Move predict-refine to libcrystfel

3 files changed, 804 insertions, 2 deletions

diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 8e5acaaf..1a0c3efe 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -9,7 +9,7 @@ libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/reflist-utils.c src/filters.c \
                          src/render.c src/index.c src/dirax.c src/mosflm.c \
                          src/cell-utils.c src/integer_matrix.c src/crystal.c \
-                         src/xds.c src/integration.c \
+                         src/xds.c src/integration.c src/predict-refine.c \
                          src/histogram.c src/events.c
 
 if HAVE_FFTW
@@ -28,7 +28,7 @@ libcrystfel_la_include_HEADERS = ${top_srcdir}/version.h \
                                  src/filters.h src/dirax.h src/mosflm.h \
                                  src/cell-utils.h \
                                  src/integer_matrix.h src/crystal.h \
-                                 src/xds.h \
+                                 src/xds.h src/predict-refine.h \
                                  src/integration.h src/histogram.h \
                                  src/events.h src/asdf.h
 
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
new file mode 100644
index 00000000..2d845feb
--- /dev/null
+++ b/libcrystfel/src/predict-refine.c
@@ -0,0 +1,757 @@
+/*
+ * predict-refine.c
+ *
+ * Prediction 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 "image.h"
+#include "geometry.h"
+#include "cell-utils.h"
+
+
+/* Maximum number of iterations of NLSq to do for each image per macrocycle. */
+#define MAX_CYCLES (10)
+
+/* Weighting of excitation error term (m^-1) compared to position term (m) */
+#define EXC_WEIGHT (4e-20)
+
+/* Parameters to refine */
+static const enum gparam rv[] =
+{
+	GPARAM_ASX,
+	GPARAM_ASY,
+	GPARAM_ASZ,
+	GPARAM_BSX,
+	GPARAM_BSY,
+	GPARAM_BSZ,
+	GPARAM_CSX,
+	GPARAM_CSY,
+	GPARAM_CSZ,
+	GPARAM_DETX,
+	GPARAM_DETY,
+};
+
+static const int num_params = 11;
+
+struct reflpeak {
+	Reflection *refl;
+	struct imagefeature *peak;
+	double Ih;   /* normalised */
+	struct panel *panel;  /* panel the reflection appears on
+                               * (we assume this never changes) */
+};
+
+
+static void twod_mapping(double fs, double ss, double *px, double *py,
+                         struct panel *p)
+{
+	double xs, ys;
+
+	xs = fs*p->fsx + ss*p->ssx;
+	ys = fs*p->fsy + ss*p->ssy;
+
+	*px = (xs + p->cnx) / p->res;
+	*py = (ys + p->cny) / p->res;
+}
+
+
+static double r_dev(struct reflpeak *rp)
+{
+	/* Excitation error term */
+	double rlow, rhigh, p;
+	get_partial(rp->refl, &rlow, &rhigh, &p);
+	return (rlow+rhigh)/2.0;
+}
+
+
+static double x_dev(struct reflpeak *rp, struct detector *det)
+{
+	/* Peak position term */
+	double xpk, ypk, xh, yh;
+	double fsh, ssh;
+	twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
+	get_detector_pos(rp->refl, &fsh, &ssh);
+	twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
+	return xh-xpk;
+}
+
+
+static double y_dev(struct reflpeak *rp, struct detector *det)
+{
+	/* Peak position term */
+	double xpk, ypk, xh, yh;
+	double fsh, ssh;
+	twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
+	get_detector_pos(rp->refl, &fsh, &ssh);
+	twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
+	return yh-ypk;
+}
+
+
