Fix lots of memory leaks

src/hdf5-file.c

@@ -47,6 +47,7 @@ struct hdfile *hdfile_open(const char *filename)
 	f = malloc(sizeof(struct hdfile));
 	if ( f == NULL ) return NULL;
 	f->image = NULL;
+	f->image_dirty = 1;
 
 	f->fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
 	if ( f->fh < 0 ) {
@@ -55,8 +56,6 @@ struct hdfile *hdfile_open(const char *filename)
 		return NULL;
 	}
 
-	f->image_dirty = 1;
-
 	return f;
 }
 
@@ -104,7 +103,13 @@ int hdfile_get_height(struct hdfile *f)
 void hdfile_close(struct hdfile *f)
 {
 	H5Fclose(f->fh);
-	free(f->image);
+	if ( f->image != NULL ) {
+		if ( f->image->features != NULL ) {
+			image_feature_list_free(f->image->features);
+		}
+		free(f->image->data);
+		free(f->image);
+	}
 	free(f);
 }
 
@@ -160,6 +165,7 @@ int16_t *hdfile_get_image_binned(struct hdfile *f, int binning, int16_t *max)
 		image = malloc(sizeof(struct image));
 		if ( image == NULL ) return NULL;
 		image->features = NULL;
+		image->data = NULL;
 
 		hdf5_read(f, image);
 
@@ -167,7 +173,7 @@ int16_t *hdfile_get_image_binned(struct hdfile *f, int binning, int16_t *max)
 		if ( f->image != NULL ) {
 			image->features = f->image->features;
 			if ( f->image->data != NULL ) free(f->image->data);
-			free(f->image);
+			free(f->image->data);
 		}
 
 		f->image = image;
@@ -490,7 +496,7 @@ int hdfile_set_first_image(struct hdfile *f, const char *group)
 	char **names;
 	int *is_group;
 	int *is_image;
-	int n, i;
+	int n, i, j;
 
 	names = hdfile_read_group(f, &n, group, &is_group, &is_image);
 	if ( n == 0 ) return 1;
@@ -498,15 +504,30 @@ int hdfile_set_first_image(struct hdfile *f, const char *group)
 	for ( i=0; i<n; i++ ) {
 
 		if ( is_image[i] ) {
+			int j;
 			hdfile_set_image(f, names[i]);
+			for ( j=0; j<n; j++ ) free(names[j]);
+			free(is_image);
+			free(is_group);
+			free(names);
 			return 0;
 		} else if ( is_group[i] ) {
 			if ( !hdfile_set_first_image(f, names[i]) ) {
+				int j;
+				for ( j=0; j<n; j++ ) free(names[j]);
+				free(is_image);
+				free(is_group);
+				free(names);
 				return 0;
 			}
 		}
 
 	}
 
+	for ( j=0; j<n; j++ ) free(names[j]);
+	free(is_image);
+	free(is_group);
+	free(names);
+
 	return 1;
 }

src/indexamajig.c

@@ -20,6 +20,7 @@
 #include <string.h>
 #include <unistd.h>
 #include <getopt.h>
+#include <hdf5.h>
 
 #include "utils.h"
 #include "hdf5-file.h"
@@ -124,6 +125,7 @@ int main(int argc, char *argv[])
 
 		image.features = NULL;
 		image.molecule = NULL;
+		image.data = NULL;
 
 		STATUS("Processing '%s'\n", line);
 
@@ -162,6 +164,9 @@ int main(int argc, char *argv[])
 
 		}
 
+		free(image.data);
+		hdfile_close(hdfile);
+
 	} while ( rval != NULL );
 
 	fclose(fh);