diff options
Diffstat (limited to 'src/index.c')
| -rw-r--r-- | src/index.c | 274 |
1 files changed, 0 insertions, 274 deletions
diff --git a/src/index.c b/src/index.c deleted file mode 100644 index d5e76c50..00000000 --- a/src/index.c +++ /dev/null @@ -1,274 +0,0 @@ -/* - * 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 "detector.h" -#include "index.h" -#include "index-priv.h" -#include "reax.h" -#include "geometry.h" - - -/* Base class constructor for unspecialised indexing private data */ -IndexingPrivate *indexing_private(IndexingMethod indm) -{ - struct _indexingprivate *priv; - priv = calloc(1, sizeof(struct _indexingprivate)); - priv->indm = indm; - return priv; -} - - -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, - double nominal_photon_energy) -{ - 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] ) { - 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; - case INDEXING_REAX : - iprivs[n] = reax_prepare(); - 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; - case INDEXING_REAX : - reax_cleanup(priv[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; - - } -} - - -void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm, - int cellr, int verbose, IndexingPrivate **ipriv, - int config_insane) -{ - int i; - int n = 0; - - if ( indm == NULL ) return; - - map_all_peaks(image); - image->indexed_cell = NULL; - - while ( indm[n] != INDEXING_NONE ) { - - image->ncells = 0; - - /* Index as appropriate */ - switch ( indm[n] ) { - case INDEXING_NONE : - return; - case INDEXING_DIRAX : - run_dirax(image); - break; - case INDEXING_MOSFLM : - run_mosflm(image, cell); - break; - case INDEXING_REAX : - reax_index(ipriv[n], image, cell); - break; - } - if ( image->ncells == 0 ) { - n++; - continue; - } - - for ( i=0; i<image->ncells; i++ ) { - - UnitCell *new_cell = NULL; - UnitCell *cand = image->candidate_cells[i]; - - 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 : - new_cell = cell_new_from_cell(cand); - break; - case CELLR_REDUCE : - new_cell = match_cell(cand, cell, verbose, 1); - break; - case CELLR_COMPARE : - new_cell = match_cell(cand, cell, verbose, 0); - break; - case CELLR_COMPARE_AB : - new_cell = match_cell_ab(cand, cell); - break; - } - - /* No cell? Move on to the next candidate */ - if ( new_cell == NULL ) continue; - - /* Sanity check */ - image->reflections = find_intersections(image, new_cell); - image->indexed_cell = new_cell; - - if ( !config_insane && !peak_sanity_check(image) ) { - cell_free(new_cell); - image->indexed_cell = NULL; - continue; - } - - 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 and no success */ - cell_free(image->candidate_cells[i]); - } -} - - -IndexingMethod *build_indexer_list(const char *str, int *need_cell) -{ - int n, i; - char **methods; - IndexingMethod *list; - int tmp; - - if ( need_cell == NULL ) need_cell = &tmp; - *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 if ( strcmp(methods[i], "reax") == 0) { - list[i] = INDEXING_REAX; - *need_cell = 1; - } else { - ERROR("Unrecognised indexing method '%s'\n", - methods[i]); - return NULL; - } - - free(methods[i]); - - } - free(methods); - list[i] = INDEXING_NONE; - - return list; -} |