CavBubbleDiameter.m

clc;
clear;

basedir='...\Visualization\';

LP=[300 400 500 600 700 800 900];
magf=35;% (pixels/mm)

LPmJ=0.1122*LP-20.61;

Nl=7;
Nr=5;

x0=zeros(Nl,Nr);
y0=zeros(Nl,Nr);
bubble_diameter=zeros(Nl,Nr);
bubble_area=zeros(Nl,Nr);
cropy=200:640;


for i=1:Nl
    
    for j=1:Nr
        
        
        % Read frame
        A=imread([basedir,'LP',num2str(LP(i),'%03.0f'),filesep,'run',int2str(j),'\cam1__C001H001S0001000010.tif']);
            
        img=A(end:-1:1,:);
        
        
        % crop image
        img = img(cropy,:);
        % flip the image upside down
        img = flipud(img);
        
        img(img>100)=255;
%           % converts image to black and white
          BW = imbinarize(img,0.99);
        
        
        % only pixels that are connected to another # pixels are kept
        BWred = bwareaopen(~BW,100);
        % fills in holes of the image
        BWfill=imfill(BWred,'holes');
        
        
        
        % finds the boundaries of the image
        [B,labelmat,N,~]= bwboundaries(BWfill);
        [~,ind]=max(cellfun('length',B));
        bound = B{ind};
        [N ind]
        % calculate geometrical properties of the bubble
        indx=find(labelmat==ind);
        bubble_area(i,j)=length(indx);      
        bubble_diameter(i,j) = sqrt(bubble_area(i,j) * 4/pi); % * pixel_pitch/magnification;
        
        if bubble_diameter(i,j)<=30
            ind=ind+1;
            bound = B{ind};
            indx=find(labelmat==ind);
            bubble_area(i,j)=length(indx);      
            bubble_diameter(i,j) = sqrt(bubble_area(i,j) * 4/pi); % * pixel_pitch/magnification;
        end
        
        btemp=bound;
        % calculate centroid
        x0(i,j) = mean(btemp(:,2));
        y0(i,j) = mean(btemp(:,1));
        
        
        
%         [x0 y0 bubble_diameter]
%%
%         figure(1);imshow(BWfill(:,:));hold on;
% %         btemp=bound{1};
%         plot(btemp(:,2),btemp(:,1),'r-','LineWidth',2);
%         hold off;
%         pause(0.3);

    end
end