partialator: Scale (strictly) using strong reflections only

6 files changed, 548 insertions, 363 deletions

diff --git a/Makefile.am b/Makefile.am
index e8782455..1940affc 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -95,7 +95,7 @@ src_render_hkl_SOURCES = src/render_hkl.c
 endif
 
 src_partialator_SOURCES = src/partialator.c src/post-refinement.c \
-                          src/merge.c src/rejection.c
+                          src/merge.c src/rejection.c src/scaling.c
 
 src_ambigator_SOURCES = src/ambigator.c
 
@@ -133,7 +133,7 @@ EXTRA_DIST += src/dw-hdfsee.h src/hdfsee.h src/render_hkl.h \
               src/cl-utils.h src/hdfsee-render.h src/diffraction.h \
               src/diffraction-gpu.h src/pattern_sim.h src/list_tmp.h \
               src/im-sandbox.h src/process_image.h src/multihistogram.h \
-              src/rejection.h
+              src/rejection.h src/scaling.h
 
 crystfeldir = $(datadir)/crystfel
 crystfel_DATA = data/diffraction.cl data/hdfsee.ui
diff --git a/src/partialator.c b/src/partialator.c
index 26c72696..6de69cd2 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -54,6 +54,7 @@
 #include <cell-utils.h>
 
 #include "version.h"
+#include "scaling.h"
 #include "post-refinement.h"
 #include "merge.h"
 #include "rejection.h"
@@ -564,23 +565,35 @@ static void write_pgraph(RefList *full, Crystal **crystals, int n_crystals,
 }
 
 
-static void normalise_scales(Crystal **crystals, int n_crystals)
+static void all_residuals(Crystal **crystals, int n_crystals, RefList *full,
+                          double *presidual, double *pfree_residual,
+                          double *plog_residual, double *pfree_log_residual)
 {
 	int i;
-	int n = 0;
-	double sum_B = 0.0;
-	double mean_B;
+
+	*presidual = 0.0;
+	*pfree_residual = 0.0;
+	*plog_residual = 0.0;
+	*pfree_log_residual = 0.0;
 
 	for ( i=0; i<n_crystals; i++ ) {
-		if ( crystal_get_user_flag(crystals[i]) != 0 ) continue;
-		sum_B += crystal_get_Bfac(crystals[i]);
-		n++;
-	}
-	mean_B = sum_B / n;
-	STATUS("Mean B = %e A^2\n", mean_B*1e20);
-	for ( i=0; i<n_crystals; i++ ) {
-		double B = crystal_get_Bfac(crystals[i]);
-		crystal_set_Bfac(crystals[i], B-mean_B);
+
+		double r, free_r, log_r, free_log_r;
+
+		if ( crystal_get_user_flag(crystals[i]) ) continue;
+
+		r = residual(crystals[i], full, 0, NULL, NULL);
+		free_r = residual(crystals[i], full, 1, NULL, NULL);
+		log_r = log_residual(crystals[i], full, 0, NULL, NULL);
+		free_log_r = log_residual(crystals[i], full, 1, NULL, NULL);
+
+		if ( isnan(r) || isnan(free_r)
+		  || isnan(log_r) || isnan(free_log_r) ) continue;
+
+		*presidual += r;
+		*pfree_residual += free_r;
+		*plog_residual += log_r;
+		*pfree_log_residual += free_log_r;
 	}
 }
 
@@ -993,40 +1006,50 @@ int main(int argc, char *argv[])
 	STATUS("Checking patterns.\n");
 	//early_rejection(crystals, n_crystals);
 
-	/* Make initial estimates */
+	/* Initial rejection, figures of merit etc */
 	full = merge_intensities(crystals, n_crystals, nthreads, pmodel,
 	                         min_measurements, push_res, 1);
-
 	check_rejection(crystals, n_crystals, full);
-
+	show_all_residuals(crystals, n_crystals, full);
 	write_pgraph(full, crystals, n_crystals, 0);
 
 	/* Iterate */
 	for ( i=0; i<n_iter; i++ ) {
 
-		show_all_residuals(crystals, n_crystals, full);
-
-		STATUS("Refinement cycle %i of %i\n", i+1, n_iter);
+		STATUS("Scaling and refinement cycle %i of %i\n", i+1, n_iter);
 
