blobTrackBinarize.m

%
% binarization
%
function [bw,u,uceroded] = blobTrackBinarize(g2,i,maskInside,q);

background           = q.background;
useEnhancement       = q.useEnhancement;


% i = 5600;
try
    u= g2.read(i);
catch
    disp(sprintf('Skipping frame %d for reading problems.',i));
    % sometimes the video reader marks frames tha do not actually exist!
    bw = [];
    u = [];
    return
end

u = rgb2gray(u);

if ~isempty(background)
   ub = double(u)-background;
else
    ub = u;
end



  ubReversed = imcomplement((ub));

  if useEnhancement
      ucg = imadjust(ubReversed);
  else
      ucg = ubReversed;
  end

 
 
 % smarts 
 if ~isempty(maskInside)
    % ucg = ucg./max(ucg(:));
     ucg = mbimg.mask.applyMask(ucg,maskInside);
 end
 
 
 useSingleErosion = true;
 if useSingleErosion
%      ucgi = (imerode(ucg,strel('diamond',20)));
%      ucgi = ucgi./max(ucgi(:));
%      
%      t = graythresh(ucgi);
%      t = 0.8;
%      
     
     uceroded = imerode(ucg,strel('diamond',q.erosion));

     %bw = im2bw(mbimg.binarize(mbimg.normalize(uceroded),q.binarizationThreshold));
     bw = mbimg.binarize(mbimg.normalize(uceroded),q.binarizationThreshold);
     return
     
 end

 
 if useEnhancement
     % direct 
     ucgi = imerode(ucg,strel('diamond',5));
     t = graythresh(ucgi);
     bw = im2bw(ucgi,t);
     return
     
 end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 
% elliminates ears
%

elliminateEars = true;
if elliminateEars
    sec = strel('diamond',9); % structuring element
    uh = imclose(ucg,sec);
else
    uh = ucg;
end

%
% erode tails
%
see = strel('diamond',12); % structuring element
ue = imerode(uh,see);
ue = mat2gray(ue);


% gets blobs
%t = graythresh(ue);

%ue =  mat2gray(ucg);

try
    thresh = multithresh(ue,3);
catch
    thresh = multithresh(ue,2);
end

t = thresh(end);


%ue = mbimg.mask.applyMask(ue,maskInside);

bwn = im2bw(ue,t);


%
% 
% erode tails
%
%

seo = strel('diamond',12); % structuring element
bw = imopen(bwn,seo);

if length(find(bw))<30
    bw = bwn;
   %error('Norl! the mouse disapeared!'); 
end


if length(find(bw))<30
   
   %error('Norl! the mouse disapeared!'); 
   bw = [];
end