From eeb079dbdd1f28c0850bacb09af2829e785d596b Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 30 Nov 2010 16:42:23 +0100
Subject: Add missing files from previous commit

---
 src/hrs-scaling.c | 132 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 src/hrs-scaling.h |  26 +++++++++++
 2 files changed, 158 insertions(+)
 create mode 100644 src/hrs-scaling.c
 create mode 100644 src/hrs-scaling.h

diff --git a/src/hrs-scaling.c b/src/hrs-scaling.c
new file mode 100644
index 00000000..83c18e17
--- /dev/null
+++ b/src/hrs-scaling.c
@@ -0,0 +1,132 @@
+/*
+ * hrs-scaling.c
+ *
+ * Intensity scaling using generalised HRS target function
+ *
+ * (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 <assert.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_linalg.h>
+
+#include "image.h"
+#include "peaks.h"
+#include "symmetry.h"
+#include "geometry.h"
+#include "cell.h"
+
+
+static void show_matrix_eqn(gsl_matrix *M, gsl_vector *v, int r)
+{
+	int i, j;
+
+	for ( i=0; i<r; i++ ) {
+		STATUS("[ ");
+		for ( j=0; j<r; j++ ) {
+			STATUS("%+9.3e ", gsl_matrix_get(M, i, j));
+		}
+		STATUS("][ a%2i ] = [ %+9.3e ]\n", i, gsl_vector_get(v, i));
+	}
+}
+
+
+/* Scale the stack of images */
+void scale_intensities(struct image *images, int n, const char *sym)
+{
+#if 0
+	gsl_matrix *M;
+	gsl_vector *v;
+	gsl_vector *shifts;
+	int j;
+
+	M = gsl_matrix_calloc(n, n);
+	v = gsl_vector_calloc(n);
+
+	for ( j=0; j<n; j++ ) {
+
+		signed int hind, kind, lind;
+		signed int ha, ka, la;
+		double I_full, delta_I;
+		float I_partial;
+		float xc, yc;
+		int h;
+		struct image *image = &images[j];
+		struct cpeak *spots = image->cpeaks;
+
+		for ( h=0; h<image->n_cpeaks; h++ ) {
+
+			int g;
+			double v_c, gr, I_full;
+
+			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;
+
+			if ( integrate_peak(image, spots[h].x, spots[h].y,
+				            &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
+				continue;
+			}
+
+			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 / image->osf);
+
+
+			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],
+				               image->profile_radius)
+				    * gradient(image, k, spots[h],
+				               image->profile_radius);
+				M_c *= pow(I_full, 2.0);
+
+				gsl_matrix_set(M, g, k, M_curr + M_c);
+
+			}
+
+			gr = gradient(image, k, spots[h],
+			              image->profile_radius);
+			v_c = delta_I * I_full * gr;
+			gsl_vector_set(v, k, v_c);
+
+		}
+
+	}
+	show_matrix_eqn(M, v, NUM_PARAMS);
+
+	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);
+#endif
+}
diff --git a/src/hrs-scaling.h b/src/hrs-scaling.h
new file mode 100644
index 00000000..28343283
--- /dev/null
+++ b/src/hrs-scaling.h
@@ -0,0 +1,26 @@
+/*
+ * hrs-scaling.h
+ *
+ * Intensity scaling using generalised HRS target function
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifndef HRS_SCALING_H
+#define HRS_SCALING_H
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include "image.h"
+
+extern void scale_intensities(struct image *image, int n, const char *sym);
+
+
+#endif	/* HRS_SCALING_H */
-- 
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