-		/* Refine all crystals to get the best fit */
-		refine_all(crystals, n_crystals, full, nthreads, pmodel,
-		           no_scale, no_pr, max_B);
+		if ( !no_scale ) {
+			scale_all(crystals, n_crystals, nthreads, pmodel,
+			          max_B);
+			reflist_free(full);
+			full = merge_intensities(crystals, n_crystals, nthreads,
+			                         pmodel, min_measurements,
+			                         push_res, 1);
+		}
 
-		show_all_residuals(crystals, n_crystals, full);
+		if ( !no_pr ) {
+			refine_all(crystals, n_crystals, full, nthreads,
+			           pmodel);
+			reflist_free(full);
+			full = merge_intensities(crystals, n_crystals, nthreads,
+			                         pmodel, min_measurements,
+			                         push_res, 1);
+		}
 
 		check_rejection(crystals, n_crystals, full);
-		normalise_scales(crystals, n_crystals);
-
-		/* Re-estimate all the full intensities */
 		reflist_free(full);
 		full = merge_intensities(crystals, n_crystals, nthreads,
-		                         pmodel, min_measurements, push_res, 1);
-
+		                         pmodel, min_measurements,
+		                         push_res, 1);
+		show_all_residuals(crystals, n_crystals, full);
 		write_pgraph(full, crystals, n_crystals, i+1);
 
 	}
 
+	full = merge_intensities(crystals, n_crystals, nthreads, pmodel,
+	                         min_measurements, push_res, 1);
 	show_all_residuals(crystals, n_crystals, full);
+	write_pgraph(full, crystals, n_crystals, n_iter+1);
 
 	/* Output results */
 	STATUS("Writing overall results to %s\n", outfile);
diff --git a/src/post-refinement.c b/src/post-refinement.c
index cf3108db..487ce872 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -216,21 +216,9 @@ double gradient(Crystal *cr, int k, Reflection *refl, PartialityModel pmodel)
 	struct image *image = crystal_get_image(cr);
 	double R = crystal_get_profile_radius(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;
@@ -347,18 +335,6 @@ static void apply_shift(Crystal *cr, int k, double 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 :
@@ -379,141 +355,6 @@ static void apply_shift(Crystal *cr, int k, double shift)
 }
 
 
-/* Perform one cycle of scaling of 'cr' against 'full' */
-static double scale_iterate(Crystal *cr, const RefList *full,
-                            PartialityModel pmodel)
-{
-	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;
-
-	rv[num_params++] = GPARAM_OSF;
-	rv[num_params++] = GPARAM_BFAC;
-
-	M = gsl_matrix_calloc(num_params, num_params);
-	v = gsl_vector_calloc(num_params);
-
-	reflections = crystal_get_reflections(cr);
-	G = crystal_get_osf(cr);
-	B = crystal_get_Bfac(cr);
-
-	/* Scaling terms */
-	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];
-
-		/* If reflection is free-flagged, don't use it here */
-		if ( get_flag(refl) ) continue;
-
-		/* 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);
-		p = get_partiality(refl);
-
-		/* Scale only using strong reflections */
-		if ( I_partial <= 3.0*esd ) continue; /* Also because of log */
-		if ( get_redundancy(match) < 2 ) continue;
-		if ( I_full <= 0 ) continue;  /* Because log */
-		if ( p <= 0.0 ) continue; /* Because of log */
-
-		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 ( nref < num_params ) {
-		crystal_set_user_flag(cr, PRFLAG_FEWREFL);
-		gsl_matrix_free(M);
-		gsl_vector_free(v);
-		return 0.0;
-	}
-
-	max_shift = 0.0;
-	shifts = solve_svd(v, M, NULL, 0);
-	if ( shifts != NULL ) {
-
-		for ( param=0; param<num_params; param++ ) {
-			double shift = gsl_vector_get(shifts, param);
-			apply_shift(cr, rv[param], shift);
-			if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
-		}
-
-	} else {
-		crystal_set_user_flag(cr, PRFLAG_SOLVEFAIL);
-	}
-
-	gsl_matrix_free(M);
-	gsl_vector_free(v);
-	gsl_vector_free(shifts);
-
-	return max_shift;
-}
-
-
 /* Perform one cycle of post refinement on 'image' against 'full' */
 static double pr_iterate(Crystal *cr, const RefList *full,
                          PartialityModel pmodel,
@@ -667,74 +508,8 @@ static double pr_iterate(Crystal *cr, const RefList *full,
 }
 
