1 files changed, 5 insertions, 107 deletions

diff --git a/src/partialator.c b/src/partialator.c
index 46353c25..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"
@@ -84,111 +85,6 @@ static void show_help(const char *s)
 }
 
 
-struct refine_args
-{
-	RefList *full;
-	Crystal *crystal;
-	PartialityModel pmodel;
-	int no_scale;
-	struct prdata prdata;
-};
-
-
-struct queue_args
-{
-	int n_started;
-	int n_done;
-	Crystal **crystals;
-	int n_crystals;
-	struct refine_args task_defaults;
-	double initial_residual;
-	double initial_free_residual;
-	double final_residual;
-	double final_free_residual;
-};
-
-
-static void refine_image(void *task, int id)
-{
-	struct refine_args *pargs = task;
-	Crystal *cr = pargs->crystal;
-
-	pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel,
-	                          pargs->no_scale);
-}
-
-
-static void *get_image(void *vqargs)
-{
-	struct refine_args *task;
-	struct queue_args *qargs = vqargs;
-
-	task = malloc(sizeof(struct refine_args));
-	memcpy(task, &qargs->task_defaults, sizeof(struct refine_args));
-
-	task->crystal = qargs->crystals[qargs->n_started];
-
-	qargs->n_started++;
-
-	return task;
-}
-
-
-static void done_image(void *vqargs, void *task)
-{
-	struct queue_args *qargs = vqargs;
-	struct refine_args *pargs = task;
-
-	qargs->n_done++;
-	qargs->initial_residual += pargs->prdata.initial_residual;
-	qargs->initial_free_residual += pargs->prdata.initial_free_residual;
-	qargs->final_residual += pargs->prdata.final_residual;
-	qargs->final_free_residual += pargs->prdata.final_free_residual;
-
-	progress_bar(qargs->n_done, qargs->n_crystals, "Refining");
-	free(task);
-}
-
-
-static void refine_all(Crystal **crystals, int n_crystals,
-                       RefList *full, int nthreads, PartialityModel pmodel,
-                       int no_scale,
-                       double *initial_residual, double *initial_free_residual,
-                       double *final_residual, double *final_free_residual)
-{
-	struct refine_args task_defaults;
-	struct queue_args qargs;
-
-	task_defaults.full = full;
-	task_defaults.crystal = NULL;
-	task_defaults.pmodel = pmodel;
-	task_defaults.prdata.refined = 0;
-	task_defaults.prdata.n_filtered = 0;
-	task_defaults.no_scale = no_scale;
-
-	qargs.task_defaults = task_defaults;
-	qargs.n_started = 0;
-	qargs.n_done = 0;
-	qargs.n_crystals = n_crystals;
-	qargs.crystals = crystals;
-	qargs.initial_residual = 0.0;
-	qargs.initial_free_residual = 0.0;
-	qargs.final_residual = 0.0;
-	qargs.final_free_residual = 0.0;
-
-	/* Don't have threads which are doing nothing */
-	if ( n_crystals < nthreads ) nthreads = n_crystals;
-
-	run_threads(nthreads, refine_image, get_image, done_image,
-	            &qargs, n_crystals, 0, 0, 0);
-
-	*initial_residual = qargs.initial_residual;
-	*initial_free_residual = qargs.initial_free_residual;
-	*final_residual = qargs.final_residual;
-	*final_free_residual = qargs.final_free_residual;
-}
-
-
 static void display_progress(int n_images, int n_crystals)
 {
 	if ( !isatty(STDERR_FILENO) ) return;
@@ -475,6 +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;
@@ -510,6 +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 */
@@ -831,7 +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",