aboutsummaryrefslogtreecommitdiff
path: root/src/index.c
diff options
context:
space:
mode:
Diffstat (limited to 'src/index.c')
-rw-r--r--src/index.c274
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;
-}