Merge branch 'master' into simple-search

Conflicts:

	src/refine.c

18 files changed, 621 insertions, 127 deletions

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..97650f2
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,9 @@
+Makefile
+Makefile.in
+aclocal.m4
+autom4te.cache
+config.h
+config.log
+config.status
+configure
+stamp-h1
diff --git a/Makefile.am b/Makefile.am
index 3bd800e..e59af98 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,7 +1,8 @@
-EXTRA_DIST = configure src/displaywindow.h src/trackball.h src/reflections.h src/control.h src/readpng.h src/mrc.h src/imagedisplay.h src/main.h \
-		data/displaywindow.ui src/utils.h src/itrans.h src/qdrp.h src/cache.h src/itrans-threshold.h src/basis.h \
-		src/itrans-zaefferer.h src/itrans-stat.h src/mapping.h src/reproject.h src/prealign.h \
-		src/dirax.h src/image.h src/refine.h src/gtk-valuegraph.h src/intensities.h src/glbits.h src/gtk-valuegraph.h
+EXTRA_DIST = configure src/displaywindow.h src/trackball.h src/reflections.h src/control.h src/readpng.h src/mrc.h \
+		src/imagedisplay.h src/main.h data/displaywindow.ui src/utils.h src/itrans.h src/qdrp.h src/cache.h \
+		src/itrans-threshold.h src/basis.h src/itrans-zaefferer.h src/itrans-stat.h src/mapping.h \
+		src/reproject.h src/prealign.h src/dirax.h src/image.h src/refine.h src/gtk-valuegraph.h \
+		src/intensities.h src/glbits.h src/gtk-valuegraph.h
 SUBDIRS = src data
-TESTS = src/refinetest2d src/refinetest3d
+TESTS = src/refinetest2d src/refinetest3d1 src/refinetest3d2 src/refinetest3d3
 
diff --git a/autogen.sh b/autogen.sh
new file mode 100755
index 0000000..bf85949
--- /dev/null
+++ b/autogen.sh
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+aclocal
+autoconf
+#libtoolize
+autoheader
+automake -a
+
diff --git a/src/.gitignore b/src/.gitignore
new file mode 100644
index 0000000..1fbde8f
--- /dev/null
+++ b/src/.gitignore
@@ -0,0 +1,7 @@
+*.o
+.deps
+refinetest2d
+refinetest3d1
+refinetest3d2
+refinetest3d3
+dtr
diff --git a/src/Makefile.am b/src/Makefile.am
index 117b738..d6e39c6 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,15 +1,21 @@
-bin_PROGRAMS = dtr refinetest2d refinetest3d
+bin_PROGRAMS = dtr refinetest2d refinetest3d1 refinetest3d2 refinetest3d3
 
-dtr_SOURCES = main.c displaywindow.c trackball.c reflections.c readpng.c mrc.c imagedisplay.c utils.c itrans.c qdrp.c cache.c \
-		itrans-threshold.c itrans-zaefferer.c itrans-stat.c control.c mapping.c reproject.c prealign.c basis.c \
-		dirax.c image.c refine.c gtk-valuegraph.c intensities.c glbits.c
+dtr_SOURCES = main.c displaywindow.c trackball.c reflections.c readpng.c mrc.c imagedisplay.c utils.c itrans.c qdrp.c \
+		cache.c itrans-threshold.c itrans-zaefferer.c itrans-stat.c control.c mapping.c reproject.c prealign.c \
+		basis.c dirax.c image.c refine.c gtk-valuegraph.c intensities.c glbits.c
 dtr_LDADD = @LIBS@ @GTK_LIBS@ -lm @GTKGLEXT_LIBS@ -lgsl -lgslcblas -lutil
 
 refinetest2d_SOURCES = refinetest2d.c reflections.c basis.c utils.c reproject.c image.c refine.c mapping.c control.c
 refinetest2d_LDADD = @LIBS@ @GTK_LIBS@ -lm -lgsl -lgslcblas -lutil
 
-refinetest3d_SOURCES = refinetest3d.c reflections.c basis.c utils.c reproject.c image.c refine.c mapping.c control.c
-refinetest3d_LDADD = @LIBS@ @GTK_LIBS@ -lm -lgsl -lgslcblas -lutil
+refinetest3d1_SOURCES = refinetest3d1.c reflections.c basis.c utils.c reproject.c image.c refine.c mapping.c control.c
+refinetest3d1_LDADD = @LIBS@ @GTK_LIBS@ -lm -lgsl -lgslcblas -lutil
+
+refinetest3d2_SOURCES = refinetest3d2.c reflections.c basis.c utils.c reproject.c image.c refine.c mapping.c control.c
+refinetest3d2_LDADD = @LIBS@ @GTK_LIBS@ -lm -lgsl -lgslcblas -lutil
+
+refinetest3d3_SOURCES = refinetest3d3.c reflections.c basis.c utils.c reproject.c image.c refine.c mapping.c control.c
+refinetest3d3_LDADD = @LIBS@ @GTK_LIBS@ -lm -lgsl -lgslcblas -lutil
 
 AM_CFLAGS = -Wall -g @CFLAGS@ @GTK_CFLAGS@ @GTKGLEXT_CFLAGS@
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I/usr/include/GL
diff --git a/src/control.h b/src/control.h
index 4b97970..5dcbc89 100644
--- a/src/control.h
+++ b/src/control.h
@@ -3,7 +3,7 @@
  *
  * Common control structure
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -76,7 +76,7 @@ typedef struct cctx_struct {
 	struct imagelist_struct		*images;
 	
 	/* "Output" */
-	struct reflectionlist_struct	*reflectionlist;	/* Measured reflections (and stuff added to get displayed with them) */
+	struct reflectionlist_struct	*reflectionlist;	/* Measured reflections */
 	struct dw_struct		*dw;
 	struct basis_struct		*cell;			/* Current estimate of the reciprocal unit cell */
 	struct reflectionlist_struct	*cell_lattice;		/* Reflections calculated from 'cell' */
diff --git a/src/displaywindow.c b/src/displaywindow.c
index a038c8c..fe97f73 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -130,15 +130,16 @@ static void displaywindow_about(GtkWidget *widget, DisplayWindow *dw) {
 	
 	gtk_about_dialog_set_name(GTK_ABOUT_DIALOG(window), PACKAGE_NAME);
 	gtk_about_dialog_set_version(GTK_ABOUT_DIALOG(window), PACKAGE_VERSION);
-	gtk_about_dialog_set_copyright(GTK_ABOUT_DIALOG(window), "(c) 2006-2007 Thomas White and contributors");
+	gtk_about_dialog_set_copyright(GTK_ABOUT_DIALOG(window), "(c) 2006-2008 Thomas White and contributors");
 	gtk_about_dialog_set_comments(GTK_ABOUT_DIALOG(window), "Diffraction Tomography Reconstruction");
-	gtk_about_dialog_set_license(GTK_ABOUT_DIALOG(window), "(c) 2006-2007 Thomas White <taw27@cam.ac.uk>\n"
-								"Virtual trackball (c) Copyright 1993, 1994, Silicon Graphics, Inc.\n"
-								"See Credits for a full list of contributors\n"
-								"\n"
-								"Research funded by:\n"
-								"FEI Electron Optics B.V.\n"
-								"The Engineering and Physical Sciences Research Council");
+	gtk_about_dialog_set_license(GTK_ABOUT_DIALOG(window),
+						"(c) 2006-2008 Thomas White <taw27@cam.ac.uk>\n"
+						"Virtual trackball (c) Copyright 1993, 1994, Silicon Graphics, Inc.\n"
+						"See Credits for a full list of contributors\n"
+						"\n"
+						"Research funded by:\n"
+						"FEI Electron Optics B.V.\n"
+						"The Engineering and Physical Sciences Research Council");
 	gtk_about_dialog_set_website(GTK_ABOUT_DIALOG(window), "http://www-hrem.msm.cam.ac.uk/");
 	gtk_about_dialog_set_authors(GTK_ABOUT_DIALOG(window), authors);
 	
