%This program extracts the data from the image stack
clear;
clc;

dirname='E:\';
files=dir('*.tif');
fileIndex = find(~[files.isdir]);

for k = 1:length(fileIndex);
    
    fname=files(fileIndex(k)).name;
    
    info = imfinfo(fname);
    num_images = numel(info);

    %reading the frames
    Frame= cell([num_images,1]);
    for i=1:num_images
        [X] = imread(fname,i, 'Info', info);
        Frame{i}=X;
    end
    
    %Making a sequence
    I = imread(fname,1, 'Info', info);
    
    % Preallocate the array
    sequence(:,:,1) = I;
    
    %Create image sequence array
    for p = 2:80 %% only the first 80 frames of the movie, this is enough to choose a frame which can give us the right contrast
        sequence(:,:,p) = imread(fname,p, 'Info', info);
        % Process sequence
        AdjSequence(:,:,p)=imadjust(sequence(:,:,p));
    end
    
    %View results
    implay(AdjSequence(:,:,:))
    pause(1);
    
    %select the frame you want to analyze
    FtoAnalyze=input('Select the frame you want to analyze:');
    
    figure()
    imagen=Frame{FtoAnalyze};
    SelCell=imadjust(imagen);
    imshow(SelCell);
    fileN=fname(1:end-4);
    a=[dirname '\' fileN];
    title(a)
    xlabel('Select the cells you want to analyze')
    hold on;
    
    %%% ask how many cells are there in the image
    
    %%%for each of the cells, create a mask:
    cellTot= input('Enter the number of cells you want to select plus the local:');
    for cellIndex=1:cellTot
        h=imellipse;
        EllPosition{cellIndex}= wait(h);
        BW = createMask(h);
        %figure, imshow(BW)
    
        %for each of the masks multiplies the mask for the sequence and
        %calculates the average intensity in each frame
        
        for i=1:num_images
            Objeto=immultiply(Frame{i},BW);
            %figure, imshow(Objeto)
    
            % find the mean intensity values of the selection
            objave(i)= mean2(Objeto);% this gives the mean intensity
            %of the whole image, now we have to normailze to the selected
            %region 
            
            ind=find(Objeto);
            RegionPix=numel(ind);
            RegionFraction=RegionPix/numel(Objeto);
            AvgInt=objave./RegionFraction;
            
        end
        
        RAWInt{cellIndex}= AvgInt;% AvgInt;%RAW intensity
        
        end
    
    
    %creating the string to name the cells in the excel sheet
        myName{1}=['PrimaryLocal'];
    for i=2:cellTot
        myName{i}=['Cell_' num2str(i-1)];
    end
    
    headers = [a, myName];
    
    %creating the content of the file
    RAWMatrix=RAWInt{1};
    for i=2:cellTot
        RAWMatrix=[RAWMatrix;RAWInt{i}];
    end
    
     xlswrite('RAWData.xls', RAWMatrix',2*k);
     xlswrite('RAWData.xls', headers,(2*k)-1);

     
% Writing the max indent frame     
     p={'MaxIndentFrame';FtoAnalyze};
     xlswrite('RAWData.xls', p,(2*k)-1,'A3')
     

      
%%% saving the ellipse position
      Alphabet='ABCDEFGHIJKLMNOPQRSTUVWXYZ';

for i=1:cellTot
          myName2{(2*i)-1}=['Ellipse_x' num2str(i)];   
          myName2{2*i}=['Ellipse_y' num2str(i)];       
          
end
headers2 = [myName2];
xlswrite('RAWData.xls', headers2,(2*k)-1,'A7');

    
%writing the ellipse positions in the excel file
      %label: EllPosition{1};
      xlswrite('RAWData.xls', EllPosition,(2*k)-1,'A8');
      
    for i=1:cellTot
        letter=[Alphabet((2*i)-1)];
        myName3{i}=[letter num2str(8)];
        xlswrite('RAWData.xls', EllPosition{i},(2*k)-1,myName3{i});
        end
    
    %ploting the intensity profiles for each of the cells
    figure()
    plot(RAWInt{1},'r');
    title(a)
    legend('Primary', 'Location', 'Best');
    legendtext ='Primary Local';
        hold all;

    for cellIndex=2:cellTot

    % Set the coloring code!
    %Graph colours:
    %So I make a string like this:
    colours='bgmckbgmck';
    
    %And use the loop counter to select a colour character from the 'colours' string:
    %cellIndex 
       plot(RAWInt{cellIndex},[colours(cellIndex)]); hold on;
       Cell{cellIndex}=['Cell_' num2str(cellIndex)];
       hold all; 
    end
 
    legend('Primary','Cell_1','Cell_2', 'Cell_3','Cell_4','Cell_5', 'Cell_6', 'Cell_7', 'Cell_8', 'Cell_9')
        
    plot(FtoAnalyze, RAWInt{1},'y.');
    
    fileN=fname(1:end-4);
    SaveAllFigures(fileN,'emf')
    
    for i=1:cellTot
         Area{i}=area(EllPosition{i}(:,1), EllPosition{i}(:,2));%area
         Center{i}=mean(EllPosition{i}); %center
        letter4=[Alphabet(i+1)]; 
        q={'Area';Area{i}; 'Center'; Center{i}(1);Center{i}(2) };
        myName4{i}=[letter4 num2str(2)];
        
        xlswrite('RAWData.xls', q,(2*k)-1,myName4{i});
        
    end 
        
    
    close(gcf);
    close(gcf);
    
end