Begin.m

clc; clear;

fid = fopen('results/LiverDice_lambda.txt','w');
fprintf(fid,'%s\t%s\t%s\n','patientID','lambda', 'Dice');
fclose(fid);

topLevelFolder = '/rsrch1/ip/rglenn1/data/Processed';
files = dir(topLevelFolder);
% Get a logical vector that tells which is a directory.
dirFlags = [files.isdir];
% Extract only those that are directories.
subFolders = files(dirFlags); % A structure with extra info.
% Get only the folder names into a cell array.
subFolderNames = {subFolders(3:end).name}; % Start at 3 to skip . and ..
% Optional fun : Print folder names to command window.
patientDice = zeros(size(length(subFolderNames)));
disp(subFolderNames);

filename = sprintf('results/liver_dices.txt');
fid = fopen(filename,'w'); 
fprintf(fid,'paitentID\tDice\t\n');
fclose(fid);

for k = 1 :length(subFolderNames)
    patient = topLevelFolder+ "/"+subFolderNames{k};
	fprintf('Sub folder #%d = %s\n', k, patient);
    info = niftiinfo(patient + "/Art.bc.nii.gz");
    fprintf('BitsPerPixel %d', info.BitsPerPixel);
    art = niftiread(info);

    
    truth = niftiread(patient + '/Truth.raw.nii.gz');
    if (size(art,1) ~= size(truth,1)) || (size(art, 2) ~= size(truth, 2))
        disp("sizes are different");
        truth = imresize3(truth, size(art));
    end


    quantList = zeros(size(length(art(1,1,:))));
    segnifit = zeros(size(art),'single');
    truth = single(truth);


    outdir = append('results/', subFolderNames{k});
    mkdir(outdir);
    
    filename = append(outdir,'/anay.txt');

    fid = fopen(filename,'w');
    fprintf(fid,'%s\t%s\t%s\t%s\n','n', 'quant', 'threshold', 'dice');
    fclose(fid);

    filename = sprintf('%s/liver_dice.txt',outdir);
    fid = fopen(filename,'w');
    fprintf(fid,'%s\t%s\t%s\t%s\t\n','patient', 'i', 'lamba', 'dice');
    fclose(fid);

     
    
    for n = 60 : 60%length(art(1,1,:))
        fprintf("scan num:%d\n",n);
        if n > length(art(1,1,:))
            n = 40;
        end

        img = art(:,:,n);
        imgtruth = truth(:,:,n);
        test = imbinarize(imgtruth);
        fprintf("check sum: %f\n", sum(test(:)));
        if (sum(test(:)) < 100) 
            fprintf("Sum less than 10 need new test image %f\n",sum(test(:)) );
            fprintf("changing value n %f\n", n);
            n = 83;
            if n > length(art(1,1,:))
                fprintf("changing value n %f\n", n);
                n = 30;
            end
            img = art(:,:,n);
            imgtruth = truth(:,:,n);
            test = imbinarize(imgtruth);  
        end
        if (sum(test(:)) < 10) 
            fprintf("Sum less than 10 need new test image %f\n",sum(test(:)) );
       
            
            fprintf("changing value n %f\n", n);
            n = 50;
            img = art(:,:,n);
            imgtruth = truth(:,:,n);

        end
        fprintf("check value n %f\n", n);
        %Perform Algorithm

        
        %img = TransformImage2(img, 10, 50);
        img = sgolayfilt(double(img), 3, 7, [], 2);
        %img = imcontrast(single(img));
        %imshow(img, []);
        lamblist = [-1.0, -0.4, -0.2, 0.1, 0.2, 0.3, 0.5, 0.6, 0.7, 0.8, 0.9, ...
            1.0, 1.25, 1.5, 1.75, 2.0, 2.25, 2.5, 2.75, 3.0, 3.25, 3.5, 3.75, 4.0,...
            4.25, 4.5, 4.75, 5.0];
        [segimg, lambBest, bestDice] = fuzzyimage((img), (imgtruth), n, outdir, subFolderNames{k}, lamblist );
        %segimg = img;
       
        segnifit(:,:,n) = single(segimg);
        %imshow(imgtruth, []);
%        if info.BitsPerPixel == 16
%             segnifit(:,:,n) = int16(segimg);
%        elseif info.BitsPerPixel == 32
%             segnifit(:,:,n) = single(segimg);
%        else   
%             segnifit(:,:,n) = double(segimg);
%        end
    end
    % Calculate Dice
    dice = calculateDice((segnifit),(truth));
   
    filename = sprintf('results/liver_dices.txt');
    fid = fopen(filename,'a+'); 
    fprintf(fid,'%s \t %f \t %f \n', subFolderNames{k}, bestDice, lambBest);
    fclose(fid);

    info = niftiinfo(patient + "/Art.bc.nii.gz");
    if info.BitsPerPixel == 16
        filename = sprintf('%s/QIS.nii',outdir);
        disp(filename);
        info.BitsPerPixel = 16;
     
        niftiwrite(int16(segnifit),filename, info, 'Version', 'NIfTI1',  'Compressed',true);

    elseif info.BitsPerPixel == 32
        filename = sprintf('%s/QIS.nii',outdir);
        disp(filename);
        info.BitsPerPixel = 32;

        niftiwrite(single(segnifit),filename, info, 'Version', 'NIfTI1',  'Compressed',true);
    else
        filename = sprintf('%s/QIS.nii',outdir);
        disp(filename);
        info.BitsPerPixel = 64;
      
        niftiwrite(double(segnifit),filename, info, 'Version', 'NIfTI1',  'Compressed',true);

     end
end

function biggerIm = resizeImage(img, scaleFactor)
     
    biggerIm = zeros(size(img));   
    for i = 1 : length(img(1,1,:))
        n = 1;  
        I =(mat2gray(img(:,:,i)));
        %Idouble = im2double(I); 
        %avg = mean2(Idouble);
        %sigma = std2(Idouble);
        img_c = imadjust(I,[],[],0.95);
        %img_c = imadjust(I,[avg-n*sigma avg+n*sigma],[]);
        %img_c = int16(img(:,:,n));

        biggerIm(:,:,n) = img_c; 
    end
end