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-rw-r--r--libcrystfel/CMakeLists.txt2
-rw-r--r--libcrystfel/doc/index.md1
-rw-r--r--libcrystfel/src/statistics.c683
-rw-r--r--libcrystfel/src/statistics.h73
-rw-r--r--src/check_hkl.c1
-rw-r--r--src/compare_hkl.c1
-rw-r--r--src/process_hkl.c1
7 files changed, 0 insertions, 762 deletions
diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt
index 55c2c0f5..6d0cd8dc 100644
--- a/libcrystfel/CMakeLists.txt
+++ b/libcrystfel/CMakeLists.txt
@@ -47,7 +47,6 @@ set(LIBCRYSTFEL_SOURCES
src/hdf5-file.c
src/geometry.c
src/peakfinder8.c
- src/statistics.c
src/symmetry.c
src/stream.c
src/peaks.c
@@ -85,7 +84,6 @@ set(LIBCRYSTFEL_HEADERS
src/cell.h
src/reflist-utils.h
src/thread-pool.h
- src/statistics.h
src/utils.h
src/detector.h
src/geometry.h
diff --git a/libcrystfel/doc/index.md b/libcrystfel/doc/index.md
index d806a2e5..16868fef 100644
--- a/libcrystfel/doc/index.md
+++ b/libcrystfel/doc/index.md
@@ -35,7 +35,6 @@ API documentation
* \ref peaks.h "Main peak search functions"
* \ref peakfinder8.h "The peakfinder8 algorithm"
* \ref filters.h "Image (noise) filters"
-* \ref statistics.h "R-values and other statistics"
* \ref symmetry.h "Point group symmetry"
* Mathematical constructions:
* \ref integer_matrix.h "Integer matrices"
diff --git a/libcrystfel/src/statistics.c b/libcrystfel/src/statistics.c
deleted file mode 100644
index ff8f233c..00000000
--- a/libcrystfel/src/statistics.c
+++ /dev/null
@@ -1,683 +0,0 @@
-/*
- * statistics.c
- *
- * Structure-factor statistics
- *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
- *
- * Authors:
- * 2009-2012 Thomas White <taw@physics.org>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-#include <stdlib.h>
-#include <gsl/gsl_errno.h>
-#include <gsl/gsl_min.h>
-#include <gsl/gsl_statistics.h>
-
-#include "statistics.h"
-#include "utils.h"
-
-/** \file statistics.h */
-
-
-struct r_params {
- RefList *list1;
- RefList *list2;
- int fom; /* Which FoM to use (see the enum just below) */
-};
-
-enum {
- R_1_ZERO,
- R_1_IGNORE,
- R_2,
- R_1_I,
- R_DIFF_ZERO,
- R_DIFF_IGNORE,
- R_DIFF_INTENSITY,
-};
-
-
-/* Return the least squares optimal scaling factor when comparing intensities.
- * list1,list2 are the two intensity lists to compare.
- */
-double stat_scale_intensity(RefList *list1, RefList *list2)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- top += i1 * i2;
- bot += i2 * i2;
-
- }
-
- return top/bot;
-}
-
-
-/* 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,
- * not square rooted intensities).
- */
-static double stat_scale_sqrti(RefList *list1, RefList *list2)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- if ( i1 < 0.0 ) continue;
- f1 = sqrt(i1);
-
- if ( i2 < 0.0 ) continue;
- f2 = sqrt(i2);
-
- top += f1 * f2;
- bot += f2 * f2;
-
- }
-
- return top/bot;
-}
-
-
-static double internal_r1_ignorenegs(RefList *list1, RefList *list2,
- double scale)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- if ( i1 < 0.0 ) continue;
- f1 = sqrt(i1);
-
- if ( i2 < 0.0 ) continue;
- f2 = sqrt(i2);
- f2 *= scale;
-
- top += fabs(f1 - f2);
- bot += f1;
-
- }
-
- return top/bot;
-}
-
-
-static double internal_r1_negstozero(RefList *list1, RefList *list2,
- double scale)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- f1 = i1 > 0.0 ? sqrt(i1) : 0.0;
-
- f2 = i2 > 0.0 ? sqrt(i2) : 0.0;
- f2 *= scale;
-
- top += fabs(f1 - f2);
- bot += f1;
-
- }
-
- return top/bot;
-}
-
-
-static double internal_r2(RefList *list1, RefList *list2, double scale)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- i2 *= scale;
-
- top += pow(i1 - i2, 2.0);
- bot += pow(i1, 2.0);
-
- }
-
- return sqrt(top/bot);
-}
-
-
-static double internal_r_i(RefList *list1, RefList *list2, double scale)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
- i2 *= scale;
-
- top += fabs(i1-i2);
- bot += fabs(i1);
-
- }
-
- return top/bot;
-}
-
-
-static double internal_rdiff_intensity(RefList *list1, RefList *list2,
- double scale)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
- i2 *= scale;
-
- top += fabs(i1 - i2);
- bot += i1 + i2;
-
- }
