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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 "mosflm.h"
#include "sfac.h"
#include "detector.h"
#include "index.h"
#include "index-priv.h"
#include "templates.h"
/* Base class constructor for unspecialised indexing private data */
static IndexingPrivate *indexing_private(IndexingMethod indm)
{
struct _indexingprivate *priv;
priv = calloc(1, sizeof(struct _indexingprivate));
priv->indm = indm;
return priv;
}
IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
const char *filename, struct detector *det,
double nominal_photon_energy)
{
switch ( indm ) {
case INDEXING_NONE :
return indexing_private(indm);
case INDEXING_DIRAX :
return indexing_private(indm);
case INDEXING_MOSFLM :
return indexing_private(indm);
case INDEXING_TEMPLATE :
return generate_templates(cell, filename, det,
nominal_photon_energy);
}
return 0;
}
void cleanup_indexing(IndexingPrivate *priv)
{
switch ( priv->indm ) {
case INDEXING_NONE :
free(priv);
break;
case INDEXING_DIRAX :
free(priv);
break;
case INDEXING_MOSFLM :
free(priv);
break;
case INDEXING_TEMPLATE :
free_templates(priv);
}
}
static void write_drx(struct image *image)
{
FILE *fh;
int i;
char filename[1024];
snprintf(filename, 1023, "xfel-%i.drx", image->id);
fh = fopen(filename, "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);
}
static void write_mosflm(struct image *image)
{
FILE *fh;
int i;
char filename[1024];
double cl=100; /* fake camera length in mm */
double pix=0;
double height=0;
double sigma=0;
snprintf(filename, 1023, "xfel-%i.spt", image->id);
fh = fopen(filename, "w");
if ( !fh ) {
ERROR("Couldn't open temporary file xfel.spt\n");
return;
}
fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, 1, 1, 0);
fprintf(fh, "%10d %10d\n", 1, 1);
fprintf(fh, "%10.5f %10.5f", 0, 0);
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, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
f->x, f->y, 0, 0, height, sigma);
}
fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
-999,-999,-999,-999,-999,-999);
fclose(fh);
}
void map_all_peaks(struct image *image)
{
int i;
/* Map positions to 3D */
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
struct rvec r;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
r = get_q(image, f->x, f->y, 1, NULL, 1.0/image->lambda);
f->rx = r.u; f->ry = r.v; f->rz = r.w;
}
}
void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
int cellr, int verbose, IndexingPrivate *ipriv)
{
int i;
map_all_peaks(image);
write_drx(image);
image->ncells = 0;
/* Index (or not) as appropriate */
switch ( indm ) {
case INDEXING_NONE :
return;
case INDEXING_DIRAX :
run_dirax(image);
break;
case INDEXING_MOSFLM :
run_mosflm(image);
break;
case INDEXING_TEMPLATE :
match_templates(image, ipriv);
break;
}
if ( image->ncells == 0 ) {
STATUS("No candidate cells found.\n");
return;
}
if ( (cellr == CELLR_NONE) || (indm == INDEXING_TEMPLATE) ) {
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");
}
/* Match or reduce the cell as appropriate */
switch ( cellr ) {
case CELLR_NONE :
/* Never happens */
break;
case CELLR_REDUCE :
new_cell = match_cell(image->candidate_cells[i],
cell, verbose, 1);
break;
case CELLR_COMPARE :
new_cell = match_cell(image->candidate_cells[i],
cell, verbose, 0);
break;
}
image->indexed_cell = new_cell;
if ( new_cell != NULL ) {
STATUS("Matched on attempt %i.\n", i);
goto done;
}
}
done:
for ( i=0; i<image->ncells; i++ ) {
cell_free(image->candidate_cells[i]);
}
}
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