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authorThomas White <taw@physics.org>2015-05-15 17:10:06 +0200
committerThomas White <taw@physics.org>2015-05-19 13:57:52 +0200
commit454466a948ddeebbf09dd18489caa37a12eaf04c (patch)
treeae5e53fd4ad32fc1c09171fdc1af1e23cd640d1b /src
parent66e032a4380f223cc4534362cdea954302f8239e (diff)
Strip out old scaling code
Diffstat (limited to 'src')
-rw-r--r--src/hrs-scaling.c576
-rw-r--r--src/merge.c241
-rw-r--r--src/merge.h (renamed from src/hrs-scaling.h)14
-rw-r--r--src/partialator.c2
4 files changed, 247 insertions, 586 deletions
diff --git a/src/hrs-scaling.c b/src/hrs-scaling.c
deleted file mode 100644
index e8376573..00000000
--- a/src/hrs-scaling.c
+++ /dev/null
@@ -1,576 +0,0 @@
-/*
- * hrs-scaling.c
- *
- * Intensity scaling using generalised HRS target function
- *
- * 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_fit.h>
-
-#include "image.h"
-#include "peaks.h"
-#include "symmetry.h"
-#include "geometry.h"
-#include "cell.h"
-#include "utils.h"
-#include "reflist.h"
-#include "cell-utils.h"
-
-
-/* Minimum partiality of a reflection for it to be used for scaling */
-#define MIN_PART_SCALE (0.05)
-
-/* Minimum partiality of a reflection for it to be merged */
-#define MIN_PART_MERGE (0.05)
-
-/* Maximum number of iterations of scaling per macrocycle. */
-#define MAX_CYCLES (100)
-
-
-struct scale_queue_args
-{
- RefList *reference;
- Crystal **crystals;
- int n_started;
- PartialityModel pmodel;
- UnitCell *cell;
-};
-
-
-struct scale_worker_args
-{
- Crystal *crystal;
- RefList *reference;
- PartialityModel pmodel;
- int crystal_number;
-};
-
-
-static void *create_scale_job(void *vqargs)
-{
- struct scale_worker_args *wargs;
- struct scale_queue_args *qargs = vqargs;
-
- wargs = malloc(sizeof(struct scale_worker_args));
- wargs->reference = qargs->reference;
- wargs->pmodel = qargs->pmodel;
-
- wargs->crystal_number = qargs->n_started;
- wargs->crystal = qargs->crystals[qargs->n_started++];
-
- return wargs;
-}
-
-
-static void run_scale_job(void *vwargs, int cookie)
-{
- struct scale_worker_args *wargs = vwargs;
- Crystal *cr = wargs->crystal;
- RefList *reference = wargs->reference;
- Reflection *refl;
- RefListIterator *iter;
- int n = 0;
- double *x;
- double *y;
- double *w;
- int max_n = 256;
- double c0, c1, cov00, cov01, cov11, chisq;
- double G, B;
- int r;
-
- /* If this crystal's scaling was dodgy, it doesn't contribute to the
- * merged intensities */
- if ( crystal_get_user_flag(cr) != 0 ) return;
-
- x = malloc(max_n*sizeof(double));
- y = malloc(max_n*sizeof(double));
- w = malloc(max_n*sizeof(double));
- if ( (x==NULL) || (y==NULL) || (w==NULL) ) {
- ERROR("Failed to allocate memory for scaling.\n");
- return;
- }
-
- for ( refl = first_refl(crystal_get_reflections(cr), &iter);
- refl != NULL;
- refl = next_refl(refl, iter) )
- {
- signed int h, k, l;
- double Ih, Ihl, corr;
- Reflection *r;
- double res;
-
- get_indices(refl, &h, &k, &l);
- res = resolution(crystal_get_cell(cr), h, k, l);
-
- if ( (get_partiality(refl) < MIN_PART_SCALE)
- || (get_intensity(refl) < 5.0*get_esd_intensity(refl)) ) {
- continue;
- }
-
- /* Look up by asymmetric indices */
- r = find_refl(reference, h, k, l);
