Move post refinement stuff to a new file

5 files changed, 272 insertions, 200 deletions

diff --git a/src/Makefile.am b/src/Makefile.am
index dbbdc9a2..5599da98 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -64,7 +64,7 @@ calibrate_detector_LDADD = @LIBS@
 
 facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
                    image.c geometry.c reflections.c stream.c thread-pool.c \
-                   beam-parameters.c symmetry.c
+                   beam-parameters.c symmetry.c post-refinement.c
 facetron_LDADD = @LIBS@
 
 cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c detector.c render.c \
@@ -87,4 +87,4 @@ EXTRA_DIST = cell.h hdf5-file.h image.h  utils.h diffraction.h detector.h \
              render.h hdfsee.h dirax.h peaks.h index.h  filters.h \
              diffraction-gpu.h cl-utils.h symmetry.h \
              povray.h index-priv.h geometry.h templates.h render_hkl.h \
-             stream.h thread-pool.h beam-parameters.h
+             stream.h thread-pool.h beam-parameters.h post-refinement.h
diff --git a/src/Makefile.in b/src/Makefile.in
index 00f9af02..fbdcd53c 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -84,7 +84,8 @@ am_facetron_OBJECTS = facetron.$(OBJEXT) cell.$(OBJEXT) \
 	hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
 	peaks.$(OBJEXT) image.$(OBJEXT) geometry.$(OBJEXT) \
 	reflections.$(OBJEXT) stream.$(OBJEXT) thread-pool.$(OBJEXT) \
-	beam-parameters.$(OBJEXT) symmetry.$(OBJEXT)
+	beam-parameters.$(OBJEXT) symmetry.$(OBJEXT) \
+	post-refinement.$(OBJEXT)
 facetron_OBJECTS = $(am_facetron_OBJECTS)
 facetron_DEPENDENCIES =
 am_get_hkl_OBJECTS = get_hkl.$(OBJEXT) sfac.$(OBJEXT) cell.$(OBJEXT) \
@@ -324,7 +325,7 @@ calibrate_detector_SOURCES = calibrate_detector.c utils.c hdf5-file.c image.c \
 calibrate_detector_LDADD = @LIBS@
 facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
                    image.c geometry.c reflections.c stream.c thread-pool.c \
-                   beam-parameters.c symmetry.c
+                   beam-parameters.c symmetry.c post-refinement.c
 
 facetron_LDADD = @LIBS@
 cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c detector.c render.c \
@@ -345,7 +346,7 @@ EXTRA_DIST = cell.h hdf5-file.h image.h  utils.h diffraction.h detector.h \
              render.h hdfsee.h dirax.h peaks.h index.h  filters.h \
              diffraction-gpu.h cl-utils.h symmetry.h \
              povray.h index-priv.h geometry.h templates.h render_hkl.h \
-             stream.h thread-pool.h beam-parameters.h
+             stream.h thread-pool.h beam-parameters.h post-refinement.h
 
 all: all-am
 
@@ -491,6 +492,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/indexamajig.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pattern_sim.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/peaks.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/post-refinement.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/povray.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/powder_plot.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/process_hkl.Po@am__quote@
diff --git a/src/facetron.c b/src/facetron.c
index cf4f099e..9ea7bcea 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -22,9 +22,6 @@
 #include <getopt.h>
 #include <assert.h>
 #include <pthread.h>
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_vector.h>
-#include <gsl/gsl_linalg.h>
 
 #include "utils.h"
 #include "hdf5-file.h"
@@ -35,18 +32,12 @@
 #include "peaks.h"
 #include "thread-pool.h"
 #include "beam-parameters.h"
+#include "post-refinement.h"
 
 
 /* Maximum number of iterations of NLSq to do for each image per macrocycle. */
 #define MAX_CYCLES (100)
 
-/* Refineable parameters */
-enum {
-	REF_SCALE,
-	REF_DIV,
-	NUM_PARAMS
-};
-
 
 static void show_help(const char *s)
 {
@@ -83,190 +74,6 @@ struct refine_args
 };
 
