partialator: Remove --reference

It's not a good idea, and PR works well enough now that we no longer need this for testing

4 files changed, 13 insertions, 65 deletions

diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 12b4de10..66e614cc 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -63,13 +63,6 @@ Run \fIn\fR cycles of scaling and post refinement.
 Fix all the overall scaling factors to be unity.
 
 .PD 0
-.IP "\fB-r\fR \fIfilename\fR"
-.IP \fB--reference=\fR\fIfilename\fR
-.PD
-Refine and scale patterns against the reflections in \fIfilename\fR, instead of
-comparing them against each other.
-
-.PD 0
 .IP "\fB-m\fR \fImodel\fR"
 .IP \fB--model=\fR\fImodel\fR
 .PD
diff --git a/src/hrs-scaling.c b/src/hrs-scaling.c
index 9602836b..cba21b74 100644
--- a/src/hrs-scaling.c
+++ b/src/hrs-scaling.c
@@ -480,7 +480,7 @@ static int test_convergence(double *old_osfs, int n, Crystal **crystals)
 
 
 /* Scale the stack of images */
-RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
+RefList *scale_intensities(Crystal **crystals, int n,
                            int n_threads, int noscale, PartialityModel pmodel,
                            int min_redundancy)
 {
@@ -501,10 +501,8 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 		return full;
 	}
 
-	/* No reference -> create an initial list to refine against */
-	if ( gref == NULL ) {
-		full = lsq_intensities(crystals, n, n_threads, pmodel);
-	}
+	/* Create an initial list to refine against */
+	full = lsq_intensities(crystals, n, n_threads, pmodel);
 
 	old_osfs = malloc(n*sizeof(double));
 	if ( old_osfs == NULL ) return NULL;
@@ -513,7 +511,6 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 	i = 0;
 	do {
 
-		RefList *reference;
 		double total_sf = 0.0;
 		int n_sf = 0;
 		double norm_sf;
@@ -524,14 +521,7 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 			crystal_set_user_flag(crystals[j], 0);
 		}
 
-		/* Refine against reference or current "full" estimates */
-		if ( gref != NULL ) {
-			reference = gref;
-		} else {
-			reference = full;
-		}
-
-		iterate_scale(crystals, n, reference, n_threads, pmodel);
+		iterate_scale(crystals, n, full, n_threads, pmodel);
 
 		/* Normalise the scale factors */
 		for ( j=0; j<n; j++ ) {
@@ -550,11 +540,9 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 		reject_outliers(old_osfs, n, crystals);
 		done = test_convergence(old_osfs, n, crystals);
 
-		/* No reference -> generate list for next iteration */
-		if ( gref == NULL ) {
-			reflist_free(full);
-			full = lsq_intensities(crystals, n, n_threads, pmodel);
-		}
+		/* Generate list for next iteration */
+		reflist_free(full);
+		full = lsq_intensities(crystals, n, n_threads, pmodel);
 
 		i++;
 
@@ -564,10 +552,6 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 		ERROR("Warning: Scaling did not converge.\n");
 	}
 
-	if ( gref != NULL ) {
-		full = lsq_intensities(crystals, n, n_threads, pmodel);
-	} /* else we already did it */
-
 	calculate_esds(crystals, n, full, n_threads, min_redundancy, pmodel);
 
 	free(old_osfs);
diff --git a/src/hrs-scaling.h b/src/hrs-scaling.h
index 0979bb98..16368b79 100644
--- a/src/hrs-scaling.h
+++ b/src/hrs-scaling.h
@@ -39,8 +39,7 @@
 #include "reflist.h"
 #include "geometry.h"
 
