Index: /trunk/src/phys_ima.m
===================================================================
--- /trunk/src/phys_ima.m	(revision 891)
+++ /trunk/src/phys_ima.m	(revision 892)
@@ -1,2 +1,3 @@
+
 % phys_ima: transform several images in phys coordinates on a common pixel grid
 %------------------------------------------------------------------------
@@ -61,10 +62,10 @@
            SliceCoord=Calib.SliceCoord(ZIndex,:);
            zphys=SliceCoord(3); %to generalize for non-parallel planes
-           if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') 
-                H=Calib.InterfaceCoord(3);
-                if H>zphys
-                    zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object)
-                end
-           end
+%            if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') 
+%                 H=Calib.InterfaceCoord(3);
+%                 if H>zphys
+%                     zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object)
+%                 end
+%            end
         end
         xima=0.5:npx-0.5;%image coordinates of corners
Index: /trunk/src/px_XYZ.m
===================================================================
--- /trunk/src/px_XYZ.m	(revision 891)
+++ /trunk/src/px_XYZ.m	(revision 892)
@@ -48,5 +48,5 @@
         if H>Zphys
             Zphys=H-(H-Zphys)/Calib.RefractionIndex; %corrected z (virtual object)
-            test_refraction=1;
+          %  test_refraction=1;
         end
     end
Index: /trunk/src/uvmat.m
===================================================================
--- /trunk/src/uvmat.m	(revision 891)
+++ /trunk/src/uvmat.m	(revision 892)
@@ -1083,5 +1083,5 @@
 
 UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface 
-check=0;
+% check=0;
 if isfield(UvData,'XmlData')&&isfield(UvData.XmlData{1},'GeometryCalib')&& isfield(UvData.XmlData{1}.GeometryCalib,'SliceCoord')
     GeometryCalib=UvData.XmlData{1}.GeometryCalib;
@@ -1101,6 +1101,8 @@
 end	
 RefractionIndex=1.33;
+CheckRefraction=0;% default value of the check box refraction 
 if isfield(GeometryCalib,'RefractionIndex')
     RefractionIndex=GeometryCalib.RefractionIndex;
+    CheckRefraction=1;
 end	
 SliceAngle=[0 0 0];
@@ -1141,7 +1143,7 @@
     'String',num2str(InterfaceCoord),'Visible','off','FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_H'': z position of the water surface (=Z_1 in air)');%edit box
 %  raw 3 of the GUI
-uicontrol('Style','checkbox','Units','normalized', 'Position', [2*ii+ww 0.95-3*ii-2*hh 2*ww hh],'tag','CheckRefraction','BackgroundColor',BackgroundColor,...
+hcheckrefraction=uicontrol('Style','checkbox','Units','normalized', 'Position', [2*ii+ww 0.95-3*ii-2*hh 2*ww hh],'tag','CheckRefraction','BackgroundColor',BackgroundColor,...
     'Callback',@(hObject,eventdata)set_slice_CheckRefraction_Callback(hObject,eventdata),...
-    'String','refraction','Value',0,'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''CheckRefraction'':=1 to provide refraction correction');
+    'String','refraction','Value',CheckRefraction,'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''CheckRefraction'':=1 to provide refraction correction');
 uicontrol('Style','text','Units','normalized', 'Position', [2*ii+2*ww 0.95-3*ii-1.75*hh ww hh/2],'BackgroundColor',BackgroundColor,'Tag','Refraction_title',...
     'String','index','Visible','off','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
@@ -1165,6 +1167,4 @@
     'String','tild angle y axis','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title
 %  raw 6 of the GUI
-% uicontrol('Style','text','Units','normalized', 'Position', [ii 0.95-5*ii-4.75*hh 2*ww hh/2],'BackgroundColor',BackgroundColor,'Tag','NbSlice_title',...
-%     'String','tilt angle','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
 uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceAngle_1_1','BackgroundColor',[1 1 1],...
     'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_1'':first slice angle of inclination around the x axis');%edit box
@@ -1185,4 +1185,5 @@
     'String','Cancel','FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''Cancel'': quit GUI without action');
 drawnow
+set_slice_CheckRefraction_Callback(hcheckrefraction,[])
 
 %------------------------------------------------------------------------
@@ -1235,4 +1236,7 @@
     GeometryCalib.InterfaceCoord=[0 0 SliceData.H];
     GeometryCalib.RefractionIndex=SliceData.RefractionIndex;
+elseif isfield(GeometryCalib,'RefractionIndex')
+    GeometryCalib=rmfield(GeometryCalib,'RefractionIndex');
+    GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord');  
 end