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/*
* rejection.c
*
* Crystal rejection for scaling
*
* 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_statistics.h>
#include "crystal.h"
#include "reflist.h"
#include "rejection.h"
#include "cell-utils.h"
#include "post-refinement.h"
static double mean_intensity(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
double total = 0.0;
int n = 0;
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
total += get_intensity(refl);
n++;
}
return total/n;
}
/* Reject really obvious outliers */
void early_rejection(Crystal **crystals, int n)
{
int i;
double m = 0.0;
double mean_m;
FILE *fh = fopen("reject.dat", "w");
int n_flag = 0;
for ( i=0; i<n; i++ ) {
double u;
RefList *list = crystal_get_reflections(crystals[i]);
u = mean_intensity(list);
m += u;
fprintf(fh, "%i %f\n", i, u);
}
mean_m = m/n;
for ( i=0; i<n; i++ ) {
double u;
RefList *list = crystal_get_reflections(crystals[i]);
u = mean_intensity(list);
if ( u/mean_m < 0.2 ) {
crystal_set_user_flag(crystals[i], 5);
n_flag++;
}
}
fclose(fh);
STATUS("Mean intensity/peak = %f ADU\n", m/n);
STATUS("%i crystals flagged\n", n_flag);
}
static void check_cc(Crystal *cr, RefList *full)
{
RefList *list = crystal_get_reflections(cr);
Reflection *refl;
RefListIterator *iter;
double G = crystal_get_osf(cr);
double B = crystal_get_Bfac(cr);
UnitCell *cell = crystal_get_cell(cr);
double *vec1, *vec2;
int n, i;
double cc;
n = num_reflections(list);
vec1 = malloc(n*sizeof(double));
vec2 = malloc(n*sizeof(double));
if ( (vec1 == NULL) || (vec2 == NULL) ) {
ERROR("Not enough memory to check CCs\n");
return;
}
i = 0;
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double pobs, pcalc;
double res, corr, Ipart;
Reflection *match;
if ( !get_flag(refl) ) continue; /* Not free-flagged */
get_indices(refl, &h, &k, &l);
res = resolution(cell, h, k, l);
if ( 2.0*res > crystal_get_resolution_limit(cr) ) continue;
match = find_refl(full, h, k, l);
if ( match == NULL ) continue;
/* Calculated partiality */
pcalc = get_partiality(refl);
/* Observed partiality */
corr = exp(-G) * exp(B*res*res) * get_lorentz(refl);
Ipart = get_intensity(refl) * corr;
pobs = Ipart / get_intensity(match);
vec1[i] = pobs;
vec2[i] = pcalc;
i++;
}
cc = gsl_stats_correlation(vec1, 1, vec2, 1, i);
//printf("%f\n", cc);
if ( cc < 0.5 ) crystal_set_user_flag(cr, PRFLAG_CC);
free(vec1);
free(vec2);
}
static void check_ccs(Crystal **crystals, int n_crystals, RefList *full)
{
int i;
for ( i=0; i<n_crystals; i++ ) {
check_cc(crystals[i], full);
}
}
static void show_duds(Crystal **crystals, int n_crystals)
{
int j;
int bads[32];
int any_bad = 0;
for ( j=0; j<32; j++ ) bads[j] = 0;
for ( j=0; j<n_crystals; j++ ) {
int flag;
flag = crystal_get_user_flag(crystals[j]);
assert(flag < 32);
bads[flag]++;
if ( flag != PRFLAG_OK ) any_bad++;
}
if ( any_bad ) {
STATUS("%i bad crystals:\n", any_bad);
for ( j=0; j<32; j++ ) {
if ( bads[j] ) {
STATUS(" %i %s\n", bads[j], str_prflag(j));
}
}
}
}
void check_rejection(Crystal **crystals, int n, RefList *full)
{
int i;
int n_acc = 0;
/* Check according to CCs FIXME: Disabled */
//if ( full != NULL ) check_ccs(crystals, n, full);
for ( i=0; i<n; i++ ) {
/* Reject if B factor modulus is very large */
if ( fabs(crystal_get_Bfac(crystals[i])) > 1e-18 ) {
crystal_set_user_flag(crystals[i], PRFLAG_BIGB);
}
if ( crystal_get_user_flag(crystals[i]) == 0 ) n_acc++;
}
show_duds(crystals, n);
if ( n_acc < 2 ) {
ERROR("Not enough crystals left to proceed (%i). Sorry.\n",
n_acc);
exit(1);
}
}
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