name_root=['D:\technical\codes\IfU-IPG-PTV\working_folder_colloid_dup/'];


for_small_stuff=3;
hist_scale=30;
for_max_search=30;

img=1;
i=19740;
name=[name_root,'img\cam',num2Str(img),'.',num2Str(i)];
I = imread(name);
%imshow(I);

filt1 = imopen(I, ones(for_small_stuff,for_small_stuff));%remove stuff that has less than 3 by 3 area
filt1 = adapthisteq(filt1, 'ClipLimit',0.1,'NumTiles',[hist_scale hist_scale],'NBins',256);
%imshow(filt1);
for_max = imextendedmax(filt1,for_max_search);
L2 = bwlabel(for_max);
%hold on;
stats2  = regionprops(L2,'Centroid');
%length(stats2)
for_max=for_max-for_max;
for j = 1:length(stats2)
   for_max(round(stats2(j).Centroid(2)),round(stats2(j).Centroid(1)))=255;
end


for_perim = imclose(filt1, ones(for_small_stuff,for_small_stuff));
for_perim = im2bw(for_perim, graythresh(I));
%imshow(for_perim);
perim = bwperim(for_perim);
%overlay1 = imoverlay(filt1, perim, [0.3 1 0.3]);%
%imshow(overlay1)


for_water = imcomplement(filt1);
%imshow(for_water);
%imshow(for_perim)
%imshow(for_max)
for_water = imimposemin(for_water,  ~for_perim |for_max);
L = watershed(for_water);
stats3  = regionprops(L,'Centroid');
% imshow(label2rgb(L))
% 
% hold on;
% for j = 1:length(stats2)
%     plot(stats2(j).Centroid(1),stats2(j).Centroid(2),'r.');
% end
% for j = 1:length(stats3)
%     plot(stats3(j).Centroid(1),stats3(j).Centroid(2),'k.');
% end

% title(sprintf('image %d, frame %d',img,i))

ad_border=zeros(1024,1280);
for i=1+1:1024-1
    for j=1+1:1280-1
        if L(i,j)==0
            if L(i+1,j)>1 & L(i-1,j)>1 & L(i+1,j)~=L(i-1,j)
                ad_border(i,j)=1;
            end
            if L(i,j+1)>1 & L(i,j-1)>1 & L(i,j+1)~=L(i,j-1)
                ad_border(i,j)=1;
            end
            if L(i+1,j+1)>1 & L(i-1,j-1)>1 & L(i+1,j+1)~=L(i-1,j-1)
                ad_border(i,j)=1;
            end
            if L(i+1,j-1)>1 & L(i-1,j+1)>1 & L(i+1,j-1)~=L(i-1,j+1)
                ad_border(i,j)=1;
            end
        end
    end
end
ad_border=logical(ad_border);
figure;
overlay = imoverlay(label2rgb(L),ad_border, [0 0 0]);%
imshow(overlay);
hold on;
for j = 1:length(stats3)
    plot(stats3(j).Centroid(1),stats3(j).Centroid(2),'k.');
end
title(sprintf('image %d, frame %d',img,i))


figure;
overlay2 = imoverlay(filt1, perim, [0.3 1 0.3]);%
imshow(overlay2)
title(sprintf('image %d, frame %d',img,i))


num_max=length(stats2)
num_cells=length(stats3)