 
-/* Return the gradient of parameter 'k' given the current status of 'image'. */
-static double gradient(struct image *image, int k,
-                       struct cpeak spot, double I_partial)
-{
-	double ds;
-	double nom, den;
-
-	ds = 2.0 * resolution(image->indexed_cell, spot.h, spot.k, spot.l);
-
-	switch ( k ) {
-
-	case REF_SCALE :
-		return I_partial;
-
-	case REF_DIV :
-		nom = sqrt(2.0) * ds * sin(image->div);
-		den = sqrt(1.0 - cos(image->div));
-		return nom/den;
-
-	}
-
-	ERROR("No gradient defined for parameter %i\n", k);
-	abort();
-}
-
-
-/* Apply the given shift to the 'k'th parameter of 'image'. */
-static void apply_shift(struct image *image, int k, double shift)
-{
-	switch ( k ) {
-
-	case REF_SCALE :
-		image->osf += shift;
-		break;
-
-	case REF_DIV :
-		STATUS("Shifting div by %e\n", shift);
-		image->div += shift;
-		break;
-
-	default :
-		ERROR("No shift defined for parameter %i\n", k);
-		abort();
-
-	}
-}
-
-
-static double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
-                               const char *sym, double *i_full, FILE *graph)
-{
-	int h;
-	double delta_I = 0.0;
-
-	for ( h=0; h<n; h++ ) {
-
-		signed int hind, kind, lind;
-		signed int ha, ka, la;
-		double I_full;
-		float I_partial;
-		float xc, yc;
-
-		hind = spots[h].h;
-		kind = spots[h].k;
-		lind = spots[h].l;
-
-		/* Don't attempt to use spots with very small
-		 * partialities, since it won't be accurate. */
-		if ( spots[h].p < 0.1 ) continue;
-
-		/* Actual measurement of this reflection from this
-		 * pattern? */
-		/* FIXME: Coordinates aren't whole numbers */
-		if ( integrate_peak(image, spots[h].x, spots[h].y,
-		                    &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
-			continue;
-		}
-		I_partial *= image->osf;
-
-		get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
-		I_full = lookup_intensity(i_full, ha, ka, la);
-		delta_I += fabs(I_partial - spots[h].p * I_full);
-
-		if ( graph != NULL ) {
-			fprintf(graph, "%3i %3i %3i %5.2f (at %5.2f,%5.2f)"
-			               " %5.2f %5.2f\n",
-			       hind, kind, lind, I_partial/spots[h].p, xc, yc,
-			       spots[h].p, I_partial / I_full);
-		}
-
-	}
-
-	return delta_I / (double)n;
-}
-
-
-static double iterate(struct image *image, double *i_full, const char *sym,
-                      struct cpeak **pspots, int *n)
-{
-	gsl_matrix *M;
-	gsl_vector *v;
-	gsl_vector *shifts;
-	int h, param;
-	struct cpeak *spots = *pspots;
-
-	M = gsl_matrix_calloc(NUM_PARAMS, NUM_PARAMS);
-	v = gsl_vector_calloc(NUM_PARAMS);
-
-	/* Construct the equations, one per reflection in this image */
-	for ( h=0; h<*n; h++ ) {
-
-		signed int hind, kind, lind;
-		signed int ha, ka, la;
-		double I_full, delta_I;
-		float I_partial;
-		float xc, yc;
-		int k;
-
-		hind = spots[h].h;
-		kind = spots[h].k;
-		lind = spots[h].l;
-
-		/* Don't attempt to use spots with very small
-		 * partialities, since it won't be accurate. */
-		if ( spots[h].p < 0.1 ) continue;
-
-		/* Actual measurement of this reflection from this
-		 * pattern? */
-		/* FIXME: Coordinates aren't whole numbers */
-		if ( integrate_peak(image, spots[h].x, spots[h].y,
-		                    &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
-			continue;
-		}
-		I_partial *= image->osf;
-
-		get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
-		I_full = lookup_intensity(i_full, ha, ka, la);
-		delta_I = I_partial - spots[h].p * I_full;
-
-		for ( k=0; k<NUM_PARAMS; k++ ) {
-
-			int g;
-			double v_c;
-
-			for ( g=0; g<NUM_PARAMS; g++ ) {
-
-				double M_curr, M_c;
-
-				M_curr = gsl_matrix_get(M, g, k);
-