 
-static double log_residual(Crystal *cr, const RefList *full, int free,
-                           int *pn_used, const char *filename)
-{
-	double dev = 0.0;
-	double G, B;
-	Reflection *refl;
-	RefListIterator *iter;
-	int n_used = 0;
-	FILE *fh = NULL;
-
-	G = crystal_get_osf(cr);
-	B = crystal_get_Bfac(cr);
-	if ( filename != NULL ) {
-		fh = fopen(filename, "a");
-		if ( fh == NULL ) {
-			ERROR("Failed to open '%s'\n", filename);
-		}
-	}
-
-	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;
-
-		if ( free && !get_flag(refl) ) continue;
-
-		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 ( I_partial <= 3.0*esd ) continue; /* Also because of log */
-		if ( get_redundancy(match) < 2 ) continue;
-		if ( I_full <= 0 ) continue;  /* Because log */
-		if ( p <= 0.0 ) continue; /* Because of log */
-
-		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 %e\n",
-			        h, k, l, s, dev);
-		}
-
-	}
-
-	if ( fh != NULL ) fclose(fh);
-
-	if ( pn_used != NULL ) *pn_used = n_used;
-	return dev;
-}
-
-
-static double residual(Crystal *cr, const RefList *full, int free,
-                       int *pn_used, const char *filename)
+double residual(Crystal *cr, const RefList *full, int free,
+                int *pn_used, const char *filename)
 {
 	double dev = 0.0;
 	double G, B;
@@ -799,39 +574,6 @@ static double residual(Crystal *cr, const RefList *full, int free,
 }
 
 
-void all_residuals(Crystal **crystals, int n_crystals, RefList *full,
-                   double *presidual, double *pfree_residual,
-                   double *plog_residual, double *pfree_log_residual)
-{
-	int i;
-
-	*presidual = 0.0;
-	*pfree_residual = 0.0;
-	*plog_residual = 0.0;
-	*pfree_log_residual = 0.0;
-
-	for ( i=0; i<n_crystals; i++ ) {
-
-		double r, free_r, log_r, free_log_r;
-
-		if ( crystal_get_user_flag(crystals[i]) ) continue;
-
-		r = residual(crystals[i], full, 0, NULL, NULL);
-		free_r = residual(crystals[i], full, 1, NULL, NULL);
-		log_r = log_residual(crystals[i], full, 0, NULL, NULL);
-		free_log_r = log_residual(crystals[i], full, 1, NULL, NULL);
-
-		if ( isnan(r) || isnan(free_r)
-		  || isnan(log_r) || isnan(free_log_r) ) continue;
-
-		*presidual += r;
-		*pfree_residual += free_r;
-		*plog_residual += log_r;
-		*pfree_log_residual += free_log_r;
-	}
-}
-
-
 static void write_residual_graph(Crystal *cr, const RefList *full)
 {
 	int i;
@@ -877,49 +619,6 @@ static void write_residual_graph(Crystal *cr, const RefList *full)
 }
 
 
-static void do_scale_refine(Crystal *cr, const RefList *full,
-                            PartialityModel pmodel, int verbose)
-{
-	int i, done;
-	double old_dev;
-
-	old_dev = log_residual(cr, full, 0, NULL, NULL);
-
-	if ( verbose ) {
-		STATUS("Initial G=%.2f, B=%e\n",
-		       crystal_get_osf(cr), crystal_get_Bfac(cr));
-		STATUS("Scaling initial  dev =  %10.5e, free dev = %10.5e\n",
-		       old_dev, log_residual(cr, full, 1, NULL, NULL));
-	}
-
-	i = 0;
-	done = 0;
-	do {
-
-		double dev;
-
-		scale_iterate(cr, full, pmodel);
-
-		dev = log_residual(cr, full, 0, 0, NULL);
-		if ( fabs(dev - old_dev) < dev*0.01 ) done = 1;
-
-		if ( verbose ) {
-			STATUS("Scaling %2i: dev = %10.5e, free dev = %10.5e\n",
-			       i+1, dev, log_residual(cr, full, 0, 0, NULL));
-		}
-
-		i++;
-		old_dev = dev;
-
-	} while ( i < MAX_CYCLES && !done );
-
-	if ( verbose ) {
-		STATUS("Final G=%.2f, B=%e\n", crystal_get_osf(cr),
-		       crystal_get_Bfac(cr));
-	}
-}
-
-
 static void do_pr_refine(Crystal *cr, const RefList *full,
                          PartialityModel pmodel, int verbose)
 {
@@ -977,8 +676,7 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 
 
 static struct prdata pr_refine(Crystal *cr, const RefList *full,
-                               PartialityModel pmodel, int no_scale, int no_pr,
-                               double max_B)
+                               PartialityModel pmodel)
 {
 	int verbose = 0;
 	struct prdata prdata;
@@ -986,23 +684,11 @@ static struct prdata pr_refine(Crystal *cr, const RefList *full,
 	prdata.refined = 0;
 	prdata.n_filtered = 0;
 