- if ( r == NULL ) {
- continue;
- }
-
- corr = get_lorentz(refl) / get_partiality(refl);
-
- Ih = get_intensity(r);
- Ihl = get_intensity(refl) * corr;
-
- if ( Ihl <= 0.0 ) continue;
- if ( Ih <= 0.0 ) continue;
- if ( isnan(Ihl) || isinf(Ihl) ) continue;
- if ( isnan(Ih) || isinf(Ih) ) continue;
-
- if ( n == max_n ) {
- max_n *= 2;
- x = realloc(x, max_n*sizeof(double));
- y = realloc(y, max_n*sizeof(double));
- w = realloc(w, max_n*sizeof(double));
- if ( (x==NULL) || (y==NULL) || (w==NULL) ) {
- ERROR("Failed to allocate memory for scaling.\n");
- return;
- }
- }
-
- x[n] = res*res;
- y[n] = log(Ihl/Ih);
- w[n] = 1.0;
- n++;
-
- }
-
- if ( n < 2 ) {
- crystal_set_user_flag(cr, 1);
- return;
- }
-
- r = gsl_fit_wlinear(x, 1, w, 1, y, 1, n, &c0, &c1,
- &cov00, &cov01, &cov11, &chisq);
-
- G = 1.0/exp(c0);
- B = -c1/2.0;
-
- free(x);
- free(y);
- free(w);
- if ( r || isnan(c0) ) {
- crystal_set_user_flag(cr, 1);
- return;
- }
-
- crystal_set_osf(cr, G);
- crystal_set_Bfac(cr, B);
-}
-
-
-static void finalise_scale_job(void *vqargs, void *vwargs)
-{
- struct scale_worker_args *wargs = vwargs;
- free(wargs);
-}
-
-
-static void iterate_scale(Crystal **crystals, int n, RefList *reference,
- int n_threads, PartialityModel pmodel)
-{
- struct scale_queue_args qargs;
-
- assert(reference != NULL);
-
- qargs.reference = reference;
- qargs.n_started = 0;
- qargs.crystals = crystals;
- qargs.pmodel = pmodel;
-
- run_threads(n_threads, run_scale_job, create_scale_job,
- finalise_scale_job, &qargs, n, 0, 0, 0);
-}
-
-
-struct merge_queue_args
-{
- RefList *full;
- pthread_rwlock_t full_lock;
- Crystal **crystals;
- int n_started;
- PartialityModel pmodel;
- double push_res;
-};
-
-
-struct merge_worker_args
-{
- struct merge_queue_args *qargs;
- Crystal *crystal;
- int crystal_number;
-};
-
-
-static void *create_merge_job(void *vqargs)
-{
- struct merge_worker_args *wargs;
- struct merge_queue_args *qargs = vqargs;
-
- wargs = malloc(sizeof(struct merge_worker_args));
- wargs->qargs = qargs;
- wargs->crystal_number = qargs->n_started;
- wargs->crystal = qargs->crystals[qargs->n_started++];
-
- return wargs;
-}
-
-
-static void run_merge_job(void *vwargs, int cookie)
-{
- struct merge_worker_args *wargs = vwargs;
- Crystal *cr = wargs->crystal;
- RefList *full = wargs->qargs->full;
- double push_res = wargs->qargs->push_res;
- Reflection *refl;
- RefListIterator *iter;
- double G, B;
-
- /* If this crystal's scaling was dodgy, it doesn't contribute to the
- * merged intensities */
- if ( crystal_get_user_flag(cr) != 0 ) return;
-
- 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) )
- {
- Reflection *f;
- signed int h, k, l;
- double mean, sumweight, M2, temp, delta, R;
- double corr, res, w, esd;
-
- if ( get_partiality(refl) < MIN_PART_MERGE ) continue;
-
- get_indices(refl, &h, &k, &l);
- pthread_rwlock_rdlock(&wargs->qargs->full_lock);
- f = find_refl(full, h, k, l);
- if ( f == NULL ) {
-
- /* Swap read lock for write lock */
- pthread_rwlock_unlock(&wargs->qargs->full_lock);
- pthread_rwlock_wrlock(&wargs->qargs->full_lock);
-
- /* In the gap between the unlock and the wrlock, the
- * reflection might have been created by another thread.