+static void UNUSED write_pairs(const char *filename, struct reflpeak *rps,
+                               int n, struct detector *det)
+{
+	int i;
+	FILE *fh;
+
+	fh = fopen(filename, "w");
+	if ( fh == NULL ) {
+		ERROR("Failed to open '%s'\n", filename);
+		return;
+	}
+
+	for ( i=0; i<n; i++ ) {
+
+		double write_fs, write_ss;
+		double fs, ss;
+		struct panel *p;
+
+		fs = rps[i].peak->fs;
+		ss = rps[i].peak->ss;
+
+		p = find_panel(det, fs, ss);
+		write_fs = fs - p->min_fs + p->orig_min_fs;
+		write_ss = ss - p->min_ss + p->orig_min_ss;
+
+		fprintf(fh, "%7.2f %7.2f dev r,x,y: %9f %9f %9f %9f\n",
+		        write_fs, write_ss,
+		        r_dev(&rps[i])/1e9, fabs(r_dev(&rps[i])/1e9),
+		        x_dev(&rps[i], det),
+		        y_dev(&rps[i], det));
+
+	}
+
+	fclose(fh);
+
+	STATUS("Wrote %i pairs to %s\n", n, filename);
+}
+
+
+static int cmpd2(const void *av, const void *bv)
+{
+	struct reflpeak *a, *b;
+
+	a = (struct reflpeak *)av;
+	b = (struct reflpeak *)bv;
+
+	if ( fabs(r_dev(a)) < fabs(r_dev(b)) ) return -1;
+	return 1;
+}
+
+
+static int check_outlier_transition(struct reflpeak *rps, int n,
+                                    struct detector *det)
+{
+	int i;
+
+	if ( n < 3 ) return n;
+
+	qsort(rps, n, sizeof(struct reflpeak), cmpd2);
+	//write_pairs("pairs-before-outlier.lst", rps, n, det);
+
+	for ( i=1; i<n-1; i++ ) {
+
+		int j;
+		double grad = fabs(r_dev(&rps[i])) / i;
+
+		for ( j=i+1; j<n; j++ ) {
+			if ( fabs(r_dev(&rps[j])) < 0.001e9+grad*j ) {
+				break;
+			}
+		}
+		if ( j == n ) {
+			//STATUS("Outlier transition found at position %i / %i\n",
+			//       i, n);
+			return i;
+		}
+	}
+
+	//STATUS("No outlier transition found.\n");
+	return n;
+}
+
+
+/* Associate a Reflection with each peak in "image" which is close to Bragg.
+ * Reflections will be added to "reflist", which can be NULL if this is not
+ * needed.  "rps" must be an array of sufficient size for all the peaks */
+static int pair_peaks(struct image *image, Crystal *cr,
+                      RefList *reflist, struct reflpeak *rps)
+{
+	int i;
+	int n_acc = 0;
+	int n = 0;
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
+	RefList *all_reflist;
+
+	all_reflist = reflist_new();
+	cell_get_cartesian(crystal_get_cell(cr),
+	                   &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+
+	/* First, create a RefList containing the most likely indices for each
+	 * peak, with no exclusion criteria */
+	for ( i=0; i<image_feature_count(image->features); i++ ) {
+
+		struct imagefeature *f;
+		double h, k, l, hd, kd, ld;
+		Reflection *refl;
+		struct panel *p;
+
+		/* Assume all image "features" are genuine peaks */
+		f = image_get_feature(image->features, i);
+		if ( f == NULL ) continue;
+
+		/* Decimal and fractional Miller indices of nearest reciprocal
+		 * lattice point */
+		hd = f->rx * ax + f->ry * ay + f->rz * az;
+		kd = f->rx * bx + f->ry * by + f->rz * bz;
+		ld = f->rx * cx + f->ry * cy + f->rz * cz;
+		h = lrint(hd);
+		k = lrint(kd);
+		l = lrint(ld);
+
+		refl = reflection_new(h, k, l);
+		if ( refl == NULL ) {
+			ERROR("Failed to create reflection\n");
+			return 0;
+		}
+
+		add_refl_to_list(refl, all_reflist);
+		set_symmetric_indices(refl, h, k, l);
+
+		/* It doesn't matter if the actual predicted location
+		 * doesn't fall on this panel.  We're only interested
+		 * in how far away it is from the peak location.