-	if ( !no_scale ) {
-		do_scale_refine(cr, full, pmodel, verbose);
-	}
-
-	/* Reject if B factor modulus is very large */
-	if ( fabs(crystal_get_Bfac(cr)) > max_B ) {
-		crystal_set_user_flag(cr, PRFLAG_BIGB);
-		return prdata;
-	}
-
 	if ( verbose ) {
 		write_residual_graph(cr, full);
 	}
 
-	if ( !no_pr ) {
-		do_pr_refine(cr, full, pmodel, verbose);
-	}
+	do_pr_refine(cr, full, pmodel, verbose);
 
 	if ( crystal_get_user_flag(cr) == 0 ) {
 		prdata.refined = 1;
@@ -1017,9 +703,6 @@ struct refine_args
 	RefList *full;
 	Crystal *crystal;
 	PartialityModel pmodel;
-	int no_scale;
-	int no_pr;
-	double max_B;
 	struct prdata prdata;
 };
 
@@ -1039,8 +722,7 @@ static void refine_image(void *task, int id)
 	struct refine_args *pargs = task;
 	Crystal *cr = pargs->crystal;
 
-	pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel,
-	                          pargs->no_scale, pargs->no_pr, pargs->max_B);
+	pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel);
 }
 
 
@@ -1072,8 +754,7 @@ static void done_image(void *vqargs, void *task)
 
 
 void refine_all(Crystal **crystals, int n_crystals,
-                RefList *full, int nthreads, PartialityModel pmodel,
-                int no_scale, int no_pr, double max_B)
+                RefList *full, int nthreads, PartialityModel pmodel)
 {
 	struct refine_args task_defaults;
 	struct queue_args qargs;
@@ -1083,9 +764,6 @@ void refine_all(Crystal **crystals, int n_crystals,
 	task_defaults.pmodel = pmodel;
 	task_defaults.prdata.refined = 0;
 	task_defaults.prdata.n_filtered = 0;
-	task_defaults.no_scale = no_scale;
-	task_defaults.no_pr = no_pr;
-	task_defaults.max_B = max_B;
 
 	qargs.task_defaults = task_defaults;
 	qargs.n_started = 0;
diff --git a/src/post-refinement.h b/src/post-refinement.h
index b3509501..7f395013 100644
--- a/src/post-refinement.h
+++ b/src/post-refinement.h
@@ -57,15 +57,13 @@ enum prflag
 extern const char *str_prflag(enum prflag flag);
 
 extern void refine_all(Crystal **crystals, int n_crystals,
-                       RefList *full, int nthreads, PartialityModel pmodel,
-                       int no_scale, int no_pr, double max_B);
+                       RefList *full, int nthreads, PartialityModel pmodel);
 
 /* Exported so it can be poked by tests/pr_p_gradient_check */
 extern double gradient(Crystal *cr, int k, Reflection *refl,
                        PartialityModel pmodel);
 
-extern void all_residuals(Crystal **crystals, int n_crystals, RefList *full,
-                          double *residual, double *free_residual,
-                          double *log_residual, double *free_log_residual);
+extern double residual(Crystal *cr, const RefList *full, int free,
+                       int *pn_used, const char *filename);
 
