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+/*
+ * index.c
+ *
+ * Perform indexing (somehow)
+ *
+ * (c) 2006-2009 Thomas White <taw@physics.org>
+ *
+ * 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"
+
+
+static int map_position(struct image *image, double x, double y,
+ double *rx, double *ry, double *rz)
+{
+ /* "Input" space */
+ double d;
+
+ /* Angular description of reflection */
+ double theta, psi, k;
+
+ x -= image->x_centre;
+ y -= image->y_centre;
+ k = 1.0 / image->lambda;
+
+ /* FIXME: Don't process lower CCD for now */
+ if ( y < 0 ) return 0;
+
+ if ( image->fmode == FORMULATION_CLEN ) {
+
+ /* Convert pixels to metres */
+ x /= image->resolution;
+ y /= image->resolution; /* Convert pixels to metres */
+ d = sqrt((x*x) + (y*y));
+ theta = atan2(d, image->camera_len);
+
+ } else if (image->fmode == FORMULATION_PIXELSIZE ) {
+
+ /* Convert pixels to metres^-1 */
+ x *= image->pixel_size;
+ y *= image->pixel_size; /* Convert pixels to metres^-1 */
+ d = sqrt((x*x) + (y*y));
+ theta = atan2(d, k);
+
+ } else {
+ ERROR("Unrecognised formulation mode in mapping_scale.\n");
+ return -1;
+ }
+
+ psi = atan2(y, x);
+
+ *rx = k*sin(theta)*cos(psi);
+ *ry = k*sin(theta)*sin(psi);
+ *rz = k - k*cos(theta);
+
+ return 0;
+}
+
+
+void index_pattern(struct image *image, int no_index, int dump_peaks,
+ int use_dirax)
+{
+ int i;
+
+ /* Perform 'fine' peak search */
+ search_peaks(image, dump_peaks);
+
+ /* Map positions to 3D. FIXME: Handle lower detector */
+ for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+ struct imagefeature *f;
+
+ f = image_get_feature(image->features, i);
+ map_position(image, f->x, f->y, &f->rx, &f->ry, &f->rz);
+
+ }
+
+ if ( use_dirax ) {
+ run_dirax(image, no_index);
+ return;
+ }
+}