+		 * The predicted position and excitation errors will be
+		 * filled in by update_partialities(). */
+		p = find_panel(image->det, f->fs, f->ss);
+		set_panel(refl, p);
+
+		rps[n].refl = refl;
+		rps[n].peak = f;
+		rps[n].panel = p;
+		n++;
+
+	}
+
+	/* Get the excitation errors and detector positions for the candidate
+	 * reflections */
+	crystal_set_reflections(cr, all_reflist);
+	update_partialities(cr, PMODEL_SCSPHERE);
+
+	/* Pass over the peaks again, keeping only the ones which look like
+	 * good pairings */
+	for ( i=0; i<n; i++ ) {
+
+		double fs, ss, pd;
+		signed int h, k, l;
+		Reflection *refl = rps[i].refl;
+
+		get_indices(refl, &h, &k, &l);
+
+		/* Is the supposed reflection anywhere near the peak? */
+		get_detector_pos(refl, &fs, &ss);
+		pd = pow(fs - rps[i].peak->fs, 2.0)
+		   + pow(ss - rps[i].peak->ss, 2.0);
+		if ( pd > 10.0 * 10.0 ) continue;
+
+		rps[n_acc] = rps[i];
+		rps[n_acc].refl = reflection_new(h, k, l);
+		copy_data(rps[n_acc].refl, refl);
+		if ( reflist != NULL ) {
+			add_refl_to_list(rps[n_acc].refl, reflist);
+		}
+		n_acc++;
+
+	}
+	reflist_free(all_reflist);
+
+	/* Sort the pairings by excitation error and look for a transition
+	 * between good pairings and outliers */
+	n_acc = check_outlier_transition(rps, n_acc, image->det);
+
+	return n_acc;
+}
+
+
+void refine_radius(Crystal *cr, struct image *image)
+{
+	int n, n_acc;
+	struct reflpeak *rps;
+	RefList *reflist;
+
+	/* Maximum possible size */
+	rps = malloc(image_feature_count(image->features)
+	                  * sizeof(struct reflpeak));
+	if ( rps == NULL ) return;
+
+	reflist = reflist_new();
+	n_acc = pair_peaks(image, cr, reflist, rps);
+	if ( n_acc < 3 ) {
+		ERROR("Too few paired peaks (%i) to determine radius\n", n_acc);
+		free(rps);
+		return;
+	}
+	crystal_set_reflections(cr, reflist);
+	update_partialities(cr, PMODEL_SCSPHERE);
+	crystal_set_reflections(cr, NULL);
+
+	qsort(rps, n_acc, sizeof(struct reflpeak), cmpd2);
+	n = (n_acc-1) - n_acc/50;
+	if ( n < 2 ) n = 2; /* n_acc is always >= 2 */
+	crystal_set_profile_radius(cr, fabs(r_dev(&rps[n])));
+
+	reflist_free(reflist);
+	free(rps);
+}
+
+
+/* Returns d(xh-xpk)/dP, where P = any parameter */
+static double x_gradient(int param, struct reflpeak *rp, struct detector *det,
+                         double lambda, UnitCell *cell)
+{
+	signed int h, k, l;
+	double xpk, ypk, xh, yh;
+	double fsh, ssh;
+	double x, z, wn;
+	double ax, ay, az, bx, by, bz, cx, cy, cz;
+
+	twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
+	get_detector_pos(rp->refl, &fsh, &ssh);
+	twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
+	get_indices(rp->refl, &h, &k, &l);
+
+	wn = 1.0 / lambda;
+
+	cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+	x = h*ax + k*bx + l*cx;
+	z = h*az + k*bz + l*cz;
+
+	switch ( param ) {
+
+		case GPARAM_ASX :
+		return h * rp->panel->clen / (wn+z);
