Remove old "statistics" module with R factors etc

compare_hkl does all of these, much better than these functions.

4 files changed, 0 insertions, 759 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 */