Fix memory leaks and other memory problems

git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@197 bf6ca9ba-c028-0410-8290-897cf20841d1

8 files changed, 29 insertions, 19 deletions

diff --git a/src/cache.c b/src/cache.c
index 8f05e05..f7e6b7f 100644
--- a/src/cache.c
+++ b/src/cache.c
@@ -129,6 +129,7 @@ int cache_load(ImageList *images, const char *filename) {
 	if ( fread(index, index_size, 1, fh) != 1 ) {
 		fprintf(stderr, "Couldn't read index.\n");
 		fclose(fh);
+		free(index);
 		return -1;
 	}
 	
@@ -179,6 +180,7 @@ int cache_load(ImageList *images, const char *filename) {
 	}
 	
 	fclose(fh);
+	free(index);
 	
 	return 0;
 }
diff --git a/src/displaywindow.c b/src/displaywindow.c
index 324b921..0eed64c 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -874,6 +874,7 @@ static void displaywindow_gl_free_resources(DisplayWindow *dw) {
 
 	if ( dw->gl_use_buffers ) {
 		glDeleteBuffersARB(1, &dw->gl_ref_vertex_buffer);
+		glDeleteBuffersARB(1, &dw->gl_ref_normal_buffer);
 		glDeleteBuffersARB(1, &dw->gl_marker_vertex_buffer);
 		glDeleteBuffersARB(1, &dw->gl_marker_normal_buffer);
 		glDeleteBuffersARB(1, &dw->gl_gen_vertex_buffer);
diff --git a/src/gtk-valuegraph.c b/src/gtk-valuegraph.c
index 555cec9..e0bc112 100644
--- a/src/gtk-valuegraph.c
+++ b/src/gtk-valuegraph.c
@@ -179,6 +179,8 @@ static gint gtk_value_graph_draw(GtkWidget *graph, GdkEventExpose *event, gpoint
 	cairo_set_source_rgb(cr, 0.0, 0.0, 1.0);
 	cairo_stroke(cr);
 	
+	cairo_destroy(cr);
+	
 	return 0;
 
 }
diff --git a/src/imagedisplay.c b/src/imagedisplay.c
index 8714722..8e1858e 100644
--- a/src/imagedisplay.c
+++ b/src/imagedisplay.c
@@ -147,6 +147,10 @@ static void imagedisplay_destroyed(GtkWidget *widget, ImageDisplay *imagedisplay
 	g_object_unref(G_OBJECT(imagedisplay->gc_tiltaxis));
 	g_object_unref(G_OBJECT(imagedisplay->gc_marks_1));
 	g_object_unref(G_OBJECT(imagedisplay->gc_marks_2));
+	
+	if ( imagedisplay->flags & IMAGEDISPLAY_FREE ) {
+		free(imagedisplay->imagerecord.image);
+	}
 
 	free(imagedisplay);
 	
diff --git a/src/imagedisplay.h b/src/imagedisplay.h
index d404bcb..7b16dc2 100644
--- a/src/imagedisplay.h
+++ b/src/imagedisplay.h
@@ -25,7 +25,8 @@ typedef enum {
 	IMAGEDISPLAY_NONE		= 0,
 	IMAGEDISPLAY_SHOW_CENTRE	= 1<<1,
 	IMAGEDISPLAY_SHOW_TILT_AXIS	= 1<<2,
-	IMAGEDISPLAY_QUIT_IF_CLOSED	= 1<<3
+	IMAGEDISPLAY_QUIT_IF_CLOSED	= 1<<3,
+	IMAGEDISPLAY_FREE		= 1<<4
 } ImageDisplayFlags;
 
 typedef enum {
diff --git a/src/mrc.h b/src/mrc.h
index 6414dfe..6a66142 100644
--- a/src/mrc.h
+++ b/src/mrc.h
@@ -45,27 +45,27 @@ typedef struct struct_mrcheader {
 	float		amin;
 	float		amax;
 	float		amean;
-	uint16_t		ispg;		/* Space group number */
-	uint16_t		nsymbt;
+	uint16_t	ispg;		/* Space group number */
+	uint16_t	nsymbt;
 	int32_t		next;
-	uint16_t		dvid;
+	uint16_t	dvid;
 	char		extra[30];
-	uint16_t		numintegers;
-	uint16_t		numfloats;
-	uint16_t		sub;
-	uint16_t		zfac;
+	uint16_t	numintegers;
+	uint16_t	numfloats;
+	uint16_t	sub;
+	uint16_t	zfac;
 	float		min2;
 	float		max2;
 	float		min3;	
 	float		max3;	
 	float		min4;	
 	float		max4;
-	uint16_t		idtype;
-	uint16_t		lens;
-	uint16_t		nd1;
-	uint16_t		nd2;
-	uint16_t		vd1;
-	uint16_t		vd2;
+	uint16_t	idtype;
+	uint16_t	lens;
+	uint16_t	nd1;
+	uint16_t	nd2;
+	uint16_t	vd1;
+	uint16_t	vd2;
 	float		tiltangles[9];
 	float		zorg;
 	float		xorg;
diff --git a/src/prealign.c b/src/prealign.c
index 09785d2..9aaa72b 100644
--- a/src/prealign.c
+++ b/src/prealign.c
@@ -173,7 +173,7 @@ void prealign_sum_stack(ImageList *list, int have_centres) {
 	total_record.image = image_total;
 	total_record.width = twidth;
 	total_record.height = theight;
-	sum_id = imagedisplay_open(total_record, "Sum of All Images", IMAGEDISPLAY_SHOW_CENTRE | IMAGEDISPLAY_SHOW_TILT_AXIS);
+	sum_id = imagedisplay_open(total_record, "Sum of All Images", IMAGEDISPLAY_SHOW_CENTRE | IMAGEDISPLAY_SHOW_TILT_AXIS | IMAGEDISPLAY_FREE);
 
 }
 
diff --git a/src/refine.c b/src/refine.c
index 85573b6..b68220b 100644
--- a/src/refine.c
+++ b/src/refine.c
@@ -346,11 +346,11 @@ static int refine_sequence_sweep(ControlContext *ctx, double *fit, double *warp)
 			series_dev_n++;
 			
 			image_feature_list_free(rflist);
-
+			
 		} else {
-
+			
 			/* Even-numbered images: fit */
-			refine_fit_image(ctx->cell, &ctx->images->images[ctx->reproject_cur_image], ctx->cell_lattice);
+			refine_fit_image(ctx->cell, &ctx->images->images[i], ctx->cell_lattice);
 			displaywindow_update(ctx->dw);
 
 		}
@@ -408,7 +408,7 @@ static gint refine_sequence(GtkWidget *step_button, ControlContext *ctx) {
 			ctx->images->images[i].omega -= omega_offs;
 		}
 		memcpy(ctx->cell, &cell_copy, sizeof(Basis));
-
+		
 	}
 	
 	window_fit = gtk_window_new(GTK_WINDOW_TOPLEVEL);