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+/*
+ * post-refinement.c
+ *
+ * Post refinement
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <gsl/gsl_poly.h>
+#include <assert.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_linalg.h>
+
+#include "image.h"
+#include "post-refinement.h"
+#include "peaks.h"
+#include "symmetry.h"
+#include "geometry.h"
+
+
+/* Return the gradient of parameter 'k' given the current status of 'image'. */
+double gradient(struct image *image, int k,
+ struct cpeak spot, double I_partial)
+{
+ double ds;
+ double nom, den;
+
+ ds = 2.0 * resolution(image->indexed_cell, spot.h, spot.k, spot.l);
+
+ switch ( k ) {
+
+ case REF_SCALE :
+ return I_partial;
+
+ case REF_DIV :
+ nom = sqrt(2.0) * ds * sin(image->div);
+ den = sqrt(1.0 - cos(image->div));
+ return nom/den;
+
+ }
+
+ ERROR("No gradient defined for parameter %i\n", k);
+ abort();
+}
+
+
+/* Apply the given shift to the 'k'th parameter of 'image'. */
+void apply_shift(struct image *image, int k, double shift)
+{
+ switch ( k ) {
+
+ case REF_SCALE :
+ image->osf += shift;
+ break;
+
+ case REF_DIV :
+ STATUS("Shifting div by %e\n", shift);
+ image->div += shift;
+ break;
+
+ default :
+ ERROR("No shift defined for parameter %i\n", k);
+ abort();
+
+ }
+}
+
+
+double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
+ const char *sym, double *i_full, FILE *graph)
+{
+ int h;
+ double delta_I = 0.0;
+
+ for ( h=0; h<n; h++ ) {
+
+ signed int hind, kind, lind;
+ signed int ha, ka, la;
+ double I_full;
+ float I_partial;
+ float xc, yc;
+
+ hind = spots[h].h;
+ kind = spots[h].k;
+ lind = spots[h].l;
+
+ /* Don't attempt to use spots with very small
+ * partialities, since it won't be accurate. */
+ if ( spots[h].p < 0.1 ) continue;
+
+ /* Actual measurement of this reflection from this
+ * pattern? */
+ /* FIXME: Coordinates aren't whole numbers */
+ if ( integrate_peak(image, spots[h].x, spots[h].y,
+ &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
+ continue;
+ }
+ I_partial *= image->osf;
+
+ get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
+ I_full = lookup_intensity(i_full, ha, ka, la);
+ delta_I += fabs(I_partial - spots[h].p * I_full);
+
+ if ( graph != NULL ) {
+ fprintf(graph, "%3i %3i %3i %5.2f (at %5.2f,%5.2f)"
+ " %5.2f %5.2f\n",
+ hind, kind, lind, I_partial/spots[h].p, xc, yc,
+ spots[h].p, I_partial / I_full);
+ }
+
+ }
+
+ return delta_I / (double)n;
+}
+
+
+/* Perform one cycle of post refinement on 'image' against 'i_full' */
+double pr_iterate(struct image *image, double *i_full, const char *sym,
+ struct cpeak **pspots, int *n)
+{
+ gsl_matrix *M;
+ gsl_vector *v;
+ gsl_vector *shifts;
+ int h, param;
+ struct cpeak *spots = *pspots;
+
+ M = gsl_matrix_calloc(NUM_PARAMS, NUM_PARAMS);
+ v = gsl_vector_calloc(NUM_PARAMS);
+
+ /* Construct the equations, one per reflection in this image */
+ for ( h=0; h<*n; h++ ) {
+
+ signed int hind, kind, lind;
+ signed int ha, ka, la;
+ double I_full, delta_I;
+ float I_partial;
+ float xc, yc;
+ int k;
+
+ hind = spots[h].h;
+ kind = spots[h].k;
+ lind = spots[h].l;
+
+ /* Don't attempt to use spots with very small
+ * partialities, since it won't be accurate. */
+ if ( spots[h].p < 0.1 ) continue;
+
+ /* Actual measurement of this reflection from this
+ * pattern? */
+ /* FIXME: Coordinates aren't whole numbers */
+ if ( integrate_peak(image, spots[h].x, spots[h].y,
+ &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
+ continue;
+ }
+ I_partial *= image->osf;
+
+ get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
+ I_full = lookup_intensity(i_full, ha, ka, la);
+ delta_I = I_partial - spots[h].p * I_full;
+
+ for ( k=0; k<NUM_PARAMS; k++ ) {
+
+ int g;
+ double v_c;
+
+ for ( g=0; g<NUM_PARAMS; g++ ) {
+
+ double M_curr, M_c;
+
+ M_curr = gsl_matrix_get(M, g, k);
+
+ M_c = gradient(image, g, spots[h], I_partial)
+ * gradient(image, k, spots[h], I_partial);
+ M_c *= pow(I_full, 2.0);
+
+ gsl_matrix_set(M, g, k, M_curr + M_c);
+
+ }
+
+ v_c = delta_I * I_full * gradient(image, k, spots[h],
+ I_partial);
+ gsl_vector_set(v, k, v_c);
+
+ }
+
+ }
+
+ shifts = gsl_vector_alloc(NUM_PARAMS);
+ gsl_linalg_HH_solve(M, v, shifts);
+ for ( param=0; param<NUM_PARAMS; param++ ) {
+ double shift = gsl_vector_get(shifts, param);
+ apply_shift(image, param, shift);
+ }
+
+ gsl_matrix_free(M);
+ gsl_vector_free(v);
+ gsl_vector_free(shifts);
+
+ free(spots);
+ spots = find_intersections(image, image->indexed_cell, n, 0);
+ *pspots = spots;
+ return mean_partial_dev(image, spots, *n, sym, i_full, NULL);
+}