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/*
* index.c
*
* Perform indexing (somehow)
*
* Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Lorenzo Galli
*
* Authors:
* 2010-2013 Thomas White <taw@physics.org>
* 2010-2011 Richard Kirian <rkirian@asu.edu>
* 2012 Lorenzo Galli
*
* This file is part of CrystFEL.
*
* CrystFEL is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* CrystFEL is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#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 "detector.h"
#include "index.h"
#include "index-priv.h"
#include "reax.h"
#include "geometry.h"
#include "cell-utils.h"
static const char *maybes(int n)
{
if ( n == 1 ) return "";
return "s";
}
IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
const char *filename, struct detector *det,
struct beam_params *beam, float *ltl)
{
int n;
int nm = 0;
IndexingPrivate **iprivs;
while ( indm[nm] != INDEXING_NONE ) nm++;
STATUS("Preparing %i indexing method%s.\n", nm, maybes(nm));
iprivs = malloc((nm+1) * sizeof(IndexingPrivate *));
for ( n=0; n<nm; n++ ) {
switch ( indm[n] & INDEXING_METHOD_MASK ) {
case INDEXING_DIRAX :
iprivs[n] = dirax_prepare(indm[nm], cell, filename, det,
beam, ltl);
break;
case INDEXING_MOSFLM :
iprivs[n] = NULL;
break;
case INDEXING_REAX :
iprivs[n] = reax_prepare(cell, filename, det, beam);
break;
default :
ERROR("Don't know how to prepare indexing method %i\n",
indm[n]);
break;
}
}
iprivs[n] = NULL;
return iprivs;
}
void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs)
{
int n = 0;
if ( indms == NULL ) return; /* Nothing to do */
if ( privs == NULL ) return; /* Nothing to do */
while ( indms[n] != INDEXING_NONE ) {
switch ( indms[n] & INDEXING_METHOD_MASK ) {
case INDEXING_NONE :
case INDEXING_DIRAX :
case INDEXING_MOSFLM :
/* No cleanup */
break;
case INDEXING_REAX :
reax_cleanup(privs[n]);
break;
default :
ERROR("Don't know how to clean up indexing method %i\n",
indms[n]);
break;
}
n++;
}
}
void map_all_peaks(struct image *image)
{
int i, n;
n = image_feature_count(image->features);
/* Map positions to 3D */
for ( i=0; i<n; i++ ) {
struct imagefeature *f;
struct rvec r;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
f->rx = r.u; f->ry = r.v; f->rz = r.w;
}
}
/* Return non-zero for "success" */
static int try_indexer(struct image *image, IndexingMethod indm,
IndexingPrivate *ipriv)
{
switch ( indm & INDEXING_METHOD_MASK ) {
case INDEXING_NONE :
break;
case INDEXING_DIRAX :
return run_dirax(image, ipriv);
break;
case INDEXING_MOSFLM :
return run_mosflm(image, ipriv);
break;
case INDEXING_REAX :
return reax_index(image, ipriv);
break;
default :
ERROR("Unrecognised indexing method: %i\n", indm);
break;
}
return 0;
}
void index_pattern(struct image *image,
IndexingMethod *indms, IndexingPrivate **iprivs)
{
int n = 0;
if ( indms == NULL ) return;
map_all_peaks(image);
image->crystals = NULL;
image->n_crystals = 0;
while ( indms[n] != INDEXING_NONE ) {
if ( try_indexer(image, indms[n], iprivs[n]) ) break;
n++;
}
}
/* Set the default indexer flags. May need tweaking depending on the method */
static IndexingMethod defaults(IndexingMethod a)
{
return a | INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_PEAKS;
}
/* Set the indexer flags for "raw mode" ("--cell-reduction=none") */
static IndexingMethod set_raw(IndexingMethod a)
{
/* Disable all unit cell checks */
a &= ~(INDEXING_CHECK_CELL_COMBINATIONS | INDEXING_CHECK_CELL_AXES);
return a;
}
/* Set the indexer flags for "bad mode" ("--insane) */
static IndexingMethod set_bad(IndexingMethod a)
{
/* Disable the peak check */
return a & ~INDEXING_CHECK_PEAKS;
}
/* Set the indexer flags for "axes mode" ("--cell-reduction=compare") */
static IndexingMethod set_axes(IndexingMethod a)
{
return (a & ~INDEXING_CHECK_CELL_COMBINATIONS)
| INDEXING_CHECK_CELL_AXES;
}
IndexingMethod *build_indexer_list(const char *str)
{
int n, i;
char **methods;
IndexingMethod *list;
int tmp;
int nmeth = 0;
n = assplode(str, ",-", &methods, ASSPLODE_NONE);
list = malloc((n+1)*sizeof(IndexingMethod));
nmeth = -1; /* So that the first method is #0 */
for ( i=0; i<n; i++ ) {
if ( strcmp(methods[i], "dirax") == 0) {
list[++nmeth] = defaults(INDEXING_DIRAX);
} else if ( strcmp(methods[i], "mosflm") == 0) {
list[++nmeth] = defaults(INDEXING_MOSFLM);
} else if ( strcmp(methods[i], "reax") == 0) {
/* ReAx doesn't need any cell check */
list[++nmeth] = set_raw(defaults(INDEXING_REAX));
} else if ( strcmp(methods[i], "raw") == 0) {
list[nmeth] = set_raw(list[nmeth]);
} else if ( strcmp(methods[i], "bad") == 0) {
list[nmeth] = set_bad(list[nmeth]);
} else if ( strcmp(methods[i], "axes") == 0) {
list[nmeth] = set_axes(list[nmeth]);
} else {
ERROR("Bad list of indexing methods: '%s'\n", str);
return NULL;
}
free(methods[i]);
}
free(methods);
list[++nmeth] = INDEXING_NONE;
return list;
}
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