Remove anything which deletes a reflection or optimises a RefList

4 files changed, 20 insertions, 126 deletions

diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 08cbabbd..0ed48311 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -265,9 +265,9 @@ int main(int argc, char *argv[])
 	int ncom;
 	RefList *list1;
 	RefList *list2;
+	RefList *list1_transformed;
 	RefList *list2_transformed;
 	RefList *ratio;
-	RefList *deleteme;
 	int config_shells = 0;
 	char *pdb = NULL;
 	int rej1 = 0;
@@ -384,9 +384,9 @@ int main(int argc, char *argv[])
 	}
 
 	/* Find common reflections (taking symmetry into account) */
+	list1_transformed = reflist_new();
 	list2_transformed = reflist_new();
 	ratio = reflist_new();
-	deleteme = reflist_new();
 	for ( refl1 = first_refl(list1, &iter);
 	      refl1 != NULL;
 	      refl1 = next_refl(refl1, iter) )
@@ -403,11 +403,11 @@ int main(int argc, char *argv[])
 		get_indices(refl1, &h, &k, &l);
 
 		if ( !find_equiv_in_list(list2, h, k, l, sym, &he, &ke, &le) ) {
-			/* No common reflection */
-			add_refl(deleteme, h, k, l);
 			continue;
 		}
 
+		copy_data(add_refl(list1_transformed, h, k, l), refl1);
+
 		refl2 = find_refl(list2, he, ke, le);
 		assert(refl2 != NULL);
 
@@ -457,22 +457,7 @@ int main(int argc, char *argv[])
 	STATUS("%i,%i reflections: %i in common\n",
 	       num_reflections(list1), num_reflections(list2), ncom);
 
-	/* Trim reflections from 'list1' which had no equivalents in 'list2' */
-	for ( refl1 = first_refl(deleteme, &iter);
-	      refl1 != NULL;
-	      refl1 = next_refl(refl1, iter) ) {
-
-		signed int h, k, l;
-		Reflection *del;
-
-		get_indices(refl1, &h, &k, &l);
-		del = find_refl(list1, h, k, l);
-		assert(del != NULL);
-
-		delete_refl(del);
-
-	}
-	reflist_free(deleteme);
+	reflist_free(list1);
 	reflist_free(list2);
 
 	/* Trimming the other way round is not necessary,
@@ -480,49 +465,51 @@ int main(int argc, char *argv[])
 	arr2 = intensities_from_list(list2_transformed);
 	reflist_free(list2_transformed);
 
-	R1 = stat_r1_ignore(list1, arr2, &scale_r1fi, config_unity);
+	R1 = stat_r1_ignore(list1_transformed, arr2, &scale_r1fi, config_unity);
 	STATUS("R1(F) = %5.4f %% (scale=%5.2e)"
 	       " (ignoring negative intensities)\n",
 	       R1*100.0, scale_r1fi);
 
-	R1 = stat_r1_zero(list1, arr2, &scale_r1, config_unity);
+	R1 = stat_r1_zero(list1_transformed, arr2, &scale_r1, config_unity);
 	STATUS("R1(F) = %5.4f %% (scale=%5.2e)"
 	       " (zeroing negative intensities)\n",
 	       R1*100.0, scale_r1);
 
-	R2 = stat_r2(list1, arr2, &scale_r2, config_unity);
+	R2 = stat_r2(list1_transformed, arr2, &scale_r2, config_unity);
 	STATUS("R2(I) = %5.4f %% (scale=%5.2e)\n", R2*100.0, scale_r2);
 
-	R1i = stat_r1_i(list1, arr2, &scale_r1i, config_unity);
+	R1i = stat_r1_i(list1_transformed, arr2, &scale_r1i, config_unity);
 	STATUS("R1(I) = %5.4f %% (scale=%5.2e)\n", R1i*100.0, scale_r1i);
 
-	Rdiff = stat_rdiff_ignore(list1, arr2, &scale_rdig, config_unity);
+	Rdiff = stat_rdiff_ignore(list1_transformed, arr2, &scale_rdig,
+	                          config_unity);
 	STATUS("Rint(F) = %5.4f %% (scale=%5.2e)"
 	       " (ignoring negative intensities)\n",
 	       Rdiff*100.0, scale_rdig);
 
-	Rdiff = stat_rdiff_zero(list1, arr2, &scale, config_unity);
+	Rdiff = stat_rdiff_zero(list1_transformed, arr2, &scale, config_unity);
 	STATUS("Rint(F) = %5.4f %% (scale=%5.2e)"
 	       " (zeroing negative intensities)\n",
 	       Rdiff*100.0, scale);
 
-	Rdiff = stat_rdiff_intensity(list1, arr2, &scale_rintint, config_unity);
+	Rdiff = stat_rdiff_intensity(list1_transformed, arr2, &scale_rintint,
+	                             config_unity);
 	STATUS("Rint(I) = %5.4f %% (scale=%5.2e)\n",
 	       Rdiff*100.0, scale_rintint);
 
-	pearson = stat_pearson_i(list1, arr2);
+	pearson = stat_pearson_i(list1_transformed, arr2);
 	STATUS("Pearson r(I) = %5.4f\n", pearson);
 