- * So, we must check again */
- f = find_refl(full, h, k, l);
- if ( f == NULL ) {
- f = add_refl(full, h, k, l);
- lock_reflection(f);
- pthread_rwlock_unlock(&wargs->qargs->full_lock);
- set_intensity(f, 0.0);
- set_temp1(f, 0.0);
- set_temp2(f, 0.0);
-
- } else {
-
- /* Someone else created it */
- lock_reflection(f);
- pthread_rwlock_unlock(&wargs->qargs->full_lock);
-
- }
-
- } else {
-
- lock_reflection(f);
- pthread_rwlock_unlock(&wargs->qargs->full_lock);
-
- }
-
- mean = get_intensity(f);
- sumweight = get_temp1(f);
- M2 = get_temp2(f);
-
- res = resolution(crystal_get_cell(cr), h, k, l);
-
- if ( 2.0*res > crystal_get_resolution_limit(cr)+push_res ) {
- unlock_reflection(f);
- continue;
- }
-
- /* Total (multiplicative) correction factor */
- corr = exp(-G) * exp(B*res*res) * get_lorentz(refl)
- / get_partiality(refl);
-
- esd = get_esd_intensity(refl) * corr;
- w = 1.0;
-
- /* Running mean and variance calculation */
- temp = w + sumweight;
- delta = get_intensity(refl)*corr - mean;
- R = delta * w / temp;
- set_intensity(f, mean + R);
- set_temp2(f, M2 + sumweight * delta * R);
- set_temp1(f, temp);
- set_redundancy(f, get_redundancy(f)+1);
- unlock_reflection(f);
- }
-}
-
-
-static void finalise_merge_job(void *vqargs, void *vwargs)
-{
- free(vwargs);
-}
-
-
-RefList *lsq_intensities(Crystal **crystals, int n, int n_threads,
- PartialityModel pmodel, int min_meas, double push_res)
-{
- RefList *full;
- RefList *full2;
- struct merge_queue_args qargs;
- Reflection *refl;
- RefListIterator *iter;
-
- full = reflist_new();
-
- qargs.full = full;
- qargs.n_started = 0;
- qargs.crystals = crystals;
- qargs.pmodel = pmodel;
- qargs.push_res = push_res;
- pthread_rwlock_init(&qargs.full_lock, NULL);
-
- run_threads(n_threads, run_merge_job, create_merge_job,
- finalise_merge_job, &qargs, n, 0, 0, 0);
-
- pthread_rwlock_destroy(&qargs.full_lock);
-
- /* Calculate ESDs from variances, including only reflections with
- * enough measurements */
- full2 = reflist_new();
- if ( full2 == NULL ) return NULL;
- for ( refl = first_refl(full, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) )
- {
- double var;
- int red;
-
- red = get_redundancy(refl);
- var = get_temp2(refl) / get_temp1(refl);
- set_esd_intensity(refl, sqrt(var)/sqrt(red));
-
- if ( red >= min_meas ) {
-
- signed int h, k, l;
- Reflection *r2;
-
- get_indices(refl, &h, &k, &l);
- r2 = add_refl(full2, h, k, l);
- copy_data(r2, refl);
- }
- }
-
- reflist_free(full);
- return full2;
-}
-
-
-static void reject_outliers(double *old_osfs, int n, Crystal **crystals)
-{
- int i;
-
- for ( i=0; i<n; i++ ) {
-
- double osf = crystal_get_osf(crystals[i]);
- double Bfac = crystal_get_Bfac(crystals[i]);
- int bad = 0;
-
- if ( isnan(osf) || (osf < 0.0) ) bad = 1;
- if ( isnan(Bfac) || (Bfac<-100e-20) || (Bfac>100e-20) ) bad = 1;
-
- if ( bad ) {
- crystal_set_user_flag(crystals[i], 1);
