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.

4 files changed, 47 insertions, 50 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;
 }
 
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 7e4bad1f..beb66810 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -110,6 +110,12 @@ typedef enum
 } DataSourceType;
 
 
+struct crystal_refls
+{
+	Crystal *cr;
+	RefList *refls;
+};
+
 struct image
 {
 	/** The image data, by panel */
@@ -124,8 +130,8 @@ struct image
 	/** Non-zero if the frame was determined to be a "hit" */
 	int                     hit;
 
-	/**Array of crystals in the image */
-	Crystal                 **crystals;
+	/** Array of crystals (with reflection lists) in the image */
+	struct crystal_refls   *crystals;
 
 	/** The number of crystals in the image (size of \p crystals) */
 	int                     n_crystals;
@@ -218,6 +224,8 @@ extern ImageFeatureList *sort_peaks(ImageFeatureList *flist);
 extern ImageFeatureList *image_feature_list_copy(const ImageFeatureList *flist);
 
 extern void image_add_crystal(struct image *image, Crystal *cryst);
+extern void image_add_crystal_refls(struct image *image,
+                                    Crystal *cryst, RefList *reflist);
 extern int remove_flagged_crystals(struct image *image);
 extern void free_all_crystals(struct image *image);
 
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 4c35d2ca..7aea3b59 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -699,7 +699,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		int this_crystal = image->n_crystals - i - 1;
 
 		/* ... starting at the end of the (complete) list ... */
-		Crystal *cr = image->crystals[this_crystal];
+		Crystal *cr = image->crystals[this_crystal].cr;
 
 		crystal_set_profile_radius(cr, 0.02e9);
 		crystal_set_mosaicity(cr, 0.0);
@@ -756,7 +756,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		profile_start("cell-compare-to-others");
 		for ( j=0; j<this_crystal; j++ ) {
 
-			Crystal *that_cr = image->crystals[j];
+			Crystal *that_cr = image->crystals[j].cr;
 			/* 'tols' is in frac (not %) and radians */
 			const double tols[] = {0.1, 0.1, 0.1,
 			                       deg2rad(5.0),
@@ -908,7 +908,7 @@ static int finished_retry(IndexingMethod indm, IndexingFlags flags,
 		if ( flags & INDEXING_MULTI ) {
 			/* Remove "used" spots and try for another lattice */
 			Crystal *cr;
-			cr = image->crystals[image->n_crystals-1];
+			cr = image->crystals[image->n_crystals-1].cr;
 			return delete_explained_peaks(image, cr);
 		} else {
 			return 1;
@@ -945,8 +945,7 @@ void index_pattern_4(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 	if ( ipriv == NULL ) return;
 
-	image->crystals = NULL;
-	image->n_crystals = 0;
+	free_all_crystals(image);
 
 	/* No peaks? */
 	if ( image->features == NULL ) return;
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index edbeb7af..ffe68162 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -338,11 +338,9 @@ static int num_integrated_reflections(RefList *list)
 }
 
 
-static int write_crystal(Stream *st, Crystal *cr,
-                         int include_reflections)
+static int write_crystal(Stream *st, Crystal *cr, RefList *reflist)
 {
 	UnitCell *cell;
-	RefList *reflist;
 	double asx, asy, asz;
 	double bsx, bsy, bsz;
 	double csx, csy, csz;
@@ -389,7 +387,6 @@ static int write_crystal(Stream *st, Crystal *cr,
 	fprintf(st->fh, "predict_refine/det_shift x = %.3f y = %.3f mm\n",
 	        det_shift_x*1e3, det_shift_y*1e3);
 
-	reflist = crystal_get_reflections(cr);
 	if ( reflist != NULL ) {
 
 		fprintf(st->fh, "diffraction_resolution_limit"
@@ -406,20 +403,17 @@ static int write_crystal(Stream *st, Crystal *cr,
 
 	}
 
-	if ( include_reflections ) {
-
-		if ( reflist != NULL ) {
+	if ( reflist != NULL ) {
 
-			fprintf(st->fh, STREAM_REFLECTION_START_MARKER"\n");
-			ret = write_stream_reflections(st->fh, reflist,
-			                               st->dtempl_write);
-			fprintf(st->fh, STREAM_REFLECTION_END_MARKER"\n");
+		fprintf(st->fh, STREAM_REFLECTION_START_MARKER"\n");
+		ret = write_stream_reflections(st->fh, reflist,
+		                               st->dtempl_write);
+		fprintf(st->fh, STREAM_REFLECTION_END_MARKER"\n");
 
-		} else {
+	} else {
 
-			fprintf(st->fh, "No integrated reflections.\n");
+		fprintf(st->fh, "No integrated reflections.\n");
 
-		}
 	}
 
 	fprintf(st->fh, STREAM_CRYSTAL_END_MARKER"\n");
@@ -512,11 +506,11 @@ int stream_write_chunk(Stream *st, const struct image *i,
 	}
 
 	for ( j=0; j<i->n_crystals; j++ ) {
-		if ( crystal_get_user_flag(i->crystals[j]) ) {
+		if ( crystal_get_user_flag(i->crystals[j].cr) ) {
 			continue;
 		}
-		ret = write_crystal(st, i->crystals[j],
-		                    srf & STREAM_REFLECTIONS);
+		ret = write_crystal(st, i->crystals[j].cr,
+		                    srf & STREAM_REFLECTIONS ? i->crystals[j].refls : NULL);
 	}
 
 	fprintf(st->fh, STREAM_CHUNK_END_MARKER"\n");
@@ -564,8 +558,7 @@ static void read_crystal(Stream *st, struct image *image,
 	char unique_axis = '*';
 	LatticeType lattice_type = L_TRICLINIC;
 	Crystal *cr;
-	int n;
-	Crystal **crystals_new;
+	RefList *reflist = NULL;
 	double shift_x, shift_y;
 
 	as.u = 0.0;  as.v = 0.0;  as.w = 0.0;
@@ -664,8 +657,6 @@ static void read_crystal(Stream *st, struct image *image,
 		if ( (strcmp(line, STREAM_REFLECTION_START_MARKER) == 0)
 		  && (srf & STREAM_REFLECTIONS) )
 		{
-
-			RefList *reflist;
 			reflist = read_stream_reflections_2_3(st);
 			if ( reflist == NULL ) {
 				ERROR("Failed while reading reflections\n");
@@ -673,9 +664,6 @@ static void read_crystal(Stream *st, struct image *image,
 				ERROR("Event = %s\n", image->ev);
 				break;
 			}
-
-			crystal_set_reflections(cr, reflist);
-
 		}
 
 		if ( strcmp(line, STREAM_CRYSTAL_END_MARKER) == 0 ) break;
@@ -713,17 +701,7 @@ static void read_crystal(Stream *st, struct image *image,
 	/* Unused at the moment */
 	crystal_set_mosaicity(cr, 0.0);
 
-	/* Add crystal to the list for this image */
-	n = image->n_crystals+1;
-	crystals_new = cfrealloc(image->crystals, n*sizeof(Crystal *));
-
-	if ( crystals_new == NULL ) {
-		ERROR("Failed to expand crystal list!\n");
-	} else {
-		image->crystals = crystals_new;
-		image->crystals[image->n_crystals++] = cr;
-	}
-
+	image_add_crystal_refls(image, cr, reflist);
 }