static void scan_partialities(RefList *reflections, RefList *compare,
int *valid, long double *vals[3], int idx)
{
int i;
Reflection *refl;
RefListIterator *iter;
i = 0;
for ( refl = first_refl(reflections, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
Reflection *refl2;
get_indices(refl, &h, &k, &l);
refl2 = find_refl(compare, h, k, l);
if ( refl2 == NULL ) {
valid[i] = 0;
i++;
continue;
}
vals[idx][i] = get_lorentz(refl2);
i++;
}
}
/* Perform one cycle of post refinement on 'image' against 'full' */
static double pr_iterate(Crystal *cr, const RefList *full,
PartialityModel pmodel, int *n_filtered)
{
gsl_matrix *M;
gsl_vector *v;
gsl_vector *shifts;
int param;
Reflection *refl;
RefListIterator *iter;
RefList *reflections;
double max_shift;
int nref = 0;
const int verbose = 0;
int num_params = 0;
enum gparam rv[32];
*n_filtered = 0;
/* If partiality model is anything other than "unity", refine all the
* geometrical parameters */
if ( pmodel != PMODEL_UNITY ) {
rv[num_params++] = GPARAM_ASX;
rv[num_params++] = GPARAM_ASY;
rv[num_params++] = GPARAM_ASZ;
rv[num_params++] = GPARAM_BSX;
rv[num_params++] = GPARAM_BSY;
rv[num_params++] = GPARAM_BSZ;
rv[num_params++] = GPARAM_CSX;
rv[num_params++] = GPARAM_CSY;
rv[num_params++] = GPARAM_CSZ;
}
STATUS("Refining %i parameters.\n", num_params);
reflections = crystal_get_reflections(cr);
M = gsl_matrix_calloc(num_params, num_params);
v = gsl_vector_calloc(num_params);
/* Construct the equations, one per reflection in this image */
for ( refl = first_refl(reflections, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int ha, ka, la;
double I_full, delta_I;
double w;
double I_partial;
int k;
double p, l;
Reflection *match;
double gradients[num_params];
/* Find the full version */
get_indices(refl, &ha, &ka, &la);
match = find_refl(full, ha, ka, la);
if ( match == NULL ) continue;
if ( (get_intensity(refl) < 3.0*get_esd_intensity(refl))
|| (get_partiality(refl) < MIN_PART_REFINE)
|| (get_redundancy(match) < 2) ) continue;
I_full = get_intensity(match);
/* Actual measurement of this reflection from this pattern? */
I_partial = get_intensity(refl) / crystal_get_osf(cr);
p = get_partiality(refl);
l = get_lorentz(refl);
/* Calculate the weight for this reflection */
w = pow(get_esd_intensity(refl), 2.0);
w += l * p * I_full * pow(get_esd_intensity(match), 2.0);
w = pow(w, -1.0);
/* Calculate all gradients for this reflection */
for ( k=0; k<num_params; k++ ) {
gradients[k] = p_gradient(cr, rv[k], refl, pmodel) * l;
}
for ( k=0; k<num_params; k++ ) {
int g;
double v_c, v_curr;
for ( g=0; g<num_params; g++ ) {
double M_c, M_curr;
/* Matrix is symmetric */
if ( g > k ) continue;
M_c = gradients[g] * gradients[k];
M_c *= w * pow(I_full, 2.0);
M_curr = gsl_matrix_get(M, k, g);
gsl_matrix_set(M, k, g, M_curr + M_c);
gsl_matrix_set(M, g, k, M_curr + M_c);
}
delta_I = I_partial - (l * p * I_full);
v_c = w * delta_I * I_full * gradients[k];
v_curr = gsl_vector_get(v, k);
gsl_vector_set(v, k, v_curr + v_c);
}
nref++;
}
if ( verbose ) {
STATUS("The original equation:\n");
show_matrix_eqn(M, v);
}
//STATUS("%i reflections went into the equations.\n", nref);
if ( nref == 0 ) {
crystal_set_user_flag(cr, 2);
gsl_matrix_free(M);
gsl_vector_free(v);
return 0.0;
}
max_shift = 0.0;
shifts = solve_svd(v, M, n_filtered, verbose);
if ( shifts != NULL ) {
for ( param=0; param<num_params; param++ ) {
double shift = gsl_vector_get(shifts, param);
apply_shift(cr, rv[param], shift);
//STATUS("Shift %i: %e\n", param, shift);
if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
}
} else {
crystal_set_user_flag(cr, 3);
}
gsl_matrix_free(M);
gsl_vector_free(v);
gsl_vector_free(shifts);
return max_shift;
}
