += image.x_centre;
y += image.y_centre;
/* Sanity check */
if ( (x>=0) && (x<image.width) && (y>=0) && (y<image.height) ) {
/* Record the reflection */
refl[i].x = x;
refl[i].y = y;
i++;
if ( i > MAX_IMAGE_REFLECTIONS ) {
fprintf(stderr, "Too many reflections\n");
break;
}
//printf("Reflection %i at %i,%i\n", i, refl[i-1].x, refl[i-1].y);
} else {
//fprintf(stderr, "Reflection failed sanity test (x=%f, y=%f)\n", x, y);
}
}
reflection = reflection->next;
} while ( reflection );
//printf("Found %i reflections in image\n", i);
*n = i;
return refl;
}
|