-				M_c = gradient(image, g, spots[h], I_partial)
-				    * gradient(image, k, spots[h], I_partial);
-				M_c *= pow(I_full, 2.0);
-
-				gsl_matrix_set(M, g, k, M_curr + M_c);
-
-			}
-
-			v_c = delta_I * I_full * gradient(image, k, spots[h],
-			                                  I_partial);
-			gsl_vector_set(v, k, v_c);
-
-		}
-
-	}
-
-	shifts = gsl_vector_alloc(NUM_PARAMS);
-	gsl_linalg_HH_solve(M, v, shifts);
-	for ( param=0; param<NUM_PARAMS; param++ ) {
-		double shift = gsl_vector_get(shifts, param);
-		apply_shift(image, param, shift);
-	}
-
-	gsl_matrix_free(M);
-	gsl_vector_free(v);
-	gsl_vector_free(shifts);
-
-	free(spots);
-	spots = find_intersections(image, image->indexed_cell, n, 0);
-	*pspots = spots;
-	return mean_partial_dev(image, spots, *n, sym, i_full, NULL);
-}
-
-
 static void refine_image(int mytask, void *tasks)
 {
 	struct refine_args *all_args = tasks;
@@ -299,7 +106,7 @@ static void refine_image(int mytask, void *tasks)
 	i = 0;
 	do {
 		last_dev = dev;
-		dev = iterate(image, pargs->i_full, pargs->sym, &spots, &n);
+		dev = pr_iterate(image, pargs->i_full, pargs->sym, &spots, &n);
 		STATUS("Iteration %2i: mean dev = %5.2f\n", i, dev);
 		i++;
 	} while ( (fabs(last_dev - dev) > 1.0) && (i < MAX_CYCLES) );
diff --git a/src/post-refinement.c b/src/post-refinement.c
new file mode 100644
index 00000000..5ca0dc98
--- /dev/null
+++ b/src/post-refinement.c
@@ -0,0 +1,213 @@
+/*
+ * post-refinement.c
+ *
+ * Post refinement
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <gsl/gsl_poly.h>
+#include <assert.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_linalg.h>
+
+#include "image.h"
+#include "post-refinement.h"
+#include "peaks.h"
+#include "symmetry.h"
+#include "geometry.h"
+
+
+/* Return the gradient of parameter 'k' given the current status of 'image'. */
+double gradient(struct image *image, int k,
+                       struct cpeak spot, double I_partial)
+{
+	double ds;
+	double nom, den;
+
+	ds = 2.0 * resolution(image->indexed_cell, spot.h, spot.k, spot.l);
+
+	switch ( k ) {
+
+	case REF_SCALE :
+		return I_partial;
+
+	case REF_DIV :
+		nom = sqrt(2.0) * ds * sin(image->div);
+		den = sqrt(1.0 - cos(image->div));
+		return nom/den;
+
+	}
+
+	ERROR("No gradient defined for parameter %i\n", k);
+	abort();
+}
+
+
+/* Apply the given shift to the 'k'th parameter of 'image'. */
+void apply_shift(struct image *image, int k, double shift)
+{
+	switch ( k ) {
+
+	case REF_SCALE :
+		image->osf += shift;
+		break;
+
+	case REF_DIV :
+		STATUS("Shifting div by %e\n", shift);
+		image->div += shift;
+		break;
+
+	default :
+		ERROR("No shift defined for parameter %i\n", k);
+		abort();
+
+	}
+}
+
+
+double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
+                        const char *sym, double *i_full, FILE *graph)
+{
+	int h;
+	double delta_I = 0.0;
+
+	for ( h=0; h<n; h++ ) {
+
+		signed int hind, kind, lind;
+		signed int ha, ka, la;
+		double I_full;
+		float I_partial;
+		float xc, yc;
+
+		hind = spots[h].h;
+		kind = spots[h].k;
+		lind = spots[h].l;
+
+		/* Don't attempt to use spots with very small
+		 * partialities, since it won't be accurate. */
+		if ( spots[h].p < 0.1 ) continue;
+
+		/* Actual measurement of this reflection from this
+		 * pattern? */
+		/* FIXME: Coordinates aren't whole numbers */
+		if ( integrate_peak(image, spots[h].x, spots[h].y,
+		                    &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
+			continue;
+		}
+		I_partial *= image->osf;
+
+		get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
+		I_full = lookup_intensity(i_full, ha, ka, la);
+		delta_I += fabs(I_partial - spots[h].p * I_full);
