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-rw-r--r--doc/man/compare_hkl.114
-rw-r--r--src/compare_hkl.c153
2 files changed, 139 insertions, 28 deletions
diff --git a/doc/man/compare_hkl.1 b/doc/man/compare_hkl.1
index 8ae7574c..26ec7faf 100644
--- a/doc/man/compare_hkl.1
+++ b/doc/man/compare_hkl.1
@@ -38,13 +38,13 @@ Calculate figure of merit \fIFoM\fR. Possible figures of merit are:
.RS
.IP \fBRsplit\fR
.PD
-2^(-0.5) * sum(I1-kI2) / [ 0.5*sum(I1+kI2) ]
+2^(-0.5) * sum(|I1-kI2|) / [ 0.5*sum(I1+kI2) ]
.IP \fBR1f\fR
.PD
sum(sqrt(I1)-sqrt(kI2)) / sum(sqrt(I1))
.IP \fBR1i\fR
.PD
-sum(I1-kI2) / sum(I1)
+sum(|I1-kI2|) / sum(I1)
.IP \fBR2\fR
.PD
sqrt(sum[(I1-kI2)^2] / sum(I1^2))
@@ -57,6 +57,16 @@ See Karplus and Diederichs, Science 336 (2012) p1030.
.IP \fBCCano\fR
.PD
The correlation coefficient of the Bijvoet differences of acentric reflections.
+.IP \fBCRDano\fR
+.PD
+RMS anomalous correlation ratio: The anomalous differences from each data set are plotted in a scatter graph, and the variance along both diagonals measured. See Evans, Acta Crystallographica D62 (2006) p72.
+.IP \fBRano\fR
+.PD
+sum(|I+ - I-|) / 0.5*sum(I+ - I-)
+Note that I+ will be taken to be the mean of the I+ values from both data sets, and likewise for I-.
+.IP \fBRano/Rsplit\fR
+.PD
+The ratio of Rano to Rsplit, as defined above.
.PP
I1 and I2 are the intensities of the same reflection in both reflection lists. The scale factor, k, is given by sum(I1*i2) / sum(I2^2), unless you use \fB-u\fR.
.RE
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 66b58adc..88e162b5 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -3,11 +3,11 @@
*
* Compare reflection lists
*
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2012 Thomas White <taw@physics.org>
+ * 2010-2013 Thomas White <taw@physics.org>
* 2013 Lorenzo Galli <lorenzo.galli@desy.de>
*
* This file is part of CrystFEL.
@@ -58,7 +58,9 @@ enum fom
FOM_CC,
FOM_CCSTAR,
FOM_CCANO,
- FOM_CRDANO
+ FOM_CRDANO,
+ FOM_RANO,
+ FOM_RANORSPLIT
};
@@ -72,6 +74,8 @@ static enum fom get_fom(const char *s)
if ( strcasecmp(s, "ccstar") == 0 ) return FOM_CCSTAR;
if ( strcasecmp(s, "ccano") == 0 ) return FOM_CCANO;
if ( strcasecmp(s, "crdano") == 0 ) return FOM_CRDANO;
+ if ( strcasecmp(s, "rano") == 0 ) return FOM_RANO;
+ if ( strcasecmp(s, "rano/rsplit") == 0 ) return FOM_RANORSPLIT;
ERROR("Unknown figure of merit '%s'.\n", s);
exit(1);
@@ -88,7 +92,7 @@ static void show_help(const char *s)
" -p, --pdb=<filename> PDB file to use.\n"
" --fom=<FoM> Calculate this figure of merit Choose from:\n"
" R1I, R1F, R2, Rsplit, CC, CCstar,\n"
-" CCano, CRDano.\n"
+" CCano, CRDano, Rano, Rano/Rsplit\n"
" --nshells=<n> Use <n> resolution shells.\n"
" -u Force scale factor to 1.\n"
" --shell-file=<file> Write resolution shells to <file>.\n"
@@ -116,6 +120,10 @@ struct fom_context
double *num;
double *den;
+ /* For "double" R-factors */
+ double *num2;
+ double *den2;
+
/* For CCs */
double **vec1;
double **vec2;
@@ -137,10 +145,21 @@ static struct fom_context *init_fom(enum fom fom, int nmax, int nshells)
switch ( fctx->fom ) {
+ case FOM_RANORSPLIT :
+ fctx->num2 = malloc(nshells*sizeof(double));
