calculateTForm.m

%CALCULATETFORM estimate the affine transformation to compensate for a not
%   well alligned camera image.
%
% TFORM = CALCULATETFORM(BIM, ARENASIZE)
%
% BIM a binary image of the arena. Assuming that the arena is white and the
%  largest (white) object in the image.
% ARENASIZE the (real) size of the (square) experimental arena in mm
% 
% TFORM the infered geometric transformation.
%
% Friedrich Kretschmer
% Max-Planck Institute for Brain Research
% sciclist@brain.mpg.de

function tform = calculateTForm(bim, arenaSize)
    %Find connected components
    CC = bwconncomp(bim);
    %Deteremine the number of pixels belonging to each component
    numPixels = cellfun(@numel, CC.PixelIdxList);
    [~, idx] = max(numPixels);

    %Determine the largest blob (should be the arena)
    CC.NumObjects = 1;
    CC.PixelIdxList = {CC.PixelIdxList{idx}};

    %Calculate the convex hull for the arena
    stats = regionprops(CC, 'ConvexHull');

    %Calculate the four corners of the arena
    [~, idx] = min(pdist2([0, 0], stats.ConvexHull));
    topLeft = stats.ConvexHull(idx,:);

    [~, idx] = min(pdist2([size(bim, 2), 0], stats.ConvexHull));
    topRight = stats.ConvexHull(idx,:);

    [~, idx] = min(pdist2([size(bim, 2), size(bim, 1)], stats.ConvexHull));
    bottomRight = stats.ConvexHull(idx,:);

    [~, idx] = min(pdist2([0, size(bim, 1)], stats.ConvexHull));
    bottomLeft = stats.ConvexHull(idx,:);

    arena = [0, 0;...
            arenaSize, 0;...
            arenaSize, arenaSize;...
            0, arenaSize];

    dArena = [topLeft; topRight; bottomRight; bottomLeft];

    %Estimate the affine transformation 
    tform = fitgeotrans(dArena, arena, 'affine');
end