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/*
* index.c
*
* Perform indexing (somehow)
*
* (c) 2006-2011 Thomas White <taw@physics.org>
* (c) 2010 Richard Kirian <rkirian@asu.edu>
*
* 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"
/* 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)
{
int n;
int nm = 0;
IndexingPrivate **iprivs;
while ( indm[nm] != INDEXING_NONE ) nm++;
STATUS("Preparing %i indexing methods.\n", nm);
iprivs = malloc((nm+1) * sizeof(IndexingPrivate *));
for ( n=0; n<nm; n++ ) {
switch ( indm[n] ) {
case INDEXING_NONE :
ERROR("Tried to prepare INDEXING_NONE!\n");
break;
case INDEXING_DIRAX :
iprivs[n] = indexing_private(indm[n]);
break;
case INDEXING_MOSFLM :
iprivs[n] = indexing_private(indm[n]);
break;
}
}
iprivs[n] = NULL;
return iprivs;
}
void cleanup_indexing(IndexingPrivate **priv)
{
int n = 0;
if ( priv == NULL ) return; /* Nothing to do */
while ( priv[n] != NULL ) {
switch ( priv[n]->indm ) {
case INDEXING_NONE :
free(priv[n]);
break;
case INDEXING_DIRAX :
free(priv[n]);
break;
case INDEXING_MOSFLM :
free(priv[n]);
break;
}
n++;
}
}
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, 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 config_insane)
{
int i;
int n = 0;
map_all_peaks(image);
while ( indm[n] != INDEXING_NONE ) {
image->ncells = 0;
/* Index as appropriate */
switch ( indm[n] ) {
case INDEXING_NONE :
return;
case INDEXING_DIRAX :
STATUS("Running DirAx...\n");
run_dirax(image);
break;
case INDEXING_MOSFLM :
STATUS("Running MOSFLM...\n");
run_mosflm(image, cell);
break;
}
if ( image->ncells == 0 ) {
STATUS("No candidate cells found.\n");
n++;
continue;
}
if ( cellr == CELLR_NONE ) {
image->indexed_cell = cell_new_from_cell(
image->candidate_cells[0]);
if ( verbose ) {
STATUS("--------------------\n");
STATUS("The indexed cell (matching not"
" performed):\n");
cell_print(image->indexed_cell);
STATUS("--------------------\n");
}
goto done;
}
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;
}
/* No cell? Move on to the next candidate */
if ( new_cell == NULL ) continue;
/* Sanity check */
if ( !config_insane &&
!peak_sanity_check(image, new_cell, 0, 0.1) ) {
STATUS("Failed peak sanity check.\n");
cell_free(new_cell);
continue;
}
image->indexed_cell = new_cell;
goto done; /* Success */
}
for ( i=0; i<image->ncells; i++ ) {
cell_free(image->candidate_cells[i]);
image->candidate_cells[i] = NULL;
}
/* Move on to the next indexing method */
n++;
}
done:
for ( i=0; i<image->ncells; i++ ) {
/* May free(NULL) if all algorithms were tried */
cell_free(image->candidate_cells[i]);
}
}
IndexingMethod *build_indexer_list(const char *str, int *need_cell)
{
int n, i;
char **methods;
IndexingMethod *list;
*need_cell = 0;
n = assplode(str, ",", &methods, ASSPLODE_NONE);
list = malloc((n+1)*sizeof(IndexingMethod));
for ( i=0; i<n; i++ ) {
if ( strcmp(methods[i], "dirax") == 0) {
list[i] = INDEXING_DIRAX;
} else if ( strcmp(methods[i], "mosflm") == 0) {
list[i] = INDEXING_MOSFLM;
} else {
ERROR("Unrecognised indexing method '%s'\n",
methods[i]);
return NULL;
}
free(methods[i]);
}
free(methods);
list[i] = INDEXING_NONE;
return list;
}
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