-	pearson = stat_pearson_f_ignore(list1, arr2);
+	pearson = stat_pearson_f_ignore(list1_transformed, arr2);
 	STATUS("Pearson r(F) = %5.4f (ignoring negative intensities)\n",
 	       pearson);
 
-	pearson = stat_pearson_f_zero(list1, arr2);
+	pearson = stat_pearson_f_zero(list1_transformed, arr2);
 	STATUS("Pearson r(F) = %5.4f (zeroing negative intensities)\n",
 	       pearson);
 
 	if ( config_shells ) {
-		plot_shells(list1, arr2, scale_r1i,
+		plot_shells(list1_transformed, arr2, scale_r1i,
 		            cell, sym, rmin_fix, rmax_fix);
 	}
 
diff --git a/src/partialator.c b/src/partialator.c
index ae13f147..101fe29f 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -350,7 +350,6 @@ int main(int argc, char *argv[])
 		/* This is the raw list of reflections */
 		as = asymmetric_indices(images[n_usable_patterns].reflections,
 		                        sym);
-		optimise_reflist(as);
 		reflist_free(images[n_usable_patterns].reflections);
 		images[n_usable_patterns].reflections = as;
 
diff --git a/src/reflist-utils.c b/src/reflist-utils.c
index 0ae1f31b..016fa317 100644
--- a/src/reflist-utils.c
+++ b/src/reflist-utils.c
@@ -302,10 +302,7 @@ RefList *read_reflections_from_file(FILE *fh)
 		if ( rval == NULL ) continue;
 		chomp(line);
 
-		if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) {
-			optimise_reflist(out);
-			return out;
-		}
+		if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
 
 		r = sscanf(line, "%i %i %i %f %s %f %s %i %f %f",
 		           &h, &k, &l, &intensity, phs, &sigma, ress, &cts,
@@ -321,7 +318,7 @@ RefList *read_reflections_from_file(FILE *fh)
 			double ph;
 			char *v;
 
-			refl = add_serialised_refl(out, h, k, l);
+			refl = add_refl(out, h, k, l);
 			set_int(refl, intensity);
 			set_detector_pos(refl, 0.0, fs, ss);
 			set_esd_intensity(refl, sigma);
diff --git a/tests/list_check.c b/tests/list_check.c
index 180aeb6a..5e943c72 100644
--- a/tests/list_check.c
+++ b/tests/list_check.c
@@ -87,8 +87,6 @@ static int test_lists(int num_items)
 
 	}
 
-	optimise_reflist(list);
-
 	/* Iterate over the list and check we find everything */
 	int count = 0;
 	for ( refl = first_refl(list, &iter);
@@ -154,93 +152,6 @@ static int test_lists(int num_items)
 
 	}
 
-	/* Delete some reflections */
-	for ( i=0; i<num_items/2; i++ ) {
-
-		int j;
-		signed int h, k, l;
-		Reflection *refl;
-
-		h = check[i].h;
-		k = check[i].k;
-		l = check[i].l;
-
-		refl = find_refl(list, h, k, l);
-		delete_refl(refl);
-
-		/* Update all counts */
-		for ( j=0; j<num_items; j++ ) {
-			if ( (check[j].h == h) && (check[j].k == k)
-			  && (check[j].l == l) ) check[j].num--;
-		}
-
-	}
-
-	/* Check that the deleted reflections can no longer be found */
-	for ( i=0; i<num_items; i++ ) {
-
-		signed int h, k, l;
-		Reflection *refl;
-
-		h = check[i].h;
-		k = check[i].k;
-		l = check[i].l;
-
-		if ( check[i].num > 0 ) continue;
-
-		refl = find_refl(list, h, k, l);
-		if ( refl != NULL ) {
-
-			fprintf(stderr, "Found %3i %i %3i after  deletion.\n",
-			                h, k, l);
-			return 1;
-
-		}
-
-	}
-
-	/* Delete remaining duplicates */
-	for ( i=0; i<num_items; i++ ) {
-
-		signed int h, k, l;
-		Reflection *refl;
-
-		if ( check[i].num == 0 ) continue;
-
-		h = check[i].h;
-		k = check[i].k;
-		l = check[i].l;
-		refl = find_refl(list, h, k, l);
-
-		do {
-			int j;
-			signed int ha, ka, la;
-			Reflection *next;
-			get_indices(refl, &ha, &ka, &la);
-			next = next_found_refl(refl);
-			delete_refl(refl);
-			refl = next;
-			for ( j=0; j<num_items; j++ ) {
-				if ( (check[j].h == h) && (check[j].k == k)
-				  && (check[j].l == l) ) check[j].num--;
-			}
-		} while ( refl != NULL );
-
-		if ( check[i].num != 0 ) {
-			fprintf(stderr, "Found too few duplicates (%i) for "
-			                "%3i %3i %3i\n", check[i].num, h, k, l);
-			return 1;
-		}
-
-		refl = find_refl(list, h, k, l);
-		if ( refl != NULL ) {
-			fprintf(stderr, "Found too many duplicates for "
-			                "%3i %3i %3i\n", h, k, l);
-			return 1;
-		}
-
-	}
-
 	reflist_free(list);
 	free(check);