function R = rank_indifferencezone(X,delta,imethod);
%--------------------------------------------------------------------------
% This program was used to generate indifference-zone ranking results
% for the paper (http://www.mindboggle.info/papers/):
%
% "Evaluation of 14 nonlinear deformation algorithms 
%  applied to human brain MRI registration" 
%  NeuroImage (2009), doi:10.1016/j.neuroimage.2008.12.037
%  by Arno Klein, Jesper Andersson, Babak A. Ardekani, John Ashburner, 
%     Brian Avants, Ming-Chang Chiang, Gary E. Christensen, D. Louis Collins,
%     James Gee, Pierre Hellier, Joo Hyun Song, Mark Jenkinson, Claude Lepage,
%     Daniel Rueckert, Paul Thompson, Tom Vercauteren, Roger P. Woods, 
%     J. John Mann, and Ramin V. Parsey.
%
% (c) 2008, @rno klein
%--------------------------------------------------------------------------

composite_rank=0;
if composite_rank==0
    
    R = zeros(length(X),length(X));
    for iX = 1:length(X)
      I=find(X-X(iX)>delta);
      if length(I)>0
         R(iX,I) = -1;
      end
      I=find(X-X(iX)<-delta);
      if length(I)>0
         R(iX,I) = 1;
      end
    end
    
else
    nX = length(X);
    R  = X;

    for i1=1:nX-1
      for i2=2:nX
        if i2>i1
          I=find(abs(X(i2)-X(1:i1))<=delta);
          if length(I)>0
             R(i2) = R(I(1));
          end
        end
      end
    end

    for i3=nX:-1:2
        I=find(abs(X(i3)-X)<=delta);
        if length(I)>0
           R(I) = R(I(end));
        end
    end

    tiedr=1;
    if tiedr==1
      R=tiedrank(R);
    else
      R2   = zeros(size(R));
      setr = length(R);
      while prod(R2)==0
        uR    = unique(R);
        maxR  = max(uR);
        if maxR > 0
          I     = find(R==maxR);
          R2(I) = setr;
          setr  = setr-1;
          R(I)  = 0;
        else 
          break
        end
      end  
      R = R2;
    end
end