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/*
* reproject.c
*
* Synthesize diffraction patterns
*
* (c) 2007-2008 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"
#include "imagedisplay.h"
#include "displaywindow.h"
#include "image.h"
#include "mapping.h"
/* Attempt to find partners from the feature list of "image" for each feature in "flist". */
void reproject_partner_features(ImageFeatureList *rflist, ImageRecord *image) {
int i;
for ( i=0; i<rflist->n_features; i++ ) {
//if ( !reflection_is_easy(rflist->features[i].reflection) ) continue;
double d = 0.0;
ImageFeature *partner;
int idx;
partner = image_feature_closest(image->features, rflist->features[i].x, rflist->features[i].y, &d, &idx);
if ( (d <= 20.0) && partner ) {
rflist->features[i].partner = partner;
rflist->features[i].partner_d = d;
image->features->features[idx].partner =
&rflist->features[i];
} else {
rflist->features[i].partner = NULL;
}
}
}
ImageFeatureList *reproject_get_reflections(ImageRecord *image,
ReflectionList *reflectionlist)
{
ImageFeatureList *flist;
Reflection *reflection;
double smax = 0.2e9;
double tilt, omega, k;
double nx, ny, nz; /* "normal" vector */
double kx, ky, kz; /* Electron wavevector ("normal" times 1/lambda */
double ux, uy, uz; /* "up" vector */
double rx, ry, rz; /* "right" vector */
flist = image_feature_list_new();
tilt = image->tilt;
omega = image->omega;
k = 1.0/image->lambda;
/* Calculate the (normalised) incident electron wavevector */
mapping_rotate(0.0, 0.0, 1.0, &nx, &ny, &nz, omega, tilt);
kx = nx / image->lambda;
ky = ny / image->lambda;
kz = nz / image->lambda; /* This is the centre of the Ewald sphere */
/* Determine where "up" is */
mapping_rotate(0.0, 1.0, 0.0, &ux, &uy, &uz, omega, tilt);
/* Determine where "right" is */
mapping_rotate(1.0, 0.0, 0.0, &rx, &ry, &rz, omega, tilt);
reflection = reflectionlist->reflections;
do {
double xl, yl, zl;
double a, b, c;
double s1, s2, s, t;
double g_sq, gn;
/* Get the coordinates of the reciprocal lattice point */
xl = reflection->x;
yl = reflection->y;
zl = reflection->z;
g_sq = modulus_squared(xl, yl, zl);
gn = xl*nx + yl*ny + zl*nz;
/* Next, solve the relrod equation to calculate
* the excitation error */
a = 1.0;
b = 2.0*(gn - k);
c = -2.0*gn*k + g_sq;
t = -0.5*(b + sign(b)*sqrt(b*b - 4.0*a*c));
s1 = t/a;
s2 = c/t;
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 theta;
double x, y;
/* Determine the intersection point */
xi = xl + s*nx; yi = yl + s*ny; zi = zl + s*nz;
/* Calculate Bragg angle */
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);
if ( theta > 0.0 ) {
double dx, dy, psi;
/* Calculate azimuth of point in image
* (anticlockwise from +x) */
dx = xi*rx + yi*ry + zi*rz;
dy = xi*ux + yi*uy + zi*uz;
psi = atan2(dy, dx);
/* Get image coordinates from polar
* representation */
if ( image->fmode == FORMULATION_CLEN ) {
x = image->camera_len*tan(theta)*cos(psi);
y = image->camera_len*tan(theta)*sin(psi);
x *= image->resolution;
y *= image->resolution;
} else if ( image->fmode==FORMULATION_PIXELSIZE ) {
x = tan(theta)*cos(psi) / image->lambda;
y = tan(theta)*sin(psi) / image->lambda;
x /= image->pixel_size;
y /= image->pixel_size;
} else {
fprintf(stderr,
"Unrecognised formulation mode "
"in reproject_get_reflections\n");
return NULL;
}
x += image->x_centre;
y += image->y_centre;
/* Sanity check */
if ( (x>=0) && (x<image->width)
&& (y>=0) && (y<image->height) ) {
/* Record the reflection
* Intensity should be multiplied by
* relrod spike function except
* reprojected reflections aren't used
* quantitatively for anything
*/
image_add_feature_reflection(flist, x,
y, image, reflection->intensity,
reflection);
} /* else it's outside the picture somewhere */
} /* else this is the central beam */
}
reflection = reflection->next;
} while ( reflection );
/* Partner features only if the image has a feature list. This allows
* the test programs to use this function to generate simulated data
*/
if ( image->features != NULL ) {
reproject_partner_features(flist, image);
}
return flist;
}
/* Ensure ctx->cell_lattice matches ctx->cell */
void reproject_cell_to_lattice(ControlContext *ctx) {
int i;
if ( ctx->cell_lattice ) {
reflection_list_from_new_cell(ctx->cell_lattice, ctx->cell);
} else {
ctx->cell_lattice = reflection_list_from_cell(ctx->cell);
}
displaywindow_enable_cell_functions(ctx->dw, TRUE);
/* Invalidate all the reprojected feature lists */
for ( i=0; i<ctx->images->n_images; i++ ) {
ImageRecord *image;
int j;
image = &ctx->images->images[i];
if ( image->rflist != NULL ) {
image_feature_list_free(image->rflist);
image->rflist = NULL;
}
for ( j=0; j<image->features->n_features; j++ ) {
image->features->features[i].partner = NULL;
}
}
}
/* Notify that ctx->cell has changed (also need to call displaywindow_update) */
void reproject_lattice_changed(ControlContext *ctx) {
int i;
int total_reprojected = 0;
int total_measured = 0;
int partnered_reprojected = 0;
int partnered_measured = 0;
reproject_cell_to_lattice(ctx);
for ( i=0; i<ctx->images->n_images; i++ ) {
ImageRecord *image;
int j;
image = &ctx->images->images[i];
/* Perform relrod projection */
image->rflist = reproject_get_reflections(image,
ctx->cell_lattice);
/* Loop over reprojected reflections */
for ( j=0; j<image->rflist->n_features; j++ ) {
double d;
ImageFeature f;
ImageFeature *p;
f = image->rflist->features[j];
p = image->rflist->features[j].partner;
if ( p != NULL ) {
d = distance(f.x, f.y, p->x, p->y);
partnered_reprojected++;
}
}
total_reprojected += image->rflist->n_features;
/* Loop over measured reflections */
for ( j=0; j<image->features->n_features; j++ ) {
double d;
ImageFeature f;
ImageFeature *p;
f = image->features->features[j];
p = image->features->features[j].partner;
if ( p != NULL ) {
d = distance(f.x, f.y, p->x, p->y);
partnered_measured++;
}
}
total_measured += image->features->n_features;
}
printf("%i images\n", ctx->images->n_images);
printf("%i measured reflections\n", total_measured);
printf("%i reprojected reflections\n", total_reprojected);
printf("%i partnered measured reflections\n", partnered_measured);
printf("%i partnered reprojected reflections\n", partnered_reprojected);
displaywindow_update_imagestack(ctx->dw);
}
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