Add skeleton prealignment procedure

git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@79 bf6ca9ba-c028-0410-8290-897cf20841d1

1 files changed, 17 insertions, 2 deletions

diff --git a/src/main.c b/src/main.c
index 4e5723a..5df4bcf 100644
--- a/src/main.c
+++ b/src/main.c
@@ -31,6 +31,7 @@
 #include "ipr.h"
 #include "cache.h"
 #include "mapping.h"
+#include "prealign.h"
 
 static gint main_method_window_response(GtkWidget *method_window, gint response, ControlContext *ctx) {
 
@@ -53,6 +54,12 @@ static gint main_method_window_response(GtkWidget *method_window, gint response,
 			default: ctx->psmode = PEAKSEARCH_NONE; break;	/* This happens when reading from a cache file */
 		}
 		
+		if ( gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(ctx->checkbox_prealign)) ) {
+			ctx->prealign = TRUE;
+		} else {
+			ctx->prealign = FALSE;
+		}
+		
 		gtk_widget_destroy(method_window);
 		while ( gtk_events_pending() ) gtk_main_iteration();
 		
@@ -66,6 +73,10 @@ static gint main_method_window_response(GtkWidget *method_window, gint response,
 			val=0;
 		}
 		
+		if ( ctx->prealign ) {
+			prealign_do_series(ctx);
+		}
+		
 		if ( ctx->inputfiletype != INPUT_CACHE ) {
 			mapping_create(ctx);
 		}
@@ -108,9 +119,10 @@ void main_method_dialog_open(ControlContext *ctx) {
 	vbox = gtk_vbox_new(FALSE, 0);
 	hbox = gtk_hbox_new(TRUE, 0);
 	gtk_box_pack_start(GTK_BOX(GTK_DIALOG(method_window)->vbox), GTK_WIDGET(hbox), FALSE, FALSE, 7);
-	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(vbox), FALSE, FALSE, 5);
+	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(vbox), FALSE, FALSE, 10);
 	
-	table = gtk_table_new(3, 2, FALSE);
+	table = gtk_table_new(4, 2, FALSE);
+	gtk_table_set_row_spacings(GTK_TABLE(table), 5);
 
 	method_label = gtk_label_new("Reconstruction Algorithm: ");
 	gtk_table_attach_defaults(GTK_TABLE(table), method_label, 1, 2, 1, 2);
@@ -134,6 +146,9 @@ void main_method_dialog_open(ControlContext *ctx) {
 	gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_peaksearch), 3);
 	gtk_table_attach_defaults(GTK_TABLE(table), ctx->combo_peaksearch, 2, 3, 2, 3);
 	
+	ctx->checkbox_prealign = gtk_check_button_new_with_label("Pre-align image stack");
+	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_prealign, 1, 3, 3, 4);
+	
 	if ( ctx->inputfiletype == INPUT_CACHE ) {
 		gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Get from cache file");
 		gtk_widget_set_sensitive(GTK_WIDGET(ctx->combo_peaksearch), FALSE);