@@ -223,7 +224,8 @@ static gint displaywindow_savecache(GtkWidget *widget, DisplayWindow *dw) {
 					GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
 					GTK_STOCK_SAVE, GTK_RESPONSE_ACCEPT,
 					NULL);
-	g_signal_connect(G_OBJECT(dw->savecache_window), "response", G_CALLBACK(displaywindow_savecache_response), dw->ctx);
+	g_signal_connect(G_OBJECT(dw->savecache_window), "response", G_CALLBACK(displaywindow_savecache_response),
+				dw->ctx);
 	gtk_widget_show_all(dw->savecache_window);
 
 	return 0;
@@ -272,7 +274,8 @@ static gint displaywindow_setaxis(GtkWidget *widget, DisplayWindow *dw) {
 	GtkWidget *label;
 	
 	dw->tiltaxis_window = gtk_dialog_new_with_buttons("Set Tilt Axis Position", GTK_WINDOW(dw->window),
-		GTK_DIALOG_DESTROY_WITH_PARENT,	GTK_STOCK_CANCEL, GTK_RESPONSE_CLOSE, GTK_STOCK_OK, GTK_RESPONSE_OK, NULL);
+		GTK_DIALOG_DESTROY_WITH_PARENT,	GTK_STOCK_CANCEL, GTK_RESPONSE_CLOSE, GTK_STOCK_OK, GTK_RESPONSE_OK,
+		NULL);
 	
 	vbox = gtk_vbox_new(FALSE, 0);
 	hbox = gtk_hbox_new(TRUE, 0);
@@ -378,37 +381,45 @@ static void displaywindow_addmenubar(DisplayWindow *dw) {
 
 	GtkActionEntry entries[] = {
 
-		{ "FileAction", NULL, "_File", NULL, NULL, NULL },
-		{ "SaveCacheAction", "filesave", "Save Image Analysis to _Cache", NULL, NULL, G_CALLBACK(displaywindow_savecache) },
-		{ "SaveHKLAction", GTK_STOCK_SAVE, "Save Reflections", NULL, NULL, G_CALLBACK(displaywindow_savehkl) },
-		{ "CloseAction", GTK_STOCK_QUIT, "_Quit", NULL, NULL, G_CALLBACK(displaywindow_close) },
-		
-		{ "ViewAction", NULL, "_View", NULL, NULL, NULL },
-		
-		{ "ToolsAction", NULL, "_Tools", NULL, NULL, NULL },
-		{ "DirAxAction", "dtr-dirax", "Start _DirAx", "<Ctrl>D", NULL, G_CALLBACK(displaywindow_dirax) },
-		{ "DirAxReRunAction", NULL, "Run another DirAx cycle", NULL, NULL, G_CALLBACK(displaywindow_dirax_rerun) },
-		{ "StopDirAxAction", NULL, "Stop DirAx", NULL, NULL, G_CALLBACK(displaywindow_dirax_stop) },
-		{ "RefineStepAction", "dtr-refine", "Refine Unit Cell", NULL, NULL, G_CALLBACK(displaywindow_refinestep) },
-		{ "RefineSeqAction", "dtr-refineall", "Run Refinement Sequence", NULL, NULL, G_CALLBACK(displaywindow_refinestack) },
-		{ "SetAxisAction", "dtr-tiltaxis", "Set Tilt Axis Position...", NULL, NULL, G_CALLBACK(displaywindow_setaxis) },
-		{ "IncrAxisAction", NULL, "Increase Tilt Axis Position", "<Ctrl>Up", NULL, G_CALLBACK(displaywindow_incraxis) },
-		{ "DecrAxisAction", NULL, "Decrease Tilt Axis Position", "<Ctrl>Down", NULL, G_CALLBACK(displaywindow_decraxis) },
-		{ "ExtractIntensitiesAction", "dtr-quantify", "Quantify Reflection Intensities", NULL, NULL, G_CALLBACK(displaywindow_extract) },
-		
-		{ "HelpAction", NULL, "_Help", NULL, NULL, NULL },
-		{ "AboutAction", GTK_STOCK_ABOUT, "_About DTR...", NULL, NULL, G_CALLBACK(displaywindow_about) },
-		
-		{ "ButtonDirAxAction", "dtr-dirax", "Run _DirAx", NULL, NULL, G_CALLBACK(displaywindow_dirax) },
-		{ "ButtonTiltAxisAction", "dtr-tiltaxis", "Tilt Axis", NULL, NULL, G_CALLBACK(displaywindow_setaxis) },
-		{ "ButtonRefineStepAction", "dtr-refine", "Refine", NULL, NULL, G_CALLBACK(displaywindow_refinestep) },
-		{ "ButtonRefineSeqAction", "dtr-refineall", "Sequence", NULL, NULL, G_CALLBACK(displaywindow_refinestack) },
-		{ "ButtonFirstImageAction", GTK_STOCK_GOTO_FIRST, "First Image", NULL, NULL, G_CALLBACK(displaywindow_image_first) },
-		{ "ButtonPrevImageAction", GTK_STOCK_GO_BACK, "Previous Image", NULL, NULL, G_CALLBACK(displaywindow_image_prev) },
-		{ "ButtonNextImageAction", GTK_STOCK_GO_FORWARD, "Next Image", NULL, NULL, G_CALLBACK(displaywindow_image_next) },
-		{ "ButtonLastImageAction", GTK_STOCK_GOTO_LAST, "Last Image", NULL, NULL, G_CALLBACK(displaywindow_image_last) },
-		{ "ButtonExtractIntensitiesAction", "dtr-quantify", "Quantify", NULL, NULL, G_CALLBACK(displaywindow_extract) },
-		
+	{ "FileAction", NULL, "_File", NULL, NULL, NULL },
+	{ "SaveCacheAction", "filesave", "Save Image Analysis to _Cache",
+			NULL, NULL, G_CALLBACK(displaywindow_savecache) },
+	{ "SaveHKLAction", GTK_STOCK_SAVE, "Save Reflections", NULL, NULL, G_CALLBACK(displaywindow_savehkl) },
+	{ "CloseAction", GTK_STOCK_QUIT, "_Quit", NULL, NULL, G_CALLBACK(displaywindow_close) },
+	
+	{ "ViewAction", NULL, "_View", NULL, NULL, NULL },
+	
+	{ "ToolsAction", NULL, "_Tools", NULL, NULL, NULL },
+	{ "DirAxAction", "dtr-dirax", "Start _DirAx", "<Ctrl>D", NULL, G_CALLBACK(displaywindow_dirax) },
+	{ "DirAxReRunAction", NULL, "Run another DirAx cycle", NULL, NULL, G_CALLBACK(displaywindow_dirax_rerun) },
+	{ "StopDirAxAction", NULL, "Stop DirAx", NULL, NULL, G_CALLBACK(displaywindow_dirax_stop) },
+	{ "RefineStepAction", "dtr-refine", "Refine Unit Cell", NULL, NULL, G_CALLBACK(displaywindow_refinestep) },
+	{ "RefineSeqAction", "dtr-refineall", "Run Refinement Sequence",
+			NULL, NULL, G_CALLBACK(displaywindow_refinestack) },
+	{ "SetAxisAction", "dtr-tiltaxis", "Set Tilt Axis Position...", NULL, NULL, G_CALLBACK(displaywindow_setaxis) },
+	{ "IncrAxisAction", NULL, "Increase Tilt Axis Position", "<Ctrl>Up", NULL, G_CALLBACK(displaywindow_incraxis) },
+	{ "DecrAxisAction", NULL, "Decrease Tilt Axis Position",
+			"<Ctrl>Down", NULL, G_CALLBACK(displaywindow_decraxis) },
+	{ "ExtractIntensitiesAction", "dtr-quantify", "Quantify Reflection Intensities",
+			NULL, NULL, G_CALLBACK(displaywindow_extract) },
+	
+	{ "HelpAction", NULL, "_Help", NULL, NULL, NULL },
+	{ "AboutAction", GTK_STOCK_ABOUT, "_About DTR...", NULL, NULL, G_CALLBACK(displaywindow_about) },
+	
+	{ "ButtonDirAxAction", "dtr-dirax", "Run _DirAx", NULL, NULL, G_CALLBACK(displaywindow_dirax) },
+	{ "ButtonTiltAxisAction", "dtr-tiltaxis", "Tilt Axis", NULL, NULL, G_CALLBACK(displaywindow_setaxis) },
+	{ "ButtonRefineStepAction", "dtr-refine", "Refine", NULL, NULL, G_CALLBACK(displaywindow_refinestep) },
+	{ "ButtonRefineSeqAction", "dtr-refineall", "Sequence", NULL, NULL, G_CALLBACK(displaywindow_refinestack) },
+	{ "ButtonFirstImageAction", GTK_STOCK_GOTO_FIRST, "First Image",
+			NULL, NULL, G_CALLBACK(displaywindow_image_first) },
+	{ "ButtonPrevImageAction", GTK_STOCK_GO_BACK, "Previous Image",
+			NULL, NULL, G_CALLBACK(displaywindow_image_prev) },
+	{ "ButtonNextImageAction", GTK_STOCK_GO_FORWARD, "Next Image",
+			NULL, NULL, G_CALLBACK(displaywindow_image_next) },
+	{ "ButtonLastImageAction", GTK_STOCK_GOTO_LAST, "Last Image",
+			NULL, NULL, G_CALLBACK(displaywindow_image_last) },
+	{ "ButtonExtractIntensitiesAction", "dtr-quantify", "Quantify", NULL, NULL, G_CALLBACK(displaywindow_extract) },
+	
 	};
 	guint n_entries = G_N_ELEMENTS(entries);
 	