+ fctx->den2 = malloc(nshells*sizeof(double));
+ if ( (fctx->num2 == NULL) || (fctx->den2 == NULL) ) return NULL;
+ for ( i=0; i<nshells; i++ ) {
+ fctx->num2[i] = 0.0;
+ fctx->den2[i] = 0.0;
+ }
+ /* Intentional fall-through (no break) */
+
case FOM_R1I :
case FOM_R1F :
case FOM_R2 :
case FOM_RSPLIT :
+ case FOM_RANO :
fctx->num = malloc(nshells*sizeof(double));
fctx->den = malloc(nshells*sizeof(double));
if ( (fctx->num == NULL) || (fctx->den == NULL) ) return NULL;
@@ -182,6 +201,7 @@ static void add_to_fom(struct fom_context *fctx, double i1, double i2,
double i1bij, double i2bij, int bin)
{
double f1, f2;
+ double im, imbij;
/* Negative intensities have already been weeded out. */
f1 = sqrt(i1);
@@ -225,6 +245,18 @@ static void add_to_fom(struct fom_context *fctx, double i1, double i2,
fctx->n[bin]++;
break;
+ case FOM_RANORSPLIT :
+ fctx->num2[bin] += fabs(i1 - i2);
+ fctx->den2[bin] += i1 + i2;
+ /* Intentional fall-through (no break) */
+
+ case FOM_RANO :
+ im = (i1 + i2)/2.0;
+ imbij = (i1bij + i2bij)/2.0;
+ fctx->num[bin] += fabs(im - imbij);
+ fctx->den[bin] += im + imbij;
+ break;
+
}
}
@@ -234,6 +266,8 @@ static double fom_overall(struct fom_context *fctx)
{
double overall_num = INFINITY;
double overall_den = 0.0;
+ double overall_num2 = INFINITY;
+ double overall_den2 = 0.0;
int i;
double *overall_vec1;
double *overall_vec2;
@@ -250,12 +284,28 @@ static double fom_overall(struct fom_context *fctx)
case FOM_R1F :
case FOM_R2 :
case FOM_RSPLIT :
+ case FOM_RANO :
+ overall_num = 0.0;
+ overall_den = 0.0;
+ for ( i=0; i<fctx->nshells; i++ ) {
+ overall_num += fctx->num[i];
+ overall_den += fctx->den[i];
+ }
+ break;
+
+ case FOM_RANORSPLIT :
overall_num = 0.0;
overall_den = 0.0;
for ( i=0; i<fctx->nshells; i++ ) {
overall_num += fctx->num[i];
overall_den += fctx->den[i];
}
+ overall_num2 = 0.0;
+ overall_den2 = 0.0;
+ for ( i=0; i<fctx->nshells; i++ ) {
+ overall_num2 += fctx->num2[i];
+ overall_den2 += fctx->den2[i];
+ }
break;
case FOM_CC :
@@ -326,6 +376,13 @@ static double fom_overall(struct fom_context *fctx)
case FOM_CCSTAR :
return sqrt((2.0*cc)/(1.0+cc));
+ case FOM_RANO :
+ return 2.0*(overall_num/overall_den);
+
+ case FOM_RANORSPLIT :
+ return (2.0*(overall_num/overall_den)) /
+ (2.0*(overall_num2/overall_den2) / sqrt(2.0));
+
}
ERROR("This point is never reached.\n");
@@ -364,6 +421,12 @@ static double fom_shell(struct fom_context *fctx, int i)
fctx->n[i]);
return sqrt((2.0*cc)/(1.0+cc));
+ case FOM_RANO :
+ return 2.0 * fctx->num[i]/fctx->den[i];
+
+ case FOM_RANORSPLIT :
+ return (2.0*fctx->num[i]/fctx->den[i]) /
+ (2.0*(fctx->num2[i]/fctx->den2[i]) / sqrt(2.0));
case FOM_CRDANO :
along_diagonal = malloc(fctx->n[i] * sizeof(double));
@@ -618,7 +681,9 @@ static void do_fom(RefList *list1, RefList *list2, UnitCell *cell,
i1 = get_intensity(refl1);
i2 = scale * get_intensity(refl2);
- if ( fom == FOM_CCANO || fom == FOM_CRDANO ) {
+ if ( (fom == FOM_CCANO) || (fom == FOM_CRDANO)
+ || (fom == FOM_RANO) || (fom == FOM_RANORSPLIT) )
+ {
Reflection *refl1_bij = NULL;
Reflection *refl2_bij = NULL;
@@ -691,6 +756,14 @@ static void do_fom(RefList *list1, RefList *list2, UnitCell *cell,
