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/*
* statistics.c
*
* Structure-factor statistics
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <math.h>
#include <stdlib.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_min.h>
#include <gsl/gsl_statistics.h>
#include "statistics.h"
#include "utils.h"
struct r_params {
const double *ref1;
const unsigned int *c1;
const double *ref2;
const unsigned int *c2;
int fom;
};
enum {
R_2,
R_MERGE,
};
double stat_scale_intensity(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2)
{
double top = 0.0;
double bot = 0.0;
int i;
/* Start from i=1 -> skip central beam */
for ( i=1; i<LIST_SIZE; i++ ) {
if ( c1[i] && c2[i] ) {
double i1, i2;
i1 = ref1[i] / (double)c1[i];
i2 = ref2[i] / (double)c2[i];
top += i1 * i2;
bot += i2 * i2;
} /* else reflection not common so don't worry about it */
}
return top/bot;
}
double stat_scale_sqrti(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2)
{
double top = 0.0;
double bot = 0.0;
int i;
/* Start from i=1 -> skip central beam */
for ( i=1; i<LIST_SIZE; i++ ) {
if ( c1[i] && c2[i] ) {
double f1, f2;
if ( (ref1[i]<0.0) || (ref2[i]<0.0) ) continue;
f1 = sqrt(ref1[i]) / (double)c1[i];
f2 = sqrt(ref2[i]) / (double)c2[i];
top += f1 * f2;
bot += f2 * f2;
} /* else reflection not common so don't worry about it */
}
return top/bot;
}
static double internal_r2(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2,
double scale)
{
double top = 0.0;
double bot = 0.0;
int i;
/* Start from i=1 -> skip central beam */
for ( i=1; i<LIST_SIZE; i++ ) {
if ( c1[i] && c2[i] ) {
double i1, i2;
i1 = ref1[i] / (scale*(double)c1[i]);
i2 = ref2[i] / (double)c2[i];
top += pow(fabs(i1 - i2), 2.0);
bot += pow(i1, 2.0);
} /* else reflection not measured so don't worry about it */
}
return sqrt(top/bot);
}
static double internal_rmerge(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2,
double scale)
{
double top = 0.0;
double bot = 0.0;
int i;
/* Start from i=1 -> skip central beam */
for ( i=1; i<LIST_SIZE; i++ ) {
if ( c1[i] && c2[i] ) {
double f1, f2;
if ( (ref1[i]<0.0) || (ref2[i]<0.0) ) continue;
f1 = sqrt(ref1[i]) / (scale*(double)c1[i]);
f2 = sqrt(ref2[i]) / (double)c2[i];
top += fabs(f1 - f2);
bot += f1 + f2;
} /* else reflection not measured so don't worry about it */
}
return 2.0*top/bot;
}
static double calc_r(double scale, void *params)
{
struct r_params *rp = params;
switch ( rp->fom) {
case R_MERGE :
return internal_rmerge(rp->ref1, rp->c1,
rp->ref2, rp->c2, scale);
case R_2 :
return internal_r2(rp->ref1, rp->c1,
rp->ref2, rp->c2, scale);
}
ERROR("No such FoM!\n");
abort();
}
static double r_minimised(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2,
double *scalep, int fom)
{
gsl_function F;
gsl_min_fminimizer *s;
int status;
double scale = 1.0;
struct r_params rp;
int iter = 0;
rp.ref1 = ref1;
rp.ref2 = ref2;
rp.c1 = c1;
rp.c2 = c2;
rp.fom = fom;
F.function = &calc_r;
F.params = &rp;
s = gsl_min_fminimizer_alloc(gsl_min_fminimizer_brent);
/* Initial guess */
switch ( fom ) {
case R_MERGE :
scale = stat_scale_sqrti(ref1, c1, ref2, c2);
break;
case R_2 :
scale = stat_scale_intensity(ref1, c1, ref2, c2);
break;
}
//STATUS("Initial scale factor estimate: %5.2e\n", scale);
/* Probably within an order of magnitude either side */
gsl_min_fminimizer_set(s, &F, scale, scale/10.0, scale*10.0);
do {
double lo, up;
/* Iterate */
gsl_min_fminimizer_iterate(s);
/* Get the current estimate */
scale = gsl_min_fminimizer_x_minimum(s);
lo = gsl_min_fminimizer_x_lower(s);
up = gsl_min_fminimizer_x_upper(s);
/* Check for convergence */
status = gsl_min_test_interval(lo, up, 0.001, 0.0);
iter++;
} while ( status == GSL_CONTINUE );
if (status != GSL_SUCCESS) {
ERROR("Scale factor minimisation failed.\n");
}
gsl_min_fminimizer_free(s);
//STATUS("Final scale factor: %5.2e\n", scale);
*scalep = scale;
return calc_r(scale, &rp);
}
double stat_rmerge(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2,
double *scalep)
{
return r_minimised(ref1, c1, ref2, c2, scalep, R_MERGE);
}
double stat_r2(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2,
double *scalep)
{
return r_minimised(ref1, c1, ref2, c2, scalep, R_2);
}
double stat_pearson(const double *ref1, const unsigned int *c1,
const double *ref2, const unsigned int *c2)
{
double vec1[4096];
double vec2[4096];
signed int h, k, l;
int i = 0;
for ( l=-INDMAX; l<INDMAX; l++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( h=-INDMAX; h<INDMAX; h++ ) {
double i1, i2;
unsigned int c1s, c2s;
c1s = lookup_count(c1, h, k, l);
c2s = lookup_count(c2, h, k, l);
i1 = lookup_intensity(ref1, h, k, l);
i2 = lookup_intensity(ref2, h, k, l);
if ( c1s && c2s && (i1>0.0) && (i2>0.0) ) {
vec1[i] = sqrt(i1 / (double)c1s);
vec2[i] = sqrt(i2 / (double)c2s);
i++;
}
}
}
}
return gsl_stats_correlation(vec1, 1, vec2, 1, i);
}
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