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Commit 192b3acc authored by Thomas White's avatar Thomas White
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compare_hkl: Fix appalling scaling behaviour

parent 2470a37e
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src/compare_hkl.c
View file @ 192b3acc
......@@ -49,7 +49,7 @@ static void show_help(const char *s)
}
static void plot_shells(RefList *list1, RefList *list2, double scale,
static void plot_shells(RefList *list1, double *arr2, double scale,
UnitCell *cell, const char *sym,
double rmin_fix, double rmax_fix)
{
......@@ -106,11 +106,8 @@ static void plot_shells(RefList *list1, RefList *list2, double scale,
signed int h, k, l;
double d;
Reflection *refl2;
get_indices(refl1, &h, &k, &l);
refl2 = find_refl(list2, h, k, l);
if ( refl2 == NULL ) continue; /* No common reflection */
d = resolution(cell, h, k, l) * 2.0;
if ( d > rmax ) rmax = d;
......@@ -207,11 +204,8 @@ static void plot_shells(RefList *list1, RefList *list2, double scale,
int bin;
double i1, i2;
int j;
Reflection *refl2;
get_indices(refl1, &h, &k, &l);
refl2 = find_refl(list2, h, k, l);
if ( refl2 == NULL ) continue; /* No common reflection */
d = resolution(cell, h, k, l) * 2.0;
......@@ -230,8 +224,7 @@ static void plot_shells(RefList *list1, RefList *list2, double scale,
}
i1 = get_intensity(refl1);
i2 = get_intensity(refl2);
i2 *= scale;
i2 = scale * lookup_intensity(arr2, h, k, l);
num[bin] += fabs(i1 - i2);
den += i1;
......@@ -282,6 +275,7 @@ int main(int argc, char *argv[])
float rmax_fix = -1.0;
Reflection *refl1;
RefListIterator *iter;
double *arr2;
/* Long options */
const struct option longopts[] = {
......@@ -471,49 +465,54 @@ int main(int argc, char *argv[])
reflist_free(deleteme);
reflist_free(list2);
R1 = stat_r1_ignore(list1, list2_transformed, &scale_r1fi);
/* Trimming the other way round is not necessary,
* because of these two lines */
arr2 = intensities_from_list(list2_transformed);
reflist_free(list2_transformed);
R1 = stat_r1_ignore(list1, arr2, &scale_r1fi);
STATUS("R1(F) = %5.4f %% (scale=%5.2e)"
" (ignoring negative intensities)\n",
R1*100.0, scale_r1fi);
R1 = stat_r1_zero(list1, list2_transformed, &scale_r1);
R1 = stat_r1_zero(list1, arr2, &scale_r1);
STATUS("R1(F) = %5.4f %% (scale=%5.2e)"
" (zeroing negative intensities)\n",
R1*100.0, scale_r1);
R2 = stat_r2(list1, list2_transformed, &scale_r2);
R2 = stat_r2(list1, arr2, &scale_r2);
STATUS("R2(I) = %5.4f %% (scale=%5.2e)\n", R2*100.0, scale_r2);
R1i = stat_r1_i(list1, list2_transformed, &scale_r1i);
R1i = stat_r1_i(list1, arr2, &scale_r1i);
STATUS("R1(I) = %5.4f %% (scale=%5.2e)\n", R1i*100.0, scale_r1i);
Rdiff = stat_rdiff_ignore(list1, list2_transformed, &scale_rdig);
Rdiff = stat_rdiff_ignore(list1, arr2, &scale_rdig);
STATUS("Rint(F) = %5.4f %% (scale=%5.2e)"
" (ignoring negative intensities)\n",
Rdiff*100.0, scale_rdig);
Rdiff = stat_rdiff_zero(list1, list2_transformed, &scale);
Rdiff = stat_rdiff_zero(list1, arr2, &scale);
STATUS("Rint(F) = %5.4f %% (scale=%5.2e)"
" (zeroing negative intensities)\n",
Rdiff*100.0, scale);
Rdiff = stat_rdiff_intensity(list1, list2_transformed, &scale_rintint);
Rdiff = stat_rdiff_intensity(list1, arr2, &scale_rintint);
STATUS("Rint(I) = %5.4f %% (scale=%5.2e)\n",
Rdiff*100.0, scale_rintint);
pearson = stat_pearson_i(list1, list2_transformed);
pearson = stat_pearson_i(list1, arr2);
STATUS("Pearson r(I) = %5.4f\n", pearson);
pearson = stat_pearson_f_ignore(list1, list2_transformed);
pearson = stat_pearson_f_ignore(list1, arr2);
STATUS("Pearson r(F) = %5.4f (ignoring negative intensities)\n",
pearson);
pearson = stat_pearson_f_zero(list1, list2_transformed);
pearson = stat_pearson_f_zero(list1, arr2);
STATUS("Pearson r(F) = %5.4f (zeroing negative intensities)\n",
pearson);
if ( config_shells ) {
plot_shells(list1, list2_transformed, scale_r1i,
plot_shells(list1, arr2, scale_r1i,
cell, sym, rmin_fix, rmax_fix);
}
......
src/statistics.c
View file @ 192b3acc
......@@ -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;
......
src/statistics.h
View file @ 192b3acc
......@@ -19,23 +19,23 @@
#include "reflist.h"
extern double stat_scale_intensity(RefList *list1, RefList *list2);
extern double stat_scale_intensity(RefList *list1, double *arr2);
extern double stat_r1_zero(RefList *list1, RefList *list2, double *scalep);
extern double stat_r1_ignore(RefList *list1, RefList *list2, double *scalep);
extern double stat_r1_zero(RefList *list1, double *arr2, double *scalep);
extern double stat_r1_ignore(RefList *list1, double *arr2, double *scalep);
extern double stat_r2(RefList *list1, RefList *list2, double *scalep);
extern double stat_r2(RefList *list1, double *arr2, double *scalep);
extern double stat_r1_i(RefList *list1, RefList *list2, double *scalep);
extern double stat_r1_i(RefList *list1, double *arr2, double *scalep);
extern double stat_rdiff_zero(RefList *list1, RefList *list2, double *scalep);
extern double stat_rdiff_ignore(RefList *list1, RefList *list2, double *scalep);
extern double stat_rdiff_intensity(RefList *list1, RefList *list2,
extern double stat_rdiff_zero(RefList *list1, double *arr2, double *scalep);
extern double stat_rdiff_ignore(RefList *list1, double *arr2, double *scalep);
extern double stat_rdiff_intensity(RefList *list1, double *arr2,
double *scalep);
extern double stat_pearson_i(RefList *list1, RefList *list2);
extern double stat_pearson_f_zero(RefList *list1, RefList *list2);
extern double stat_pearson_f_ignore(RefList *list1, RefList *list2);
extern double stat_pearson_i(RefList *list1, double *arr2);
extern double stat_pearson_f_zero(RefList *list1, double *arr2);
extern double stat_pearson_f_ignore(RefList *list1, double *arr2);
#endif /* STATISTICS_H */
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