@@ -425,9 +436,12 @@ static void displaywindow_addmenubar(DisplayWindow *dw) {
 	guint n_radios2 = G_N_ELEMENTS(radios2);
 	
 	GtkToggleActionEntry toggles[] = {
-		{ "CubeAction", NULL, "Show 100 nm^-1 _Cube", NULL, NULL, G_CALLBACK(displaywindow_changecube), dw->cube },
-		{ "LinesAction", NULL, "Show Indexing Lines", NULL, NULL, G_CALLBACK(displaywindow_changelines), dw->lines },
-		{ "BackgroundAction", NULL, "Show Coloured Background", NULL, NULL, G_CALLBACK(displaywindow_changebackground), dw->background },
+		{ "CubeAction", NULL, "Show 100 nm^-1 _Cube",
+			NULL, NULL, G_CALLBACK(displaywindow_changecube), dw->cube },
+		{ "LinesAction", NULL, "Show Indexing Lines",
+			NULL, NULL, G_CALLBACK(displaywindow_changelines), dw->lines },
+		{ "BackgroundAction", NULL, "Show Coloured Background",
+			NULL, NULL, G_CALLBACK(displaywindow_changebackground), dw->background },
 	};
 	guint n_toggles = G_N_ELEMENTS(toggles);
 
@@ -435,8 +449,10 @@ static void displaywindow_addmenubar(DisplayWindow *dw) {
 
 	dw->action_group = gtk_action_group_new("dtrdisplaywindow");
 	gtk_action_group_add_actions(dw->action_group, entries, n_entries, dw);
-	gtk_action_group_add_radio_actions(dw->action_group, radios, n_radios, -1, G_CALLBACK(displaywindow_changeview), dw);
-	gtk_action_group_add_radio_actions(dw->action_group, radios2, n_radios2, -1, G_CALLBACK(displaywindow_changemode), dw);
+	gtk_action_group_add_radio_actions(dw->action_group, radios, n_radios,
+						-1, G_CALLBACK(displaywindow_changeview), dw);
+	gtk_action_group_add_radio_actions(dw->action_group, radios2, n_radios2,
+						-1, G_CALLBACK(displaywindow_changemode), dw);
 	gtk_action_group_add_toggle_actions(dw->action_group, toggles, n_toggles, dw);
 	
 	dw->ui = gtk_ui_manager_new();
@@ -497,9 +513,10 @@ void displaywindow_update_imagestack(DisplayWindow *dw) {
 		/* Now connect partners */
 		for ( j=0; j<image->rflist->n_features; j++ ) {
 			if ( image->rflist->features[j].partner ) {
-				imagedisplay_add_line(dw->stack, image->rflist->features[j].x, image->rflist->features[j].y,
-								 image->rflist->features[j].partner->x, image->rflist->features[j].partner->y,
-								 IMAGEDISPLAY_MARK_LINE_1);
+				imagedisplay_add_line(dw->stack,
+					image->rflist->features[j].x, image->rflist->features[j].y,
+					image->rflist->features[j].partner->x, image->rflist->features[j].partner->y,
+					IMAGEDISPLAY_MARK_LINE_1);
 			}
 		}
 	}
@@ -535,6 +552,15 @@ void displaywindow_update_imagestack(DisplayWindow *dw) {
 	
 }
 
+static void displaywindow_switch_page(GtkNotebook *notebook, GtkNotebookPage *page, guint page_num, DisplayWindow *dw) {
+	if ( dw->realised && (page_num == 0) ) {
+		int i;
+		for ( i=0; i<2; i++ ) {
+			glbits_expose(dw->drawing_area, NULL, dw);
+		}
+	}
+}
+
 DisplayWindow *displaywindow_open(ControlContext *ctx) {
 
 	const char *filename;
@@ -569,6 +595,7 @@ DisplayWindow *displaywindow_open(ControlContext *ctx) {
 	dw->lines = FALSE;
 	dw->background = TRUE;
 	dw->cur_image = 0;
+	dw->realised = 0;
 	
 	dw->window = gtk_window_new(GTK_WINDOW_TOPLEVEL);
 	gtk_window_set_title(GTK_WINDOW(dw->window), title);
@@ -577,10 +604,6 @@ DisplayWindow *displaywindow_open(ControlContext *ctx) {
 	gtk_container_add(GTK_CONTAINER(dw->window), dw->bigvbox);
 	displaywindow_addmenubar(dw);
 	
-	dw->status_bar = gtk_statusbar_new();
-	gtk_statusbar_set_has_resize_grip(GTK_STATUSBAR(dw->status_bar), FALSE);
-	gtk_box_pack_end(GTK_BOX(dw->bigvbox), dw->status_bar, FALSE, FALSE, 0);
-	
 	g_signal_connect(GTK_OBJECT(dw->window), "destroy", G_CALLBACK(displaywindow_closedown), dw);
 	
 	notebook = gtk_notebook_new();
@@ -598,12 +621,15 @@ DisplayWindow *displaywindow_open(ControlContext *ctx) {
 	gtk_widget_set_size_request(dw->drawing_area, 640, 640);
 	gtk_widget_set_gl_capability(dw->drawing_area, glconfig, NULL, TRUE, GDK_GL_RGBA_TYPE);
 	gtk_notebook_append_page(GTK_NOTEBOOK(notebook), dw->drawing_area, gtk_label_new("Reconstruction"));
-	gtk_widget_add_events(dw->drawing_area, GDK_BUTTON1_MOTION_MASK | GDK_BUTTON_PRESS_MASK | GDK_VISIBILITY_NOTIFY_MASK);
+	gtk_widget_add_events(dw->drawing_area,
+				GDK_BUTTON1_MOTION_MASK | GDK_BUTTON_PRESS_MASK | GDK_VISIBILITY_NOTIFY_MASK);
 	g_signal_connect(GTK_OBJECT(dw->drawing_area), "configure_event", G_CALLBACK(glbits_configure), dw);
 	g_signal_connect(GTK_OBJECT(dw->drawing_area), "realize", G_CALLBACK(glbits_realise), dw);
 	g_signal_connect(GTK_OBJECT(dw->drawing_area), "expose_event", G_CALLBACK(glbits_expose), dw);
-	g_signal_connect(GTK_OBJECT(dw->drawing_area), "button_press_event", G_CALLBACK(displaywindow_gl_button_press), dw);
-	g_signal_connect(GTK_OBJECT(dw->drawing_area), "motion_notify_event", G_CALLBACK(displaywindow_gl_motion_notify), dw);
+	g_signal_connect(GTK_OBJECT(dw->drawing_area), "button_press_event",
+				G_CALLBACK(displaywindow_gl_button_press), dw);
+	g_signal_connect(GTK_OBJECT(dw->drawing_area), "motion_notify_event",
+				G_CALLBACK(displaywindow_gl_motion_notify), dw);
 	g_signal_connect(GTK_OBJECT(dw->drawing_area), "destroy", G_CALLBACK(displaywindow_gl_destroyed), dw);
 	
 	if ( ctx->images->n_images > 0 ) {
@@ -612,9 +638,12 @@ DisplayWindow *displaywindow_open(ControlContext *ctx) {
 		gtk_notebook_append_page(GTK_NOTEBOOK(notebook), dw->stack->vbox, gtk_label_new("Image Stack"));
 		displaywindow_update_imagestack(dw);
 	} else {
-		gtk_notebook_append_page(GTK_NOTEBOOK(notebook), gtk_label_new("No Images to Display"), gtk_label_new("Image Stack"));
+		gtk_notebook_append_page(GTK_NOTEBOOK(notebook), gtk_label_new("No Images to Display"),
+						gtk_label_new("Image Stack"));
 	}
 	