-extern RefList *scale_intensities(Crystal **crystals, int n,
-                                  RefList *reference, int n_threads,
+extern RefList *scale_intensities(Crystal **crystals, int n, int n_threads,
                                   int noscale, PartialityModel pmodel,
                                   int min_redundancy);
 
diff --git a/src/partialator.c b/src/partialator.c
index 10290fd6..8823990f 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -71,7 +71,6 @@ static void show_help(const char *s)
 "  -y, --symmetry=<sym>       Merge according to symmetry <sym>.\n"
 "  -n, --iterations=<n>       Run <n> cycles of scaling and post-refinement.\n"
 "      --no-scale             Fix all the scaling factors at unity.\n"
-"  -r, --reference=<file>     Refine images against reflections in <file>,\n"
 "  -m, --model=<model>        Specify partiality model.\n"
 "      --min-measurements=<n> Minimum number of measurements to require.\n"
 "      --no-polarisation      Disable polarisation correction.\n"
@@ -206,8 +205,6 @@ int main(int argc, char *argv[])
 	RefList *full;
 	int n_images = 0;
 	int n_crystals = 0;
-	char *reference_file = NULL;
-	RefList *reference = NULL;
 	char cmdline[1024];
 	SRContext *sr;
 	int noscale = 0;
@@ -250,7 +247,7 @@ int main(int argc, char *argv[])
 	}
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:o:g:b:y:n:r:j:m:",
+	while ((c = getopt_long(argc, argv, "hi:o:g:b:y:n:j:m:",
 	                        longopts, NULL)) != -1)
 	{
 
@@ -289,10 +286,6 @@ int main(int argc, char *argv[])
 			pmodel_str = strdup(optarg);
 			break;
 
-			case 'r' :
-			reference_file = strdup(optarg);
-			break;
-
 			case 2 :
 			errno = 0;
 			min_measurements = strtod(optarg, &rval);
@@ -353,21 +346,6 @@ int main(int argc, char *argv[])
 		}
 	}
 
-	if ( reference_file != NULL ) {
-
-		RefList *list;
-
-		list = read_reflections(reference_file);
-		if ( list == NULL ) {
-			ERROR("Failed to read '%s'\n", reference_file);
-			return 1;
-		}
-		free(reference_file);
-		reference = asymmetric_indices(list, sym);
-		reflist_free(list);
-
-	}
-
 	gsl_set_error_handler_off();
 
 	/* Fill in what we know about the images so far */
@@ -477,7 +455,7 @@ int main(int argc, char *argv[])
 	/* Make initial estimates */
 	STATUS("Performing initial scaling.\n");
 	if ( noscale ) STATUS("Scale factors fixed at 1.\n");
-	full = scale_intensities(crystals, n_crystals, reference,
+	full = scale_intensities(crystals, n_crystals,
 	                         nthreads, noscale, pmodel, min_measurements);
 
 	srdata.crystals = crystals;
@@ -497,15 +475,13 @@ int main(int argc, char *argv[])
 		int n_lost = 0;
 		int n_dud = 0;
 		int j;
-		RefList *comp;
 
 		STATUS("Post refinement cycle %i of %i\n", i+1, n_iter);
 
 		srdata.n_filtered = 0;
 
 		/* Refine the geometry of all patterns to get the best fit */
-		comp = (reference == NULL) ? full : reference;
-		refine_all(crystals, n_crystals, comp, nthreads, pmodel,
+		refine_all(crystals, n_crystals, full, nthreads, pmodel,
 		           &srdata);
 
 		for ( j=0; j<n_crystals; j++ ) {
@@ -533,9 +509,8 @@ int main(int argc, char *argv[])
 		}
 		/* Re-estimate all the full intensities */
 		reflist_free(full);
-		full = scale_intensities(crystals, n_crystals,
-		                         reference, nthreads, noscale, pmodel,
-		                         min_measurements);
+		full = scale_intensities(crystals, n_crystals, nthreads,
+		                         noscale, pmodel, min_measurements);
 
 		srdata.full = full;
 
@@ -572,9 +547,6 @@ int main(int argc, char *argv[])
 	free(sym);
 	free(outfile);
 	free(crystals);
-	if ( reference != NULL ) {
-		reflist_free(reference);
-	}
 	for ( i=0; i<n_images; i++ ) {
 		free(images[i].filename);
 	}