+
+		case GPARAM_BSX :
+		return k * rp->panel->clen / (wn+z);
+
+		case GPARAM_CSX :
+		return l * rp->panel->clen / (wn+z);
+
+		case GPARAM_ASY :
+		return 0.0;
+
+		case GPARAM_BSY :
+		return 0.0;
+
+		case GPARAM_CSY :
+		return 0.0;
+
+		case GPARAM_ASZ :
+		return -h * x * rp->panel->clen / (wn*wn + 2*wn*z + z*z);
+
+		case GPARAM_BSZ :
+		return -k * x * rp->panel->clen / (wn*wn + 2*wn*z + z*z);
+
+		case GPARAM_CSZ :
+		return -l * x * rp->panel->clen / (wn*wn + 2*wn*z + z*z);
+
+		case GPARAM_DETX :
+		return -1;
+
+		case GPARAM_DETY :
+		return 0;
+
+		case GPARAM_CLEN :
+		return x / (wn+z);
+
+	}
+
+	ERROR("Positional gradient requested for parameter %i?\n", param);
+	abort();
+}
+
+
+/* Returns d(yh-ypk)/dP, where P = any parameter */
+static double y_gradient(int param, struct reflpeak *rp, struct detector *det,
+                         double lambda, UnitCell *cell)
+{
+	signed int h, k, l;
+	double xpk, ypk, xh, yh;
+	double fsh, ssh;
+	double y, z, wn;
+	double ax, ay, az, bx, by, bz, cx, cy, cz;
+
+	twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
+	get_detector_pos(rp->refl, &fsh, &ssh);
+	twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
+	get_indices(rp->refl, &h, &k, &l);
+
+	wn = 1.0 / lambda;
+
+	cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+	y = h*ay + k*by + l*cy;
+	z = h*az + k*bz + l*cz;
+
+	switch ( param ) {
+
+		case GPARAM_ASX :
+		return 0.0;
+
+		case GPARAM_BSX :
+		return 0.0;
+
+		case GPARAM_CSX :
+		return 0.0;
+
+		case GPARAM_ASY :
+		return h * rp->panel->clen / (wn+z);
+
+		case GPARAM_BSY :
+		return k * rp->panel->clen / (wn+z);
+
+		case GPARAM_CSY :
+		return l * rp->panel->clen / (wn+z);
+
+		case GPARAM_ASZ :
+		return -h * y * rp->panel->clen / (wn*wn + 2*wn*z + z*z);
+
+		case GPARAM_BSZ :
+		return -k * y * rp->panel->clen / (wn*wn + 2*wn*z + z*z);
+
+		case GPARAM_CSZ :
+		return -l * y * rp->panel->clen / (wn*wn + 2*wn*z + z*z);
+
+		case GPARAM_DETX :
+		return 0;
+
+		case GPARAM_DETY :
+		return -1;
+
+		case GPARAM_CLEN :
+		return y / (wn+z);
+
+	}
+
+	ERROR("Positional gradient requested for parameter %i?\n", param);
+	abort();
+}
+
+
+static void update_detector(struct detector *det, double xoffs, double yoffs,
+                            double coffs)
+{
+	int i;
+
+	for ( i=0; i<det->n_panels; i++ ) {
+		struct panel *p = &det->panels[i];
+		p->cnx += xoffs * p->res;
+		p->cny += yoffs * p->res;
+		p->clen += coffs;
+	}
+}
+
+
+static int iterate(struct reflpeak *rps, int n, UnitCell *cell,
+                   struct image *image,
+                   double *total_x, double *total_y, double *total_z)
+{
+	int i;
+	gsl_matrix *M;
+	gsl_vector *v;
+	gsl_vector *shifts;
+	double asx, asy, asz;
+	double bsx, bsy, bsz;
+	double csx, csy, csz;
+
+	/* Number of parameters to refine */
+	M = gsl_matrix_calloc(num_params, num_params);
