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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"
static void write_drx(struct image *image)
{
FILE *fh;
int i;
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 verbose)
{
int i;
int nc = 0;
/* Map positions to 3D */
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
int c;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
c = map_position(image, f->x, f->y, &f->rx, &f->ry, &f->rz);
if ( c != 0 ) nc++;
}
if ( nc ) {
ERROR("Failed to map %i reflections\n", nc);
}
write_drx(image);
image->ncells = 0;
/* Index (or not) as appropriate */
if ( indm == INDEXING_NONE ) return;
if ( indm == INDEXING_DIRAX ) run_dirax(image);
if ( image->ncells == 0 ) {
STATUS("No candidate cells found.\n");
return;
}
if ( no_match ) {
image->indexed_cell = image->candidate_cells[0];
if ( verbose ) {
STATUS("--------------------\n");
STATUS("The indexed cell (matching not performed):\n");
cell_print(image->indexed_cell);
STATUS("--------------------\n");
}
return;
}
for ( i=0; i<image->ncells; i++ ) {
UnitCell *new_cell = NULL;
if ( verbose ) {
STATUS("--------------------\n");
STATUS("Candidate cell %i (before matching):\n", i);
cell_print(image->candidate_cells[i]);
STATUS("--------------------\n");
}
new_cell = match_cell(image->candidate_cells[i],
image->molecule->cell, verbose);
image->indexed_cell = new_cell;
if ( new_cell == NULL ) {
STATUS("Cell %i not matched.\n", i);
} else {
goto done;
}
}
done:
for ( i=0; i<image->ncells; i++ ) {
free(image->candidate_cells[i]);
}
}
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