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
|
/*
* mapping.c
*
* 3D Mapping
*
* (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "reflections.h"
#include "control.h"
#include "image.h"
#include "displaywindow.h"
#include "cache.h"
#include "utils.h"
void mapping_rotate(double x, double y, double z, double *ddx, double *ddy, double *ddz, double omega, double tilt) {
double nx, ny, nz;
double x_temp, y_temp, z_temp;
/* First: rotate image clockwise until tilt axis is aligned horizontally. */
nx = x*cos(omega) + y*sin(omega);
ny = -x*sin(omega) + y*cos(omega);
nz = z;
/* Now, tilt about the x-axis ANTICLOCKWISE around +x, i.e. the "wrong" way.
This is because the crystal is rotated in the experiment, not the Ewald sphere. */
x_temp = nx; y_temp = ny; z_temp = nz;
nx = x_temp;
ny = cos(tilt)*y_temp + sin(tilt)*z_temp;
nz = -sin(tilt)*y_temp + cos(tilt)*z_temp;
/* Finally, reverse the omega rotation to restore the location of the image in 3D space */
x_temp = nx; y_temp = ny; z_temp = nz;
nx = x_temp*cos(-omega) + y_temp*sin(-omega);
ny = -x_temp*sin(-omega) + y_temp*cos(-omega);
nz = z_temp;
*ddx = nx;
*ddy = ny;
*ddz = nz;
}
int mapping_map_to_space(ImageFeature *refl, double *ddx, double *ddy, double *ddz, double *twotheta) {
/* "Input" space */
double d, x, y;
ImageRecord *imagerecord;
/* Angular description of reflection */
double theta, psi, k;
/* Reciprocal space */
double tilt;
double omega;
double x_temp, y_temp, z_temp;
imagerecord = refl->parent;
x = refl->x - imagerecord->x_centre; y = refl->y - imagerecord->y_centre;
tilt = imagerecord->tilt;
omega = imagerecord->omega;
k = 1/imagerecord->lambda;
/* Calculate an angular description of the reflection */
if ( imagerecord->fmode == FORMULATION_CLEN ) {
x /= imagerecord->resolution;
y /= imagerecord->resolution; /* Convert pixels to metres */
d = sqrt((x*x) + (y*y));
theta = atan2(d, imagerecord->camera_len);
} else if (imagerecord->fmode == FORMULATION_PIXELSIZE ) {
x *= imagerecord->pixel_size;
y *= imagerecord->pixel_size; /* Convert pixels to metres^-1 */
d = sqrt((x*x) + (y*y));
theta = atan2(d, k);
} else {
fprintf(stderr, "Unrecognised formulation mode in mapping_map_to_space.\n");
return -1;
}
psi = atan2(y, x);
x_temp = k*sin(theta)*cos(psi);
y_temp = k*sin(theta)*sin(psi);
z_temp = k - k*cos(theta);
mapping_rotate(x_temp, y_temp, z_temp, ddx, ddy, ddz, omega, tilt);
*twotheta = theta; /* Radians. I've used the "wrong" nomenclature above */
return 0;
}
int mapping_scale(ImageFeature *refl, double *ddx, double *ddy) {
double x, y;
ImageRecord *imagerecord;
double k;
imagerecord = refl->parent;
x = refl->x - imagerecord->x_centre;
y = refl->y - imagerecord->y_centre;
k = 1/imagerecord->lambda;
if ( imagerecord->fmode == FORMULATION_CLEN ) {
x /= imagerecord->resolution;
y /= imagerecord->resolution; /* Convert pixels to metres */
*ddx = x * k / imagerecord->camera_len;
*ddy = y * k / imagerecord->camera_len;
} else if (imagerecord->fmode == FORMULATION_PIXELSIZE ) {
*ddx = x * imagerecord->pixel_size;
*ddy = y * imagerecord->pixel_size; /* Convert pixels to metres^-1 */
} else {
fprintf(stderr, "Unrecognised formulation mode in mapping_scale.\n");
return -1;
}
return 0;
}
/* Return the length of a 1 nm^-1 scale bar in the given image (in pixels)
* Result only strictly valid at the centre of the image */
double mapping_scale_bar_length(ImageRecord *image) {
switch ( image->fmode ) {
case FORMULATION_PIXELSIZE : return 1.0e9/image->pixel_size;
case FORMULATION_CLEN : return 1.0e9*image->resolution*image->camera_len*image->lambda;
default : fprintf(stderr, "Unrecognised formulation mode in mapping_scale_bar_length.\n");
}
return 0.0;
}
void mapping_map_features(ControlContext *ctx) {
int i;
/* Create reflection list for measured reflections */
if ( ctx->reflectionlist ) reflectionlist_free(ctx->reflectionlist);
ctx->reflectionlist = reflectionlist_new();
printf("MP: Mapping to 3D..."); fflush(stdout);
for ( i=0; i<ctx->images->n_images; i++ ) {
int j;
/* Iterate over the features in this image */
for ( j=0; j<ctx->images->images[i].features->n_features; j++ ) {
double nx, ny, nz, twotheta;
if ( !mapping_map_to_space(&ctx->images->images[i].features->features[j],
&nx, &ny, &nz, &twotheta) ) {
reflection_add(ctx->reflectionlist, nx, ny, nz,
ctx->images->images[i].features->features[j].intensity, REFLECTION_NORMAL);
} else {
printf("Couldn't map\n");
}
}
}
printf("done.\n");
}
void mapping_adjust_axis(ControlContext *ctx, double offset) {
int i;
for ( i=0; i<ctx->images->n_images; i++ ) {
printf("Image #%3i: old omega=%f deg, new omega=%f deg\n", i, rad2deg(ctx->images->images[i].omega),
rad2deg(ctx->images->images[i].omega+offset));
ctx->images->images[i].omega += offset;
}
mapping_map_features(ctx);
if ( ctx->dw ) {
displaywindow_update_imagestack(ctx->dw);
displaywindow_update(ctx->dw);
}
}
|
