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Samuel Callahan
SCallahan/
ComputerVision-LungCancer
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[b4b313]: / Image features calculation code / Not Working / shape.m

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tic

files = dir('segmented_nodules/*.dcm');

count = 0;

fid = fopen ('nodules_features.txt', 'wt');

fid2 = fopen ('nodules_many_regions.txt', 'wt');

fprintf(fid,'%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s \n','ImageName','Area','ConvexArea','Circularity','Perimeter','ConvexPerimeter','Roughness','EquivDiameter','MajorAxisLength','MinorAxisLength','Elongation','Compactness','Eccentricity','Solidity','Extent','RadialDistanceSD','MinIntensity','MaxIntensity','MeanIntensity','SDIntensity','MinIntensityBG','MaxIntensityBG','MeanIntensityBG','SDIntensityBG','IntesityDifference');

fprintf(fid2,'%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s \n','ImageName','Area','ConvexArea','Circularity','Perimeter','ConvexPerimeter','Roughness','EquivDiameter','MajorAxisLength','MinorAxisLength','Elongation','Compactness','Eccentricity','Solidity','Extent','RadialDistanceSD','MinIntensity','MaxIntensity','MeanIntensity','SDIntensity','MinIntensityBG','MaxIntensityBG','MeanIntensityBG','SDIntensityBG','IntesityDifference');

for i = 1:size(files,1)

    fn = sprintf('%s/%s', 'segmented_nodules', char(files(i).name));

    fn2 = sprintf('%s/%s', 'segmented_background', char(files(i).name));

    info = dicominfo(fn);

    info4 = dicominfo(fn2);

    I = dicomread(info);

    I4 = dicomread(info4);

    BW = (I~=-2000);

    L = bwlabel(BW);

    a = L;

    flag = 0;

    if (nanmax(a(:)) > 1)

        flag = 1;

    end

    a(a~=0 & a~=1) = 0;

    STATS = regionprops (a,'Area', 'Extent', 'Perimeter', 'Centroid', 'ConvexArea', 'ConvexImage', 'Solidity', 'Eccentricity', 'MajorAxisLength', 'EquivDiameter', 'MinorAxisLength');

    STATS.ConvexPerimeter = 2 * (sqrt(pi*STATS.ConvexArea));

    STATS.Circularity = (4*pi*STATS.Area)/(STATS.ConvexPerimeter .^ 2);

    STATS.Elongation = STATS.MajorAxisLength/STATS.MinorAxisLength;

    b = double(I);

    b(b==-2000) = NaN;

    b4 = double(I4);

    b4(b4==-2000) = NaN;

    STATS.MinIntensity = nanmin(b(:));

    STATS.MaxIntensity = nanmax(b(:));

    STATS.MeanIntensity = nanmean(b(:));

    STATS.SDIntensity = nanstd(b(:));

    STATS.MinIntensityBG = nanmin(b4(:));

    STATS.MaxIntensityBG = nanmax(b4(:));

    STATS.SDIntensityBG = nanstd(b4(:));    

    STATS.MeanIntensityBG = nanmean(b4(:));

    STATS.IntensityDifference = abs(STATS.MeanIntensity - STATS.MeanIntensityBG);

    fprintf(files(i).name,',',STATS(1).Area,',', STATS(1).Extent,',', STATS(1).Perimeter,'\n');

    count = count+1

    fn2 = sprintf('%s/%s', 'contours', char(files(i).name));

    info2 = dicominfo(fn2);

    I2 = dicomread(info2);

    d = NaN;

    j = 0;

    for r = 1:size(I2,1)

        for c = 1:size(I2,2)

            if (I2(r,c) == 1)

                j = j + 1;

                d(j) = sqrt(double((c-(STATS.Centroid(1)^2))+(r-(STATS.Centroid(2)^2))));

            end

        end

    end

    STATS.RadialDistanceSD = nanstd(d(:));

    STATS.Perimeter = j;

    I3 = bwperim(STATS.ConvexImage);

    j = 0;

    for r = 1:size(I3,1)

        for c = 1:size(I3,2)

            if (I3(r,c) == 1)

                j = j + 1;

            end

        end

    end

    STATS.ConvexPerimeter = j;

    STATS.Roughness = STATS.ConvexPerimeter/STATS.Perimeter;

    STATS.Compactness = STATS.Perimeter^2/(4*pi*STATS.Area);

    if (flag == 0)

        fprintf(fid,'%s,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f \n',files(i).name,STATS.Area,STATS.ConvexArea,STATS.Circularity,STATS.Perimeter,STATS.ConvexPerimeter,STATS.Roughness,STATS.EquivDiameter,STATS.MajorAxisLength,STATS.MinorAxisLength,STATS.Elongation,STATS.Compactness,STATS.Eccentricity,STATS.Solidity,STATS.Extent,STATS.RadialDistanceSD,STATS.MinIntensity,STATS.MaxIntensity,STATS.MeanIntensity,STATS.SDIntensity,STATS.MinIntensityBG,STATS.MaxIntensityBG,STATS.MeanIntensityBG,STATS.SDIntensityBG,STATS.IntensityDifference);

    else

        fprintf(fid2,'%s,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f \n',files(i).name,STATS.Area,STATS.ConvexArea,STATS.Circularity,STATS.Perimeter,STATS.ConvexPerimeter,STATS.Roughness,STATS.EquivDiameter,STATS.MajorAxisLength,STATS.MinorAxisLength,STATS.Elongation,STATS.Compactness,STATS.Eccentricity,STATS.Solidity,STATS.Extent,STATS.RadialDistanceSD,STATS.MinIntensity,STATS.MaxIntensity,STATS.MeanIntensity,STATS.SDIntensity,STATS.MinIntensityBG,STATS.MaxIntensityBG,STATS.MeanIntensityBG,STATS.SDIntensityBG,STATS.IntensityDifference);

    end

end

fclose(fid);

fclose(fid2);

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