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%TRACKFILE track a mouse in the openfield experiment
%
%TRACKFILE(FILENAME, ARENASIZE, THRESH, BORDER)
%
% FILENAME the input video file
% ARENASIZE the size of the (square) experimental arena in mm
% THRESH the threshold to apply for segmentation (0-1)
% BORDER an additional border that is substracted from the image on all
% sides to avoid tracking problems due to minimal misalignements
%
% the function will generate a .mat file containing the x,y position
% of the mouse (mousePos), the affine transformation matrix (tform)
% that was used to warp the image based on the four corners of the arena
% and the given size of the arena (arenaSize).
%
% Friedrich Kretschmer
% Max-Planck Institute for Brain Research
% sciclist@brain.mpg.de
function trackFile(fileName, arenaSize, thresh, border)
%Save a video containing the tracking result
doSaveDemo = true;
[pathstr, name, ~] = fileparts(fileName);
vid = VideoReader(fileName);
%First frame is used to estimate the affine transformation matrix
im = vid.read(1);
%Threshold image
bim = im2bw(im, thresh);
%Estimate affine transformation
tform = calculateTForm(bim, arenaSize);
nFrames = round(vid.Duration * vid.FrameRate);
frameRate = vid.FrameRate;
mousePos = NaN(nFrames, 2);
if doSaveDemo
vidWriter = VideoWriter([pathstr, filesep, name, '_tracked.avi']);
open(vidWriter);
fig = figure('NumberTitle', 'off', 'Position', [100,100,482,500]);
ax = axes('Parent', fig, 'Units', 'normalized', 'Position', [0,0,1,1]);
pim = imshow(zeros(arenaSize-(2*border), arenaSize-(2*border), 3), 'Parent', ax);
hold on
p = plot(0,0, 'r+', 'markerSize', 14, 'LineWidth', 2);
axis equal
end
for frameIdx = 1:nFrames
try
im = vid.read(frameIdx);
%Threshold image
bim = im2bw(im, thresh);
%And warp the image according to the affine transformation
wim = imwarp(bim, tform, 'OutputView', imref2d([arenaSize, arenaSize]));
%Remove border from image (might not be perfectly aligned and
%black affects tracking
bwim = wim((border+1):end-border,(border+1):end-border);
% Detect the mouse
CC = bwconncomp(~bwim);
%Deteremine the number of pixels belonging to each component
numPixels = cellfun(@numel, CC.PixelIdxList);
[~, idx] = max(numPixels);
%Determine the largest blob (should be the mouse)
if ~isempty(idx)
CC.NumObjects = 1;
CC.PixelIdxList = {CC.PixelIdxList{idx}};
stats = regionprops(CC, 'Centroid');
mousePos(frameIdx, :) = stats.Centroid + [border+1, border+1];
else
mousePos(frameIdx,:) = [NaN,NaN];
end
%Generate an image overlayed with the tracking result
if doSaveDemo
wim = imwarp(im, tform, 'OutputView', imref2d([arenaSize, arenaSize]));
set(pim, 'CData', wim((border+1):end-border,(border+1):end-border,:));
set(fig, 'Name', [name, ': ', num2str(frameIdx),'/',num2str(nFrames)]);
hold on
if ~isempty(idx)
set(p, 'XData', stats.Centroid(1), 'YData', stats.Centroid(2));
else
set(p, 'XData', 0, 'YData', 0);
end
drawnow();
writeVideo(vidWriter, getframe(fig));
end
catch exception
%The number of frames is often incorrectly read.
if(strcmp(exception.identifier, 'MATLAB:audiovideo:VideoReader:invalidFrameVarFrameRate'))
%Just interrupt if file ends early
break
else
rethrow(exception);
end
end
end
%Save results
save([pathstr, filesep, name], 'mousePos', 'tform', 'arenaSize', 'frameRate');
if doSaveDemo
close(vidWriter);
close(fig);
end
end