compare_hkl: Fix appalling scaling behaviour

1 files changed, 57 insertions, 92 deletions

diff --git a/src/statistics.c b/src/statistics.c
index 77e7919f..da9a06c6 100644
--- a/src/statistics.c
+++ b/src/statistics.c
@@ -26,7 +26,7 @@
 
 struct r_params {
 	RefList *list1;
-	RefList *list2;
+	double *arr2;
 	int fom;              /* Which FoM to use (see the enum just below) */
 };
 
@@ -42,10 +42,10 @@ enum {
 
 
 /* Return the least squares optimal scaling factor when comparing intensities.
- * list1,list2 are the two intensity lists to compare.  "items" is a ReflItemList
+ * list1,arr2 are the two intensity lists to compare.  "items" is a ReflItemList
  * containing the reflections which should be taken into account.
  */
-double stat_scale_intensity(RefList *list1, RefList *list2)
+double stat_scale_intensity(RefList *list1, double *arr2)
 {
 	double top = 0.0;
 	double bot = 0.0;
@@ -58,14 +58,11 @@ double stat_scale_intensity(RefList *list1, RefList *list2)
 
 		double i1, i2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		top += i1 * i2;
 		bot += i2 * i2;
@@ -79,11 +76,11 @@ double stat_scale_intensity(RefList *list1, RefList *list2)
 /* Return the least squares optimal scaling factor when comparing the square
  * roots of the intensities (i.e. one approximation to the structure factor
  * moduli).
- * list1,list2 are the two intensity lists to compare (they contain intensities,
+ * list1,arr2 are the two intensity lists to compare (they contain intensities,
  * not square rooted intensities).  "items" is a ReflItemList containing the
  * reflections which should be taken into account.
  */
-static double stat_scale_sqrti(RefList *list1, RefList *list2)
+static double stat_scale_sqrti(RefList *list1, double *arr2)
 {
 	double top = 0.0;
 	double bot = 0.0;
@@ -97,14 +94,11 @@ static double stat_scale_sqrti(RefList *list1, RefList *list2)
 		double i1, i2;
 		double f1, f2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		if ( i1 < 0.0 ) continue;
 		f1 = sqrt(i1);
@@ -121,7 +115,7 @@ static double stat_scale_sqrti(RefList *list1, RefList *list2)
 }
 
 
-static double internal_r1_ignorenegs(RefList *list1, RefList *list2,
+static double internal_r1_ignorenegs(RefList *list1, double *arr2,
                                      double scale)
 {
 	double top = 0.0;
@@ -136,14 +130,11 @@ static double internal_r1_ignorenegs(RefList *list1, RefList *list2,
 		double i1, i2;
 		double f1, f2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		if ( i1 < 0.0 ) continue;
 		f1 = sqrt(i1);
@@ -161,7 +152,7 @@ static double internal_r1_ignorenegs(RefList *list1, RefList *list2,
 }
 
 
-static double internal_r1_negstozero(RefList *list1, RefList *list2,
+static double internal_r1_negstozero(RefList *list1, double *arr2,
                                      double scale)
 {
 	double top = 0.0;
@@ -176,14 +167,11 @@ static double internal_r1_negstozero(RefList *list1, RefList *list2,
 		double i1, i2;
 		double f1, f2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		f1 = i1 > 0.0 ? sqrt(i1) : 0.0;
 
@@ -199,7 +187,7 @@ static double internal_r1_negstozero(RefList *list1, RefList *list2,
 }
 
 
-static double internal_r2(RefList *list1, RefList *list2, double scale)
+static double internal_r2(RefList *list1, double *arr2, double scale)
 {
 	double top = 0.0;
 	double bot = 0.0;
@@ -212,14 +200,12 @@ static double internal_r2(RefList *list1, RefList *list2, double scale)
 
 		double i1, i2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = scale * get_intensity(refl2);
+		i2 *= scale;
 
 		top += pow(i1 - i2, 2.0);
 		bot += pow(i1, 2.0);
@@ -230,7 +216,7 @@ static double internal_r2(RefList *list1, RefList *list2, double scale)
 }
 
 
-static double internal_r_i(RefList *list1, RefList *list2, double scale)
+static double internal_r_i(RefList *list1, double *arr2, double scale)
 {
 	double top = 0.0;
 	double bot = 0.0;
@@ -243,14 +229,12 @@ static double internal_r_i(RefList *list1, RefList *list2, double scale)
 
 		double i1, i2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = scale * get_intensity(refl2);
+		i2 *= scale;
 
 		top += fabs(i1-i2);
 		bot += fabs(i1);
@@ -261,7 +245,7 @@ static double internal_r_i(RefList *list1, RefList *list2, double scale)
 }
 