+	g_signal_connect(GTK_OBJECT(notebook), "switch-page", G_CALLBACK(displaywindow_switch_page), dw);
+	
 	displaywindow_enable_cell_functions(dw, FALSE);
 	displaywindow_update_dirax(ctx, dw);
 	d = gtk_ui_manager_get_widget(dw->ui, "/ui/displaywindow/file/savehkl");
diff --git a/src/displaywindow.h b/src/displaywindow.h
index d0173f4..052e7d3 100644
--- a/src/displaywindow.h
+++ b/src/displaywindow.h
@@ -3,7 +3,7 @@
  *
  * The display window
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -39,7 +39,6 @@ typedef struct dw_struct {
 	GtkActionGroup		*action_group;
 	GtkWidget		*window;
 	GtkWidget		*bigvbox;
-	GtkWidget		*status_bar;
 	GtkWidget		*drawing_area;
 	GtkWidget		*savecache_window;
 	
@@ -68,6 +67,7 @@ typedef struct dw_struct {
 	GLuint			gl_vshader_lightpp;
 	GLuint			gl_fshader_lightpp;
 	GLuint			gl_program_lightpp;
+	int			realised;
 	
 	/* Display parameters */
 	DisplayWindowView	view;
diff --git a/src/glbits.c b/src/glbits.c
index d32fc0c..ba03adf 100644
--- a/src/glbits.c
+++ b/src/glbits.c
@@ -676,8 +676,8 @@ gint glbits_expose(GtkWidget *widget, GdkEventExpose *event, DisplayWindow *dw)
 		GLfloat w = dw->drawing_area->allocation.width;
 		GLfloat h = dw->drawing_area->allocation.height;
 		GLfloat aspect = w/h;
-		GLfloat bg_top[] = { 0.6, 0.9, 0.8, 1.0 };
-		GLfloat bg_bot[] = { 0.3, 0.7, 0.5, 1.0 };
+		GLfloat bg_top[] = { 0.0, 0.3, 1.0, 1.0 };
+		GLfloat bg_bot[] = { 0.0, 0.7, 1.0, 1.0 };
 		
 		glMatrixMode(GL_MODELVIEW);
 		glLoadIdentity();
@@ -934,6 +934,7 @@ gint glbits_realise(GtkWidget *widget, DisplayWindow *dw) {
 		
 	glbits_set_ortho(dw, w, h);
 	glbits_first_prepare(dw);
+	dw->realised = 1;
 	
 	gdk_gl_drawable_gl_end(gldrawable);
 
diff --git a/src/imagedisplay.c b/src/imagedisplay.c
index 00b7285..42026d2 100644
--- a/src/imagedisplay.c
+++ b/src/imagedisplay.c
@@ -3,7 +3,7 @@
  *
  * Show raw and processed images
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -23,6 +23,7 @@
 
 #include "imagedisplay.h"
 #include "utils.h"
+#include "mapping.h"
 
 /* Free pixbuf data when reference count drops to zero */
 static void imagedisplay_free_data(guchar *image_eightbit, ImageDisplay *imagedisplay) {
@@ -167,6 +168,33 @@ void imagedisplay_close(ImageDisplay *imagedisplay) {
 	}
 }
 
+static void imagedisplay_add_scalebar(ImageDisplay *imagedisplay, GtkWidget *drawingarea,
+							double scale, double xoffs, double yoffs) {
+
+	PangoLayout *layout;
+	double sb;
+	PangoRectangle rect;
+	int bwidth, bheight;
+	int view_height = imagedisplay->view_height;
+	
+	sb = mapping_scale_bar_length(&imagedisplay->imagerecord);
+	layout = gtk_widget_create_pango_layout(drawingarea, "1 nm^-1");
+	pango_layout_get_pixel_extents(layout, &rect, NULL);
+	
+	bwidth = (sb*scale)+20;
+	bheight = rect.height+30;
+	if ( rect.width > bwidth ) bwidth = rect.width+20;
+	gdk_draw_rectangle(drawingarea->window, drawingarea->style->bg_gc[GTK_WIDGET_STATE(drawingarea)], TRUE,
+				xoffs+20, yoffs+view_height-20-bheight,
+				bwidth, bheight);
+	gdk_draw_line(drawingarea->window, imagedisplay->gc_scalebar,
+				xoffs+30, yoffs+view_height-30,
+				xoffs+30+(scale*sb), yoffs+view_height-30);
+	gdk_draw_layout(drawingarea->window, drawingarea->style->fg_gc[GTK_WIDGET_STATE(drawingarea)],
+				xoffs+30, yoffs+view_height-20-bheight+10, layout);
+
+}
+
 #define imagedisplay_draw_line(gc,x1,y1,x2,y2) (gdk_draw_line(drawingarea->window,gc, \
 						xoffs+(x1), yoffs+imagedisplay->view_height-1-(y1), \
 						xoffs+(x2), yoffs+imagedisplay->view_height-1-(y2)))
@@ -181,7 +209,8 @@ static gboolean imagedisplay_redraw(GtkWidget *drawingarea, GdkEventExpose *even
 	yoffs = ((double)imagedisplay->drawingarea_height - imagedisplay->view_height) / 2;
 	scale = (double)imagedisplay->view_width/imagedisplay->imagerecord.width;
 	
-	gdk_draw_pixbuf(drawingarea->window, drawingarea->style->bg_gc[GTK_WIDGET_STATE(drawingarea)], imagedisplay->pixbuf_scaled,
+	gdk_draw_pixbuf(drawingarea->window, drawingarea->style->bg_gc[GTK_WIDGET_STATE(drawingarea)],
+			imagedisplay->pixbuf_scaled,
 			0, 0, xoffs, yoffs, imagedisplay->view_width, imagedisplay->view_height,
 			GDK_RGB_DITHER_NONE, 0, 0);
 	
@@ -201,6 +230,9 @@ static gboolean imagedisplay_redraw(GtkWidget *drawingarea, GdkEventExpose *even
 					* tan(imagedisplay->imagerecord.omega)) * scale);
 	}
 	
+	/* Add scale bar */
+	imagedisplay_add_scalebar(imagedisplay, drawingarea, scale, xoffs, yoffs);
+	
 	/* NB This calls the function above, which sorts out stuff */
 	if ( imagedisplay->flags & IMAGEDISPLAY_SHOW_CENTRE ) {
 		imagedisplay_draw_line(imagedisplay->gc_centre,
@@ -245,8 +277,9 @@ static gboolean imagedisplay_redraw(GtkWidget *drawingarea, GdkEventExpose *even
 			default : gc = imagedisplay->gc_marks_1; break;
 		}
 		
-		if ( (cur->type == IMAGEDISPLAY_MARK_CIRCLE_1) || (cur->type == IMAGEDISPLAY_MARK_CIRCLE_2)
-			 || (cur->type == IMAGEDISPLAY_MARK_CIRCLE_3) ) {
+		if ( (cur->type == IMAGEDISPLAY_MARK_CIRCLE_1)
+		  || (cur->type == IMAGEDISPLAY_MARK_CIRCLE_2)
+		  || (cur->type == IMAGEDISPLAY_MARK_CIRCLE_3) ) {
 		
 			double r;
 		
@@ -307,6 +340,11 @@ static gint imagedisplay_realize(GtkWidget *widget, ImageDisplay *imagedisplay)
 	gdk_color_parse("#00ddff", &colour);
 	gdk_gc_set_rgb_fg_color(imagedisplay->gc_marks_3, &colour);
 
