%% Master file for segmenting gamma prime particles

close all
[fname, pathname] = uigetfile({'*.tif', 'image files (*.tif)'}, ...
    'Select the original intensity *.tif image');
filename = [pathname fname];
scrsz = get(0,'ScreenSize');
clear pathname

% filename is the original intensity image
I = imread(filename);
I = imcrop(I); close(1)
filename = strrep(filename,'.tif','_crop.tif');
imwrite(I,filename,'tif')

% Find previously segmented objects
if exist(strrep(filename,'.tif','_auto1.tif')) == 2
    J_master = imread(strrep(filename,'.tif','_auto1.tif'));
else
    J_master = I == -1;
end

%% Detect seeds & Grow region

% Crop the original area (or else it is really slow)
I = imread(filename);
I(:,1) = 255; I(:,end) = 255; 
I(1,:) = 255; I(end,:) = 255; 
clear I2
K4 = bwperim(J_master);
I_tmp = I; I_tmp(K4) = 255; 
I2(:,:,1) = I_tmp;
I_tmp = I; I_tmp(K4) = 0; 
I2(:,:,2) = I_tmp;
I_tmp = I; I_tmp(K4) = 0; 
I2(:,:,3) = I_tmp;
[I2 rect] = imcrop(I2);
rect = round(rect);
I = I(rect(2):rect(2)+rect(4)-1,rect(1):rect(1)+rect(3)-1);
clear I2 I_tmp K4
close all

% Select the points
% Hit return to exit
figure('Name','Select point(s) and hit return to exit','NumberTitle','off')
imshow(I,[]);
set(gcf,'Position',[1 1 scrsz(3) scrsz(4)])
[y1,x1] = ginput; 
x1 = round(x1); y1 = round(y1);
close(1)

% Grow region

% What are the optimum parameters based on Tschopp et al MS&T (2010)?
% Parameters get passed into the region growing algorithm
parameters.fill_holes_flag = 0;    
parameters.fill_holes_mod = 100;
parameters.output_flag = 1;
parameters.output_mod = 200;
parameters.min_size = 100;
parameters.max_size = 10000000;
parameters.whole_region = 0;
parameters.boundary_layer = 15; 
parameters.image_growth_flag = 0;
parameters.image_growth_file = 'image99.tif';
parameters.decreasing_max = 10;
parameters.trace_boundary = 0;
parameters.threshplot = 0;
parameters.nhood_size = 5;      %m
parameters.nhood_median = 9;    %c
parameters.f_ceiling = 1;       
parameters.w1_reduce = 1;

% The function that executes it all!
tic
[J,thresh_plot] = segment_particle_RegionGrow(I,x1,y1,parameters);
K = J_master(rect(2):rect(2)+rect(4)-1,rect(1):rect(1)+rect(3)-1);
K(J) = 1;
J_master(rect(2):rect(2)+rect(4)-1,rect(1):rect(1)+rect(3)-1) = K;
close all
toc

%% Save segmentation

imwrite(J_master, strrep(filename,'.tif','_auto1.tif'),'tif')

I = imread(filename);
I(:,1) = 255; I(:,end) = 255; 
I(1,:) = 255; I(end,:) = 255; 

clear I2
K4 = bwperim(J_master);
I_tmp = I; I_tmp(K4) = 255; 
I2(:,:,1) = I_tmp;
I_tmp = I; I_tmp(K4) = 0; 
I2(:,:,2) = I_tmp;
I_tmp = I; I_tmp(K4) = 0; 
I2(:,:,3) = I_tmp;
imwrite(I2, strrep(filename,'.tif','_auto2.tif'),'tif')
clear I2 I_tmp K4