Use libcrystfel memory allocation routines everywhere

1 files changed, 33 insertions, 33 deletions

diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 71dd7413..edbeb7af 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -453,7 +453,7 @@ int stream_write_chunk(Stream *st, const struct image *i,
 	fprintf(st->fh, "hit = %i\n", i->hit);
 	indexer = indexer_str(i->indexed_by);
 	fprintf(st->fh, "indexed_by = %s\n", indexer);
-	free(indexer);
+	cffree(indexer);
 	if ( i->indexed_by != INDEXING_NONE ) {
 		fprintf(st->fh, "n_indexing_tries = %i\n", i->n_indexing_tries);
 	}
@@ -715,7 +715,7 @@ static void read_crystal(Stream *st, struct image *image,
 
 	/* Add crystal to the list for this image */
 	n = image->n_crystals+1;
-	crystals_new = realloc(image->crystals, n*sizeof(Crystal *));
+	crystals_new = cfrealloc(image->crystals, n*sizeof(Crystal *));
 
 	if ( crystals_new == NULL ) {
 		ERROR("Failed to expand crystal list!\n");
@@ -733,7 +733,7 @@ static void parse_header(const char *line_in, struct image *image,
 	char *line;
 	char *pos;
 
-	line = strdup(line_in);
+	line = cfstrdup(line_in);
 	chomp(line);
 
 	pos = strchr(line, ' ');
@@ -816,12 +816,12 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
 		chomp(line);
 
 		if ( strncmp(line, "Image filename: ", 16) == 0 ) {
-			image->filename = strdup(line+16);
+			image->filename = cfstrdup(line+16);
 			have_filename = 1;
 		}
 
 		if ( strncmp(line, "Event: ", 7) == 0 ) {
-			image->ev = strdup(line+7);
+			image->ev = cfstrdup(line+7);
 		}
 
 		if ( strncmp(line, "hdf5/", 5) == 0 ) {
@@ -928,7 +928,7 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
 char *stream_audit_info(Stream *st)
 {
 	if ( st->audit_info == NULL ) return NULL;
-	return strdup(st->audit_info);
+	return cfstrdup(st->audit_info);
 }
 
 
@@ -945,7 +945,7 @@ static int read_geometry_file(Stream *st)
 	const size_t max_geom_len = 1024*1024;
 	char *geom;
 
-	geom = malloc(max_geom_len);
+	geom = cfmalloc(max_geom_len);
 	if ( geom == NULL ) {
 		ERROR("Failed to allocate memory for geometry file\n");
 		return 1;
@@ -962,7 +962,7 @@ static int read_geometry_file(Stream *st)
 		if ( rval == NULL ) {
 			ERROR("Failed to read stream geometry file.\n");
 			stream_close(st);
-			free(geom);
+			cffree(geom);
 			return 1;
 		}
 
@@ -975,7 +975,7 @@ static int read_geometry_file(Stream *st)
 		if ( len > max_geom_len-1 ) {
 			ERROR("Stream's geometry file is too long (%li > %i).\n",
 			      (long)len, (int)max_geom_len);
-			free(geom);
+			cffree(geom);
 			return 1;
 		} else {
 			strcat(geom, line);
@@ -994,7 +994,7 @@ static int read_headers(Stream *st)
 	int done = 0;
 	size_t len = 0;
 
-	st->audit_info = malloc(4096);
+	st->audit_info = cfmalloc(4096);
 	if ( st->audit_info == NULL ) {
 		ERROR("Failed to allocate memory for audit information\n");
 		return 1;
@@ -1041,7 +1041,7 @@ Stream *stream_open_for_read(const char *filename)
 {
 	Stream *st;
 
-	st = malloc(sizeof(struct _stream));
+	st = cfmalloc(sizeof(struct _stream));
 	if ( st == NULL ) return NULL;
 	st->old_indexers = 0;
 	st->audit_info = NULL;
@@ -1058,7 +1058,7 @@ Stream *stream_open_for_read(const char *filename)
 	}
 
 	if ( st->fh == NULL ) {
-		free(st);
+		cffree(st);
 		return NULL;
 	}
 
@@ -1108,7 +1108,7 @@ Stream *stream_open_fd_for_write(int fd, const DataTemplate *dtempl)
 {
 	Stream *st;
 
