From 623939fb6bd9475935546b9539f404eaaff41a3f Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Mon, 11 Jul 2011 16:55:35 +0200
Subject: Use new Kabsch algorithm for faster scaling

---
 src/reflist.c | 102 ++++++++++++++++++++++++++++++++++++----------------------
 1 file changed, 64 insertions(+), 38 deletions(-)

(limited to 'src/reflist.c')

diff --git a/src/reflist.c b/src/reflist.c
index b51af27c..5b594d76 100644
--- a/src/reflist.c
+++ b/src/reflist.c
@@ -81,9 +81,9 @@ struct _refldata {
 	/* Redundancy */
 	int redundancy;
 
-	/* Total squared difference between all estimates of this reflection
-	 * and the estimated mean value */
-	double sum_squared_dev;
+	/* User-specified temporary values */
+	double temp1;
+	double temp2;
 };
 
 
@@ -423,47 +423,61 @@ int get_redundancy(const Reflection *refl)
 
 
 /**
- * get_sum_squared_dev:
+ * get_esd_intensity:
  * @refl: A %Reflection
  *
- * The sum squared deviation is used to estimate the standard errors on the
- * intensities during 'Monte Carlo' merging.
+ * Returns: the standard error in the intensity measurement (as returned by
+ * get_intensity()) for this reflection.
+ *
+ **/
+double get_esd_intensity(const Reflection *refl)
+{
+	return refl->data.esd_i;
+}
+
+
+/**
+ * get_phase:
+ * @refl: A %Reflection
  *
- * Returns: the sum of the squared deviations between the intensities and the
- * mean intensity from all measurements of the reflection (and probably its
- * symmetry equivalents according to some point group).
+ * Returns: the phase for this reflection.
  *
  **/
-double get_sum_squared_dev(const Reflection *refl)
+double get_phase(const Reflection *refl)
 {
-	return refl->data.sum_squared_dev;
+	return refl->data.phase;
 }
 
 
 /**
- * get_esd_intensity:
+ * get_temp1:
  * @refl: A %Reflection
  *
- * Returns: the standard error in the intensity measurement (as returned by
- * get_intensity()) for this reflection.
+ * The temporary values can be used according to the needs of the calling
+ * program.
+ *
+ * Returns: the first temporary value for this reflection.
  *
  **/
-double get_esd_intensity(const Reflection *refl)
+double get_temp1(const Reflection *refl)
 {
-	return refl->data.esd_i;
+	return refl->data.temp1;
 }
 
 
 /**
- * get_phase:
+ * get_temp2:
  * @refl: A %Reflection
  *
- * Returns: the phase for this reflection.
+ * The temporary values can be used according to the needs of the calling
+ * program.
+ *
+ * Returns: the second temporary value for this reflection.
  *
  **/
-double get_phase(const Reflection *refl)
+double get_temp2(const Reflection *refl)
 {
-	return refl->data.phase;
+	return refl->data.temp2;
 }
 
 
@@ -584,24 +598,6 @@ void set_redundancy(Reflection *refl, int red)
 }
 
 
-/**
- * set_sum_squared_dev:
- * @refl: A %Reflection
- * @dev: New sum squared deviation for the reflection
- *
- * The sum squared deviation is used to estimate the standard errors on the
- * intensities during 'Monte Carlo' merging.  It is defined as the sum of the
- * squared deviations between the intensities and the mean intensity from all
- * measurements of the reflection (and probably its symmetry equivalents
- * according to some point group).
- *
- **/
-void set_sum_squared_dev(Reflection *refl, double dev)
-{
-	refl->data.sum_squared_dev = dev;
-}
-
-
 /**
  * set_esd_intensity:
  * @refl: A %Reflection
@@ -648,6 +644,36 @@ void set_symmetric_indices(Reflection *refl,
 }
 
 
+/**
+ * set_temp1
+ * @refl: A %Reflection
+ * @temp: New temporary value for the reflection
+ *
+ * The temporary values can be used according to the needs of the calling
+ * program.
+ *
+ **/
+void set_temp1(Reflection *refl, double temp)
+{
+	refl->data.temp1 = temp;
+}
+
+
+/**
+ * set_temp2
+ * @refl: A %Reflection
+ * @temp: New temporary value for the reflection
+ *
+ * The temporary values can be used according to the needs of the calling
+ * program.
+ *
+ **/
+void set_temp2(Reflection *refl, double temp)
+{
+	refl->data.temp2 = temp;
+}
+
+
 /********************************* Insertion **********************************/
 
 static Reflection *rotate_once(Reflection *refl, int dir)
-- 
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