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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 <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"
#include "cell.h"
/* Returns dp/dr at "r" */
static double partiality_gradient(double r, double profile_radius)
{
double q, dpdq, dqdr;
/* Calculate degree of penetration */
q = (r + profile_radius)/(2.0*profile_radius);
/* dp/dq */
dpdq = 6.0*(q-pow(q, 2.0));
/* dq/dr */
dqdr = 1.0 / (2.0*profile_radius);
return dpdq * dqdr;
}
/* Returns dp/drad at "r" */
static double partiality_rgradient(double r, double profile_radius)
{
double q, dpdq, dqdrad;
/* Calculate degree of penetration */
q = (r + profile_radius)/(2.0*profile_radius);
/* dp/dq */
dpdq = 6.0*(q-pow(q, 2.0));
/* dq/drad */
dqdrad = 0.5 * (1.0 - r * pow(profile_radius, -2.0));
return dpdq * dqdrad;
}
/* 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 r)
{
double ds, tt, azi;
double nom, den;
double g = 0.0;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double xl, yl, zl;
cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
xl = spot.h*asx + spot.k*bsx + spot.l*csx;
yl = spot.h*asy + spot.k*bsy + spot.l*csy;
zl = spot.h*asz + spot.k*bsz + spot.l*csz;
ds = 2.0 * resolution(image->indexed_cell, spot.h, spot.k, spot.l);
tt = angle_between(0.0, 0.0, 1.0, xl, yl, zl+k);
azi = angle_between(1.0, 0.0, 0.0, xl, yl, 0.0);
/* Calculate the gradient of partiality wrt excitation error. */
if ( spot.clamp1 == 0 ) {
g += partiality_gradient(spot.r1, r);
}
if ( spot.clamp2 == 0 ) {
g += partiality_gradient(spot.r2, r);
}
/* For many gradients, just multiply the above number by the gradient
* of excitation error wrt whatever. */
switch ( k ) {
case REF_SCALE :
return I_partial;
case REF_DIV :
nom = sqrt(2.0) * ds * sin(image->div/2.0);
den = sqrt(1.0 - cos(image->div/2.0));
return (nom/den) * g;
case REF_R :
if ( spot.clamp1 == 0 ) {
g += partiality_rgradient(spot.r1, r);
}
if ( spot.clamp2 == 0 ) {
g += partiality_rgradient(spot.r2, r);
}
return g;
/* Cell parameters and orientation */
case REF_ASX :
return spot.h * pow(sin(tt), -1.0) * cos(azi) * g;
case REF_BSX :
return spot.k * pow(sin(tt), -1.0) * cos(azi) * g;
case REF_CSX :
return spot.l * pow(sin(tt), -1.0) * cos(azi) * g;
case REF_ASY :
return spot.h * pow(sin(tt), -1.0) * sin(azi) * g;
case REF_BSY :
return spot.k * pow(sin(tt), -1.0) * sin(azi) * g;
case REF_CSY :
return spot.l * pow(sin(tt), -1.0) * sin(azi) * g;
case REF_ASZ :
return spot.h * pow(cos(tt), -1.0) * g;
case REF_BSZ :
return spot.k * pow(cos(tt), -1.0) * g;
case REF_CSZ :
return spot.l * pow(cos(tt), -1.0) * g;
}
ERROR("No gradient defined for parameter %i\n", k);
abort();
}
static void apply_cell_shift(UnitCell *cell, int k, double shift)
{
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
switch ( k )
{
case REF_ASX : asx += shift; break;
case REF_ASY : asy += shift; break;
case REF_ASZ : asz += shift; break;
case REF_BSX : bsx += shift; break;
case REF_BSY : bsy += shift; break;
case REF_BSZ : bsz += shift; break;
case REF_CSX : csx += shift; break;
case REF_CSY : csy += shift; break;
case REF_CSZ : csz += shift; break;
}
cell_set_reciprocal(cell, asx, asy, asz,
bsx, bsy, bsz,
csx, csy, csz);
if ( k == REF_CSZ ) {
double a, b, c, al, be, ga;
cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
STATUS("New cell: %5.2f %5.2f %5.2f nm %5.2f %5.2f %5.2f deg\n",
a/1.0e-9, b/1.0e-9, c/1.0e-9,
rad2deg(al), rad2deg(be), rad2deg(ga));
}
}
/* 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;
case REF_R :
STATUS("Shifting r by %e\n", shift);
image->profile_radius += shift;
break;
case REF_ASX :
case REF_ASY :
case REF_ASZ :
case REF_BSX :
case REF_BSY :
case REF_BSZ :
case REF_CSX :
case REF_CSY :
case REF_CSZ :
apply_cell_shift(image->indexed_cell, k, 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, n_used;
double delta_I = 0.0;
n_used = 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);
n_used++;
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_used;
}
/* 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, gr;
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,
image->profile_radius)
* gradient(image, k, spots[h], I_partial,
image->profile_radius);
M_c *= pow(I_full, 2.0);
gsl_matrix_set(M, g, k, M_curr + M_c);
}
gr = gradient(image, k, spots[h], I_partial,
image->profile_radius);
v_c = delta_I * I_full * gr;
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);
}
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