 
-static double internal_rdiff_intensity(RefList *list1, RefList *list2,
+static double internal_rdiff_intensity(RefList *list1, double *arr2,
                                        double scale)
 {
 	double top = 0.0;
@@ -275,14 +259,11 @@ static double internal_rdiff_intensity(RefList *list1, RefList *list2,
 
 		double i1, i2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		i2 *= scale;
 
@@ -295,7 +276,7 @@ static double internal_rdiff_intensity(RefList *list1, RefList *list2,
 }
 
 
-static double internal_rdiff_negstozero(RefList *list1, RefList *list2,
+static double internal_rdiff_negstozero(RefList *list1, double *arr2,
                                         double scale)
 {
 	double top = 0.0;
@@ -310,14 +291,11 @@ static double internal_rdiff_negstozero(RefList *list1, RefList *list2,
 		double i1, i2;
 		double f1, f2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		f1 = i1 > 0.0 ? sqrt(i1) : 0.0;
 
@@ -333,7 +311,7 @@ static double internal_rdiff_negstozero(RefList *list1, RefList *list2,
 }
 
 
-static double internal_rdiff_ignorenegs(RefList *list1, RefList *list2,
+static double internal_rdiff_ignorenegs(RefList *list1, double *arr2,
                                         double scale)
 {
 	double top = 0.0;
@@ -348,14 +326,11 @@ static double internal_rdiff_ignorenegs(RefList *list1, RefList *list2,
 		double i1, i2;
 		double f1, f2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		if ( i1 < 0.0 ) continue;
 		f1 = sqrt(i1);
@@ -379,21 +354,21 @@ static double calc_r(double scale, void *params)
 
 	switch ( rp->fom) {
 	case R_1_ZERO :
-		return internal_r1_negstozero(rp->list1, rp->list2, scale);
+		return internal_r1_negstozero(rp->list1, rp->arr2, scale);
 	case R_1_IGNORE :
-		return internal_r1_ignorenegs(rp->list1, rp->list2, scale);
+		return internal_r1_ignorenegs(rp->list1, rp->arr2, scale);
 	case R_2 :
-		return internal_r2(rp->list1, rp->list2, scale);
+		return internal_r2(rp->list1, rp->arr2, scale);
 
 	case R_1_I :
-		return internal_r_i(rp->list1, rp->list2, scale);
+		return internal_r_i(rp->list1, rp->arr2, scale);
 
 	case R_DIFF_ZERO :
-		return internal_rdiff_negstozero(rp->list1, rp->list2,scale);
+		return internal_rdiff_negstozero(rp->list1, rp->arr2,scale);
 	case R_DIFF_IGNORE :
-		return internal_rdiff_ignorenegs(rp->list1, rp->list2, scale);
+		return internal_rdiff_ignorenegs(rp->list1, rp->arr2, scale);
 	case R_DIFF_INTENSITY :
-		return internal_rdiff_intensity(rp->list1, rp->list2, scale);
+		return internal_rdiff_intensity(rp->list1, rp->arr2, scale);
 	}
 
 	ERROR("No such FoM!\n");
@@ -401,8 +376,7 @@ static double calc_r(double scale, void *params)
 }
 
 
-static double r_minimised(RefList *list1, RefList *list2,
-                          double *scalep, int fom)
+static double r_minimised(RefList *list1, double *arr2, double *scalep, int fom)
 {
 	gsl_function F;
 	gsl_min_fminimizer *s;
@@ -412,7 +386,7 @@ static double r_minimised(RefList *list1, RefList *list2,
 	int iter = 0;
 
 	rp.list1 = list1;
-	rp.list2 = list2;
+	rp.arr2 = arr2;
 	rp.fom = fom;
 
 	F.function = &calc_r;
@@ -426,12 +400,12 @@ static double r_minimised(RefList *list1, RefList *list2,
 	case R_1_IGNORE :
 	case R_DIFF_ZERO :
 	case R_DIFF_IGNORE :
-		scale = stat_scale_sqrti(list1, list2);
+		scale = stat_scale_sqrti(list1, arr2);
 		break;
 	case R_2 :
 	case R_1_I :
 	case R_DIFF_INTENSITY :
-		scale = stat_scale_intensity(list1, list2);
+		scale = stat_scale_intensity(list1, arr2);
 		break;
 	}
 	//STATUS("Initial scale factor estimate: %5.2e\n", scale);
@@ -470,52 +444,52 @@ static double r_minimised(RefList *list1, RefList *list2,
 }
 