STATUS("Overall CRDano = %.7f\n", fom_overall(fctx));
break;
+ case FOM_RANO :
+ STATUS("Overall Rano = %.2f %%\n", 100.0*fom_overall(fctx));
+ break;
+
+ case FOM_RANORSPLIT :
+ STATUS("Overall Rano/Rsplit = %.7f\n", fom_overall(fctx));
+ break;
+
}
fh = fopen(filename, "w");
@@ -741,6 +814,14 @@ static void do_fom(RefList *list1, RefList *list2, UnitCell *cell,
fprintf(fh, "%s CRDano nref%s\n", t1, t2);
break;
+ case FOM_RANO :
+ fprintf(fh, "%s Rano/%% nref%s\n", t1, t2);
+ break;
+
+ case FOM_RANORSPLIT :
+ fprintf(fh, "%s Rano/Rsplit nref%s\n", t1, t2);
+ break;
+
}
for ( i=0; i<nshells; i++ ) {
@@ -756,6 +837,7 @@ static void do_fom(RefList *list1, RefList *list2, UnitCell *cell,
case FOM_R1F :
case FOM_R2 :
case FOM_RSPLIT :
+ case FOM_RANO :
if ( config_intshells ) {
fprintf(fh, "%10.3f %10.2f %10i\n",
cen, r*100.0, cts[i]);
@@ -778,6 +860,17 @@ static void do_fom(RefList *list1, RefList *list2, UnitCell *cell,
}
break;
+ case FOM_RANORSPLIT :
+ if ( config_intshells ) {
+ fprintf(fh, "%10.3f %10.7f %10i\n",
+ cen, r, cts[i]);
+ } else {
+ fprintf(fh, "%10.3f %10.7f %10i %10.2f\n",
+ cen*1.0e-9, r, cts[i], (1.0/cen)*1e10);
+ }
+ break;
+
+
}
}
@@ -932,6 +1025,8 @@ int main(int argc, char *argv[])
case FOM_CCSTAR :
case FOM_CCANO :
case FOM_CRDANO :
+ case FOM_RANO :
+ case FOM_RANORSPLIT :
break;
}
}
@@ -942,24 +1037,30 @@ int main(int argc, char *argv[])
sym = get_pointgroup(sym_str);
free(sym_str);
- if ( (fom == FOM_CCANO || fom == FOM_CRDANO ) &&
- is_centrosymmetric(sym) ) {
-
- /* Refuse to calculate CCano or CRDano with a
- * centrosymmetric point group.
- * It'll "work", in the sense of producing a number, but the
- * number won't have anything to do with anomalous signal. */
-
- ERROR("You are trying to calculate CCano or CRDano with a"
- " centrosymmetric point group.\n");
- ERROR("This is a silly thing to do, and I'm refusing to help"
- " you do it.\n");
- ERROR("Please review your earlier processing steps and try"
- " again using a non-centrosymmetric point group for"
- " '-y'.\n");
-
- return 1;
+ if ( is_centrosymmetric(sym) ) {
+ switch ( fom )
+ {
+ case FOM_R1F :
+ case FOM_R2 :
+ case FOM_R1I :
+ case FOM_RSPLIT :
+ case FOM_CC :
+ case FOM_CCSTAR :
+ break;
+ case FOM_CCANO :
+ case FOM_CRDANO :
+ case FOM_RANO :
+ case FOM_RANORSPLIT :
+ ERROR("You are trying to measure an anomalous signal in"
+ " a centrosymmetric point group.\n");
+ ERROR("This is a silly thing to do, and I'm refusing to"
+ " help you do it.\n");
+ ERROR("Please review your earlier processing steps and"
+ " try again using a non-centrosymmetric point"
+ " group for '-y'.\n");
+ return 1;
+ }
}
afile = strdup(argv[optind++]);
@@ -1086,8 +1187,9 @@ int main(int argc, char *argv[])
}
}
- if ( fom == FOM_CCANO || fom == FOM_CRDANO ) {
-
+ if ( (fom == FOM_CCANO) || (fom == FOM_CRDANO)
+ || (fom == FOM_RANO) || (fom == FOM_RANORSPLIT) )
+ {
Reflection *refl1_bij = NULL;
Reflection *refl2_bij = NULL;
signed int hb, kb, lb;
@@ -1113,7 +1215,6 @@ int main(int argc, char *argv[])
nbij++;
continue;
}
-
}
refl1_acc = add_refl(list1_acc, h, k, l);
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-24 10:23:07 +0000