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/*
* post-refinement.c
*
* Post refinement
*
* Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2015 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
* CrystFEL is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* CrystFEL is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#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 <gsl/gsl_eigen.h>
#include <gsl/gsl_blas.h>
#include "image.h"
#include "post-refinement.h"
#include "peaks.h"
#include "symmetry.h"
#include "geometry.h"
#include "cell.h"
#include "cell-utils.h"
/* Minimum partiality of a reflection for it to be used for refinement */
#define MIN_PART_REFINE (0.1)
/* Maximum number of iterations of NLSq to do for each image per macrocycle. */
#define MAX_CYCLES (10)
/* Returns dp(gauss)/dr at "r" */
static double gaussian_fraction_gradient(double r, double R)
{
const double ng = 2.6;
const double sig = R/ng;
/* If the Ewald sphere isn't within the profile, the gradient is zero */
if ( r < -R ) return 0.0;
if ( r > +R ) return 0.0;
return exp(-pow(r/sig, 2.0)/2.0) / (sig*sqrt(2.0*M_PI));
}
/* Returns dp(sph)/dr at "r" */
static double sphere_fraction_gradient(double r, double pr)
{
double q, dpdq, dqdr;
/* If the Ewald sphere isn't within the profile, the gradient is zero */
if ( r < -pr ) return 0.0;
if ( r > +pr ) return 0.0;
q = (r + pr)/(2.0*pr);
dpdq = 6.0*(q - q*q);
dqdr = 1.0 / (2.0*pr);
return dpdq * dqdr;
}
/* Returns dp/dr at "r" */
static double partiality_gradient(double r, double pr,
PartialityModel pmodel,
double rlow, double rhigh)
{
double A, D;
D = rlow - rhigh;
switch ( pmodel ) {
default:
case PMODEL_UNITY:
return 0.0;
case PMODEL_SCSPHERE:
A = sphere_fraction_gradient(r, pr)/D;
return 4.0*pr*A/3.0;
case PMODEL_SCGAUSSIAN:
A = gaussian_fraction_gradient(r, pr)/D;
return 4.0*pr*A/3.0;
}
}
static double sphere_fraction_rgradient(double r, double R)
{
/* If the Ewald sphere isn't within the profile, the gradient is zero */
if ( r < -R ) return 0.0;
if ( r > +R ) return 0.0;
return -(3.0*r/(4.0*R*R)) * (1.0 - r*r/(R*R));
}
static double gaussian_fraction_rgradient(double r, double R)
{
const double ng = 2.6;
const double sig = R/ng;
/* If the Ewald sphere isn't within the profile, the gradient is zero */
if ( r < -R ) return 0.0;
if ( r > +R ) return 0.0;
return -(ng*r/(sqrt(2.0*M_PI)*R*R))*exp(-r*r/(2.0*sig*sig));
}
static double volume_fraction_rgradient(double r, double pr,
PartialityModel pmodel)
{
switch ( pmodel )
{
case PMODEL_UNITY :
return 1.0;
case PMODEL_SCSPHERE :
return sphere_fraction_rgradient(r, pr);
case PMODEL_SCGAUSSIAN :
return gaussian_fraction_rgradient(r, pr);
}
ERROR("No pmodel in volume_fraction_rgradient!\n");
return 1.0;
}
static double volume_fraction(double rlow, double rhigh, double pr,
PartialityModel pmodel)
{
switch ( pmodel )
{
case PMODEL_UNITY :
return 1.0;
case PMODEL_SCSPHERE :
return sphere_fraction(rlow, rhigh, pr);
case PMODEL_SCGAUSSIAN :
return gaussian_fraction(rlow, rhigh, pr);
}
ERROR("No pmodel in volume_fraction!\n");
return 1.0;
}
/* Return the gradient of "fx" wrt parameter 'k' given the current
* status of the crystal. */
double gradient(Crystal *cr, int k, Reflection *refl, PartialityModel pmodel)
{
double glow, ghigh;
double rlow, rhigh, p;
struct image *image = crystal_get_image(cr);
double R = crystal_get_profile_radius(cr);
double osf = crystal_get_osf(cr);
double gr;
signed int hi, ki, li;
double s;
