blobTrackExtractMouse.m

% Extracts the biggest blob out of a binary image
%
%

function [bwmouse, o] = blobTrackExtractMouse(bw,varargin);

o  =mbparse.output();

p = inputParser();
p.addParamValue('maxPixels',5000);
p.addParamValue('minPixels',200);
p.addParamValue('backgroundMask',[]);

p.parse(varargin{:});
q = p.Results();


cc = bwconncomp(bw);


bwe = [];

neededMany = false;

if neededMany
    while cc.NumObjects == 1
        se = strel('diamond',4); % structuring element
        if isempty(bwe)
            bwe = bw;
        end
        
        % erode a little bit more
        bwe = imerode(bwe,se);
        
        cc = bwconncomp(bwe);
        disp('eroding a little bit');
    end
end








% check the size of secon componet
indexSecondBest = 1;

for i=1:length(cc.PixelIdxList)
   myArea(i) = length(cc.PixelIdxList{i}); 
end

[nestArea,orderedIndices] = sort(myArea,'descend');

indexSecondBest = orderedIndices(1);


mousePixelIndices = cc.PixelIdxList{indexSecondBest};
N = length(cc.PixelIdxList{indexSecondBest});

io = bw(cc.PixelIdxList{indexSecondBest});
bwmouse = false(size(bw));
bwmouse(mousePixelIndices) = true;

s  = regionprops(bwmouse, 'centroid');
o.assignprop('Centroid',s.Centroid);
o.assignprop('Area',N);

%o.echo('mouse has %d pixels ',N);