-
- return 2.0*top/bot;
-}
-
-
-static double internal_rdiff_negstozero(RefList *list1, RefList *list2,
- double scale)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- f1 = i1 > 0.0 ? sqrt(i1) : 0.0;
-
- f2 = i2 > 0.0 ? sqrt(i2) : 0.0;
- f2 *= scale;
-
- top += fabs(f1 - f2);
- bot += f1 + f2;
-
- }
-
- return 2.0*top/bot;
-}
-
-
-static double internal_rdiff_ignorenegs(RefList *list1, RefList *list2,
- double scale)
-{
- double top = 0.0;
- double bot = 0.0;
- Reflection *refl1;
- RefListIterator *iter;
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- if ( i1 < 0.0 ) continue;
- f1 = sqrt(i1);
-
- if ( i2 < 0.0 ) continue;
- f2 = sqrt(i2);
- f2 *= scale;
-
- top += fabs(f1 - f2);
- bot += f1 + f2;
-
- }
-
- return 2.0*top/bot;
-}
-
-
-static double calc_r(double scale, void *params)
-{
- struct r_params *rp = params;
-
- switch ( rp->fom ) {
-
- case R_1_ZERO :
- return internal_r1_negstozero(rp->list1, rp->list2, scale);
-
- case R_1_IGNORE :
- return internal_r1_ignorenegs(rp->list1, rp->list2, scale);
-
- case R_2 :
- return internal_r2(rp->list1, rp->list2, scale);
-
- case R_1_I :
- return internal_r_i(rp->list1, rp->list2, scale);
-
- case R_DIFF_ZERO :
- return internal_rdiff_negstozero(rp->list1, rp->list2,scale);
-
- case R_DIFF_IGNORE :
- return internal_rdiff_ignorenegs(rp->list1, rp->list2, scale);
-
- case R_DIFF_INTENSITY :
- return internal_rdiff_intensity(rp->list1, rp->list2, scale);
-
- }
-
- ERROR("No such FoM!\n");
- abort();
-}
-
-
-static double r_minimised(RefList *list1, RefList *list2, double *scalep, int fom,
- int u)
-{
- gsl_function F;
- gsl_min_fminimizer *s;
- int status;
- double scale = 1.0;
- struct r_params rp;
- int iter = 0;
-
- rp.list1 = list1;
- rp.list2 = list2;
- rp.fom = fom;
-
- if ( u ) {
-
- scale = 1.0;
-
- } else {
-
- F.function = &calc_r;
- F.params = &rp;
-
- s = gsl_min_fminimizer_alloc(gsl_min_fminimizer_brent);
-
- /* Initial guess */
- switch ( fom ) {
-
- case R_1_ZERO :
- case R_1_IGNORE :
- case R_DIFF_ZERO :
- case R_DIFF_IGNORE :
- scale = stat_scale_sqrti(list1, list2);
- break;
-
- case R_2 :
- case R_1_I :
- case R_DIFF_INTENSITY :
- scale = stat_scale_intensity(list1, list2);
- break;
-
- }
- //STATUS("Initial scale factor estimate: %5.2e\n", scale);
-
- /* Probably within an order of magnitude either side */
- gsl_min_fminimizer_set(s, &F, scale, scale/10.0, scale*10.0);
-
- do {
-
- double lo, up;
-
- /* Iterate */
- if ( gsl_min_fminimizer_iterate(s) ) {
- ERROR("Failed to find scale factor.\n");
- return NAN;
- }
-
- /* Get the current estimate */
- scale = gsl_min_fminimizer_x_minimum(s);
- lo = gsl_min_fminimizer_x_lower(s);
- up = gsl_min_fminimizer_x_upper(s);
-
- /* Check for convergence */
- status = gsl_min_test_interval(lo, up, 0.001, 0.0);
-
- iter++;
-
- } while ( status == GSL_CONTINUE );
-
- if ( status != GSL_SUCCESS ) {
- ERROR("Scale factor minimisation failed.\n");
- }
-
- gsl_min_fminimizer_free(s);
-
- }
-
- //STATUS("Final scale factor: %5.2e\n", scale);
- *scalep = scale;
- return calc_r(scale, &rp);
-}
-
-
-double stat_r1_ignore(RefList *list1, RefList *list2, double *scalep, int u)
-{
- return r_minimised(list1, list2, scalep, R_1_IGNORE, u);
-}
-
-
-double stat_r1_zero(RefList *list1, RefList *list2, double *scalep, int u)
-{
- return r_minimised(list1, list2, scalep, R_1_ZERO, u);
-}
-
-
-double stat_r2(RefList *list1, RefList *list2, double *scalep, int u)
-{
- return r_minimised(list1, list2, scalep, R_2, u);
-}
-
-
-double stat_r1_i(RefList *list1, RefList *list2, double *scalep, int u)
-{
- return r_minimised(list1, list2, scalep, R_1_I, u);
-}
-
-
-double stat_rdiff_zero(RefList *list1, RefList *list2, double *scalep, int u)
-{
- return r_minimised(list1, list2, scalep, R_DIFF_ZERO, u);
-}
-
-
-double stat_rdiff_ignore(RefList *list1, RefList *list2, double *scalep, int u)
-{
- return r_minimised(list1, list2, scalep, R_DIFF_IGNORE, u);
-}
-
-
-double stat_rdiff_intensity(RefList *list1, RefList *list2, double *scalep, int u)
-{
- return r_minimised(list1, list2, scalep, R_DIFF_INTENSITY, u);
-}
-
-
