cell_connect_tracks.m

function cell_connect_tracks(case_string)

track_dir = fullfile('cases',case_string,'tracks');

num_frms = numel(dir([track_dir ,'/*.mat']));

tracks_euler = zeros(num_frms,1000,9);

for volume = 1 : num_frms-1
    
    load([track_dir,'/tracks_',num2str(volume,'%.4d'),'.mat']);
    
    tracks_euler(volume,1:size(tracks,1),:) = tracks;
    
end;

num_of_tracks = 0;

tracks_lagrangian = zeros(num_frms,4,1000);

for volume = 1 : num_frms
    
    for p = 1:size(tracks_euler,2)
        
        if tracks_euler(volume,p,1) ~= 0
            
            num_of_tracks = num_of_tracks + 1;
            
            tracks_lagrangian(volume,:,num_of_tracks) = tracks_euler(volume,p,[1,4:6]);
            tracks_lagrangian(volume+1,:,num_of_tracks) = tracks_euler(volume,p,[2,7:9]);
            target_num = tracks_euler(volume,p,2);
            tracks_euler(volume,p,:) = zeros(1,9);
            
            for nxt_v = volume + 1 : num_frms
                
                ind = tracks_euler(nxt_v,:,1) == target_num;
                
                if sum(ind) == 0
                    break
                end
                
                tracks_lagrangian(nxt_v,:,num_of_tracks) = tracks_euler(nxt_v,ind,[1,4:6]);
                tracks_lagrangian(nxt_v+1,:,num_of_tracks) = tracks_euler(nxt_v,ind,[2,7:9]);
                
                target_num = tracks_euler(nxt_v,ind,2);
                tracks_euler(nxt_v,ind,:) = zeros(1,9);
            end
        end
    end
    
end

% display(sprintf('Number of tracks : %.4d',num_of_tracks));


fst_frame = zeros(1, num_of_tracks);
lst_frame = zeros(1, num_of_tracks);

for p = 1 : num_of_tracks
    
    current_track = tracks_lagrangian(:,:,p);
    ind = find(current_track(:,1) ~=0);
    fst_frame(p) = min(ind);
    lst_frame(p) = max(ind);
    
end;


for p1 = 1 : num_of_tracks
    
    p1_t =  lst_frame(p1);
    if p1_t == 0
        continue
    end
    
    p1_p = tracks_lagrangian(p1_t ,2:4,p1);
    
    for p2 = 1 : num_of_tracks
        
        p2_t =  fst_frame(p2);
        if p2_t == 0
            continue
        end
        
        p2_p = tracks_lagrangian(p2_t ,2:4,p2);
        
        dis = sum((p1_p-p2_p).^2)^0.5;
        
        if (p1_t == p2_t)&&(dis<5)
            tracks_lagrangian(fst_frame(p2):lst_frame(p2),:,p1) = tracks_lagrangian(fst_frame(p2):lst_frame(p2) ,:,p2);
            lst_frame(p1) = lst_frame(p2);
            fst_frame(p2) = 0;
            lst_frame(p2) = 0;
        end;
        
        if (p1_t + 1 == p2_t)&&(dis<10)
            tracks_lagrangian(fst_frame(p2):lst_frame(p2),:,p1) = tracks_lagrangian(fst_frame(p2):lst_frame(p2) ,:,p2);
            tracks_lagrangian(lst_frame(p1)+1,:,p1)  =  ...
                (tracks_lagrangian(lst_frame(p1),:,p1) + tracks_lagrangian(lst_frame(p1)+2,:,p1) )/2;
            lst_frame(p1) = lst_frame(p2);
            fst_frame(p2) = 0;
            lst_frame(p2) = 0;
        end;
        
    end
end

ind = find(fst_frame ~=0);
tracks_lagrangian = tracks_lagrangian(:,:,ind);
num_of_tracks = length(ind);
% display(sprintf('Number of tracks after connection : %.4d',num_of_tracks));

duration = zeros(num_of_tracks,1);
position = zeros(num_of_tracks,3);
displacement = zeros(num_of_tracks,1);

for p = 1 : num_of_tracks
    
    current_track = tracks_lagrangian(:,:,p);
    
    ind = find(current_track(:,1) ~= 0);
    s0 = current_track(ind(1),2:4);
    st = current_track(ind(end),2:4);
    
    duration(p) = length(ind);
    position(p,:) = mean(current_track(ind,2:4),1);
    displacement(p) = sum((st - s0).^2)^0.5;
    
end

% [duration,order] = sort(duration,'descend');
[duration,order] = sort(displacement,'descend');
tracks_order = tracks_lagrangian(:,:,order);
save(fullfile(track_dir,'tracks.mat'),'tracks_order')