clearvars

sdirectory2 = '/Users/elisnewham/Desktop/Elis cementum work/8 bit straightened/t56/increment models/'; %insert folder containing cmeentum increment models here
textFiles2 = dir([sdirectory2 '*.txt']);
NumberTransects=length(textFiles2);

clearvars midLine imageTortuosityVec graphTortuosityVec 

for j=1:NumberTransects
    clearvars imageTortuosity
    filename=[sdirectory2 textFiles2(j).name];
    img=load(filename);
    imgBW=im2bw(img);
    
    [row,col]=find(img);
    startPoint=min(col);
    endPoint=max(col);
    for i=startPoint:endPoint
        colVec=img(:,i);
        [val,loc]=max(colVec);
        midLine(i)=loc;
    end
    [row,col]=find(midLine);
    firstPixel=min(col);
    midLine(1:firstPixel)=[];
    [m,n]=size(midLine);
    px=[1:n];
    
    [row,col]=find(midLine);
    startPoint=min(col);
    endPoint=max(col);
    firstVal=midLine(startPoint);
    lastVal=midLine(endPoint);
    difference=firstVal-lastVal;
    vertDifference=sqrt(difference^2);
    horizDifference=endPoint-startPoint;
    hypotenuse=sqrt((vertDifference^2)+(horizDifference^2));
    
    diffMidline=diff(midLine);
    
    pathlength=max(find(midLine))+sum(diffMidline.^2);
    
    imageTortuosity=pathlength./hypotenuse;
    
    [arclen,seglen]=arclength(px,midLine);
    
    graphTortuosity=arclen./hypotenuse;
    
    imageTortuosityVec(j)=imageTortuosity;
    graphTortuosityVec(j)=graphTortuosity;
    
    
end

finalImageTort=sort(imageTortuosityVec);
finalGraphTort=sort(graphTortuosityVec);