function [RegionImage,RegionBinaryImage,RegionX,RegionY]=PreProcessRegion(RegionLoc,INPUT_IM,SmallObjThres,RoundThresh,EnableFiltering)
% This function deletes the small and the rounded objects and creates
% the images of the zone to be process by the entropyfilter.
% Use:
% [RegionImage,RegionBinaryImage]=PreProcessRegion(RegionLoc,INPUT_IM,SmallObjThres,EnableFiltering)
% Where--
% RegionLoc=>Region area loaded from locations file
% INPUT_IM =>Input Image variable
% SmallObjThres => Threshold to define an object as small and delete it
% RoundThresh => Coeff to define an object as round and delete it
% EnableFiltering => Flag (1 or 0) to Enable filtering small and rounded
% objects
% (c) Gustavo Liņan Cembrano
% IMSE-CNM-CSIC
% linan@imse-cnm.csic.es

Region=zeros(size(INPUT_IM,1),size(INPUT_IM,2));
Region(RegionLoc)=1;
RegionProps=regionprops(Region,'centroid');
RegionX=RegionProps.Centroid(1);
RegionY=RegionProps.Centroid(2);
RegionBinaryImage=regionprops(Region,'Image');
RegionBinaryImage=RegionBinaryImage.Image;
RegionBBox=regionprops(Region,'BoundingBox');
RegionBBox=RegionBBox.BoundingBox;
RegionBBox=round(RegionBBox);
RegionImage=uint8(zeros(size(RegionBinaryImage,1),...
    size(RegionBinaryImage,2),...
    3));
RegionImage(:,:,1)=INPUT_IM(RegionBBox(2):RegionBBox(2)+RegionBBox(4)-1,...
    RegionBBox(1):RegionBBox(1)+RegionBBox(3)-1,...
    1);
RegionImage(:,:,2)=INPUT_IM(RegionBBox(2):RegionBBox(2)+RegionBBox(4)-1,...
    RegionBBox(1):RegionBBox(1)+RegionBBox(3)-1,...
    2);
RegionImage(:,:,3)=INPUT_IM(RegionBBox(2):RegionBBox(2)+RegionBBox(4)-1,...
    RegionBBox(1):RegionBBox(1)+RegionBBox(3)-1,...
    3);

if(EnableFiltering)
    %% Removing rounded&small objects from image and substituting them by average around them
    threshold=graythresh(RegionImage);
    bw = im2bw(RegionImage,threshold);
    %Erasing small objects
    bw2 = bwareaopen(bw,SmallObjThres);
    SmallObjects=xor(bw,bw2);
    [L,NUM] = bwlabel(SmallObjects,8);
    fprintf('Deleted %d Small Objects in Region\n',NUM);
    
    RegionBinaryImage=and(RegionBinaryImage,not(SmallObjects));
    % fill a gap in the pen's cap
    se = strel('disk',2);
    bw = imclose(bw2,se);
    
    % fill any holes, so that regionprops can be used to estimate
    % the area enclosed by each of the boundaries
    
    bw = imfill(bw,'holes');
    [B,L] = bwboundaries(bw,'noholes');
    stats = regionprops(L,'Area','Centroid','PixelIdxList');
    
    threshold = RoundThresh; %the closer to 1 the more round
    % loop over the boundaries
    Deleted=0;
    for k = 1:length(B)
        
        % obtain (X,Y) boundary coordinates corresponding to label 'k'
        boundary = B{k};
        
        % compute a simple estimate of the object's perimeter
        delta_sq = diff(boundary).^2;
        perimeter = sum(sqrt(sum(delta_sq,2)));
        
        % obtain the area calculation corresponding to label 'k'
        area = stats(k).Area;
        
        % compute the roundness metric
        metric = 4*pi*area/perimeter^2;
        
        % mark objects above the threshold with a black circle
        if metric > threshold
            Deleted=Deleted+1;
            RegionBinaryImage(stats(k).PixelIdxList)=0;
        end
        
    end
    fprintf('Deleted %d round objects in Region\n',Deleted);
end

end