+	imagedisplay->gc_scalebar = gdk_gc_new(imagedisplay->drawingarea->window);
+	gdk_color_parse("#000000", &colour);
+	gdk_gc_set_rgb_fg_color(imagedisplay->gc_scalebar, &colour);
+	gdk_gc_set_line_attributes(imagedisplay->gc_scalebar, 5, GDK_LINE_SOLID, GDK_CAP_BUTT, GDK_JOIN_MITER);
+
 	imagedisplay->realised = TRUE;
 
 	return 0;
@@ -351,10 +389,14 @@ ImageDisplay *imagedisplay_new_nowindow(ImageRecord imagerecord, ImageDisplayFla
 					G_CALLBACK(imagedisplay->mouse_click_func), callback_data);
 	}
 	
-	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "realize", G_CALLBACK(imagedisplay_realize), imagedisplay);
-	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "destroy", G_CALLBACK(imagedisplay_destroyed), imagedisplay);
-	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "configure_event", G_CALLBACK(imagedisplay_configure_event), imagedisplay);
-	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "expose-event", G_CALLBACK(imagedisplay_redraw), imagedisplay);
+	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "realize",
+				G_CALLBACK(imagedisplay_realize), imagedisplay);
+	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "destroy",
+				G_CALLBACK(imagedisplay_destroyed), imagedisplay);
+	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "configure_event",
+				G_CALLBACK(imagedisplay_configure_event), imagedisplay);
+	g_signal_connect(GTK_OBJECT(imagedisplay->drawingarea), "expose-event",
+				G_CALLBACK(imagedisplay_redraw), imagedisplay);
 	
 	return imagedisplay;
 
@@ -362,7 +404,8 @@ ImageDisplay *imagedisplay_new_nowindow(ImageRecord imagerecord, ImageDisplayFla
 
 /* Display an image */
 ImageDisplay *imagedisplay_open_with_message(ImageRecord imagerecord, const char *title, const char *message,
-						ImageDisplayFlags flags, GCallback mouse_click_func, gpointer callback_data) {
+						ImageDisplayFlags flags, GCallback mouse_click_func,
+						gpointer callback_data) {
 
 	ImageDisplay *imagedisplay;
 	GdkGeometry geom;
@@ -375,7 +418,8 @@ ImageDisplay *imagedisplay_open_with_message(ImageRecord imagerecord, const char
 	gtk_window_set_title(GTK_WINDOW(imagedisplay->window), imagedisplay->title);
 	
 	geom.min_width = 128;	geom.min_height = 128;
-	gtk_window_set_geometry_hints(GTK_WINDOW(imagedisplay->window), GTK_WIDGET(imagedisplay->drawingarea), &geom, GDK_HINT_MIN_SIZE);
+	gtk_window_set_geometry_hints(GTK_WINDOW(imagedisplay->window), GTK_WIDGET(imagedisplay->drawingarea),
+					&geom, GDK_HINT_MIN_SIZE);
 	
 	gtk_window_set_default_size(GTK_WINDOW(imagedisplay->window), 512, 512);
 	
@@ -411,7 +455,8 @@ void imagedisplay_add_mark(ImageDisplay *imagedisplay, double x, double y, Image
 
 }
 
-void imagedisplay_add_line(ImageDisplay *imagedisplay, double x1, double y1, double x2, double y2, ImageDisplayMarkType type) {
+void imagedisplay_add_line(ImageDisplay *imagedisplay, double x1, double y1,
+				double x2, double y2, ImageDisplayMarkType type) {
 
 	ImageDisplayMark *new;
 	
@@ -436,6 +481,7 @@ void imagedisplay_add_line(ImageDisplay *imagedisplay, double x1, double y1, dou
 
 void imagedisplay_force_redraw(ImageDisplay *imagedisplay) {
 	imagedisplay_rescale(imagedisplay, imagedisplay->drawingarea_width, imagedisplay->drawingarea_height);
-	gtk_widget_queue_draw_area(imagedisplay->drawingarea, 0, 0, imagedisplay->drawingarea_width, imagedisplay->drawingarea_height);
+	gtk_widget_queue_draw_area(imagedisplay->drawingarea, 0, 0, imagedisplay->drawingarea_width,
+								    imagedisplay->drawingarea_height);
 }
 
diff --git a/src/imagedisplay.h b/src/imagedisplay.h
index 325ea96..3462a83 100644
--- a/src/imagedisplay.h
+++ b/src/imagedisplay.h
@@ -3,7 +3,7 @@
  *
  * Show raw and processed images
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -70,6 +70,7 @@ typedef struct imagedisplay_struct {
 	GdkGC			*gc_marks_1;
 	GdkGC			*gc_marks_2;
 	GdkGC			*gc_marks_3;
+	GdkGC			*gc_scalebar;
 	gboolean		realised;
 	
 	unsigned int		drawingarea_width;
@@ -80,12 +81,20 @@ typedef struct imagedisplay_struct {
 } ImageDisplay;
 
 extern ImageDisplay *imagedisplay_open(ImageRecord image, const char *title, ImageDisplayFlags flags);
+
 extern ImageDisplay *imagedisplay_open_with_message(ImageRecord image, const char *title, const char *message,
-						ImageDisplayFlags flags, GCallback mouse_click_func, gpointer callback_data);
+						ImageDisplayFlags flags, GCallback mouse_click_func,
+						gpointer callback_data);
+
 extern ImageDisplay *imagedisplay_new_nowindow(ImageRecord imagerecord, ImageDisplayFlags flags, const char *message,
-					GCallback mouse_click_func, gpointer callback_data);
-extern void imagedisplay_add_mark(ImageDisplay *imagedisplay, double x, double y, ImageDisplayMarkType type, double weight);
-extern void imagedisplay_add_line(ImageDisplay *imagedisplay, double x1, double y1, double x2, double y2, ImageDisplayMarkType type);
+						GCallback mouse_click_func, gpointer callback_data);
+
+extern void imagedisplay_add_mark(ImageDisplay *imagedisplay, double x, double y, ImageDisplayMarkType type,
+						double weight);
+
+extern void imagedisplay_add_line(ImageDisplay *imagedisplay, double x1, double y1,
+						double x2, double y2, ImageDisplayMarkType type);
+
 extern void imagedisplay_force_redraw(ImageDisplay *imagedisplay);
 extern void imagedisplay_put_data(ImageDisplay *imagedisplay, ImageRecord imagerecord);
 extern void imagedisplay_close(ImageDisplay *imagedisplay);
diff --git a/src/mapping.c b/src/mapping.c
index c9872f9..4897450 100644
--- a/src/mapping.c
+++ b/src/mapping.c
@@ -3,7 +3,7 @@
  *
  * 3D Mapping
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -128,6 +128,20 @@ int mapping_scale(ImageFeature *refl, double *ddx, double *ddy) {
 	
 }
 
+/* Return the length of a 1 nm^-1 scale bar in the given image (in pixels)
+ *  Result only strictly valid at the centre of the image */
+double mapping_scale_bar_length(ImageRecord *image) {
+
+	switch ( image->fmode ) {
+		case FORMULATION_PIXELSIZE : return 1.0e9/image->pixel_size;
+		case FORMULATION_CLEN : return image->camera_len*image->lambda;
+		default : fprintf(stderr, "Unrecognised formulation mode in mapping_scale_bar_length.\n");
+	}
+	
+	return 0.0;
+
+}
+
 void mapping_map_features(ControlContext *ctx) {
 
 	int i;
@@ -146,7 +160,8 @@ void mapping_map_features(ControlContext *ctx) {
 		
 			double nx, ny, nz, twotheta;
 			
-			if ( !mapping_map_to_space(&ctx->images->images[i].features->features[j], &nx, &ny, &nz, &twotheta) ) {
+			if ( !mapping_map_to_space(&ctx->images->images[i].features->features[j],
+											&nx, &ny, &nz, &twotheta) ) {
 				reflection_add(ctx->reflectionlist, nx, ny, nz,
 					ctx->images->images[i].features->features[j].intensity, REFLECTION_NORMAL);
 			}
diff --git a/src/mapping.h b/src/mapping.h
index 8b23550..82d2f04 100644
--- a/src/mapping.h
+++ b/src/mapping.h
@@ -3,7 +3,7 @@
  *
  * 3D Mapping
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -18,10 +18,13 @@
 
 #include "reflections.h"
 #include "control.h"
+#include "image.h"
 
