Crystals shouldn't own RefLists (part 2)

This commit replaces image.crystals with an array of small structs, each
consisting of a Crystal-RefList pair.  index.c and stream.c are updated,
more to follow.

1 files changed, 20 insertions, 8 deletions

diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 9e9af85c..142598e3 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -317,35 +317,45 @@ void image_remove_feature(ImageFeatureList *flist, int idx)
 }
 
 
-void image_add_crystal(struct image *image, Crystal *cryst)
+void image_add_crystal_refls(struct image *image,
+                             Crystal *cryst,
+                             RefList *reflist)
 {
-	Crystal **crs;
+	struct crystal_refls *crs;
 	int n;
 
 	n = image->n_crystals;
-	crs = cfrealloc(image->crystals, (n+1)*sizeof(Crystal *));
+	crs = cfrealloc(image->crystals, (n+1)*sizeof(struct crystal_refls));
 	if ( crs == NULL ) {
 		ERROR("Failed to allocate memory for crystals.\n");
 		return;
 	}
 
-	crs[n] = cryst;
+	crs[n].cr = cryst;
+	crs[n].refls = reflist;
 	image->crystals = crs;
 	image->n_crystals = n+1;
 }
 
 
+void image_add_crystal(struct image *image, Crystal *cryst)
+{
+	image_add_crystal_refls(image, cryst, NULL);
+}
+
+
 int remove_flagged_crystals(struct image *image)
 {
 	int i;
 	int n_bad = 0;
 
 	for ( i=0; i<image->n_crystals; i++ ) {
-		if ( crystal_get_user_flag(image->crystals[i]) ) {
+		if ( crystal_get_user_flag(image->crystals[i].cr) ) {
 			int j;
-			Crystal *deleteme = image->crystals[i];
+			Crystal *deleteme = image->crystals[i].cr;
 			cell_free(crystal_get_cell(deleteme));
 			crystal_free(deleteme);
+			reflist_free(image->crystals[i].refls);
 			for ( j=i; j<image->n_crystals-1; j++ ) {
 				image->crystals[j] = image->crystals[j+1];
 			}
@@ -365,11 +375,13 @@ void free_all_crystals(struct image *image)
 	int i;
 	if ( image->crystals == NULL ) return;
 	for ( i=0; i<image->n_crystals; i++ ) {
-		Crystal *cr = image->crystals[i];
+		Crystal *cr = image->crystals[i].cr;
 		cell_free(crystal_get_cell(cr));
-		crystal_free(image->crystals[i]);
+		crystal_free(image->crystals[i].cr);
+		reflist_free(image->crystals[i].refls);
 	}
 	cffree(image->crystals);
+	image->crystals = NULL;
 	image->n_crystals = 0;
 }