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/*
* index.c
*
* Perform indexing (somehow)
*
* (c) 2006-2010 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 <string.h>
#include <assert.h>
#include "image.h"
#include "utils.h"
#include "peaks.h"
#include "dirax.h"
#include "sfac.h"
#include "detector.h"
#include "index.h"
/* x,y in pixels relative to central beam */
int map_position(struct image *image, double dx, double dy,
double *rx, double *ry, double *rz)
{
double d;
double twotheta, psi;
const double k = 1.0 / image->lambda;
int p;
int found = 0;
double x = 0.0;
double y = 0.0;
/* Perform the detector mapping for these coordinates */
for ( p=0; p<image->det.n_panels; p++ ) {
if ( (dx >= image->det.panels[p].min_x)
&& (dx <= image->det.panels[p].max_x)
&& (dy >= image->det.panels[p].min_y)
&& (dy <= image->det.panels[p].max_y) ) {
x = ((double)dx - image->det.panels[p].cx);
y = ((double)dy - image->det.panels[p].cy);
found = 1;
}
}
if ( !found ) {
ERROR("No mapping found for %f,%f\n", dx, dy);
return 0;
}
if ( image->fmode == FORMULATION_CLEN ) {
/* Convert pixels to metres */
x /= image->resolution;
y /= image->resolution; /* Convert pixels to metres */
d = sqrt((x*x) + (y*y));
twotheta = atan2(d, image->camera_len);
} else if (image->fmode == FORMULATION_PIXELSIZE ) {
/* Convert pixels to metres^-1 */
x *= image->pixel_size;
y *= image->pixel_size; /* Convert pixels to metres^-1 */
d = sqrt((x*x) + (y*y));
twotheta = atan2(d, k);
} else {
ERROR("Unrecognised formulation mode in mapping_scale.\n");
return -1;
}
psi = atan2(y, x);
*rx = k*sin(twotheta)*cos(psi);
*ry = k*sin(twotheta)*sin(psi);
*rz = k - k*cos(twotheta);
return 0;
}
static void write_drx(struct image *image)
{
FILE *fh;
int i;
STATUS("Writing xfel.drx file. Remember that it uses units of "
"reciprocal Angstroms!\n");
fh = fopen("xfel.drx", "w");
if ( !fh ) {
ERROR("Couldn't open temporary file xfel.drx\n");
return;
}
fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
fprintf(fh, "%10f %10f %10f %8f\n",
f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0);
}
fclose(fh);
}
void index_pattern(struct image *image, IndexingMethod indm, int no_match)
{
int i;
UnitCell *new_cell = NULL;
int nc = 0;
/* Map positions to 3D */
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
if ( map_position(image, f->x, f->y, &f->rx, &f->ry, &f->rz) ) {
nc++;
}
}
if ( nc ) {
ERROR("Failed to map %i reflections\n", nc);
}
write_drx(image);
/* Index (or not) as appropriate */
if ( indm == INDEXING_NONE ) return;
if ( indm == INDEXING_DIRAX ) run_dirax(image);
if ( image->indexed_cell == NULL ) {
STATUS("No cell found.\n");
return;
}
if ( !no_match ) {
new_cell = match_cell(image->indexed_cell,
image->molecule->cell);
free(image->indexed_cell);
image->indexed_cell = new_cell;
}
}
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