% MATLAB R2019b
% 
% This script reads a microscope image of hand-picked zircon mounts and 
% overlays contours generated by 'ImageProcess_Zr-contour-xy.py' from the
% same image. The contours can be manually adjusted from the user. The new
% contour is accepted by a double click and by typing 'n'(-Enter) or rejected by
% typing 'y'(-Enter) into the command window. Then the next contour pops up a.s.o.  
% As an output a table with the area value of the contoured object is generated.
%
% USER INPUT:
% Image - filename.png (line 25)
% x|y coordinates of the contour vertices - filename.csv (line 28 and 29)
%
% Created: 12/08/2021
% Last Modified: 07/09/2021
% Author: Isabel Zutterkirch

clc
clear
close all

%% INPUT

% image
I= imread('filename.png');
% x- and y-coordinate of the contour vertices, which are generated by the 
% python script "ImageProcess_Zr-contour-xy.py" 
x= regexp(fileread('filename.csv'),'[\n\r]+','split');
y= regexp(fileread('filename.csv'),'[\n\r]+','split');

%% PROCESSING

% iteration over contour vertices
% to minimize the amount of vertices, set the number to only take the nth
n=10;
% tracking the iteration, area in the table will be 0 when the contour is 
% rejected, see if-statement
j=0;
% storage for the accepted polygons
NewPoly=[];
% iteration
for i= 1:1:length(x)
    strx = regexprep(x{1,i},',',' ');
    stry = regexprep(y{1,i},',',' ');
    xcoo= str2num(strx);
    ycoo= str2num(stry);
    % take nth element on list
    xcoo_modi= xcoo(1:n:end);
    ycoo_modi= ycoo(1:n:end);
    % create tuple and transpose
    pgon=[xcoo_modi;ycoo_modi];
    pgon_transposed= pgon.';
    % plot image and polygon
    imshow(I);
    h= drawpolygon('Position', pgon_transposed);
    xlim([min(xcoo_modi)-50 max(xcoo_modi)+50])
    ylim([min(ycoo_modi)-20 max(ycoo_modi)+20])
    % wait for user modification until user double clicks
    wait(h)
    % get new positions
    pos= h.Position();
    % figure()
    new_polygon=polyshape(pos(:,1).', pos(:,2).');
    plot(new_polygon)
    NewPoly= [NewPoly,new_polygon];
    % tracking the iteration and adding the area value to the list 'A'
    j=j+1;
    prompt= 'Would you like to reject the contour? y/n (or s for stop): ';
    str= input(prompt,'s');
    if str == 'n'
        A(j)= area(new_polygon);
        area(new_polygon)
    elseif str == 's'
        break
    elseif i== length(x)
        break
    else
        
    end
end
% transpose A
a= A.';

%% OUTPUT

% csv table with area values
csvwrite('2123198_bw_Area.csv',a)
% optional for checking save desired variables in a matrix
%save ('2123198_Poly.mat','I','x','y','a','NewPoly')