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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"
/* 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;
} else {
rflist->features[i].partner = NULL;
}
}
}
ImageFeatureList *reproject_get_reflections(ImageRecord *image, ReflectionList *reflectionlist) {
ImageFeatureList *flist;
Reflection *reflection;
double smax = 0.4e9;
double tilt, omega, k;
double nx, ny, nz; /* "normal" vector */
double kx, ky, kz; /* Electron wavevector ("normal" times 1/lambda */
double ux, uy, uz, uxt, uyt, uzt; /* "up" vector (and calculation intermediates) */
//int done_debug = 0;
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 */
//reflection_add(ctx->reflectionlist, kx, ky, kz, 1, REFLECTION_VECTOR_MARKER_1);
/* Determine where "up" is
* See above. */
uxt = 0.0; uyt = 1.0; uzt = 0.0;
ux = uxt; uy = cos(tilt)*uyt + sin(tilt)*uzt; uz = -sin(tilt)*uyt + cos(tilt)*uzt;
uxt = ux; uyt = uy; uzt = uz;
ux = uxt*cos(-omega) + uyt*-sin(omega); uy = -uxt*sin(omega) + uyt*cos(omega); uz = uzt;
//reflection_add(ctx->reflectionlist, ux*50e9, uy*50e9, uz*50e9, 1, REFLECTION_VECTOR_MARKER_2);
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 cx, cy, cz;
double theta;
double x, y;
double rx, ry, rz;
/* 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 psi, disc;
//reflection_add(ctx->reflectionlist, xl, yl, zl, 1, REFLECTION_GENERATED);
//reflection_add(ctx->reflectionlist, xi, yi, zi, 1, REFLECTION_MARKER);
/* Calculate azimuth of point in image (clockwise from "up", will be changed later) */
cx = yi*nz-zi*ny; cy = nx*zi-nz*xi; cz = ny*xi-nx*yi; /* c = i x n */
psi = angle_between(cx, cy, cz, ux, uy, uz);
/* Finally, resolve the +/- Pi ambiguity from the previous step */
rx = cy*nz-cz*ny; ry = nx*cz-nz*cx; rz = ny*cx-nx*cy; /* r = [i x n] x n */
disc = angle_between(rx, ry, rz, ux, uy, uz);
// if ( (i==20) && !done_debug ) {
// reflection_add(ctx->reflectionlist, xi, yi, zi, 1, REFLECTION_VECTOR_MARKER_3);
// reflection_add(ctx->reflectionlist, cx, cy, cz, 1, REFLECTION_VECTOR_MARKER_4);
// reflection_add(ctx->reflectionlist, rx, ry, rz, 1, REFLECTION_VECTOR_MARKER_4);
// printf("psi=%f deg, disc=%f deg\n", rad2deg(psi), rad2deg(disc));
// }
if ( (psi >= M_PI_2) && (disc >= M_PI_2) ) {
psi -= M_PI_2; /* Case 1 */
// if ( (i==20) && !done_debug ) printf("case 1\n");
} else if ( (psi >= M_PI_2) && (disc < M_PI_2) ) {
psi = 3*M_PI_2 - psi; /* Case 2 */
// if ( (i==20) && !done_debug ) printf("case 2\n");
} else if ( (psi < M_PI_2) && (disc < M_PI_2) ) {
psi = 3*M_PI_2 - psi; /* Case 3 */
// if ( (i==20) && !done_debug ) printf("case 3\n");
} else if ( (psi < M_PI_2) && (disc >= M_PI_2) ) {
psi = 3*M_PI_2 + psi; /* Case 4 */
// if ( (i==20) && !done_debug ) printf("case 4\n");
}
// if ( (i==20) && !done_debug ) printf("final psi=%f clockwise from 'up'\n", rad2deg(psi));
psi = M_PI_2 - psi; /* Anticlockwise from "+x" instead of clockwise from "up" */
// if ( (i==20) && !done_debug ) printf("final psi=%f anticlockwise from +x\n", rad2deg(psi));
psi += omega;
// if ( (i==20) && !done_debug ) printf("final psi=%f anticlockwise from +tilt axis\n", rad2deg(psi));
// if ( (i==20) && !done_debug ) done_debug = 1;
/* Calculate 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 */
image_add_feature_reflection(flist, x, y, image, reflection->intensity, reflection);
/* Intensity should be multiplied by relrod spike function except
* reprojected reflections aren't used quantitatively for anything */
//printf("Reflection at %f, %f\n", x, y);
} /* else it's outside the picture somewhere */
} /* else this is the central beam so don't worry about it */
}
reflection = reflection->next;
} while ( reflection );
/* Partner features only if the image has a feature list. This allows the test
* program 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++ ) {
image_feature_list_free(ctx->images->images[i].rflist);
ctx->images->images[i].rflist = NULL;
}
}
/* Notify that ctx->cell has changed (also need to call displaywindow_update) */
void reproject_lattice_changed(ControlContext *ctx) {
reproject_cell_to_lattice(ctx);
displaywindow_update_imagestack(ctx->dw);
}
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