 #endif	/* POST_REFINEMENT_H */
diff --git a/src/scaling.c b/src/scaling.c
new file mode 100644
index 00000000..b3b9137e
--- /dev/null
+++ b/src/scaling.c
@@ -0,0 +1,439 @@
+/*
+ * scaling.c
+ *
+ * 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_matrix.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_eigen.h>
+#include <gsl/gsl_blas.h>
+
+#include "merge.h"
+#include "post-refinement.h"
+#include "symmetry.h"
+#include "cell.h"
+#include "cell-utils.h"
+
+
+/* Maximum number of iterations of NLSq to do for each image per macrocycle. */
+#define MAX_CYCLES (10)
+
+
+/* Apply the given shift to the 'k'th parameter of 'image'. */
+static void apply_shift(Crystal *cr, int k, double shift)
+{
+	double t;
+
+	switch ( k ) {
+
+		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;
+
+		default :
+		ERROR("No shift defined for parameter %i\n", k);
+		abort();
+
+	}
+}
+
+
+/* Perform one cycle of scaling of 'cr' against 'full' */
+static double scale_iterate(Crystal *cr, const RefList *full,
+                            PartialityModel pmodel)
+{
+	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;
+
+	rv[num_params++] = GPARAM_OSF;
+	rv[num_params++] = GPARAM_BFAC;
+
+	M = gsl_matrix_calloc(num_params, num_params);
+	v = gsl_vector_calloc(num_params);
+
+	reflections = crystal_get_reflections(cr);
+	G = crystal_get_osf(cr);
+	B = crystal_get_Bfac(cr);
+
+	/* Scaling terms */
+	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];
+
+		/* If reflection is free-flagged, don't use it here */
+		if ( get_flag(refl) ) continue;
+
+		/* 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);
+		p = get_partiality(refl);
+
+		/* Scale only using strong reflections */
+		if ( I_partial <= 3.0*esd ) continue; /* Also because of log */
+		if ( get_redundancy(match) < 2 ) continue;
+		if ( I_full <= 0 ) continue;  /* Because log */
+		if ( p <= 0.0 ) continue; /* Because of log */
+
+		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++ ) {
+
+			if ( rv[k] == GPARAM_OSF ) {
+				gradients[k] = 1.0;
+			} else if ( rv[k] == GPARAM_BFAC ) {
+				gradients[k] = -s*s;
+			} else {
+				ERROR("Unrecognised scaling gradient.\n");
+				abort();
+			}
+		}
+
+		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 ( nref < num_params ) {
+		crystal_set_user_flag(cr, PRFLAG_FEWREFL);
+		gsl_matrix_free(M);
+		gsl_vector_free(v);
+		return 0.0;
+	}
+
+	max_shift = 0.0;
+	shifts = solve_svd(v, M, NULL, 0);
+	if ( shifts != NULL ) {
+
+		for ( param=0; param<num_params; param++ ) {
+			double shift = gsl_vector_get(shifts, param);
+			apply_shift(cr, rv[param], shift);
+			if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
+		}
+
+	} else {
+		crystal_set_user_flag(cr, PRFLAG_SOLVEFAIL);
+	}
+
+	gsl_matrix_free(M);
+	gsl_vector_free(v);
+	gsl_vector_free(shifts);
+
+	return max_shift;
+}
+
+
+double log_residual(Crystal *cr, const RefList *full, int free,
+                    int *pn_used, const char *filename)
+{
+	double dev = 0.0;
+	double G, B;
+	Reflection *refl;
+	RefListIterator *iter;
+	int n_used = 0;
+	FILE *fh = NULL;
+
+	G = crystal_get_osf(cr);
+	B = crystal_get_Bfac(cr);
+	if ( filename != NULL ) {
+		fh = fopen(filename, "a");
+		if ( fh == NULL ) {
+			ERROR("Failed to open '%s'\n", filename);
+		}
+	}
+
+	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;
+
+		if ( free && !get_flag(refl) ) continue;
+
+		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 ( I_partial <= 3.0*esd ) continue; /* Also because of log */
+		if ( get_redundancy(match) < 2 ) continue;
+		if ( I_full <= 0 ) continue;  /* Because log */
+		if ( p <= 0.0 ) continue; /* Because of log */
+
+		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 %e\n",
+			        h, k, l, s, dev);
+		}
+
+	}
+
+	if ( fh != NULL ) fclose(fh);
+
+	if ( pn_used != NULL ) *pn_used = n_used;
+	return dev;
+}
+
+
+static void do_scale_refine(Crystal *cr, const RefList *full,