-double stat_pearson_i(RefList *list1, RefList *list2)
-{
- double *vec1, *vec2;
- int ni = num_reflections(list1);
- double val;
- int nacc = 0;
- Reflection *refl1;
- RefListIterator *iter;
-
- vec1 = malloc(ni*sizeof(double));
- vec2 = malloc(ni*sizeof(double));
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- vec1[nacc] = i1;
- vec2[nacc] = i2;
- nacc++;
- }
-
- val = gsl_stats_correlation(vec1, 1, vec2, 1, nacc);
- free(vec1);
- free(vec2);
-
- return val;
-}
-
-
-double stat_pearson_f_ignore(RefList *list1, RefList *list2)
-{
- double *vec1, *vec2;
- int ni = num_reflections(list1);
- double val;
- int nacc = 0;
- Reflection *refl1;
- RefListIterator *iter;
-
- vec1 = malloc(ni*sizeof(double));
- vec2 = malloc(ni*sizeof(double));
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- if ( i1 < 0.0 ) continue;
- if ( i2 < 0.0 ) continue;
-
- f1 = sqrt(i1);
- f2 = sqrt(i2);
-
- vec1[nacc] = f1;
- vec2[nacc] = f2;
- nacc++;
-
- }
-
- val = gsl_stats_correlation(vec1, 1, vec2, 1, nacc);
- free(vec1);
- free(vec2);
-
- return val;
-}
-
-
-double stat_pearson_f_zero(RefList *list1, RefList *list2)
-{
- double *vec1, *vec2;
- int ni = num_reflections(list1);
- double val;
- int nacc = 0;
- Reflection *refl1;
- RefListIterator *iter;
-
- vec1 = malloc(ni*sizeof(double));
- vec2 = malloc(ni*sizeof(double));
-
- for ( refl1 = first_refl(list1, &iter);
- refl1 != NULL;
- refl1 = next_refl(refl1, iter) )
- {
- 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 */
-
- i1 = get_intensity(refl1);
- i2 = get_intensity(refl2);
-
- f1 = i1 > 0.0 ? sqrt(i1) : 0.0;
- f2 = i2 > 0.0 ? sqrt(i2) : 0.0;
-
- vec1[nacc] = f1;
- vec2[nacc] = f2;
- nacc++;
-
- }
-
- val = gsl_stats_correlation(vec1, 1, vec2, 1, nacc);
- free(vec1);
- free(vec2);
-
- return val;
-}
diff --git a/libcrystfel/src/statistics.h b/libcrystfel/src/statistics.h
deleted file mode 100644
index 4e2d2aff..00000000
--- a/libcrystfel/src/statistics.h
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * statistics.h
- *
- * Structure-factor statistics
- *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
- *
- * Authors:
- * 2009-2012 Thomas White <taw@physics.org>
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef STATISTICS_H
-#define STATISTICS_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#include "reflist.h"
-
-/**
- * \file statistics.h
- * Intensity statistic calculations
- */
-
-extern double stat_scale_intensity(RefList *list1, RefList *list2);
-
-extern double stat_r1_zero(RefList *list1, RefList *list2,
- double *scalep, int u);
-extern double stat_r1_ignore(RefList *list1, RefList *list2,
- double *scalep, int u);
-
-extern double stat_r2(RefList *list1, RefList *list2, double *scalep, int u);
-
-extern double stat_r1_i(RefList *list1, RefList *list2, double *scalep, int u);
-
-extern double stat_rdiff_zero(RefList *list1, RefList *list2,
- double *scalep, int u);
-extern double stat_rdiff_ignore(RefList *list1, RefList *list2,
- double *scalep, int u);
-extern double stat_rdiff_intensity(RefList *list1, RefList *list2,
- double *scalep, int u);
-
-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);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* STATISTICS_H */
diff --git a/src/check_hkl.c b/src/check_hkl.c
index 224ccc00..ca096ae8 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -41,7 +41,6 @@
#include <assert.h>
#include "utils.h"
-#include "statistics.h"
#include "symmetry.h"
#include "reflist.h"
#include "reflist-utils.h"
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 5812cad2..479d7332 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -44,7 +44,6 @@
#include <gsl/gsl_fit.h>
#include "utils.h"
-#include "statistics.h"
#include "symmetry.h"
#include "reflist-utils.h"
#include "cell-utils.h"
diff --git a/src/process_hkl.c b/src/process_hkl.c
index ab5b9af1..393dc3e8 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -44,7 +44,6 @@
#include <getopt.h>
#include "utils.h"
-#include "statistics.h"
#include "reflist-utils.h"
#include "symmetry.h"
#include "stream.h"
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-30 21:37:55 +0000