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/*
* basis.c
*
* Find approximate lattices to feed various procedures
*
* (c) 2007 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "utils.h"
#include "reflections.h"
#include "basis.h"
static double basis_efom(ReflectionList *reflectionlist, Basis *basis) {
int n_indexed, n_counted;
Reflection *cur;
cur = reflectionlist->reflections;
n_indexed = 0;
n_counted = 0;
while ( cur ) {
if ( cur->type == REFLECTION_NORMAL ) {
/* Can this basis "approximately" account for this reflection? */
double det;
double a11, a12, a13, a21, a22, a23, a31, a32, a33;
double h, k, l;
/* Set up the coordinate transform from hkl to xyz */
a11 = basis->a.x; a12 = basis->a.y; a13 = basis->a.z;
a21 = basis->b.x; a22 = basis->b.y; a23 = basis->b.z;
a31 = basis->c.x; a32 = basis->c.y; a33 = basis->c.z;
/* Invert the matrix to get hkl from xyz */
det = a11*(a22*a33 - a23*a32) - a12*(a21*a33 - a23*a31) + a13*(a21*a32 - a22*a31);
h = ((a22*a33-a23*a32)*cur->x + (a23*a31-a21*a33)*cur->y + (a21*a32-a22*a31)*cur->z) / det;
k = ((a13*a32-a12*a33)*cur->x + (a11*a33-a13*a31)*cur->y + (a12*a31-a11*a32)*cur->z) / det;
l = ((a12*a23-a13*a22)*cur->x + (a13*a21-a11*a23)*cur->y + (a11*a22-a12*a21)*cur->z) / det;
/* Calculate the deviations in terms of |a|, |b| and |c| */
h = fabs(h); k = fabs(k); l = fabs(l);
h -= floor(h); k -= floor(k); l -= floor(l);
if ( h == 1.0 ) h = 0.0;
if ( k == 1.0 ) k = 0.0;
if ( l == 1.0 ) l = 0.0;
/* Define "approximately" here. Circle in basis space becomes an ellipsoid in reciprocal space */
if ( h*h + k*k + l*l <= 0.1*0.1*0.1 ) n_indexed++;
n_counted++;
}
cur = cur->next;
}
return (double)n_indexed / n_counted;
}
static int basis_lfom(ControlContext *ctx, double vx, double vy, double vz) {
Reflection *tcentre;
int lfom;
double tol;
int j;
lfom = 0;
tol = modulus(vx, vy, vz)/10.0;
tcentre = ctx->reflectionlist->reflections;
do {
for ( j=-20; j<=20; j++ ) {
Reflection *check;
check = reflection_find_nearest(ctx->reflectionlist, tcentre->x+vx*j, tcentre->y+vy*j, tcentre->z+vz*j);
if ( check && (distance3d(check->x, check->y, check->z, tcentre->x+vx*j, tcentre->y+vy*j, tcentre->z+vz*j) < tol) ) {
lfom++;
}
}
tcentre = tcentre->next;
} while ( tcentre );
return lfom;
}
static ReflectionList *basis_find_seeds(ControlContext *ctx) {
double tilt_min;
double tilt_max;
double tilt_mid;
ImageRecord *imagerecord;
double x_temp, y_temp, z_temp;
double scale;
double x, y, z;
Reflection *centre;
int i;
ReflectionList *seeds;
seeds = reflection_init();
/* Locate the 'plane' in the middle of the "wedge".
* This whole procedure assumes there is just one tilt axis. */
tilt_min = control_min_tilt(ctx);
tilt_max = control_max_tilt(ctx);
tilt_mid = tilt_min + (tilt_max-tilt_min)/2;
imagerecord = control_image_nearest_tilt(ctx, tilt_mid);
/* Apply the last two steps of the mapping transform to get the direction from the origin
* towards the middle of the wedge */
x_temp = 0.0;
y_temp = cos(deg2rad(imagerecord->tilt));
z_temp = -sin(deg2rad(imagerecord->tilt));
x = x_temp*cos(-deg2rad(imagerecord->omega)) + y_temp*sin(-deg2rad(imagerecord->omega));
y = -x_temp*sin(-deg2rad(imagerecord->omega)) + y_temp*cos(-deg2rad(imagerecord->omega));
z = z_temp;
/* Find the point in the middle of the "wedge" */
scale = reflection_largest_g(ctx->reflectionlist)/4;
x *= scale;
y *= scale;
z *= scale;
reflection_add(ctx->reflectionlist, x, y, z, 1.0, REFLECTION_VECTOR_MARKER_2);
/* Find an "origin" reflection */
centre = reflection_find_nearest(ctx->reflectionlist, x, y, z);
if ( !centre ) return NULL;
centre->found = 1;
reflection_add(ctx->reflectionlist, centre->x, centre->y, centre->z, 1.0, REFLECTION_GENERATED);
for ( i=1; i<=10; i++ ) {
Reflection *vector;
int accept;
double vx, vy, vz;
do {
Reflection *check;
int lfom;
accept = 1;
/* Find a "candidate vector" reflection */
vector = reflection_find_nearest_longer(ctx->reflectionlist, centre->x, centre->y, centre->z, 1e9); /* 0.5 A^-1 */
if ( !vector ) {
printf("BS: Couldn't find enough seeds\n");
return NULL;
}
vector->found = 1;
/* Get vector components (not the coordinates the vector was calculated from!) */
vx = vector->x - centre->x;
vy = vector->y - centre->y;
vz = vector->z - centre->z;
/* Proximity test */
check = reflection_find_nearest_type(ctx->reflectionlist, vx, vy, vz, REFLECTION_NORMAL);
if ( check ) {
if ( distance3d(vx, vy, vz, check->x, check->y, check->z) < 1e9 ) {
/* Too close to another seed */
accept = 0;
continue;
}
}
/* lFOM test */
lfom = basis_lfom(ctx, vx, vy, vz);
if ( lfom < 1 ) {
accept = 0;
continue;
}
printf("lfom=%i\n", lfom);
} while ( !accept );
reflection_add(seeds, vx, vy, vz, 1.0, REFLECTION_NORMAL);
reflection_add(ctx->reflectionlist, vx, vy, vz, 1.0, REFLECTION_MARKER);
}
return seeds;
}
Basis *basis_find(ControlContext *ctx) {
Basis *basis;
ReflectionList *seeds;
Reflection *ref;
int i;
/* Get the shortlist of seeds */
seeds = basis_find_seeds(ctx);
/* Assemble the seeds into a basis */
basis = malloc(sizeof(Basis));
ref = seeds->reflections;
for ( i=1; i<=3; i++ ) {
double vx, vy, vz;
vx = ref->x;
vy = ref->y;
vz = ref->z;
switch ( i ) {
case 1 : {
basis->a.x = vx;
basis->a.y = vy;
basis->a.z = vz;
}
case 2 : {
basis->b.x = vx;
basis->b.y = vy;
basis->b.z = vz;
}
case 3 : {
basis->c.x = vx;
basis->c.y = vy;
basis->c.z = vz;
}
}
ref = ref->next;
}
printf("BS: eFOM = %7.3f %%\n", basis_efom(ctx->reflectionlist, basis)*100);
return basis;
}
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