Move indexing and rendering to libcrystfel

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;
-}