malaria detection code

src/rashmi's code/CellSegmentation.m

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+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);--