-extern void mapping_rotate(double x, double y, double z, double *ddx, double *ddy, double *ddz, double omega, double tilt);
+extern void mapping_rotate(double x, double y, double z, double *ddx, double *ddy, double *ddz,
+			   double omega, double tilt);
 extern int mapping_map_to_space(ImageFeature *refl, double *ddx, double *ddy, double *ddz, double *twotheta);
 extern int mapping_scale(ImageFeature *refl, double *ddx, double *ddy);
+extern double mapping_scale_bar_length(ImageRecord *image);
 
 extern void mapping_adjust_axis(ControlContext *ctx, double offset);
 extern void mapping_map_features(ControlContext *ctx);
diff --git a/src/refine.c b/src/refine.c
index 20fc431..5d1b59a 100644
--- a/src/refine.c
+++ b/src/refine.c
@@ -272,7 +272,8 @@ double refine_do_cell(ControlContext *ctx) {
 			rf->partner->x = old_x;
 			rf->partner->y = old_y;
 			#if REFINE_DEBUG
-			printf("=> %+10.5f %+10.5f nm^-1\n", dx/DISPFACTOR, dy/DISPFACTOR);
+			double mod = sqrt(dx*dx + dy*dy)/DISPFACTOR;
+			printf("=> %+10.5f %+10.5f nm^-1 (length %10.5f nm^1)\n", dx/DISPFACTOR, dy/DISPFACTOR, mod);
 			#endif /* REFINE_DEBUG */
 			
 			d[f].dx = dx;
diff --git a/src/refinetest2d.c b/src/refinetest2d.c
index cdc0c8d..1c30348 100644
--- a/src/refinetest2d.c
+++ b/src/refinetest2d.c
@@ -44,47 +44,47 @@ static int check_cell(Basis *cell, Basis *cell_real) {
 	
 	fail = 0;
 	if ( fabs(cell->a.x - cell_real->a.x) > 0.01e9 ) {
-		fprintf(stderr, "refinetest3d: ax not determined correctly (got %8f, should be %8f)\n",
+		fprintf(stderr, "refinetest2d: ax not determined correctly (got %8f, should be %8f)\n",
 										cell->a.x/1e9, cell_real->a.x/1e9);
 		fail = 1;
 	}
 	if ( fabs(cell->a.y - cell_real->a.y) > 0.01e9 ) {
-		fprintf(stderr, "refinetest3d: ay not determined correctly (got %8f, should be %8f)\n",
+		fprintf(stderr, "refinetest2d: ay not determined correctly (got %8f, should be %8f)\n",
 										cell->a.y/1e9, cell_real->a.y/1e9);
 		fail = 1;
 	}
 //	if ( fabs(cell->a.z - cell_real->a.z) > 0.01e9 ) {
-//		fprintf(stderr, "refinetest3d: az not determined correctly (got %8f, should be %8f)\n",
+//		fprintf(stderr, "refinetest2d: az not determined correctly (got %8f, should be %8f)\n",
 //										cell->a.z/1e9, cell_real->a.z/1e9);
 //		fail = 1;
 //	}
 	if ( fabs(cell->b.x - cell_real->b.x) > 0.01e9 ) {
-		fprintf(stderr, "refinetest3d: bx not determined correctly (got %8f, should be %8f)\n",
+		fprintf(stderr, "refinetest2d: bx not determined correctly (got %8f, should be %8f)\n",
 										cell->b.x/1e9, cell_real->b.x/1e9);
 		fail = 1;
 	}
 	if ( fabs(cell->b.y - cell_real->b.y) > 0.01e9 ) {
-		fprintf(stderr, "refinetest3d: by not determined correctly (got %8f, should be %8f)\n",
+		fprintf(stderr, "refinetest2d: by not determined correctly (got %8f, should be %8f)\n",
 										cell->b.y/1e9, cell_real->b.y/1e9);
 		fail = 1;
 	}
 //	if ( fabs(cell->b.z - cell_real->b.z) > 0.01e9 ) {
-//		fprintf(stderr, "refinetest3d: bz not determined correctly (got %8f, should be %8f)\n",
+//		fprintf(stderr, "refinetest2d: bz not determined correctly (got %8f, should be %8f)\n",
 //										cell->b.z/1e9, cell_real->b.z/1e9);
 //		fail = 1;
 //	}
 //	if ( fabs(cell->c.x - cell_real->c.x) > 0.01e9 ) {
-//		fprintf(stderr, "refinetest3d: cx not determined correctly (got %8f, should be %8f)\n",
+//		fprintf(stderr, "refinetest2d: cx not determined correctly (got %8f, should be %8f)\n",
 //										cell->c.x/1e9, cell_real->c.x/1e9);
 //		fail = 1;
 //	}
 //	if ( fabs(cell->c.y - cell_real->c.y) > 0.01e9 ) {
-//		fprintf(stderr, "refinetest3d: cy not determined correctly (got %8f, should be %8f)\n",
+//		fprintf(stderr, "refinetest2d: cy not determined correctly (got %8f, should be %8f)\n",
 //										cell->c.y/1e9, cell_real->c.y/1e9);
 //		fail = 1;
 //	}
 //	if ( fabs(cell->c.z - cell_real->c.z) > 0.01e9 ) {
-//		fprintf(stderr, "refinetest3d: cz not determined correctly (got %8f, should be %8f)\n",
+//		fprintf(stderr, "refinetest2d: cz not determined correctly (got %8f, should be %8f)\n",
 //										cell->c.z/1e9, cell_real->c.z/1e9);
 //		fail = 1;
 //	}
diff --git a/src/refinetest3d.c b/src/refinetest3d1.c
index cbe8be2..cd8cc84 100644
--- a/src/refinetest3d.c
+++ b/src/refinetest3d1.c
@@ -1,5 +1,5 @@
 /*
- * refinetest3d.c
+ * refinetest3d1.c
  *
  * Unit test for refinement procedure in 3D
  *
@@ -27,13 +27,6 @@
 #include "displaywindow.h"
 #include "mrc.h"
 
-/* Return a random number x, -max < x < +max */
-static double random_plusminus(double max) {
-
-	return max;
-
-}
-
 static int check_cell(Basis *cell, Basis *cell_real) {
 	
 	int fail;
@@ -86,13 +79,6 @@ static int check_cell(Basis *cell, Basis *cell_real) {
 	} else {
 		printf("by is OK.\n");
 	}
-	if ( fabs(cell->b.z - cell_real->b.z) > 0.01e9 ) {
-		fprintf(stderr, "refinetest3d: bz not determined correctly (got %8f, should be %8f)\n",
-										cell->b.z/1e9, cell_real->b.z/1e9);
-		fail = 1;
-	} else {
-		printf("bz is OK.\n");
-	}
 	if ( fabs(cell->c.x - cell_real->c.x) > 0.01e9 ) {
 		fprintf(stderr, "refinetest3d: cx not determined correctly (got %8f, should be %8f)\n",
 										cell->c.x/1e9, cell_real->c.x/1e9);
@@ -100,13 +86,6 @@ static int check_cell(Basis *cell, Basis *cell_real) {
 	} else {
 		printf("cx is OK.\n");
 	}
-	if ( fabs(cell->c.y - cell_real->c.y) > 0.01e9 ) {
-		fprintf(stderr, "refinetest3d: cy not determined correctly (got %8f, should be %8f)\n",
-										cell->c.y/1e9, cell_real->c.y/1e9);
-		fail = 1;
-	} else {
-		printf("cy is OK.\n");
-	}
 	if ( fabs(cell->c.z - cell_real->c.z) > 0.01e9 ) {
 		fprintf(stderr, "refinetest3d: cz not determined correctly (got %8f, should be %8f)\n",
 										cell->c.z/1e9, cell_real->c.z/1e9);
@@ -115,6 +94,8 @@ static int check_cell(Basis *cell, Basis *cell_real) {
 		printf("cz is OK.\n");
 	}
 	
+	printf("bz and cy not checked in this test.\n");
+	
 	return fail;
 