-	st = malloc(sizeof(struct _stream));
+	st = cfmalloc(sizeof(struct _stream));
 	if ( st == NULL ) return NULL;
 	st->old_indexers = 0;
 	st->audit_info = NULL;
@@ -1120,7 +1120,7 @@ Stream *stream_open_fd_for_write(int fd, const DataTemplate *dtempl)
 
 	st->fh = fdopen(fd, "w");
 	if ( st->fh == NULL ) {
-		free(st);
+		cffree(st);
 		return NULL;
 	}
 
@@ -1165,7 +1165,7 @@ Stream *stream_open_for_write(const char *filename,
 {
 	Stream *st;
 
-	st = malloc(sizeof(struct _stream));
+	st = cfmalloc(sizeof(struct _stream));
 	if ( st == NULL ) return NULL;
 	st->old_indexers = 0;
 	st->audit_info = NULL;
@@ -1178,7 +1178,7 @@ Stream *stream_open_for_write(const char *filename,
 	st->fh = fopen(filename, "w");
 	if ( st->fh == NULL ) {
 		ERROR("Failed to open stream.\n");
-		free(st);
+		cffree(st);
 		return NULL;
 	}
 
@@ -1209,11 +1209,11 @@ int stream_get_fd(Stream *st)
 void stream_close(Stream *st)
 {
 	if ( st == NULL ) return;
-	free(st->audit_info);
-	free(st->geometry_file);
+	cffree(st->audit_info);
+	cffree(st->geometry_file);
 	data_template_free(st->dtempl_read);
 	fclose(st->fh);
-	free(st);
+	cffree(st);
 }
 
 
@@ -1338,9 +1338,9 @@ struct _streamindex
 void stream_index_free(StreamIndex *index)
 {
 	if ( index == NULL ) return;
-	free(index->keys);
-	free(index->ptrs);
-	free(index);
+	cffree(index->keys);
+	cffree(index->ptrs);
+	cffree(index);
 }
 
 
@@ -1351,7 +1351,7 @@ static char *make_key(const char *filename,
 
 	if ( ev == NULL ) ev = "//";
 
-	key = malloc(strlen(filename)+strlen(ev)+2);
+	key = cfmalloc(strlen(filename)+strlen(ev)+2);
 	if ( key == NULL ) return NULL;
 
 	strcpy(key, filename);
@@ -1398,14 +1398,14 @@ static void add_index_record(StreamIndex *index,
 		char **new_keys;
 		long int *new_ptrs;
 
-		new_keys = realloc(index->keys,
-		                   new_max_keys*sizeof(char *));
+		new_keys = cfrealloc(index->keys,
+		                     new_max_keys*sizeof(char *));
 		if ( new_keys == NULL ) return;
 
-		new_ptrs = realloc(index->ptrs,
-		                   new_max_keys*sizeof(long int));
+		new_ptrs = cfrealloc(index->ptrs,
+		                     new_max_keys*sizeof(long int));
 		if ( new_ptrs == NULL ) {
-			free(new_keys);
+			cffree(new_keys);
 			return;
 		}
 
@@ -1436,7 +1436,7 @@ StreamIndex *stream_make_index(const char *filename)
 	fh = fopen(filename, "r");
 	if ( fh == NULL ) return NULL;
 
-	index = malloc(sizeof(StreamIndex));
+	index = cfmalloc(sizeof(StreamIndex));
 	if ( index == NULL ) {
 		fclose(fh);
 		return NULL;
@@ -1467,11 +1467,11 @@ StreamIndex *stream_make_index(const char *filename)
 		}
 
 		if ( strncmp(line, "Image filename: ", 16) == 0 ) {
-			last_filename = strdup(line+16);
+			last_filename = cfstrdup(line+16);
 		}
 
 		if ( strncmp(line, "Event: ", 7) == 0 ) {
-			last_ev = strdup(line+7);
+			last_ev = cfstrdup(line+7);
 		}
 
 		if ( strcmp(line, STREAM_CHUNK_END_MARKER) == 0 ) {
@@ -1483,8 +1483,8 @@ StreamIndex *stream_make_index(const char *filename)
 				                 last_filename,
 				                 last_ev);
 			}
-			free(last_filename);
-			free(last_ev);
+			cffree(last_filename);
+			cffree(last_ev);
 			last_start_pos = 0;
 			last_filename = NULL;
 			last_ev = NULL;