endVrept.m~

%%                             endVrept.m
% 
% Alistair Boettiger                                   Date Begun: 03/01/11
% Levine Lab                                Functionally Complete: 03/01/11
%                                                   Last Modified: 03/01/11
%

function Im_seg = endVrept(folder,name,norm,scale,f)



    Ymax = 250;
    Nstrength = .7;

   load([folder,name]); 
    age = getage(H,cent);
    disp(age);
    
        N_y = length(unique(H.*L1));
    N_r = length(unique(   H.*(L1&(1-L2).*Filt)    ));
    N_ectopic = N_r/(N_y+N_r);
    
    
   % Yellow = both;  Green = endogenous no reporter 
     Iz = uint8(zeros(h,w,3));
     Iz(:,:,1) = 255*uint8(L2n1);
     Iz(:,:,2) = 1*uint8(Ymax*(L1&L2)) + 255*uint8(L2n1) + Nstrength*handles.In ;
     Iz(:,:,3) = Nstrength*handles.In - Iz(:,:,1)  - 255*uint8(L2n1) - 1*uint8(Ymax*(L1&L2));
     Im_seg = uint8(bsxfun(@times,double(Iz)/255*norm,double(handles.In)));
     
     Im_seg = imresize(Im_seg,scale);
     Im_seg = imflip(imflip(Im_seg,f(1)),f(2));
     
     
   imshow(Im_seg);
     
     
   
   %  Yellow = both, red = missing
%         Iz = uint8(zeros(h,w,3));
%      Iz(:,:,1) = 1*uint8(Ymax*(L1&L2))+ 255*uint8(L2n1);
%      Iz(:,:,2) = 1*uint8(Ymax*(L1&L2)) + Nstrength*handles.In - 255*uint8(L2n1);
%      Iz(:,:,3) = Nstrength*handles.In - Iz(:,:,1);
%      Im_seg = uint8(bsxfun(@times,double(Iz)/255*norm,double(handles.In)));

% Green = both, yellow = missing

     Iz = uint8(zeros(h,w,3));
     Iz(:,:,1) = 255*uint8(L2n1);
     Iz(:,:,2) = 1*uint8(Ymax*(L1&L2)) + 255*uint8(L2n1) + Nstrength*handles.In ;
     Iz(:,:,3) = Nstrength*handles.In - Iz(:,:,1)  - 255*uint8(L2n1) - 1*uint8(Ymax*(L1&L2));
     Im_seg = uint8(bsxfun(@times,double(Iz)/255*norm,double(handles.In)));