partialator: Use Spectrum API

2 files changed, 39 insertions, 12 deletions

diff --git a/src/partialator.c b/src/partialator.c
index 92fcfbe4..de7eeb4b 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -570,8 +570,11 @@ static void skip_to_end(FILE *fh)
 }
 
 
-static int set_initial_params(Crystal *cr, FILE *fh)
+static int set_initial_params(Crystal *cr, FILE *fh, double force_bandwidth,
+                              double force_radius, double force_lambda)
 {
+	struct image *image = crystal_get_image(cr);
+
 	if ( fh != NULL ) {
 
 		int err;
@@ -596,6 +599,17 @@ static int set_initial_params(Crystal *cr, FILE *fh)
 
 	}
 
+	if ( force_bandwidth > 0.0 ) {
+		image->bw = force_bandwidth;
+	}
+	if ( force_radius > 0.0 ) {
+		crystal_set_profile_radius(cr, force_radius);
+	}
+	if ( force_lambda > 0.0 ) {
+		image->lambda = force_lambda;
+	}
+	image->spectrum = spectrum_generate_gaussian(image->lambda, image->bw);
+
 	return 0;
 }
 
@@ -1420,7 +1434,9 @@ int main(int argc, char *argv[])
 			crystal_set_user_flag(cr, PRFLAG_OK);
 			reflist_free(cr_refl);
 
-			if ( set_initial_params(cr, sparams_fh) ) {
+			if ( set_initial_params(cr, sparams_fh, force_bandwidth,
+			                        force_radius, force_lambda) )
+			{
 				ERROR("Failed to set initial parameters\n");
 				return 1;
 			}
@@ -1451,15 +1467,6 @@ int main(int argc, char *argv[])
 	STATUS("Initial partiality calculation...\n");
 	for ( i=0; i<n_crystals; i++ ) {
 		Crystal *cr = crystals[i];
-		if ( force_bandwidth > 0.0 ) {
-			crystal_get_image(cr)->bw = force_bandwidth;
-		}
-		if ( force_radius > 0.0 ) {
-			crystal_set_profile_radius(cr, force_radius);
-		}
-		if ( force_lambda > 0.0 ) {
-			crystal_get_image(cr)->lambda = force_lambda;
-		}
 		update_predictions(cr);
 		calculate_partialities(cr, pmodel);
 	}
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 59d44425..6db1a48a 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -153,14 +153,22 @@ static void apply_parameters(const Crystal *cr_orig, Crystal *cr_tgt,
                              struct rf_alteration alter)
 {
 	double R, lambda;
+	struct gaussian g;
+	struct image *image;
 
+	image = crystal_get_image(cr_tgt);
 	R = crystal_get_profile_radius(cr_orig);
 	lambda = crystal_get_image_const(cr_orig)->lambda;
 
 	rotate_cell_xy(crystal_get_cell_const(cr_orig), crystal_get_cell(cr_tgt),
 	               alter.rot_x, alter.rot_y);
 	crystal_set_profile_radius(cr_tgt, R+alter.delta_R);
-	crystal_get_image(cr_tgt)->lambda = lambda+alter.delta_wave;
+	image->lambda = lambda+alter.delta_wave;
+
+	g.kcen = 1.0/image->lambda;
+	g.sigma = image->bw/image->lambda;
+	g.height = 1;
+	spectrum_set_gaussians(image->spectrum, &g, 1);
 }
 
 
@@ -442,6 +450,7 @@ static void write_angle_grid(Crystal *cr, const RefList *full,
 	struct rf_priv priv;
 	RefList *list;
 	UnitCell *cell;
+	Spectrum *spectrum;
 
 	priv.cr = cr;
 	priv.full = full;
@@ -449,6 +458,8 @@ static void write_angle_grid(Crystal *cr, const RefList *full,
 	priv.scaleflags = scaleflags;
 	priv.cr_tgt = crystal_copy(cr);
 	priv.image_tgt = *crystal_get_image(cr);
+	spectrum = spectrum_new();
+	priv.image_tgt.spectrum = spectrum;
 	crystal_set_image(priv.cr_tgt, &priv.image_tgt);
 	list = copy_reflist(crystal_get_reflections(cr));
 	crystal_set_reflections(priv.cr_tgt, list);
@@ -490,6 +501,7 @@ static void write_angle_grid(Crystal *cr, const RefList *full,
 
 	reflist_free(crystal_get_reflections(priv.cr_tgt));
 	crystal_free(priv.cr_tgt);
+	spectrum_free(spectrum);
 }
 
 
@@ -502,6 +514,7 @@ static void write_radius_grid(Crystal *cr, const RefList *full,
 	struct rf_priv priv;
 	RefList *list;
 	UnitCell *cell;
+	Spectrum *spectrum;
 
 	priv.cr = cr;
 	priv.full = full;
@@ -509,6 +522,8 @@ static void write_radius_grid(Crystal *cr, const RefList *full,
 	priv.scaleflags = scaleflags;
 	priv.cr_tgt = crystal_copy(cr);
 	priv.image_tgt = *crystal_get_image(cr);
+	spectrum = spectrum_new();
+	priv.image_tgt.spectrum = spectrum;
 	crystal_set_image(priv.cr_tgt, &priv.image_tgt);
 	list = copy_reflist(crystal_get_reflections(cr));
 	crystal_set_reflections(priv.cr_tgt, list);
@@ -550,6 +565,7 @@ static void write_radius_grid(Crystal *cr, const RefList *full,
 
 	reflist_free(crystal_get_reflections(priv.cr_tgt));
 	crystal_free(priv.cr_tgt);
+	spectrum_free(spectrum);
 }
 
 
@@ -635,6 +651,7 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 	RefList *list;
 	FILE *fh = NULL;
 	UnitCell *cell;
+	Spectrum *spectrum;
 
 	try_reindex(cr, full, sym, amb, scaleflags);
 
@@ -651,6 +668,8 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 	priv.scaleflags = scaleflags;
 	priv.cr_tgt = crystal_copy(cr);
 	priv.image_tgt = *crystal_get_image(cr);
+	spectrum = spectrum_new();
+	priv.image_tgt.spectrum = spectrum;
 	crystal_set_image(priv.cr_tgt, &priv.image_tgt);
 	list = copy_reflist(crystal_get_reflections(cr));
 	crystal_set_reflections(priv.cr_tgt, list);
@@ -718,6 +737,7 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 
 	reflist_free(crystal_get_reflections(priv.cr_tgt));
 	crystal_free(priv.cr_tgt);
+	spectrum_free(spectrum);
 }