clc ;
close all;
clear all;
%mkdir Live;
mkdir slice;


%% Code to write images 



%open(NewObj1);
%open(NewObj2);
updating_array=0;
dead_cells=0;
total_dead_cells=0;
total_live_cells=0;

live_cells=0;
for videos=91:91


z=0;

VidObj = VideoReader(strcat('D:\All_videos\Yeast_1\yeast00',num2str(videos),'.avi'));



VidObjDat = read(VidObj);
Nframes = VidObj.NumberOfFrames;
vidHeight = VidObj.Height;
vidWidth = VidObj.Width;
mean_count=1;
pixel_count=1;
%% Generate Background
a = read(VidObj,1);
%%% average ten frames to generate background.
bg = 0;
count = 30 ;% set number of frame to be averaged
N = 1; % start frame number
for i = N:N+count
    bg = bg +double(rgb2gray(read(VidObj,i)));
end
bg  = uint8(bg /count); % Final Background generated.
%imshow(bg);
% set appropriate cropping for the background
%  RS = 135;% start value of the row
 %RE = 280; % end value of the row
  RS = 76;% start value of the row
   RE = 280;% start value of the row
 
%  RS = 493;% start value of the row
%  RE = 638; % end value of the row
CS = 1;% start value of the column
CE = 216; % end value of the column
% crop as per the following imshow(CS:CE,RS:RE)
%imshow(bg(:,RS:RE));



%% subtract all subsequent frames and write into a video. 
      ccount = 0;
      gccount = 0;
    framecount = 0;
 

 ccount = 0;
 MAVector = 0;
 MVector = 0;
 framenum = 0;
 pframenum = 0;

 for k =1:Nframes
 Copy=rgb2gray(read(VidObj,k));
 CurrFrame = double(rgb2gray(read(VidObj,k)));
 CurrFrame1=read(VidObj,k);
 CurrFrame1=CurrFrame1(:,RS:RE);
 Sub = double(CurrFrame(:,RS:RE)-double(bg(:,RS:RE)));
 Submin = min(Sub(:));
 Submax = max(Sub(:));
 AdjBGSub = uint8( (Sub - Submin)/(Submax-Submin) * 255);
 I = AdjBGSub;
  [A, B]=size(I);

%  a = uint8(min(Sub(:))*-1+Sub);
[~, threshold] = edge(I, 'sobel');
fudgeFactor = 1;
BWs = edge(I,'sobel', threshold * fudgeFactor);
se90 = strel('line', 3, 90);
se0 = strel('line', 3, 0);
BWsdil = imdilate(BWs, [se90 se0]);
BWdfill = imfill(BWsdil, 'holes');
BWdfillopen = imopen(BWdfill,strel('disk',5,4));
BWnobord = imclearborder(BWdfillopen, 4);
seD = strel('diamond',2);
BWfinal = imerode(BWnobord,seD);
BWfinal = imerode(BWfinal,seD);
CC =bwconncomp(BWfinal);
Areas = regionprops(CC,'Area');
MALength = regionprops(CC,'MajorAxisLength');
MinLength = regionprops(CC,'MinorAxisLength');
Centroids=regionprops(CC,'Centroid');
    
BWthresh = imcomplement(im2bw(I,0.15));
            % imshow(BWthresh);

            % figure;
            % imshow(uint8(BWthresh).*I);
            % CC_par =bwconncomp(BWthresh);
            % Centroids=regionprops(CC_par,'Centroid');
            % Areas_par = regionprops(CC_par,'Area');

for il = 1:CC.NumObjects

        if(Areas(il).Area > 40 && Areas(il).Area < 45840  )
              ccount = ccount +1;
              gccount = gccount +1;
               
                CR1=round(Centroids(il).Centroid(1))-15;
                CC1=round(Centroids(il).Centroid(2))-15;
                CR2=round(Centroids(il).Centroid(1))+15;
                CC2=round(Centroids(il).Centroid(2))+15;
                if CR1 <= 0
                CR1=1;
                end
                if CC1 <= 0
                CC1=1;
                end
                if CR2 > B
                CR2=B;
                end
                if CC2 > A
                CC2=A;
                end
                
           sliceOfImage = CurrFrame1(CC1:CC2,CR1:CR2);
          
           %imwrite(sliceOfImage,strcat('C:\Users\RBCCPS\Documents\MATLAB\slice/FrameNumber','-',num2str(k),'-',num2str(il),'.jpg'),'jpeg');
            %mean(mean_count)=mean2(I(CC1:CC2,CR1:CR2));
            %mean_count=mean_count+1;
            %mean_slice=mean2(sliceOfImage);
            [p, q]=size(sliceOfImage);
            
           % BWthresh = im2bw(sliceOfImage,0.15);
            % imshow(BWthresh);

            % figure;
            % imshow(uint8(BWthresh).*I);
            %CC1 =bwconncomp(imcomplement(BWthresh));
            % Areas_stained = regionprops(CC1,'Area');
 %           C_Percentstained = sum(struct2array(Areas_stained))/max(struct2array(Areas))*100;
%            Percentstained = horzcat(Percentstained, C_Percentstained );

             z=z+1;  %if (pixel_count ~=0)
            pixel_count_array(z)=pixel_count;
            

                
                        imwrite(sliceOfImage,strcat('C:\Users\RBCCPS\Documents\MATLAB\slice/FrameNumber','-',num2str(videos),'-',num2str(k),'-',num2str(il),'.jpg'),'jpeg');

               

                 end

            end
      end

updating_array=vertcat(updating_array(:),pixel_count_array(:));
pixel_count_array=0;
z=0;
videos
end
 %end
%end



 %end

%close(NewObj1);
%close(NewObj2);--