Crystals shouldn't own RefLists (part 6)

This fixes the remaining programs.

6 files changed, 21 insertions, 25 deletions

diff --git a/src/ambigator.c b/src/ambigator.c
index 3777cf0a..91e621ac 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -1287,7 +1287,8 @@ int main(int argc, char *argv[])
 			RefList *list;
 			UnitCell *cell;
 
-			cr = image->crystals[i];
+			cr = image->crystals[i].cr;
+			list = image->crystals[i].refls;
 			cell = crystal_get_cell(cr);
 
 			if ( n_crystals == max_crystals ) {
@@ -1308,7 +1309,6 @@ int main(int argc, char *argv[])
 
 			}
 
-			list = crystal_get_reflections(cr);
 			crystals[n_crystals] = asymm_and_merge(list, s_sym,
 			                                       cell,
 			                                       rmin, rmax,
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index 99cb284f..a92de347 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -2002,9 +2002,7 @@ static int add_stream(CellWindow *w, const char *stream_filename,
 
 		for ( i=0; i<image->n_crystals; i++ ) {
 
-			Crystal *cr;
-
-			cr = image->crystals[i];
+			Crystal *cr = image->crystals[i].cr;
 
 			if ( w->n_cells == max_cells ) {
 
diff --git a/src/crystfelimageview.c b/src/crystfelimageview.c
index 03350204..1659ae4f 100644
--- a/src/crystfelimageview.c
+++ b/src/crystfelimageview.c
@@ -707,9 +707,8 @@ static gint draw_sig(GtkWidget *window, cairo_t *cr, CrystFELImageView *iv)
 	if ( iv->show_refls ) {
 		int i;
 		for ( i=0; i<iv->image->n_crystals; i++ ) {
-			Crystal *cry = iv->image->crystals[i];
 			draw_refls(cr, iv,
-			           crystal_get_reflections(cry),
+			           iv->image->crystals[i].refls,
 			           iv->label_refls,
 			           crystal_cols[i % n_crystal_cols]);
 		}
diff --git a/src/gui_index.c b/src/gui_index.c
index 2cc8e8db..218331eb 100644
--- a/src/gui_index.c
+++ b/src/gui_index.c
@@ -636,19 +636,19 @@ static void run_indexing_once(struct crystfelproject *proj)
 	index_pattern(proj->cur_image, ipriv);
 
 	for ( i=0; i<proj->cur_image->n_crystals; i++ ) {
-		crystal_set_mosaicity(proj->cur_image->crystals[i], 0.0);
+		crystal_set_mosaicity(proj->cur_image->crystals[i].cr, 0.0);
 		if ( proj->indexing_params.use_fix_profile_radius ) {
 
 			/* Manual radius */
-			crystal_set_profile_radius(proj->cur_image->crystals[i],
+			crystal_set_profile_radius(proj->cur_image->crystals[i].cr,
 			                           proj->indexing_params.fix_profile_radius);
 
 		} else {
 
 			/* Auto radius determination */
-			crystal_set_profile_radius(proj->cur_image->crystals[i],
+			crystal_set_profile_radius(proj->cur_image->crystals[i].cr,
 			                           0.02e9);
-			if ( refine_radius(proj->cur_image->crystals[i],
+			if ( refine_radius(proj->cur_image->crystals[i].cr,
 		                           proj->cur_image) )
 			{
 				ERROR("WARNING: Radius determination failed\n");
@@ -682,7 +682,7 @@ static void run_indexing_once(struct crystfelproject *proj)
 	STATUS("Number of crystals: %i\n",
 	       proj->cur_image->n_crystals);
 	for ( i=0; i<proj->cur_image->n_crystals; i++ ) {
-		cell_print(crystal_get_cell(proj->cur_image->crystals[i]));
+		cell_print(crystal_get_cell(proj->cur_image->crystals[i].cr));
 	}
 
