% determine the change in width of lines during shrinking process

%%

clear all;

% load images
x = imread('fig7_5.png');     ** THIS LINE MIGHT BE WRONG FILE
x = sum(x,3);

%% split the images
im1 = x(1:3000,1:2300);
im2 = x(1:3000,2400:4686);

% plot in 2D before processing
figure(1)
subplot(1,2,1); imagesc(im1); colorbar; axis image;
subplot(1,2,2); imagesc(im2); colorbar; axis image;


%% SIZE OF LEFT-HS LINE
im3 = x(1851:2500,1721:2215); scale = 0.656; period = 16; thr = 0.5; % USE FOR LEFT HAND SIDE LINE
% im3 = x(1601:2500,3471:4140); scale = 1.33; period = 24; thr = 0.5; % USE FOR RIGHT HAND SIDE LINE

im3 = max(im3(:))-im3;

bg1 = im3(1:100,:);
bg2 = im3(end-100:end,:);
bg = mean([bg1(:); bg2(:)]);
im3 = im3-bg;

figure(1)
subplot(1,2,1); imagesc(im3);
subplot(1,2,2); imagesc(im3); axis image

% figure(2)


width_i = [];
for line_i = 1:length(im3)

    a = im3(line_i,:);
    a = a./max(a(:));
    b = [];
    
    % turn into single data points
    for i=1:period:length(a)
        b(end+1) = a(i); %#ok<SAGROW>
    end

    % find thresholds, via linear interpolation
%     thr = 0.5;
    thr1 = 0;
    thr2 = 0;
    for i=1:length(b)-1;

        % left threshold cross
        if (b(i)<thr && b(i+1)>thr && thr1==0) % only record first 'left' threshold
            thr1 = i + (0.5-b(i))/(b(i+1)-b(i));
        end

        % right threshold cross
        if (b(i)>thr && b(i+1)<thr)
            thr2 = i + (0.5-b(i))/(b(i+1)-b(i));
        end
    end

%     figure(2);
%     plot(1:length(a),a,'x',1:period:length(a),b,'-or');
    
    width_i(line_i) = thr2-thr1; %#ok<SAGROW>
    
end

microns = width_i./scale;
mean(microns)
std(microns)

%%
figure(3)
% g = g+0.0; g = g./max(g(:));
subplot(1,2,1); plot(f);
subplot(1,2,2); plot(g);