trackBEEtagsAcrossFrames.m

%% Beta/example code to track beetags across all frames of a video

%codelist = [109 36]; %List of codes in the frame - supplying this is more robust, but optional

[filename pathname] = uigetfile('*'); %User-specified file input - this can be modified to be automated if you need to track over lots of files
mov = VideoReader([pathname filename]); %Make a VideoReader object for the movie

nframes = mov.NumberOfFrames; %how many frames are in the video?


%Create empty frame for tracking output
trackingData = struct();

%% Loop across frames
for i = 1:nframes
    
    %% Read in each frames and track codes in it
    disp(strcat('tracking frame_', num2str(i), '_of_', num2str(nframes)));
    im = read(mov, i);
    
    %Two example options for tracking in each frame (only comment in one at a time):
    
    %example 1, maybe a little more robust but slower
    
    F = locateCodes(im, 'threshMode', 1, 'bradleyFilterSize', [15 15], 'bradleyThreshold', 3);
    
    
    %example option 2, faster, simpler - just uses a simple threshold value instead
    %of doing adaptive filtering, less good for inhomogenously lit images
    
    %F = locateCodes(im, 'thresh', 0.25);
    
    %Append this single frame data to the master tracking output
    trackingData(i).F = F;
    
end


%% if there's no 'codelist' object defined, extract it from all the unique codes tracked in the movie
if ~exist('codelist')
    for i = 1:nframes
        %for i = 1:numel(trackingData)
        curNumbers = [trackingData(i).F.number];
        %%
        if i == 1
            allNumbers = [] ;
        else
            allNumbers = [allNumbers curNumbers];
        end
        codelist = unique(allNumbers);
    end
end
%%
disp('rearranging data into easier format');
trackingDataReshaped = struct();
for i = 1:nframes
    %%
    F = trackingData(i).F;
    for j = 1:numel(codelist)
        %%
        if ~isempty(F)
            FS = F([F.number] == codelist(j));
            if ~isempty(FS)
                trackingDataReshaped(j).CentroidX(i) = FS.Centroid(1);
                trackingDataReshaped(j).CentroidY(i) = FS.Centroid(2);
                trackingDataReshaped(j).FrontX(i) = FS.frontX;
                trackingDataReshaped(j).FrontY(i) = FS.frontY;
                trackingDataReshaped(j).number(i) = FS.number;
            end
        end
    end
    
end


%% Save data
save('trackingData.mat', 'trackingDataReshaped')

%% Replay video
disp('replaying video with tracking data shown');
TD = trackingDataReshaped;

outputMovieName = 'ExampleTrackingMovie.avi';
outputMovie = 0; %Set to 1 if you want to save a movie, set to 0 if not

%If we're in movie writing mode, output the video
if outputMovie == 0
   vidObj = VideoWriter(outputMovieName);
   open(vidObj)
end

for i = 1:nframes
    %%
    im =  read(mov, i);
    imshow(im);
    hold on;
    for j = 1:numel(TD)
        if numel(TD(j).CentroidX) >= i & ~isempty(TD(j).CentroidX(i))
            try
            plot([TD(j).CentroidX(i) TD(j).FrontX(i)], [TD(j).CentroidY(i) TD(j).FrontY(i)], 'b-','LineWidth', 3);
            text(TD(j).CentroidX(i), TD(j).CentroidY(i), num2str(TD(j).number(i)),'FontSize', 25, 'Color', 'r');
            catch
                continue
            end
        end
    end
    drawnow
    currFrame = getframe;
    writeVideo(vidObj, currFrame);
    hold off;
end

close(vidObj);