DL_ImageStrat.m

function [RGB1, out] = DL_ImageStrat(IM2);
%DL_ImageStrat.m

% 'geo-plot' plotter for clustered data, and to create ( and save) imagew

% WAL3
% Dec 2018; Last revision: 12-Dec-2020

% User inputs
Draw_Line = 0; % flag to draw a line across a damaged section

% Make an intensity matched overlay:
figure();
RGB1 = XMASS_tish(IM2(:,:,1),IM2(:,:,2),IM2(:,:,3));


if Draw_Line ==1;
    % get cross-section ( through UI input)
    disp('Make a cross-section selection!');
    [x,y] = ginput(2);
    
    hold on;
    plot(x,y,'LineWidth',5,'Color',[1 1 1]);
    
    % make like 'thick'
    m = ((y(2)-y(1))/(x(2)-x(1))); % slope ( rise/run)
    counter = 1;
    
    
    % plot on top
    I = getimage(gca);
    
    for i = 1: 20; % change x and y by on
        % solve for y = mx+b
        y1(counter) = (round(m*(x(1)))+1*i);% increase 'b' by one...
        x1(counter) = (round(y1(1)/m));
        y1(counter) = -y1(counter);
        counter = counter+1;
        y1(counter) = (round(m*(x(2)))+1*i);
        x1(counter) = (round(y1(2)/m));
        y1(counter) = -y1(counter);
        counter = 1;
        temp = squeeze(improfile(I,x,y,1000));
        if i ==1;
            dat(:,:,i) = temp;
        else
            dat(:,:,i) = temp(1:size(dat,1),:);
        end
    end
    
    
    
    
    dat2 = mean(dat,3);
    smth = 300; % smoothing factor
    figure();
    hold on;
    plot(smooth(dat2(:,1),smth),'r')
    plot(smooth(dat2(:,2),smth),'g')
    plot(smooth(dat2(:,3),smth),'b')
    
end

smooth_param = 10;% how much to spatially smooth

for i = 1:3;
    C(:,:,i) =imgaussfilt(RGB1(:,:,i),smooth_param,'padding','circular');
end

% First, look at Blue vs Green
matA = C(:,:,2) - C(:,:,3);

figure();
subplot(3,1,1)
imshow(RGB1);
subplot(3,1,2)
h = imshow(RGB1);
alpha = (matA+0.2);
BW1 = imbinarize(matA);
alpha(alpha<0.25) = 0;
set(h, 'AlphaData', BW1);
subplot(3,1,3)
h2 = imshow(RGB1);
alpha = -(matA)+0.2;
alpha(alpha<0.3) = 0;
BW2 = imbinarize(alpha);
set(h2, 'AlphaData', alpha);




% Plot boundires
B = bwboundaries(BW1);

figure();
imagesc(RGB1);

hold on;
for i = 1:size(B,1)
    plot(B{i}(:,2),B{i}(:,1),'LineWidth',2,'Color',[1 1 1])
end

title('blue and green overlap');


% next, Green vs Red...
clear matA
matA = C(:,:,1) - C(:,:,2);


figure();
subplot(3,1,1)
imshow(RGB1);
subplot(3,1,2)
h = imshow(RGB1);
alpha = (matA+0.2);
BW1 = imbinarize(matA);
alpha(alpha<0.25) = 0;
set(h, 'AlphaData', BW1);
out.R = BW1;
subplot(3,1,3)
h2 = imshow(RGB1);
alpha = -(matA)+0.2;
alpha(alpha<0.3) = 0;
BW2 = imbinarize(alpha);
set(h2, 'AlphaData', alpha);
out.B = BW2;

% get ouptupts
for i = 1: 3
    out.All(:,:,i) = imbinarize(C(:,:,i));
end

% Plot boundires
B2 = bwboundaries(BW1);

figure();
imagesc(RGB1);

hold on;
for i = 1:size(B2,1)
    plot(B2{i}(:,2),B2{i}(:,1),'LineWidth',2,'Color',[1 1 1])
end
title('red and green overlap')

out.B = B;
out.B2 = B2;