blobTrack.m

% Tracks the dynamics of an object  by binarization
%
% INPUT
%  hvideo  : handle to a mbvid.mbVideoReader object
%
%  FLAGS
%
%   'frames'        : default: [] or '*' (analyhses all frames
%                      sequentially)
%
%
%   Image analysis
%   --------------
%
%  'erosion' : default 8
%
%  'binarizationThreshold' : default 0.9
% 
%
%  Depiction
%  ---------
% 
%  'show'    : default : 0 
% 
%  'nfig'    : default: 1
%
%
%   Performance
%   -----------
%
%   'NumWorkers'   : default 1 (no multicore computation) 
%   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%
%  OUTPUT
%  
%  track   :  
%
% 
%  'centers'
%
%  'areas'
%
%  'FLAGS'
% 
%
%   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% SYNTAX
%
% o = blobTrack(hvideo,'show',true);
%
% o = blobTrack(hvideo,'show',0,'mask',mask);
%
% % Checking on a single frame
% 
% o = blobTrack(hvideo,'show',true,'frames',128);

function [track,o] = blobTrack(hvideo,varargin);

o =mbparse.output();

p = inputParser();
p.addParamValue('frames',[]);
p.addParamValue('show',false);
p.addParamValue('nfig','new');

p.addParamValue('useMask',true);
p.addParamValue('useBackground',false);

p.addParamValue('updateBackground',false);
p.addParamValue('updateBackgroundInterval',20);
p.addParamValue('updateBackgroundExtent',100);
p.addParamValue('useEnhancement',false);
p.addParamValue('NumWorkers',1);
p.addParamValue('opencv',false);

p.addParamValue('mask',[]);

p.addParamValue('binarizationThreshold',0.9);
p.addParamValue('erosion',8);

p.addParamValue('intermediateSaveInterval',[]);
p.addParamValue('intermediateSaveFile','blobTracktemp.mat');

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


N = hvideo.NumberOfFrames();

if q.show
    thisFigure = mbgraph.figure(q.nfig);
end

if isempty(q.frames)
    frames = 1:N;
else
    frames = q.frames;
end

centers = zeros(0,2);
areas   =  [];
failedFrames = [];
counter = 1;

if ischar(q.mask)
   q.mask = mbio.read(q.mask);
end



%%
checkCluster = mbparse.multicore.checkPool('matlab_workers',q.NumWorkers);


tic;
if checkCluster.NumWorkersFinal == 1
    for i = frames;
        %
        % b: black and white
        %
        % bm: segmented (just the mouse)
        %
        [b,original,bm,obm,ueroded] = looped(q,hvideo,i);
        
        if isempty(bm)
            failedFrames(i) = i;
            %centers(i,:) = centers(i-1,:);
            %areas(i)     = areas(i-1) ;     
        else
            centers(i,:) = obm.Centroid;
            areas(i)     = obm.Area;
        end
        
        
        
        if q.show
            figure(thisFigure);
            subplot(2,2,1);
            imshow(original);
            
            h = mbimg.showTile('centerhv',obm.Centroid,'width',40,'height',40);
             title('estimated location on original');
            
            subplot(2,2,2);
            imshow(ueroded,[]);
            title('Erosion');
            
            subplot(2,2,3);
            imshow(b,[]);
            title('binarization');
            
             subplot(2,2,4);
            imshow(bm,[]);
            title('segmentation (connected components)');
            
            set(gcf,'name',sprintf('Frame %d',i));
            
        end
        
        counter = counter+1;
        
        if mod(counter,1000) == 0;
           o.echo('Done with %d frames',counter); 
        end
         % mbparse.intermediateResultsSave(q,counter,{areas,centers});
        
    end
    
else
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % 
    %
    
    q.background = []; % to avoid problems with the parforr
    parfor i = frames;
        
        
        
        if q.useBackground
            averageNeighboorhood = hvideo.average('frames',....
                [i-q.updateBackgroundExtent:q.updateBackgroundInterval:i+q.updateBackgroundExtent]);
        else
            averageNeighboorhood = [];
        end
        
       
        [b,original]  = blobTrackBinarize(hvideo,i,q.mask,q);
        
        if isempty(b)
             failedFrames(i) = i;
        else
            [bm,obm]      = blobTrackExtractMouse(b);
            
            if isempty(bm)
                failedFrames(i) = i;
                %centers(i,:) = centers(i-1,:);
                %areas(i)     = areas(i-1) ;
                
            else
                centers(i,:) = obm.Centroid;
                areas(i)     = obm.Area;
            end
        end
        
     
        %
        % mbparse.intermediateResultsSave(q,counter,{areas,centers});
    end
    
end
toc;

o.assignprop('centers',fliplr(centers));
o.assignprop('areas',areas);
o.assignprop('failedFrames',failedFrames);

track = mbvid.videotrack.patchtrack('video',hvideo,'data',fliplr(centers));
o.ok = true;


function [ublackAndWhite,original,uSegmented,obm,ueroded] = looped(q,hvideo,i);

if q.useBackground
    averageNeighboorhood = hvideo.average('frames',....
        [i-q.updateBackgroundExtent:q.updateBackgroundInterval:i+q.updateBackgroundExtent]);
else
    averageNeighboorhood = [];
end
q.background = averageNeighboorhood;
[ublackAndWhite,original,ueroded]  = blobTrackBinarize(hvideo,i,q.mask,q);
[uSegmented,obm]      = blobTrackExtractMouse(ublackAndWhite);