 }
diff --git a/src/process_image.c b/src/process_image.c
index 2f856594..782c97b9 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -434,20 +434,20 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	set_last_task(last_task, "prediction params");
 	if ( iargs->fix_profile_r >= 0.0 ) {
 		for ( i=0; i<image->n_crystals; i++ ) {
-			crystal_set_profile_radius(image->crystals[i],
+			crystal_set_profile_radius(image->crystals[i].cr,
 			                           iargs->fix_profile_r);
-			crystal_set_mosaicity(image->crystals[i], 0.0);
+			crystal_set_mosaicity(image->crystals[i].cr, 0.0);
 		}
 	} else {
 		for ( i=0; i<image->n_crystals; i++ ) {
-			crystal_set_profile_radius(image->crystals[i], 0.02e9);
-			crystal_set_mosaicity(image->crystals[i], 0.0);
+			crystal_set_profile_radius(image->crystals[i].cr, 0.02e9);
+			crystal_set_mosaicity(image->crystals[i].cr, 0.0);
 		}
 	}
 
 	if ( iargs->fix_profile_r < 0.0 ) {
 		for ( i=0; i<image->n_crystals; i++ ) {
-			if ( refine_radius(image->crystals[i], image) ) {
+			if ( refine_radius(image->crystals[i].cr, image) ) {
 				ERROR("WARNING: Radius determination failed\n");
 			}
 		}
@@ -479,7 +479,7 @@ streamwrite:
 
 	int n = 0;
 	for ( i=0; i<image->n_crystals; i++ ) {
-		n += crystal_get_num_implausible_reflections(image->crystals[i]);
+		n += crystal_get_num_implausible_reflections(image->crystals[i].cr);
 	}
 	if ( n > 0 ) {
 		STATUS("WARNING: %i implausibly negative reflection%s in %s "
@@ -495,7 +495,7 @@ out:
 	pthread_mutex_lock(&sb_shared->totals_lock);
 	any_crystals = 0;
 	for ( i=0; i<image->n_crystals; i++ ) {
-		if ( crystal_get_user_flag(image->crystals[i]) == 0 ) {
+		if ( crystal_get_user_flag(image->crystals[i].cr) == 0 ) {
 			sb_shared->n_crystals++;
 			any_crystals = 1;
 		}
diff --git a/src/whirligig.c b/src/whirligig.c
index 20fcfa40..aa2cf090 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -175,12 +175,11 @@ static void process_series(struct image *images, signed int *ser,
 	fprintf(fh, "%i frames in series\n\n", len);
 	fprintf(fh, "   # Serial Filename   EventID   Crystal\n");
 	for ( i=0; i<len; i++ ) {
-		Crystal *cr = images[i].crystals[ser[i]];
 		fprintf(fh, "%4i %5i %s %s %i\n", i, images[i].serial,
 		                             images[i].filename,
 		                             images[i].ev,
 		                             ser[i]);
-		p[i] = transform_reflections(crystal_get_reflections(cr),
+		p[i] = transform_reflections(images[i].crystals[ser[i]].refls,
 		                             mat[i]);
 	}
 
@@ -316,8 +315,8 @@ static IntegerMatrix *try_all(struct window *win, int n1, int n2,
 	for ( i=0; i<i1->n_crystals; i++ ) {
 	for ( j=0; j<i2->n_crystals; j++ ) {
 
-		if ( compare_permuted_cell_parameters_and_orientation(crystal_get_cell(i1->crystals[i]),
-		                                                      crystal_get_cell(i2->crystals[j]),
+		if ( compare_permuted_cell_parameters_and_orientation(crystal_get_cell(i1->crystals[i].cr),
+		                                                      crystal_get_cell(i2->crystals[j].cr),
 		                                                      tols, &m) )
 		{
 			if ( !crystal_used(win, n1, i)
@@ -377,12 +376,12 @@ static int try_join(struct window *win, int sn)
 
 	/* Get the appropriately transformed cell from the last crystal in this
 	 * series */
-	cr = win->img[sp].crystals[win->ser[sn][sp]];
+	cr = win->img[sp].crystals[win->ser[sn][sp]].cr;
 	ref = cell_transform_intmat(crystal_get_cell(cr), win->mat[sn][sp]);
 
 	for ( j=0; j<win->img[win->join_ptr].n_crystals; j++ ) {
 		Crystal *cr2;
-		cr2 = win->img[win->join_ptr].crystals[j];
+		cr2 = win->img[win->join_ptr].crystals[j].cr;
 		if ( compare_permuted_cell_parameters_and_orientation(ref, crystal_get_cell(cr2),
 		                                                      tols,
 		                                                      &win->mat[sn][win->join_ptr]) )