- //STATUS("crystal %i bad: osf=%f B=%f A^2\n",
- // i, osf, Bfac*1e20);
- } else {
- //STATUS("OK %i: osf=%f B=%f A^2\n",
- // i, osf, Bfac*1e20);
- }
-
- }
-}
-
-
-static void reset_scaling_flag(Crystal *crystal)
-{
- /* Every pattern gets another chance at being scaled, but stays flagged
- * if it was flagged for any other reason */
- if ( crystal_get_user_flag(crystal) == 1 ) {
- crystal_set_user_flag(crystal, 0);
- }
-}
-
-
-static int test_convergence(double *old_osfs, double *old_Bs, int *old_flags,
- int n, Crystal **crystals)
-{
- int i;
- double total_osf_change = 0.0;
- double total_B_change = 0.0;
- int n_change = 0;
- int n_newreject = 0;
- int n_reject = 0;
-
- for ( i=0; i<n; i++ ) {
-
- int oldf = old_flags[i];
- int newf = crystal_get_user_flag(crystals[i]);
-
- if ( (oldf==0) && (newf==0) ) {
- /* Crystal OK before and now */
- double new_osf = crystal_get_osf(crystals[i]);
- double new_B = crystal_get_Bfac(crystals[i]);
- total_osf_change += fabs(new_osf - old_osfs[i]);
- total_B_change += fabs(new_B - old_Bs[i]);
- n_change++;
-
- } else if ( (oldf==0) && (newf!=0) ) {
- /* Crystal bad now, but OK before */
- n_newreject++;
-
- }
-
- if ( newf != 0 ) {
- /* Crystal is bad now, don't care about before */
- n_reject++;
- }
- }
-
- STATUS("Mean OSF change: %10.3f Mean B change: %10.3f A^2 "
- "Newly rejected: %4i Total rejected : %4i\n",
- total_osf_change/n_change, 1e20*total_B_change/n_change,
- n_newreject, n_reject);
-
- return (total_osf_change/n_change) < 0.01;
-}
-
-
-/* Scale the stack of images */
-RefList *scale_intensities(Crystal **crystals, int n, int n_threads,
- PartialityModel pmodel, int min_redundancy)
-{
- int i;
- RefList *full = NULL;
- double *old_osfs;
- double *old_Bs;
- int *old_flags;
- int done;
-
- for ( i=0; i<n; i++ ) {
- reset_scaling_flag(crystals[i]);
- crystal_set_osf(crystals[i], 1.0);
- crystal_set_Bfac(crystals[i], 0.0);
- }
-
- /* Create an initial list to refine against */
- full = lsq_intensities(crystals, n, n_threads, pmodel, min_redundancy, 0.0);
-
- old_osfs = malloc(n*sizeof(double));
- old_Bs = malloc(n*sizeof(double));
- old_flags = malloc(n*sizeof(int));
- if ( (old_osfs == NULL) || (old_Bs == NULL) || (old_flags == NULL) ) {
- return NULL;
- }
-
- /* Iterate */
- i = 0;
- do {
-
- double total_sf = 0.0;
- double total_B = 0.0;
- int n_sf = 0;
- double norm_sf, norm_B;
- int j;
-
- for ( j=0; j<n; j++ ) {
- old_osfs[j] = crystal_get_osf(crystals[j]);
- old_Bs[j] = crystal_get_Bfac(crystals[j]);
- old_flags[j] = crystal_get_user_flag(crystals[j]);
- reset_scaling_flag(crystals[j]);
- }
-
- iterate_scale(crystals, n, full, n_threads, pmodel);
- reject_outliers(old_osfs, n, crystals);
-
- /* Normalise the scale factors */
- for ( j=0; j<n; j++ ) {
- if ( crystal_get_user_flag(crystals[j]) == 0 ) {
- total_sf += crystal_get_osf(crystals[j]);
- total_B += crystal_get_Bfac(crystals[j]);
