partialator: Add --no-pr

4 files changed, 26 insertions, 11 deletions

diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index 5c3c24bb..272c97a9 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -62,7 +62,12 @@ Run \fIn\fR cycles of scaling and post refinement.
 .PD 0
 .IP \fB--no-scale\fR
 .PD
-Fix all the overall scaling factors to be unity.
+Disable the scaling part of the refinement calculation.
+
+.PD 0
+.IP \fB--no-pr\fR
+.PD
+Disable the orientation/physics model part of the refinement calculation.
 
 .PD 0
 .IP "\fB-m\fR \fImodel\fR"
@@ -149,6 +154,10 @@ partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=uni
 .PD
 partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=0\fR
 
+.IP "Merging with partialities, with scaling but without post-refinement:"
+.PD
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1 --no-pr\fR
+
 .IP "Merging with partialities, post-refinement and scaling:"
 .PD
 partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1\fR
diff --git a/src/partialator.c b/src/partialator.c
index 4398c9f8..2ad20094 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -74,7 +74,8 @@ static void show_help(const char *s)
 "      --start-after=<n>      Skip <n> crystals at the start of the stream.\n"
 "      --stop-after=<n>       Stop after merging <n> crystals.\n"
 "  -n, --iterations=<n>       Run <n> cycles of scaling and post-refinement.\n"
-"      --no-scale             Fix all the scaling factors at unity.\n"
+"      --no-scale             Disable scale factor (G, B) refinement.\n"
+"      --no-pr                Disable orientation/physics refinement.\n"
 "  -m, --model=<model>        Specify partiality model.\n"
 "      --min-measurements=<n> Minimum number of measurements to require.\n"
 "      --no-polarisation      Disable polarisation correction.\n"
@@ -370,6 +371,7 @@ int main(int argc, char *argv[])
 	int n_crystals_seen = 0;
 	char cmdline[1024];
 	int no_scale = 0;
+	int no_pr = 0;
 	Stream *st;
 	Crystal **crystals;
 	char *pmodel_str = NULL;
@@ -405,6 +407,7 @@ int main(int argc, char *argv[])
 		{"res-push",           1, NULL,                5}, /* compat */
 
 		{"no-scale",           0, &no_scale,           1},
+		{"no-pr",              0, &no_pr,              1},
 		{"no-polarisation",    0, &polarisation,       0},
 		{"no-polarization",    0, &polarisation,       0},
 		{"polarisation",       0, &polarisation,       1}, /* compat */
@@ -726,7 +729,7 @@ int main(int argc, char *argv[])
 
 		/* Refine all crystals to get the best fit */
 		refine_all(crystals, n_crystals, full, nthreads, pmodel,
-		           no_scale, &init_dev, &init_free_dev,
+		           no_scale, no_pr, &init_dev, &init_free_dev,
 		           &final_dev, &final_free_dev);
 
 		STATUS("Overall residual: initial = %e, final = %e\n",
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 9484da43..d62d9323 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -326,8 +326,8 @@ static void apply_shift(Crystal *cr, int k, double shift)
 
 /* Perform one cycle of post refinement on 'image' against 'full' */
 static double pr_iterate(Crystal *cr, const RefList *full,
-                         PartialityModel pmodel, int no_scale, int *n_filtered,
-                         int verbose)
+                         PartialityModel pmodel, int no_scale, int no_pr,
+                         int *n_filtered, int verbose)
 {
 	gsl_matrix *M;
 	gsl_vector *v;
@@ -346,7 +346,7 @@ static double pr_iterate(Crystal *cr, const RefList *full,
 
 	/* If partiality model is anything other than "unity", refine all the
 	 * geometrical parameters */
-	if ( pmodel != PMODEL_UNITY ) {
+	if ( (pmodel != PMODEL_UNITY) && !no_pr ) {
 		rv[num_params++] = GPARAM_ASX;
 		rv[num_params++] = GPARAM_ASY;
 		rv[num_params++] = GPARAM_ASZ;
@@ -547,7 +547,7 @@ static double residual(Crystal *cr, const RefList *full, int verbose, int free)
 
 
 static struct prdata pr_refine(Crystal *cr, const RefList *full,
-                               PartialityModel pmodel, int no_scale)
+                               PartialityModel pmodel, int no_scale, int no_pr)
 {
 	int i;
 	int verbose = 0;
@@ -584,7 +584,8 @@ static struct prdata pr_refine(Crystal *cr, const RefList *full,
 		cell_get_reciprocal(crystal_get_cell(cr), &asx, &asy, &asz,
 			               &bsx, &bsy, &bsz, &csx, &csy, &csz);
 
-		pr_iterate(cr, full, pmodel, no_scale, &prdata.n_filtered, 0);
+		pr_iterate(cr, full, pmodel, no_scale, no_pr,
+		           &prdata.n_filtered, verbose);
 
 		update_partialities(cr, pmodel);
 
@@ -622,6 +623,7 @@ struct refine_args
 	Crystal *crystal;
 	PartialityModel pmodel;
 	int no_scale;
+	int no_pr;
 	struct prdata prdata;
 };
 
@@ -646,7 +648,7 @@ static void refine_image(void *task, int id)
 	Crystal *cr = pargs->crystal;
 
 	pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel,
-	                          pargs->no_scale);
+	                          pargs->no_scale, pargs->no_pr);
 }
 
 
@@ -684,7 +686,7 @@ static void done_image(void *vqargs, void *task)
 
 void refine_all(Crystal **crystals, int n_crystals,
                 RefList *full, int nthreads, PartialityModel pmodel,
-                int no_scale,
+                int no_scale, int no_pr,
                 double *initial_residual, double *initial_free_residual,
                 double *final_residual, double *final_free_residual)
 {
@@ -697,6 +699,7 @@ void refine_all(Crystal **crystals, int n_crystals,
 	task_defaults.prdata.refined = 0;
 	task_defaults.prdata.n_filtered = 0;
 	task_defaults.no_scale = no_scale;
+	task_defaults.no_pr = no_pr;
 
 	qargs.task_defaults = task_defaults;
 	qargs.n_started = 0;
diff --git a/src/post-refinement.h b/src/post-refinement.h
index a0d27591..b59ae24f 100644
--- a/src/post-refinement.h
+++ b/src/post-refinement.h
@@ -57,7 +57,7 @@ struct prdata
 
 extern void refine_all(Crystal **crystals, int n_crystals,
                        RefList *full, int nthreads, PartialityModel pmodel,
-                       int no_scale,
+                       int no_scale, int no_pr,
                        double *initial_residual, double *initial_free_residual,
                        double *final_residual, double *final_free_residual);