 }	
diff --git a/src/refinetest3d2.c b/src/refinetest3d2.c
new file mode 100644
index 0000000..38ea72e
--- /dev/null
+++ b/src/refinetest3d2.c
@@ -0,0 +1,191 @@
+/*
+ * refinetest3d2.c
+ *
+ * Unit test for refinement procedure in 3D
+ *
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
+ *
+ *  dtr - Diffraction Tomography Reconstruction
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <math.h>
+
+#include "basis.h"
+#include "reflections.h"
+#include "image.h"
+#include "reproject.h"
+#include "refine.h"
+#include "utils.h"
+#include "mapping.h"
+#include "control.h"
+#include "displaywindow.h"
+#include "mrc.h"
+
+static int check_cell(Basis *cell, Basis *cell_real) {
+	
+	int fail;
+	
+	printf("     Refinement    Actual\n");
+	printf("---------------------------\n");
+	printf("ax  %+8f     %+8f\n", cell->a.x/1e9, cell_real->a.x/1e9);
+	printf("ay  %+8f     %+8f\n", cell->a.y/1e9, cell_real->a.y/1e9);
+	printf("az  %+8f     %+8f\n", cell->a.z/1e9, cell_real->a.z/1e9);
+	printf("bx  %+8f     %+8f\n", cell->b.x/1e9, cell_real->b.x/1e9);
+	printf("by  %+8f     %+8f\n", cell->b.y/1e9, cell_real->b.y/1e9);
+	printf("bz  %+8f     %+8f\n", cell->b.z/1e9, cell_real->b.z/1e9);
+	printf("cx  %+8f     %+8f\n", cell->c.x/1e9, cell_real->c.x/1e9);
+	printf("cy  %+8f     %+8f\n", cell->c.y/1e9, cell_real->c.y/1e9);
+	printf("cz  %+8f     %+8f\n", cell->c.z/1e9, cell_real->c.z/1e9);
+	
+	fail = 0;
+	if ( fabs(cell->a.x - cell_real->a.x) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: ax not determined correctly (got %8f, should be %8f)\n",
+										cell->a.x/1e9, cell_real->a.x/1e9);
+		fail = 1;
+	} else {
+		printf("ax is OK.\n");
+	}
+	if ( fabs(cell->a.y - cell_real->a.y) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: ay not determined correctly (got %8f, should be %8f)\n",
+										cell->a.y/1e9, cell_real->a.y/1e9);
+		fail = 1;
+	} else {
+		printf("ay is OK.\n");
+	}
+	if ( fabs(cell->a.z - cell_real->a.z) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: az not determined correctly (got %8f, should be %8f)\n",
+										cell->a.z/1e9, cell_real->a.z/1e9);
+		fail = 1;
+	} else {
+		printf("az is OK.\n");
+	}
+	if ( fabs(cell->b.x - cell_real->b.x) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: bx not determined correctly (got %8f, should be %8f)\n",
+										cell->b.x/1e9, cell_real->b.x/1e9);
+		fail = 1;
+	} else {
+		printf("bx is OK.\n");
+	}
+	if ( fabs(cell->b.y - cell_real->b.y) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: by not determined correctly (got %8f, should be %8f)\n",
+										cell->b.y/1e9, cell_real->b.y/1e9);
+		fail = 1;
+	} else {
+		printf("by is OK.\n");
+	}
+	if ( fabs(cell->b.z - cell_real->b.z) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: bz not determined correctly (got %8f, should be %8f)\n",
+										cell->b.z/1e9, cell_real->b.z/1e9);
+		fail = 1;
+	} else {
+		printf("bz is OK.\n");
+	}
+	if ( fabs(cell->c.x - cell_real->c.x) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: cx not determined correctly (got %8f, should be %8f)\n",
+										cell->c.x/1e9, cell_real->c.x/1e9);
+		fail = 1;
+	} else {
+		printf("cx is OK.\n");
+	}
+	if ( fabs(cell->c.y - cell_real->c.y) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: cy not determined correctly (got %8f, should be %8f)\n",
+										cell->c.y/1e9, cell_real->c.y/1e9);
+		fail = 1;
+	} else {
+		printf("cx is OK.\n");
+	}
+	if ( fabs(cell->c.z - cell_real->c.z) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: cz not determined correctly (got %8f, should be %8f)\n",
+										cell->c.z/1e9, cell_real->c.z/1e9);
+		fail = 1;
+	} else {
+		printf("cz is OK.\n");
+	}
+	
+	return fail;
+
+}	
+
+int main(int argc, char *argv[]) {
+
+	ControlContext *ctx;
+	ReflectionList *reflections_real;
+	Basis *cell_real;
+	int fail;
+	
+	ctx = control_ctx_new();
+	ctx->omega = deg2rad(0.0);
+	ctx->lambda = lambda(300.0e3);	/* 300 keV */
+	ctx->fmode = FORMULATION_PIXELSIZE;
+	ctx->x_centre = 256;
+	ctx->y_centre = 256;
+	ctx->pixel_size = 5e7;
+	image_add(ctx->images, NULL, 512, 512, deg2rad(00.0), ctx);
+	ctx->images->images[0].features = image_feature_list_new();
+	image_add(ctx->images, NULL, 512, 512, deg2rad(90.0), ctx);
+	ctx->images->images[1].features = image_feature_list_new();
+	ctx->omega = deg2rad(90.0);
+	image_add(ctx->images, NULL, 512, 512, deg2rad(90.0), ctx);
+	ctx->images->images[2].features = image_feature_list_new();
+	
+	/* Fudge to avoid horrifying pointer-related death */
+	ctx->dw = malloc(sizeof(DisplayWindow));
+	ctx->dw->cur_image = 0;
+	
+	/* The "true" cell */
+	cell_real = malloc(sizeof(Basis));
+	cell_real->a.x = 5.0e9;  cell_real->a.y = 0.0e9;  cell_real->a.z = 0.0e9;
+	cell_real->b.x = 0.0e9;  cell_real->b.y = 5.0e9;  cell_real->b.z = 0.0e9;
+	cell_real->c.x = 0.0e9;  cell_real->c.y = 0.0e9;  cell_real->c.z = 5.0e9;
+	/* The "real" reflections */
+	reflections_real = reflection_list_from_cell(cell_real);
+	ctx->images->images[0].features = reproject_get_reflections(&ctx->images->images[0], reflections_real);
+	ctx->images->images[1].features = reproject_get_reflections(&ctx->images->images[1], reflections_real);
+	ctx->images->images[2].features = reproject_get_reflections(&ctx->images->images[2], reflections_real);
+	
+	/* The "model" cell to be refined */
+	ctx->cell = malloc(sizeof(Basis));
+	ctx->cell->a.x = 5.0e9;  ctx->cell->a.y = 0.1e9;  ctx->cell->a.z = 0.1e9;
+	ctx->cell->b.x = 0.1e9;  ctx->cell->b.y = 5.0e9;  ctx->cell->b.z = 0.1e9;
+	ctx->cell->c.x = 0.1e9;  ctx->cell->c.y = 0.1e9;  ctx->cell->c.z = 5.0e9;
+	ctx->cell_lattice = reflection_list_from_cell(ctx->cell);
+	ctx->images->images[0].rflist = reproject_get_reflections(&ctx->images->images[0], ctx->cell_lattice);
+	reproject_partner_features(ctx->images->images[0].rflist, &ctx->images->images[0]);
+	ctx->images->images[1].rflist = reproject_get_reflections(&ctx->images->images[1], ctx->cell_lattice);
+	reproject_partner_features(ctx->images->images[1].rflist, &ctx->images->images[1]);
+	ctx->images->images[2].rflist = reproject_get_reflections(&ctx->images->images[2], ctx->cell_lattice);
+	reproject_partner_features(ctx->images->images[2].rflist, &ctx->images->images[2]);
+	
+	refine_do_cell(ctx);
+	image_feature_list_free(ctx->images->images[0].rflist);
+	image_feature_list_free(ctx->images->images[1].rflist);
+	image_feature_list_free(ctx->images->images[2].rflist);
+	
+	fail = check_cell(ctx->cell, cell_real);
+	
+	free(ctx);
+	
+	if ( fail ) return 1;
+	
+	printf("\n3D refinement test OK.\n");
+	
+	return 0;
+	
+}
+
+/* Dummy function stubs */
+#include "gtk-valuegraph.h"