- n_sf++;
- }
- }
- norm_sf = total_sf / n_sf;
- norm_B = total_B / n_sf;
- for ( j=0; j<n; j++ ) {
- crystal_set_osf(crystals[j],
- crystal_get_osf(crystals[j])/norm_sf);
- crystal_set_Bfac(crystals[j],
- crystal_get_Bfac(crystals[j])-norm_B);
- }
-
- done = test_convergence(old_osfs, old_Bs, old_flags,
- n, crystals);
-
- /* Generate list for next iteration */
- reflist_free(full);
- full = lsq_intensities(crystals, n, n_threads, pmodel,
- min_redundancy, 0.0);
-
- i++;
-
- } while ( !done && (i < MAX_CYCLES) );
-
- if ( i == MAX_CYCLES ) {
- ERROR("WARNING: Scaling did not converge.\n");
- }
-
- free(old_osfs);
- free(old_Bs);
- free(old_flags);
- return full;
-}
diff --git a/src/merge.c b/src/merge.c
new file mode 100644
index 00000000..f7a654ea
--- /dev/null
+++ b/src/merge.c
@@ -0,0 +1,241 @@
+/*
+ * merge.c
+ *
+ * Parallel weighted merging of intensities
+ *
+ * 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_fit.h>
+
+#include "image.h"
+#include "peaks.h"
+#include "symmetry.h"
+#include "geometry.h"
+#include "cell.h"
+#include "utils.h"
+#include "reflist.h"
+#include "cell-utils.h"
+
+
+/* Minimum partiality of a reflection for it to be merged */
+#define MIN_PART_MERGE (0.05)
+
+
+struct merge_queue_args
+{
+ RefList *full;
+ pthread_rwlock_t full_lock;
+ Crystal **crystals;
+ int n_started;
+ PartialityModel pmodel;
+ double push_res;
+};
+
+
+struct merge_worker_args
+{
+ struct merge_queue_args *qargs;
+ Crystal *crystal;
+ int crystal_number;
+};
+
+
+static void *create_merge_job(void *vqargs)
+{
+ struct merge_worker_args *wargs;
+ struct merge_queue_args *qargs = vqargs;
+
+ wargs = malloc(sizeof(struct merge_worker_args));
+ wargs->qargs = qargs;
+ wargs->crystal_number = qargs->n_started;
+ wargs->crystal = qargs->crystals[qargs->n_started++];
+
+ return wargs;
+}
+
+
+static void run_merge_job(void *vwargs, int cookie)
+{
+ struct merge_worker_args *wargs = vwargs;
+ Crystal *cr = wargs->crystal;
+ RefList *full = wargs->qargs->full;
+ double push_res = wargs->qargs->push_res;
+ Reflection *refl;
+ RefListIterator *iter;
+ double G, B;
+
+ /* If this crystal's scaling was dodgy, it doesn't contribute to the
+ * merged intensities */
+ if ( crystal_get_user_flag(cr) != 0 ) return;
+
+ 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) )
+ {
+ Reflection *f;
+ signed int h, k, l;
+ double mean, sumweight, M2, temp, delta, R;
+ double corr, res, w, esd;
+
+ if ( get_partiality(refl) < MIN_PART_MERGE ) continue;
+
+ get_indices(refl, &h, &k, &l);
+ pthread_rwlock_rdlock(&wargs->qargs->full_lock);
+ f = find_refl(full, h, k, l);
+ if ( f == NULL ) {
+
+ /* Swap read lock for write lock */
+ pthread_rwlock_unlock(&wargs->qargs->full_lock);
+ pthread_rwlock_wrlock(&wargs->qargs->full_lock);
+
+ /* In the gap between the unlock and the wrlock, the
+ * reflection might have been created by another thread.