get_indices(refl, &hi, &ki, &li);
s = resolution(crystal_get_cell(cr), hi, ki, li);
get_partial(refl, &rlow, &rhigh, &p);
if ( k == GPARAM_OSF ) {
return 1.0;
}
if ( k == GPARAM_BFAC ) {
return -s*s;
}
if ( k == GPARAM_R ) {
double Rglow, Rghigh;
double D, psph;
D = rlow - rhigh;
psph = volume_fraction(rlow, rhigh, R, pmodel);
Rglow = volume_fraction_rgradient(rlow, R, pmodel);
Rghigh = volume_fraction_rgradient(rhigh, R, pmodel);
gr = 4.0*psph/(3.0*D) + (4.0*R/(3.0*D))*(Rglow - Rghigh);
return gr * osf;
}
/* Calculate the gradient of partiality wrt excitation error. */
glow = partiality_gradient(rlow, R, pmodel, rlow, rhigh);
ghigh = partiality_gradient(rhigh, R, pmodel, rlow, rhigh);
if ( k == GPARAM_DIV ) {
double D, psph, ds;
signed int hs, ks, ls;
D = rlow - rhigh;
psph = volume_fraction(rlow, rhigh, R, pmodel);
get_symmetric_indices(refl, &hs, &ks, &ls);
ds = 2.0 * resolution(crystal_get_cell(cr), hs, ks, ls);
gr = (ds/2.0)*(glow+ghigh) - 4.0*R*psph*ds/(3.0*D*D);
return gr * osf;
}
gr = r_gradient(crystal_get_cell(cr), k, refl, image) * (glow-ghigh);
return gr/p;
}
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 GPARAM_ASX : asx += shift; break;
case GPARAM_ASY : asy += shift; break;
case GPARAM_ASZ : asz += shift; break;
case GPARAM_BSX : bsx += shift; break;
case GPARAM_BSY : bsy += shift; break;
case GPARAM_BSZ : bsz += shift; break;
case GPARAM_CSX : csx += shift; break;
case GPARAM_CSY : csy += shift; break;
case GPARAM_CSZ : csz += shift; break;
}
cell_set_reciprocal(cell, asx, asy, asz,
bsx, bsy, bsz,
csx, csy, csz);
}
/* Apply the given shift to the 'k'th parameter of 'image'. */
static void apply_shift(Crystal *cr, int k, double shift)
{
double t;
struct image *image = crystal_get_image(cr);
if ( isnan(shift) ) {
ERROR("Refusing NaN shift for parameter %i\n", k);
ERROR("Image serial %i\n", image->serial);
return;
}
switch ( k ) {
case GPARAM_DIV :
image->div += shift;
if ( image->div < 0.0 ) image->div = 0.0;
break;
case GPARAM_R :
t = crystal_get_profile_radius(cr);
t += shift;
crystal_set_profile_radius(cr, t);
break;
case GPARAM_BFAC :
t = crystal_get_Bfac(cr);
t += shift;
crystal_set_Bfac(cr, t);
break;
case GPARAM_OSF :
t = crystal_get_osf(cr);
t += shift;
crystal_set_osf(cr, t);
break;
case GPARAM_ASX :
case GPARAM_ASY :
case GPARAM_ASZ :
case GPARAM_BSX :
case GPARAM_BSY :
case GPARAM_BSZ :
case GPARAM_CSX :
case GPARAM_CSY :
case GPARAM_CSZ :
apply_cell_shift(crystal_get_cell(cr), k, shift);
break;
default :
ERROR("No shift defined for parameter %i\n", k);
abort();
}
}
/* Perform one cycle of post refinement on 'image' against 'full' */
static double pr_iterate(Crystal *cr, const RefList *full,
PartialityModel pmodel, int no_scale, int *n_filtered,
int verbose)
{
gsl_matrix *M;
gsl_vector *v;
gsl_vector *shifts;
int param;
Reflection *refl;
RefListIterator *iter;
RefList *reflections;
double max_shift;
int nref = 0;
int num_params = 0;
enum gparam rv[32];
double G, B;
*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;
}
/* If we are scaling, refine scale factors (duh) */
if ( !no_scale ) {
rv[num_params++] = GPARAM_OSF;
rv[num_params++] = GPARAM_BFAC;
}
if ( num_params == 0 ) return 0.0;
reflections = crystal_get_reflections(cr);
M = gsl_matrix_calloc(num_params, num_params);
v = gsl_vector_calloc(num_params);
G = crystal_get_osf(cr);
B = crystal_get_Bfac(cr);
/* 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, esd;
double w;
double I_partial;
int k;
