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/*
* reflections.c
*
* Data structures in 3D space
*
* (c) 2007 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include "reflections.h"
static void reflection_addfirst(ReflectionContext *reflectionctx) {
/* Create first items on lists - saves faffing later. Corresponds to a central marker.
Reflections are only stored if they have non-zero value. */
reflectionctx->reflections = malloc(sizeof(Reflection));
reflectionctx->reflections->next = NULL;
reflectionctx->reflections->x = 0;
reflectionctx->reflections->y = 0;
reflectionctx->reflections->z = 0;
reflectionctx->reflections->type = REFLECTION_CENTRAL;
reflectionctx->last_reflection = reflectionctx->reflections;
}
ReflectionContext *reflection_init() {
ReflectionContext *reflectionctx = malloc(sizeof(ReflectionContext));
reflection_addfirst(reflectionctx);
return reflectionctx;
}
void reflection_clear(ReflectionContext *reflectionctx) {
Reflection *reflection = reflectionctx->reflections;
do {
Reflection *next = reflection->next;
free(reflection);
reflection = next;
} while ( reflection );
reflection_addfirst(reflectionctx);
}
void reflection_free(ReflectionContext *reflectionctx) {
reflection_clear(reflectionctx);
free(reflectionctx->reflections);
free(reflectionctx);
}
void reflection_add(ReflectionContext *reflectionctx, double x, double y, double z, double intensity, ReflectionType type) {
Reflection *new_reflection;
//printf("Added reflection (%f,%f,%f)\n",x,y,z);
new_reflection = malloc(sizeof(Reflection));
new_reflection->next = NULL;
new_reflection->x = x;
new_reflection->y = y;
new_reflection->z = z;
new_reflection->intensity = intensity;
new_reflection->type = type;
reflectionctx->last_reflection->next = new_reflection;
reflectionctx->last_reflection = new_reflection;
}
void reflection_add_index(ReflectionContext *reflectionctx, signed int h, signed int k, signed int l, double intensity, ReflectionType type) {
Reflection *new_reflection;
new_reflection = malloc(sizeof(Reflection));
new_reflection->next = NULL;
new_reflection->h = h;
new_reflection->k = k;
new_reflection->l = l;
new_reflection->intensity = intensity;
new_reflection->type = type;
reflectionctx->last_reflection->next = new_reflection;
reflectionctx->last_reflection = new_reflection;
}
/* x and y in metres (in real space!) */
void reflection_add_from_dp(ControlContext *ctx, double x, double y, double tilt_degrees, double intensity) {
double nx, ny, nz;
/* Real space */
double L;
double d;
/* Shared */
double theta;
double psi;
/* Reciprocal space */
double r;
double tilt;
double omega;
double x_temp, y_temp, z_temp;
tilt = 2*M_PI*(tilt_degrees/360); /* Convert to Radians */
omega = 2*M_PI*(ctx->omega/360); /* Likewise */
d = sqrt((x*x) + (y*y));
L = ctx->camera_length;
theta = atan2(d, L);
psi = atan2(y, x);
r = 1/ctx->lambda;
x_temp = r*sin(theta)*cos(psi);
y_temp = -r*sin(theta)*sin(psi); /* Minus sign to define axes as y going upwards */
z_temp = r- r*cos(theta);
/* Apply the rotations...
First: rotate image clockwise until tilt axis is aligned horizontally. */
nx = x_temp*cos(omega) + y_temp*-sin(omega);
ny = x_temp*sin(omega) + y_temp*cos(omega);
nz = z_temp;
/* 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;
reflection_add(ctx->reflectionctx, nx, ny, nz, intensity, REFLECTION_NORMAL);
}
/* Alternative formulation for when the input data is already in reciprocal space units
x and y in metres^-1 (in reciprocal space) */
void reflection_add_from_reciprocal(ControlContext *ctx, double x, double y, double tilt_degrees, double intensity) {
double nx, ny, nz;
/* Input (reciprocal space) */
double dr;
/* Shared */
double theta;
double psi;
double r;
/* Reciprocal space */
double tilt;
double omega;
double x_temp, y_temp, z_temp;
tilt = M_PI*(tilt_degrees/180); /* Convert to Radians */
omega = M_PI*(ctx->omega/180); /* Likewise */
dr = sqrt((x*x) + (y*y));
r = 1/ctx->lambda;
theta = atan2(dr, r);
psi = atan2(y, x);
x_temp = r*sin(theta)*cos(psi);
y_temp = -r*sin(theta)*sin(psi); /* Minus sign to define axes as y going upwards */
z_temp = r - r*cos(theta);
/* Apply the rotations...
First: rotate image clockwise until tilt axis is aligned horizontally. */
nx = x_temp*cos(omega) + y_temp*-sin(omega);
ny = x_temp*sin(omega) + y_temp*cos(omega);
nz = z_temp;
/* 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;
reflection_add(ctx->reflectionctx, nx, ny, nz, intensity, REFLECTION_NORMAL);
}
void reflection_add_from_reflection(ReflectionContext *rctx, Reflection *r) {
r->next = NULL;
rctx->last_reflection->next = r;
rctx->last_reflection = r;
}
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