 
-double stat_r1_ignore(RefList *list1, RefList *list2, double *scalep)
+double stat_r1_ignore(RefList *list1, double *arr2, double *scalep)
 {
-	return r_minimised(list1, list2, scalep, R_1_IGNORE);
+	return r_minimised(list1, arr2, scalep, R_1_IGNORE);
 }
 
 
-double stat_r1_zero(RefList *list1, RefList *list2, double *scalep)
+double stat_r1_zero(RefList *list1, double *arr2, double *scalep)
 {
-	return r_minimised(list1, list2, scalep, R_1_ZERO);
+	return r_minimised(list1, arr2, scalep, R_1_ZERO);
 }
 
 
-double stat_r2(RefList *list1, RefList *list2, double *scalep)
+double stat_r2(RefList *list1, double *arr2, double *scalep)
 {
-	return r_minimised(list1, list2, scalep, R_2);
+	return r_minimised(list1, arr2, scalep, R_2);
 }
 
 
-double stat_r1_i(RefList *list1, RefList *list2, double *scalep)
+double stat_r1_i(RefList *list1, double *arr2, double *scalep)
 {
-	return r_minimised(list1, list2, scalep, R_1_I);
+	return r_minimised(list1, arr2, scalep, R_1_I);
 }
 
 
-double stat_rdiff_zero(RefList *list1, RefList *list2, double *scalep)
+double stat_rdiff_zero(RefList *list1, double *arr2, double *scalep)
 {
-	return r_minimised(list1, list2, scalep, R_DIFF_ZERO);
+	return r_minimised(list1, arr2, scalep, R_DIFF_ZERO);
 }
 
 
-double stat_rdiff_ignore(RefList *list1, RefList *list2, double *scalep)
+double stat_rdiff_ignore(RefList *list1, double *arr2, double *scalep)
 {
-	return r_minimised(list1, list2, scalep, R_DIFF_IGNORE);
+	return r_minimised(list1, arr2, scalep, R_DIFF_IGNORE);
 }
 
 
-double stat_rdiff_intensity(RefList *list1, RefList *list2, double *scalep)
+double stat_rdiff_intensity(RefList *list1, double *arr2, double *scalep)
 {
-	return r_minimised(list1, list2,  scalep, R_DIFF_INTENSITY);
+	return r_minimised(list1, arr2,  scalep, R_DIFF_INTENSITY);
 }
 
 
-double stat_pearson_i(RefList *list1, RefList *list2)
+double stat_pearson_i(RefList *list1, double *arr2)
 {
 	double *vec1, *vec2;
-	int ni = num_reflections(list1) + num_reflections(list2);
+	int ni = num_reflections(list1);
 	double val;
 	int nacc = 0;
 	Reflection *refl1;
@@ -530,14 +504,11 @@ double stat_pearson_i(RefList *list1, RefList *list2)
 
 		double i1, i2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		vec1[nacc] = i1;
 		vec2[nacc] = i2;
@@ -552,10 +523,10 @@ double stat_pearson_i(RefList *list1, RefList *list2)
 }
 
 
-double stat_pearson_f_ignore(RefList *list1, RefList *list2)
+double stat_pearson_f_ignore(RefList *list1, double *arr2)
 {
 	double *vec1, *vec2;
-	int ni = num_reflections(list1) + num_reflections(list2);
+	int ni = num_reflections(list1);
 	double val;
 	int nacc = 0;
 	Reflection *refl1;
@@ -571,15 +542,12 @@ double stat_pearson_f_ignore(RefList *list1, RefList *list2)
 		double i1, i2;
 		double f1, f2;
 		signed int h, k, l;
-		Reflection *refl2;
 		int ig = 0;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		if ( i1 < 0.0 ) ig = 1;
 		f1 = sqrt(i1);
@@ -603,10 +571,10 @@ double stat_pearson_f_ignore(RefList *list1, RefList *list2)
 }
 
 
-double stat_pearson_f_zero(RefList *list1, RefList *list2)
+double stat_pearson_f_zero(RefList *list1, double *arr2)
 {
 	double *vec1, *vec2;
-	int ni = num_reflections(list1) + num_reflections(list2);
+	int ni = num_reflections(list1);
 	double val;
 	int nacc = 0;
 	Reflection *refl1;
@@ -622,14 +590,11 @@ double stat_pearson_f_zero(RefList *list1, RefList *list2)
 		double i1, i2;
 		double f1, f2;
 		signed int h, k, l;
-		Reflection *refl2;
 
 		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;  /* No common reflection */
+		i2 = lookup_intensity(arr2, h, k, l);
 
 		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
 
 		f1 = i1 > 0.0 ? sqrt(i1) : 0.0;
 		f2 = i2 > 0.0 ? sqrt(i2) : 0.0;