+ * So, we must check again */
+ f = find_refl(full, h, k, l);
+ if ( f == NULL ) {
+ f = add_refl(full, h, k, l);
+ lock_reflection(f);
+ pthread_rwlock_unlock(&wargs->qargs->full_lock);
+ set_intensity(f, 0.0);
+ set_temp1(f, 0.0);
+ set_temp2(f, 0.0);
+
+ } else {
+
+ /* Someone else created it */
+ lock_reflection(f);
+ pthread_rwlock_unlock(&wargs->qargs->full_lock);
+
+ }
+
+ } else {
+
+ lock_reflection(f);
+ pthread_rwlock_unlock(&wargs->qargs->full_lock);
+
+ }
+
+ mean = get_intensity(f);
+ sumweight = get_temp1(f);
+ M2 = get_temp2(f);
+
+ res = resolution(crystal_get_cell(cr), h, k, l);
+
+ if ( 2.0*res > crystal_get_resolution_limit(cr)+push_res ) {
+ unlock_reflection(f);
+ continue;
+ }
+
+ /* Total (multiplicative) correction factor */
+ corr = exp(-G) * exp(B*res*res) * get_lorentz(refl)
+ / get_partiality(refl);
+
+ esd = get_esd_intensity(refl) * corr;
+ w = 1.0;
+
+ /* Running mean and variance calculation */
+ temp = w + sumweight;
+ delta = get_intensity(refl)*corr - mean;
+ R = delta * w / temp;
+ set_intensity(f, mean + R);
+ set_temp2(f, M2 + sumweight * delta * R);
+ set_temp1(f, temp);
+ set_redundancy(f, get_redundancy(f)+1);
+ unlock_reflection(f);
+ }
+}
+
+
+static void finalise_merge_job(void *vqargs, void *vwargs)
+{
+ free(vwargs);
+}
+
+
+RefList *lsq_intensities(Crystal **crystals, int n, int n_threads,
+ PartialityModel pmodel, int min_meas, double push_res)
+{
+ RefList *full;
+ RefList *full2;
+ struct merge_queue_args qargs;
+ Reflection *refl;
+ RefListIterator *iter;
+
+ full = reflist_new();
+
+ qargs.full = full;
+ qargs.n_started = 0;
+ qargs.crystals = crystals;
+ qargs.pmodel = pmodel;
+ qargs.push_res = push_res;
+ pthread_rwlock_init(&qargs.full_lock, NULL);
+
+ run_threads(n_threads, run_merge_job, create_merge_job,
+ finalise_merge_job, &qargs, n, 0, 0, 0);
+
+ pthread_rwlock_destroy(&qargs.full_lock);
+
+ /* Calculate ESDs from variances, including only reflections with
+ * enough measurements */
+ full2 = reflist_new();
+ if ( full2 == NULL ) return NULL;
+ for ( refl = first_refl(full, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) )
+ {
+ double var;
+ int red;
+
+ red = get_redundancy(refl);
+ var = get_temp2(refl) / get_temp1(refl);
+ set_esd_intensity(refl, sqrt(var)/sqrt(red));
+
+ if ( red >= min_meas ) {
+
+ signed int h, k, l;
+ Reflection *r2;
+
+ get_indices(refl, &h, &k, &l);
+ r2 = add_refl(full2, h, k, l);
+ copy_data(r2, refl);
+ }
+ }
+
+ reflist_free(full);
+ return full2;
+}
diff --git a/src/hrs-scaling.h b/src/merge.h
index 42d153b0..f653ec21 100644
--- a/src/hrs-scaling.h
+++ b/src/merge.h
@@ -1,7 +1,7 @@
/*
- * hrs-scaling.h
+ * merge.h
*
- * Intensity scaling using generalised HRS target function
+ * Parallel weighted merging of intensities
*
* Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
@@ -26,8 +26,8 @@
*
*/
-#ifndef HRS_SCALING_H
-#define HRS_SCALING_H
+#ifndef MERGE_H
+#define MERGE_H
#ifdef HAVE_CONFIG_H
@@ -39,12 +39,8 @@
#include "reflist.h"
#include "geometry.h"
-extern RefList *scale_intensities(Crystal **crystals, int n, int n_threads,
- PartialityModel pmodel, int min_redundancy);
-
-
extern RefList *lsq_intensities(Crystal **crystals, int n, int n_threads,
PartialityModel pmodel, int min_meas,
double push_res);
-#endif /* HRS_SCALING_H */
+#endif /* MERGE */
diff --git a/src/partialator.c b/src/partialator.c
index 76122c12..6844d2ab 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -53,7 +53,7 @@
#include "version.h"
#include "post-refinement.h"
-#include "hrs-scaling.h"
+#include "merge.h"
#include "scaling-report.h"
#include "rejection.h"