+void displaywindow_update_imagestack(DisplayWindow *dw) { };
+void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g) { };
+void displaywindow_update(DisplayWindow *dw) { };
+void displaywindow_error(const char *msg, DisplayWindow *dw) { };
+guint gtk_value_graph_get_type() { return 0; };
+GtkWidget *gtk_value_graph_new() { return NULL; };
+void gtk_value_graph_set_data(GtkValueGraph *vg, double *data, unsigned int n) { };
+
diff --git a/src/refinetest3d3.c b/src/refinetest3d3.c
new file mode 100644
index 0000000..de8a792
--- /dev/null
+++ b/src/refinetest3d3.c
@@ -0,0 +1,187 @@
+/*
+ * refinetest3d3.c
+ *
+ * Unit test for refinement procedure in 3D
+ *
+ * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
+ *
+ *  dtr - Diffraction Tomography Reconstruction
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <math.h>
+
+#include "basis.h"
+#include "reflections.h"
+#include "image.h"
+#include "reproject.h"
+#include "refine.h"
+#include "utils.h"
+#include "mapping.h"
+#include "control.h"
+#include "displaywindow.h"
+#include "mrc.h"
+
+static int check_cell(Basis *cell, Basis *cell_real) {
+	
+	int fail;
+	
+	printf("     Refinement    Actual\n");
+	printf("---------------------------\n");
+	printf("ax  %+8f     %+8f\n", cell->a.x/1e9, cell_real->a.x/1e9);
+	printf("ay  %+8f     %+8f\n", cell->a.y/1e9, cell_real->a.y/1e9);
+	printf("az  %+8f     %+8f\n", cell->a.z/1e9, cell_real->a.z/1e9);
+	printf("bx  %+8f     %+8f\n", cell->b.x/1e9, cell_real->b.x/1e9);
+	printf("by  %+8f     %+8f\n", cell->b.y/1e9, cell_real->b.y/1e9);
+	printf("bz  %+8f     %+8f\n", cell->b.z/1e9, cell_real->b.z/1e9);
+	printf("cx  %+8f     %+8f\n", cell->c.x/1e9, cell_real->c.x/1e9);
+	printf("cy  %+8f     %+8f\n", cell->c.y/1e9, cell_real->c.y/1e9);
+	printf("cz  %+8f     %+8f\n", cell->c.z/1e9, cell_real->c.z/1e9);
+	
+	fail = 0;
+	if ( fabs(cell->a.x - cell_real->a.x) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: ax not determined correctly (got %8f, should be %8f)\n",
+										cell->a.x/1e9, cell_real->a.x/1e9);
+		fail = 1;
+	} else {
+		printf("ax is OK.\n");
+	}
+	if ( fabs(cell->a.y - cell_real->a.y) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: ay not determined correctly (got %8f, should be %8f)\n",
+										cell->a.y/1e9, cell_real->a.y/1e9);
+		fail = 1;
+	} else {
+		printf("ay is OK.\n");
+	}
+	if ( fabs(cell->a.z - cell_real->a.z) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: az not determined correctly (got %8f, should be %8f)\n",
+										cell->a.z/1e9, cell_real->a.z/1e9);
+		fail = 1;
+	} else {
+		printf("az is OK.\n");
+	}
+	if ( fabs(cell->b.x - cell_real->b.x) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: bx not determined correctly (got %8f, should be %8f)\n",
+										cell->b.x/1e9, cell_real->b.x/1e9);
+		fail = 1;
+	} else {
+		printf("bx is OK.\n");
+	}
+	if ( fabs(cell->b.y - cell_real->b.y) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: by not determined correctly (got %8f, should be %8f)\n",
+										cell->b.y/1e9, cell_real->b.y/1e9);
+		fail = 1;
+	} else {
+		printf("by is OK.\n");
+	}
+	if ( fabs(cell->b.z - cell_real->b.z) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: bz not determined correctly (got %8f, should be %8f)\n",
+										cell->b.z/1e9, cell_real->b.z/1e9);
+		fail = 1;
+	} else {
+		printf("bz is OK.\n");
+	}
+	if ( fabs(cell->c.x - cell_real->c.x) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: cx not determined correctly (got %8f, should be %8f)\n",
+										cell->c.x/1e9, cell_real->c.x/1e9);
+		fail = 1;
+	} else {
+		printf("cx is OK.\n");
+	}
+	if ( fabs(cell->c.y - cell_real->c.y) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: cy not determined correctly (got %8f, should be %8f)\n",
+										cell->c.y/1e9, cell_real->c.y/1e9);
+		fail = 1;
+	} else {
+		printf("cx is OK.\n");
+	}
+	if ( fabs(cell->c.z - cell_real->c.z) > 0.01e9 ) {
+		fprintf(stderr, "refinetest3d: cz not determined correctly (got %8f, should be %8f)\n",
+										cell->c.z/1e9, cell_real->c.z/1e9);
+		fail = 1;
+	} else {
+		printf("cz is OK.\n");
+	}
+	
+	return fail;
+
+}	
+
+int main(int argc, char *argv[]) {
+
+	ControlContext *ctx;
+	ReflectionList *reflections_real;
+	Basis *cell_real;
+	int fail;
+	int i;
+	
+	ctx = control_ctx_new();
+	ctx->omega = deg2rad(45.0);
+	ctx->lambda = lambda(300.0e3);	/* 300 keV */
+	ctx->fmode = FORMULATION_PIXELSIZE;
+	ctx->x_centre = 256;
+	ctx->y_centre = 256;
+	ctx->pixel_size = 5e7;
+	for ( i=0; i<=90; i++ ) {
+		image_add(ctx->images, NULL, 512, 512, deg2rad(i), ctx);
+		ctx->images->images[i].features = image_feature_list_new();
+	}
+	
+	/* Fudge to avoid horrifying pointer-related death */
+	ctx->dw = malloc(sizeof(DisplayWindow));
+	ctx->dw->cur_image = 0;
+	
+	/* The "true" cell */
+	cell_real = malloc(sizeof(Basis));
+	cell_real->a.x = 5.0e9;  cell_real->a.y = 0.0e9;  cell_real->a.z = 0.0e9;
+	cell_real->b.x = 0.0e9;  cell_real->b.y = 5.0e9;  cell_real->b.z = 0.0e9;
+	cell_real->c.x = 0.0e9;  cell_real->c.y = 0.0e9;  cell_real->c.z = 5.0e9;
+	/* The "real" reflections */
+	reflections_real = reflection_list_from_cell(cell_real);
+	for ( i=0; i<=90; i++ ) {
+		ctx->images->images[i].features = reproject_get_reflections(&ctx->images->images[i], reflections_real);
+	}
+	
+	/* The "model" cell to be refined */
+	ctx->cell = malloc(sizeof(Basis));
+	ctx->cell->a.x = 5.0e9;  ctx->cell->a.y = 0.1e9;  ctx->cell->a.z = 0.1e9;
+	ctx->cell->b.x = 0.1e9;  ctx->cell->b.y = 5.0e9;  ctx->cell->b.z = 0.1e9;
+	ctx->cell->c.x = 0.1e9;  ctx->cell->c.y = 0.1e9;  ctx->cell->c.z = 5.0e9;
+	ctx->cell_lattice = reflection_list_from_cell(ctx->cell);
+	for ( i=0; i<ctx->images->n_images; i++ ) {
+		ctx->images->images[i].rflist = reproject_get_reflections(&ctx->images->images[i], ctx->cell_lattice);
+		reproject_partner_features(ctx->images->images[i].rflist, &ctx->images->images[i]);
+	}
+	
+	refine_do_cell(ctx);
+	for ( i=0; i<ctx->images->n_images; i++ ) {
+		image_feature_list_free(ctx->images->images[i].rflist);
+	}
+	
+	fail = check_cell(ctx->cell, cell_real);
+	
+	free(ctx);
+	
+	if ( fail ) return 1;
+	
+	printf("\n3D refinement test OK.\n");
+	
+	return 0;
+	
+}
+
+/* Dummy function stubs */
+#include "gtk-valuegraph.h"
+void displaywindow_update_imagestack(DisplayWindow *dw) { };
+void displaywindow_enable_cell_functions(DisplayWindow *dw, gboolean g) { };
+void displaywindow_update(DisplayWindow *dw) { };
+void displaywindow_error(const char *msg, DisplayWindow *dw) { };
+guint gtk_value_graph_get_type() { return 0; };
+GtkWidget *gtk_value_graph_new() { return NULL; };
+void gtk_value_graph_set_data(GtkValueGraph *vg, double *data, unsigned int n) { };
+