partialator: Fix multiple memory leaks

5 files changed, 34 insertions, 16 deletions

diff --git a/libcrystfel/src/reflist.c b/libcrystfel/src/reflist.c
index f1d759ea..9c8a6a14 100644
--- a/libcrystfel/src/reflist.c
+++ b/libcrystfel/src/reflist.c
@@ -233,6 +233,7 @@ void reflist_free(RefList *list)
 	if ( list->head != NULL ) {
 		recursive_free(list->head);
 	} /* else empty list */
+	if ( list->notes != NULL ) free(list->notes);
 	free(list);
 }
 
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index bcd2627e..66b3b657 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1131,6 +1131,18 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 }
 
 
+void free_stuff_from_stream(struct stuff_from_stream *sfs)
+{
+	int i;
+	if ( sfs == NULL ) return;
+	for ( i=0; i<sfs->n_fields; i++ ) {
+		free(sfs->fields[i]);
+	}
+	free(sfs->fields);
+	free(sfs);
+}
+
+
 static int read_and_store_field(struct image *image, const char *line)
 {
 	char **new_fields;
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index a8e3e2ee..bd7aa690 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -106,6 +106,8 @@ extern Stream *open_stream_fd_for_write(int fd);
 extern int get_stream_fd(Stream *st);
 extern void close_stream(Stream *st);
 
+extern void free_stuff_from_stream(struct stuff_from_stream *sfs);
+
 extern int read_chunk(Stream *st, struct image *image);
 extern int read_chunk_2(Stream *st, struct image *image,
                            StreamReadFlags srf);
diff --git a/src/partialator.c b/src/partialator.c
index aacf241f..8b4893a5 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1237,6 +1237,7 @@ int main(int argc, char *argv[])
 			ERROR("Unknown partiality model '%s'.\n", pmodel_str);
 			return 1;
 		}
+		free(pmodel_str);
 	}
 
 	if ( (pmodel == PMODEL_UNITY) && !no_pr ) {
@@ -1377,6 +1378,7 @@ int main(int argc, char *argv[])
 			*image = cur;
 			image->n_crystals = 1;
 			image->crystals = &crystals[n_crystals];
+			free(cur.crystals);
 
 			/* This is the raw list of reflections */
 			cr_refl = crystal_get_reflections(cr);
@@ -1420,6 +1422,7 @@ int main(int argc, char *argv[])
 	fprintf(stderr, "\n");
 	if ( sparams_fh != NULL ) fclose(sparams_fh);
 	audit_info = stream_audit_info(st);
+	free(audit_info);
 	close_stream(st);
 
 	STATUS("Initial partiality calculation...\n");
@@ -1568,7 +1571,12 @@ int main(int argc, char *argv[])
 	/* Clean up */
 	gsl_rng_free(rng);
 	for ( i=0; i<n_crystals; i++ ) {
+		struct image *image = crystal_get_image(crystals[i]);
 		reflist_free(crystal_get_reflections(crystals[i]));
+		free_stuff_from_stream(image->stuff_from_stream);
+		free(image->filename);
+		free(image);
+		cell_free(crystal_get_cell(crystals[i]));
 		crystal_free(crystals[i]);
 	}
 	free_contribs(full);
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 4ae72685..fd0d5c4e 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -84,17 +84,14 @@ const char *str_prflag(enum prflag flag)
 }
 
 
-static UnitCell *rotate_cell_xy(const UnitCell *cell, double ang1, double ang2)
+static void rotate_cell_xy(UnitCell *cell, double ang1, double ang2)
 {
-	UnitCell *o;
 	double asx, asy, asz;
 	double bsx, bsy, bsz;
 	double csx, csy, csz;
 	double xnew, ynew, znew;
 
-	o = cell_new_from_cell(cell);
-
-	cell_get_reciprocal(o, &asx, &asy, &asz,
+	cell_get_reciprocal(cell, &asx, &asy, &asz,
 	                       &bsx, &bsy, &bsz,
 	                       &csx, &csy, &csz);
 
@@ -134,9 +131,7 @@ static UnitCell *rotate_cell_xy(const UnitCell *cell, double ang1, double ang2)
 	znew = -csx*sin(ang2) + csz*cos(ang2);
 	csx = xnew;  csy = ynew;  csz = znew;
 
-	cell_set_reciprocal(o, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
-
-	return o;
+	cell_set_reciprocal(cell, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
 }
 
 
@@ -201,7 +196,6 @@ static void apply_parameters(const gsl_vector *v, const gsl_vector *initial,
 {
 	int i;
 	double ang1, ang2, R, lambda;
-	UnitCell *cell;
 
 	/* Default parameters if not used in refinement */
 	ang1 = 0.0;
@@ -240,9 +234,7 @@ static void apply_parameters(const gsl_vector *v, const gsl_vector *initial,
 		}
 	}
 
-	cell = rotate_cell_xy(crystal_get_cell_const(cr), ang1, ang2);
-	crystal_set_cell(cr, cell);
-
+	rotate_cell_xy(crystal_get_cell(cr), ang1, ang2);
 	crystal_set_profile_radius(cr, R);
 	crystal_get_image(cr)->lambda = lambda;
 }
@@ -254,7 +246,6 @@ static double residual_f(const gsl_vector *v, void *pp)
 	RefList *list;
 	struct image im;
 	Crystal *cr;
-	UnitCell *cell;
 	double res;
 	int i;
 
@@ -263,14 +254,14 @@ static double residual_f(const gsl_vector *v, void *pp)
 	}
 
 	cr = crystal_copy(pv->cr);
-	cell = cell_new_from_cell(crystal_get_cell(cr));
-	if ( cell == NULL ) return GSL_NAN;
-	crystal_set_cell(cr, cell);
 	im = *crystal_get_image(cr);
 	crystal_set_image(cr, &im);
+	crystal_set_cell(cr, cell_new_from_cell(crystal_get_cell(cr)));
+
 	apply_parameters(v, pv->initial, pv->rv, cr);
 
 	if ( fabs(crystal_get_profile_radius(cr)) > 5e9 ) {
+		cell_free(crystal_get_cell(cr));
 		crystal_free(cr);
 		if ( pv->verbose ) STATUS("radius > 5e9\n");
 		return GSL_NAN;
@@ -278,12 +269,14 @@ static double residual_f(const gsl_vector *v, void *pp)
 
 	/* Can happen with grid scans and certain --force-radius values */
 	if ( fabs(crystal_get_profile_radius(cr)) < 0.0000001e9 ) {
+		cell_free(crystal_get_cell(cr));
 		crystal_free(cr);
 		if ( pv->verbose ) STATUS("radius very small\n");
 		return GSL_NAN;
 	}
 
 	if ( im.lambda <= 0.0 ) {
+		cell_free(crystal_get_cell(cr));
 		crystal_free(cr);
 		if ( pv->verbose ) STATUS("lambda < 0\n");
 		return GSL_NAN;
@@ -296,6 +289,8 @@ static double residual_f(const gsl_vector *v, void *pp)
 	calculate_partialities(cr, PMODEL_XSPHERE);
 
 	if ( scale_one_crystal(cr, pv->full, pv->scaleflags) ) {
+		cell_free(crystal_get_cell(cr));
+		reflist_free(crystal_get_reflections(cr));
 		crystal_free(cr);
 		if ( pv->verbose ) STATUS("Bad scaling\n");
 		return GSL_NAN;