+                            PartialityModel pmodel)
+{
+	int i, done;
+	double old_dev;
+
+	old_dev = log_residual(cr, full, 0, NULL, NULL);
+
+	i = 0;
+	done = 0;
+	do {
+
+		double dev;
+
+		scale_iterate(cr, full, pmodel);
+
+		dev = log_residual(cr, full, 0, 0, NULL);
+		if ( fabs(dev - old_dev) < dev*0.01 ) done = 1;
+
+		i++;
+		old_dev = dev;
+
+	} while ( i < MAX_CYCLES && !done );
+}
+
+
+struct scale_args
+{
+	RefList *full;
+	Crystal *crystal;
+	PartialityModel pmodel;
+	double max_B;
+};
+
+
+struct queue_args
+{
+	int n_started;
+	int n_done;
+	Crystal **crystals;
+	int n_crystals;
+	struct scale_args task_defaults;
+};
+
+
+static void scale_crystal(void *task, int id)
+{
+	struct scale_args *pargs = task;
+	do_scale_refine(pargs->crystal, pargs->full, pargs->pmodel);
+
+	/* Reject if B factor modulus is very large */
+	if ( fabs(crystal_get_Bfac(pargs->crystal)) > pargs->max_B ) {
+		crystal_set_user_flag(pargs->crystal, PRFLAG_BIGB);
+	}
+}
+
+
+static void *get_crystal(void *vqargs)
+{
+	struct scale_args *task;
+	struct queue_args *qargs = vqargs;
+
+	task = malloc(sizeof(struct scale_args));
+	memcpy(task, &qargs->task_defaults, sizeof(struct scale_args));
+
+	task->crystal = qargs->crystals[qargs->n_started];
+
+	qargs->n_started++;
+
+	return task;
+}
+
+
+static void done_crystal(void *vqargs, void *task)
+{
+	struct queue_args *qa = vqargs;
+
+	qa->n_done++;
+
+	progress_bar(qa->n_done, qa->n_crystals, "Scaling");
+	free(task);
+}
+
+
+static double total_log_r(Crystal **crystals, int n_crystals, RefList *full,
+                          int *ninc)
+{
+	int i;
+	double total = 0.0;
+	int n = 0;
+
+	for ( i=0; i<n_crystals; i++ ) {
+
+		double r;
+		if ( crystal_get_user_flag(crystals[i]) ) continue;
+		r = log_residual(crystals[i], full, 0, NULL, NULL);
+		if ( isnan(r) ) continue;
+		total += r;
+		n++;
+
+	}
+
+	if ( ninc != NULL ) *ninc = n;
+	return total;
+}
+
+
+/* Perform iterative scaling, all the way to convergence */
+void scale_all(Crystal **crystals, int n_crystals, int nthreads,
+               PartialityModel pmodel, double max_B)
+{
+	struct scale_args task_defaults;
+	struct queue_args qargs;
+	double old_res, new_res;
+
+	task_defaults.crystal = NULL;
+	task_defaults.pmodel = pmodel;
+	task_defaults.max_B = max_B;
+
+	qargs.task_defaults = task_defaults;
+	qargs.n_crystals = n_crystals;
+	qargs.crystals = crystals;
+
+	/* Don't have threads which are doing nothing */
+	if ( n_crystals < nthreads ) nthreads = n_crystals;
+
+	new_res = INFINITY;
+	do {
+		RefList *full;
+		int ninc;
+		double bef_res;
+
+		full = merge_intensities(crystals, n_crystals, nthreads,
+		                         pmodel, 2, INFINITY, 0);
+		old_res = new_res;
+		bef_res = total_log_r(crystals, n_crystals, full, NULL);
+
+		qargs.task_defaults.full = full;
+		qargs.n_started = 0;
+		qargs.n_done = 0;
+		run_threads(nthreads, scale_crystal, get_crystal, done_crystal,
+		            &qargs, n_crystals, 0, 0, 0);
+
+		new_res = total_log_r(crystals, n_crystals, full, &ninc);
+		STATUS("Log residual went from %e to %e, %i crystals\n",
+		       bef_res, new_res, ninc);
+
+		reflist_free(full);
+
+	} while ( fabs(new_res-old_res) >= 0.01*old_res );
+}
diff --git a/src/scaling.h b/src/scaling.h
new file mode 100644
index 00000000..f8eb4e9e
--- /dev/null
+++ b/src/scaling.h
@@ -0,0 +1,47 @@
+/*
+ * scaling.h
+ *
+ * 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/>.
+ *
+ */
+
+#ifndef SCALING_H
+#define SCALING_H
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include "crystal.h"
+#include "geometry.h"
+
+extern double log_residual(Crystal *cr, const RefList *full, int free,
+                           int *pn_used, const char *filename);
+
+extern void scale_all(Crystal **crystals, int n_crystals, int nthreads,
+                      PartialityModel pmodel, double max_B);
+
+#endif	/* SCALING_H */