double p, L, s;
double fx;
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;
/* Merged intensitty */
I_full = get_intensity(match);
/* Actual measurement of this reflection from this pattern */
I_partial = get_intensity(refl);
esd = get_esd_intensity(refl);
if ( (get_partiality(refl) < MIN_PART_REFINE)
|| (get_redundancy(match) < 2)
|| (I_full <= 0) || (I_partial < 3*esd) ) continue;
p = get_partiality(refl);
L = get_lorentz(refl);
s = resolution(crystal_get_cell(cr), ha, ka, la);
/* Calculate the weight for this reflection */
w = 1.0;
/* Calculate all gradients for this reflection */
for ( k=0; k<num_params; k++ ) {
gradients[k] = gradient(cr, rv[k], refl, pmodel);
}
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 = w * gradients[g] * gradients[k];
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);
}
fx = G + log(p) - log(L) - B*s*s + log(I_full);
delta_I = log(I_partial) - fx;
v_c = w * delta_I * 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 < num_params ) {
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);
if ( verbose ) STATUS("Shift %i: %e\n", param, shift);
apply_shift(cr, rv[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;
}
static double residual(Crystal *cr, const RefList *full, int verbose)
{
double dev = 0.0;
double G, B;
Reflection *refl;
RefListIterator *iter;
FILE *fh = NULL;
if ( verbose ) {
fh = fopen("residual.dat", "w");
}
G = crystal_get_osf(cr);
B = crystal_get_Bfac(cr);
for ( refl = first_refl(crystal_get_reflections(cr), &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
double p, L, s, w;
signed int h, k, l;
Reflection *match;
double esd, I_full, I_partial;
double fx, dc;
get_indices(refl, &h, &k, &l);
match = find_refl(full, h, k, l);
if ( match == NULL ) continue;
p = get_partiality(refl);
L = get_lorentz(refl);
I_partial = get_intensity(refl);
I_full = get_intensity(match);
esd = get_esd_intensity(refl);
s = resolution(crystal_get_cell(cr), h, k, l);
if ( (get_partiality(refl) < MIN_PART_REFINE)
|| (get_redundancy(match) < 2)
|| (I_full <= 0) || (I_partial < 3*esd) ) continue;
fx = G + log(p) - log(L) - B*s*s + log(I_full);
dc = log(I_partial) - fx;
w = 1.0;
dev += w*dc*dc;
if ( fh != NULL ) {
fprintf(fh, "%4i %4i %4i %e %.2f %e %f %f\n",
h, k, l, s, G, B, I_partial, I_full);
}
}
if ( fh != NULL ) fclose(fh);
return dev;
}
struct prdata pr_refine(Crystal *cr, const RefList *full,
PartialityModel pmodel, int no_scale)
{
double dev;
int i;
int verbose = 0;
struct prdata prdata;
prdata.refined = 0;
prdata.n_filtered = 0;
/* Don't refine crystal if scaling was bad */
if ( crystal_get_user_flag(cr) != 0 ) return prdata;
if ( verbose ) {
dev = residual(cr, full, 1);
STATUS("\n"); /* Deal with progress bar */
STATUS("Initial G=%.2f, B=%e\n",
crystal_get_osf(cr), crystal_get_Bfac(cr));
STATUS("Initial dev = %10.5e\n", dev);
}
i = 0;
do {
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double dev;
cell_get_reciprocal(crystal_get_cell(cr), &asx, &asy, &asz,
&bsx, &bsy, &bsz, &csx, &csy, &csz);
pr_iterate(cr, full, pmodel, no_scale, &prdata.n_filtered, 0);
update_partialities(cr, pmodel);
if ( verbose ) {
dev = residual(cr, full, 0);
STATUS("PR Iteration %2i: dev = %10.5e\n", i+1, dev);
}
i++;
} while ( i < MAX_CYCLES );
if ( crystal_get_user_flag(cr) == 0 ) {
prdata.refined = 1;
}
if ( verbose ) {
STATUS("Final G=%.2f, B=%e\n", crystal_get_osf(cr),
crystal_get_Bfac(cr));
}
return prdata;
}
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