+	v = gsl_vector_calloc(num_params);
+
+	for ( i=0; i<n; i++ ) {
+
+		int k;
+		double gradients[num_params];
+		double w;
+
+		/* Excitation error terms */
+		w = EXC_WEIGHT * rps[i].Ih;
+
+		for ( k=0; k<num_params; k++ ) {
+			gradients[k] = r_gradient(cell, rv[k], rps[i].refl,
+			                          image);
+		}
+
+		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);
+
+			}
+
+			v_c = w * r_dev(&rps[i]);
+			v_c *= -gradients[k];
+			v_curr = gsl_vector_get(v, k);
+			gsl_vector_set(v, k, v_curr + v_c);
+
+		}
+
+		/* Positional x terms */
+		for ( k=0; k<num_params; k++ ) {
+			gradients[k] = x_gradient(rv[k], &rps[i], image->det,
+			                          image->lambda, cell);
+		}
+
+		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 = 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);
+
+			}
+
+			v_c = x_dev(&rps[i], image->det);
+			v_c *= -gradients[k];
+			v_curr = gsl_vector_get(v, k);
+			gsl_vector_set(v, k, v_curr + v_c);
+
+		}
+
+		/* Positional y terms */
+		for ( k=0; k<num_params; k++ ) {
+			gradients[k] = y_gradient(rv[k], &rps[i], image->det,
+			                          image->lambda, cell);
+		}
+
+		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 = 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);
+
+			}
+
+			v_c = y_dev(&rps[i], image->det);
+			v_c *= -gradients[k];
+			v_curr = gsl_vector_get(v, k);
+			gsl_vector_set(v, k, v_curr + v_c);
+
+		}
+
+	}
+
+	//show_matrix_eqn(M, v);
+	shifts = solve_svd(v, M, NULL, 0);
+	if ( shifts == NULL ) {
+		ERROR("Failed to solve equations.\n");
+		gsl_matrix_free(M);
+		gsl_vector_free(v);
+		return 1;
+	}
+
+	for ( i=0; i<num_params; i++ ) {
+	//	STATUS("Shift %i = %e\n", i, gsl_vector_get(shifts, i));
+		if ( isnan(gsl_vector_get(shifts, i)) ) {
+			gsl_vector_set(shifts, i, 0.0);
+		}
+	}
+
+	/* Apply shifts */
+	cell_get_reciprocal(cell, &asx, &asy, &asz,
+	                          &bsx, &bsy, &bsz,
+	                          &csx, &csy, &csz);
+
+	/* Ensure the order here matches the order in rv[] */
+	asx += gsl_vector_get(shifts, 0);
+	asy += gsl_vector_get(shifts, 1);
+	asz += gsl_vector_get(shifts, 2);
+	bsx += gsl_vector_get(shifts, 3);
+	bsy += gsl_vector_get(shifts, 4);
+	bsz += gsl_vector_get(shifts, 5);
+	csx += gsl_vector_get(shifts, 6);
+	csy += gsl_vector_get(shifts, 7);
+	csz += gsl_vector_get(shifts, 8);
+	update_detector(image->det, gsl_vector_get(shifts, 9),
+	                            gsl_vector_get(shifts, 10),
+	                            gsl_vector_get(shifts, 11));
+	*total_x += gsl_vector_get(shifts, 9);
+	*total_y += gsl_vector_get(shifts, 10);
+	*total_z += gsl_vector_get(shifts, 11);
+
+	cell_set_reciprocal(cell, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+
+	gsl_vector_free(shifts);
+	gsl_matrix_free(M);
+	gsl_vector_free(v);
+
+	return 0;
+}
+
+