+
+		if ( graph != NULL ) {
+			fprintf(graph, "%3i %3i %3i %5.2f (at %5.2f,%5.2f)"
+			               " %5.2f %5.2f\n",
+			       hind, kind, lind, I_partial/spots[h].p, xc, yc,
+			       spots[h].p, I_partial / I_full);
+		}
+
+	}
+
+	return delta_I / (double)n;
+}
+
+
+/* Perform one cycle of post refinement on 'image' against 'i_full' */
+double pr_iterate(struct image *image, double *i_full, const char *sym,
+                  struct cpeak **pspots, int *n)
+{
+	gsl_matrix *M;
+	gsl_vector *v;
+	gsl_vector *shifts;
+	int h, param;
+	struct cpeak *spots = *pspots;
+
+	M = gsl_matrix_calloc(NUM_PARAMS, NUM_PARAMS);
+	v = gsl_vector_calloc(NUM_PARAMS);
+
+	/* Construct the equations, one per reflection in this image */
+	for ( h=0; h<*n; h++ ) {
+
+		signed int hind, kind, lind;
+		signed int ha, ka, la;
+		double I_full, delta_I;
+		float I_partial;
+		float xc, yc;
+		int k;
+
+		hind = spots[h].h;
+		kind = spots[h].k;
+		lind = spots[h].l;
+
+		/* Don't attempt to use spots with very small
+		 * partialities, since it won't be accurate. */
+		if ( spots[h].p < 0.1 ) continue;
+
+		/* Actual measurement of this reflection from this
+		 * pattern? */
+		/* FIXME: Coordinates aren't whole numbers */
+		if ( integrate_peak(image, spots[h].x, spots[h].y,
+		                    &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
+			continue;
+		}
+		I_partial *= image->osf;
+
+		get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
+		I_full = lookup_intensity(i_full, ha, ka, la);
+		delta_I = I_partial - spots[h].p * I_full;
+
+		for ( k=0; k<NUM_PARAMS; k++ ) {
+
+			int g;
+			double v_c;
+
+			for ( g=0; g<NUM_PARAMS; g++ ) {
+
+				double M_curr, M_c;
+
+				M_curr = gsl_matrix_get(M, g, k);
+
+				M_c = gradient(image, g, spots[h], I_partial)
+				    * gradient(image, k, spots[h], I_partial);
+				M_c *= pow(I_full, 2.0);
+
+				gsl_matrix_set(M, g, k, M_curr + M_c);
+
+			}
+
+			v_c = delta_I * I_full * gradient(image, k, spots[h],
+			                                  I_partial);
+			gsl_vector_set(v, k, v_c);
+
+		}
+
+	}
+
+	shifts = gsl_vector_alloc(NUM_PARAMS);
+	gsl_linalg_HH_solve(M, v, shifts);
+	for ( param=0; param<NUM_PARAMS; param++ ) {
+		double shift = gsl_vector_get(shifts, param);
+		apply_shift(image, param, shift);
+	}
+
+	gsl_matrix_free(M);
+	gsl_vector_free(v);
+	gsl_vector_free(shifts);
+
+	free(spots);
+	spots = find_intersections(image, image->indexed_cell, n, 0);
+	*pspots = spots;
+	return mean_partial_dev(image, spots, *n, sym, i_full, NULL);
+}
diff --git a/src/post-refinement.h b/src/post-refinement.h
new file mode 100644
index 00000000..1ef7a1fd
--- /dev/null
+++ b/src/post-refinement.h
@@ -0,0 +1,50 @@
+/*
+ * post-refinement.h
+ *
+ * Post refinement
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifndef POST_REFINEMENT_H
+#define POST_REFINEMENT_H
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdio.h>
+
+#include "image.h"
+
+
+/* Refineable parameters */
+enum {
+	REF_SCALE,
+	REF_DIV,
+	NUM_PARAMS
+};
+
+
+/* Return the gradient of parameter 'k' given the current status of 'image'. */
+double gradient(struct image *image, int k, struct cpeak spot,
+                double I_partial);
+
+/* Apply the given shift to the 'k'th parameter of 'image'. */
+void apply_shift(struct image *image, int k, double shift);
+
+
+double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
+                        const char *sym, double *i_full, FILE *graph);
+
+
+double pr_iterate(struct image *image, double *i_full, const char *sym,
+                  struct cpeak **pspots, int *n);
+
+
+#endif	/* POST_REFINEMENT_H */