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/*
* reax.c
*
* A new auto-indexer
*
* (c) 2011 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <assert.h>
#include <fftw3.h>
#include "image.h"
#include "utils.h"
#include "peaks.h"
#include "cell.h"
#include "index.h"
#include "index-priv.h"
struct dvec
{
double x;
double y;
double z;
};
struct reax_private
{
IndexingPrivate base;
struct dvec *directions;
int n_dir;
};
static double check_dir(struct dvec *dir, ImageFeatureList *flist, double modv,
int nel, double pmax, double *fft_in,
fftw_complex *fft_out, fftw_plan plan)
{
int n, i;
for ( i=0; i<nel; i++ ) {
fft_in[i] = 0.0;
}
n = image_feature_count(flist);
for ( i=0; i<n; i++ ) {
struct imagefeature *f;
double val;
int idx;
f = image_get_feature(flist, i);
if ( f == NULL ) continue;
val = f->rx*dir->x + f->ry*dir->y + f->rz*dir->z;
idx = nel/2 + nel*val/(2.0*pmax);
fft_in[idx]++;
}
fftw_execute(plan);
return 0.0;
}
void reax_index(IndexingPrivate *pp, struct image *image, UnitCell *cell)
{
int i;
struct reax_private *p;
double fom;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double mod_as;
double dx, dy, dz;
int nel, n;
double pmax;
double *fft_in;
fftw_complex *fft_out;
fftw_plan plan;
const double cellmax = 50.0e-9; /* 50 nm max cell size */
assert(pp->indm == INDEXING_REAX);
p = (struct reax_private *)pp;
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
mod_as = modulus(asx, asy, asz);
n = image_feature_count(image->features);
pmax = 0.0;
for ( i=0; i<n; i++ ) {
struct imagefeature *f;
double val;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
val = modulus(f->rx, f->ry, f->rz);
if ( val > pmax ) pmax = val;
}
nel = 2.0*pmax*5.0*cellmax;
fft_in = fftw_malloc(nel*sizeof(double));
fft_out = fftw_malloc((nel/2 + 1)*sizeof(fftw_complex));
plan = fftw_plan_dft_r2c_1d(nel, fft_in, fft_out, FFTW_ESTIMATE);
/* Search for a* */
fom = 0.0; dx = 0.0; dy = 0.0; dz = 0.0;
for ( i=0; i<p->n_dir; i++ ) {
double new_fom;
new_fom = check_dir(&p->directions[i], image->features, mod_as,
nel, pmax, fft_in, fft_out, plan);
if ( new_fom > fom ) {
fom = new_fom;
dx = p->directions[i].x;
dy = p->directions[i].x;
dz = p->directions[i].x;
}
}
fftw_destroy_plan(plan);
fftw_free(fft_in);
fftw_free(fft_out);
/* No improvement from zero? */
if ( fom == 0.0 ) return;
}
IndexingPrivate *reax_prepare()
{
struct reax_private *priv;
int ui, vi;
int samp;
double angular_inc;
priv = calloc(1, sizeof(*priv));
if ( priv == NULL ) return NULL;
priv->base.indm = INDEXING_REAX;
/* Decide on sampling interval */
angular_inc = 0.03; /* From Steller (1997) */
samp = (2.0 * M_PI) / angular_inc;
priv->n_dir = samp*samp;
priv->directions = malloc(priv->n_dir*sizeof(struct dvec));
if ( priv == NULL) {
free(priv);
return NULL;
}
/* Generate vectors for 1D Fourier transforms */
for ( ui=0; ui<samp; ui++ ) {
for ( vi=0; vi<samp; vi++ ) {
double u, v;
double th, ph;
struct dvec *dir;
u = (double)ui/samp;
v = (double)vi/samp;
/* Uniform sampling of a hemisphere */
th = 2.0 * M_PI * u; /* "Longitude" */
ph = acos(v); /* "Latitude" */
dir = &priv->directions[ui + vi*samp];
dir->x = cos(th) * sin(ph);
dir->y = sin(th) * sin(ph);
dir->z = cos(ph);
}
}
return (IndexingPrivate *)priv;
}
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