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Diffstat (limited to 'src/post-refinement.c')
| -rw-r--r-- | src/post-refinement.c | 213 |
1 files changed, 213 insertions, 0 deletions
diff --git a/src/post-refinement.c b/src/post-refinement.c new file mode 100644 index 00000000..5ca0dc98 --- /dev/null +++ b/src/post-refinement.c @@ -0,0 +1,213 @@ +/* + * 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); +} |