Fix many small memory leaks

5 files changed, 44 insertions, 11 deletions

diff --git a/src/cell.c b/src/cell.c
index 9fa506b0..c3a65066 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -81,6 +81,7 @@ UnitCell *cell_new()
 	cell->rep = CELL_REP_CRYST;
 
 	cell->pointgroup = strdup("1");
+	cell->spacegroup = strdup("P 1");
 
 	return cell;
 }
@@ -90,6 +91,7 @@ void cell_free(UnitCell *cell)
 {
 	if ( cell == NULL ) return;
 	free(cell->pointgroup);
+	free(cell->spacegroup);
 	free(cell);
 }
 
@@ -187,6 +189,8 @@ UnitCell *cell_new_from_cell(UnitCell *orig)
 	new = malloc(sizeof(UnitCell));
 
 	*new = *orig;
+	cell_set_pointgroup(new, orig->pointgroup);
+	cell_set_spacegroup(new, orig->spacegroup);
 
 	return new;
 }
@@ -207,6 +211,20 @@ void cell_set_reciprocal(UnitCell *cell,
 }
 
 
+void cell_set_spacegroup(UnitCell *cell, const char *sym)
+{
+	free(cell->spacegroup);
+	cell->spacegroup = strdup(sym);
+}
+
+
+void cell_set_pointgroup(UnitCell *cell, const char *sym)
+{
+	free(cell->pointgroup);
+	cell->pointgroup = strdup(sym);
+}
+
+
 /************************* Getter helper functions ****************************/
 
 static int cell_crystallographic_to_cartesian(UnitCell *cell,
@@ -838,8 +856,7 @@ static void cell_set_pointgroup_from_pdb(UnitCell *cell, const char *sym)
 	if ( strcmp(sym, "P 43 21 2") == 0 ) new = "422";
 
 	if ( new != NULL ) {
-		free(cell->pointgroup);
-		cell->pointgroup = strdup(new);
+		cell_set_pointgroup(cell, new);
 	} else {
 		ERROR("Can't determine point group for '%s'\n", sym);
 	}
@@ -901,13 +918,15 @@ UnitCell *load_cell_from_pdb(const char *filename)
 				sym = strndup(line+55, 10);
 				notrail(sym);
 				cell_set_pointgroup_from_pdb(cell, sym);
-				cell->spacegroup = sym;
-
+				cell_set_spacegroup(cell, sym);
+				free(sym);
 			} else {
 				cell_set_pointgroup_from_pdb(cell, "P 1");
-				cell->spacegroup = strdup("P 1");
+				cell_set_spacegroup(cell, "P 1");
 				ERROR("CRYST1 line without space group.\n");
 			}
+
+			break;  /* Done */
 		}
 
 	} while ( rval != NULL );
diff --git a/src/cell.h b/src/cell.h
index 5e9facb0..17990e2c 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -50,6 +50,8 @@ extern void cell_set_parameters(UnitCell *cell, double a, double b, double c,
 extern void cell_set_cartesian_a(UnitCell *cell, double ax, double ay, double az);
 extern void cell_set_cartesian_b(UnitCell *cell, double bx, double by, double bz);
 extern void cell_set_cartesian_c(UnitCell *cell, double cx, double cy, double cz);
+extern void cell_set_spacegroup(UnitCell *cell, const char *sym);
+extern void cell_set_pointgroup(UnitCell *cell, const char *sym);
 
 
 extern int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
diff --git a/src/index.c b/src/index.c
index ce6021da..6f9b5278 100644
--- a/src/index.c
+++ b/src/index.c
@@ -162,7 +162,8 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 		}
 
 		if ( (cellr == CELLR_NONE) || (indm[n] == INDEXING_TEMPLATE) ) {
-			image->indexed_cell = image->candidate_cells[0];
+			image->indexed_cell = cell_new_from_cell(
+			                             image->candidate_cells[0]);
 			if ( verbose ) {
 				STATUS("--------------------\n");
 				STATUS("The indexed cell (matching not"
@@ -170,7 +171,7 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 				cell_print(image->indexed_cell);
 				STATUS("--------------------\n");
 			}
-			return;
+			goto done;
 		}
 
 		for ( i=0; i<image->ncells; i++ ) {
@@ -206,6 +207,7 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 			/* Sanity check */
 			if ( !peak_sanity_check(image, new_cell, 0, 0.1) ) {
 				STATUS("Failed peak sanity check.\n");
+				cell_free(new_cell);
 				continue;
 			}
 
@@ -216,6 +218,7 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 
 		for ( i=0; i<image->ncells; i++ ) {
 			cell_free(image->candidate_cells[i]);
+			image->candidate_cells[i] = NULL;
 		}
 
 		/* Move on to the next indexing method */
@@ -225,6 +228,7 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 
 done:
 	for ( i=0; i<image->ncells; i++ ) {
+		/* May free(NULL) if all algorithms were tried */
 		cell_free(image->candidate_cells[i]);
 	}
 }
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 411a1b63..c997ed12 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -461,7 +461,10 @@ static void *get_image(void *qp)
 	} else {
 
 		rval = fgets(line, 1023, qargs->fh);
-		if ( rval == NULL ) return NULL;
+		if ( rval == NULL ) {
+			free(pargs);
+			return NULL;
+		}
 		chomp(line);
 		pargs->filename = malloc(strlen(qargs->prefix)+strlen(line)+1);
 		snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);
@@ -884,11 +887,14 @@ int main(int argc, char *argv[])
 
 	cleanup_indexing(ipriv);
 
+	free(indm);
+	free(ipriv);
 	free(prefix);
 	free(det->panels);
 	free(det);
 	cell_free(cell);
-	if ( fh != stdout ) fclose(fh);
+	if ( fh != stdin ) fclose(fh);
+	if ( ofh != stdout ) fclose(ofh);
 	free(sym);
 
 	STATUS("There were %i images, of which %i could be indexed.\n",
diff --git a/src/mosflm.c b/src/mosflm.c
index 5cd2291e..6f27eb7d 100644
--- a/src/mosflm.c
+++ b/src/mosflm.c
@@ -228,6 +228,8 @@ static void write_spt(struct image *image, const char *filename)
 
 	}
 
+	free(sptlines);
+
 	fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
 	           -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
 	fclose(fh);
@@ -262,8 +264,8 @@ static void write_img(struct image *image, const char *filename)
 	/* Header padding */
 	while ( ftell(fh) < 512 ) fprintf(fh," ");
 
-	fwrite(fh, sizeof(unsigned short int), 1, fh);
-
+	fwrite(intimage, sizeof(unsigned short int), 1, fh);
+	free(intimage);
 	fclose(fh);
 }