+static double UNUSED residual(struct reflpeak *rps, int n, struct detector *det)
+{
+	int i;
+	double res = 0.0;
+	double r;
+
+	r = 0.0;
+	for ( i=0; i<n; i++ ) {
+		r += EXC_WEIGHT * rps[i].Ih * pow(r_dev(&rps[i]), 2.0);
+	}
+	printf("%e ", r);
+	res += r;
+
+	r = 0.0;
+	for ( i=0; i<n; i++ ) {
+		r += pow(x_dev(&rps[i], det), 2.0);
+	}
+	printf("%e ", r);
+	res += r;
+
+	r = 0.0;
+	for ( i=0; i<n; i++ ) {
+		r += pow(y_dev(&rps[i], det), 2.0);
+	}
+	printf("%e\n", r);
+	res += r;
+
+	return res;
+}
+
+
+int refine_prediction(struct image *image, Crystal *cr)
+{
+	int n;
+	int i;
+	struct reflpeak *rps;
+	double max_I;
+	RefList *reflist;
+	double total_x = 0.0;
+	double total_y = 0.0;
+	double total_z = 0.0;
+	char tmp[1024];
+
+	rps = malloc(image_feature_count(image->features)
+	                       * sizeof(struct reflpeak));
+	if ( rps == NULL ) return 1;
+
+	reflist = reflist_new();
+	n = pair_peaks(image, cr, reflist, rps);
+	if ( n < 10 ) {
+		ERROR("Too few paired peaks (%i) to refine orientation.\n", n);
+		free(rps);
+		reflist_free(reflist);
+		return 1;
+	}
+	crystal_set_reflections(cr, reflist);
+
+	/* Normalise the intensities to max 1 */
+	max_I = -INFINITY;
+	for ( i=0; i<n; i++ ) {
+		double cur_I = rps[i].peak->intensity;
+		if ( cur_I > max_I ) max_I = cur_I;
+	}
+	if ( max_I <= 0.0 ) {
+		ERROR("All peaks negative?\n");
+		free(rps);
+		return 1;
+	}
+	for ( i=0; i<n; i++ ) {
+		rps[i].Ih = rps[i].peak->intensity / max_I;
+	}
+
+	//STATUS("Initial residual = %e\n", residual(rps, n, image->det));
+
+	/* Refine */
+	for ( i=0; i<MAX_CYCLES; i++ ) {
+		update_partialities(cr, PMODEL_SCSPHERE);
+		if ( iterate(rps, n, crystal_get_cell(cr), image,
+		             &total_x, &total_y, &total_z) ) return 1;
+		//STATUS("Residual after %i = %e\n", i,
+		//       residual(rps, n, image->det));
+	}
+	//STATUS("Final residual = %e\n", residual(rps, n, image->det));
+
+	snprintf(tmp, 1024, "predict_refine/det_shift x = %.3f y = %.3f mm",
+	                    total_x*1e3, total_y*1e3);
+	crystal_add_notes(cr, tmp);
+
+	crystal_set_reflections(cr, NULL);
+	reflist_free(reflist);
+
+	n = pair_peaks(image, cr, NULL, rps);
+	free(rps);
+	if ( n < 10 ) {
+		ERROR("Too few paired peaks (%i) after refinement.\n", n);
+		return 1;
+	}
+
+	return 0;
+}
diff --git a/libcrystfel/src/predict-refine.h b/libcrystfel/src/predict-refine.h
new file mode 100644
index 00000000..c763d2ca
--- /dev/null
+++ b/libcrystfel/src/predict-refine.h
@@ -0,0 +1,45 @@
+/*
+ * predict-refine.h
+ *
+ * Prediction 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/>.
+ *
+ */
+
+#ifndef PREDICT_REFINE_H
+#define PREDICT_REFINE_H
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "crystal.h"
+
+struct image;
+
+extern int refine_prediction(struct image *image, Crystal *cr);
+extern void refine_radius(Crystal *cr, struct image *image);
+
+
+#endif	/* PREDICT_REFINE_H */