smoothbinvol.m

function vol = smoothbinvol(vol, layer)
%
% vol=smoothbinvol(vol,layer)
%
% perform a memory-limited 3D image smoothing
%
% author: Qianqian Fang <q.fang at neu.edu>
%
% input:
%     vol: a 3D volumetric image to be smoothed
%     layer: number of iterations for the smoothing
%
% output:
%     vol: the volumetric image after smoothing
%
% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
%

dim = size(vol);
dxy = dim(1) * dim(2);
fulllen = prod(dim);

weight = 1 ./ 6.;
step = 4000;

% in case vol is a logical
vol = double(vol);
offs = [1, -1, dim(1), -dim(1), dxy, -dxy];

for i = 1:layer
    % find all non-zero values
    idx = find(vol);
    % get the neighbors of all the non-zero values
    % this may cause wrapping -- TODO
    val = vol(idx);
    for k = 1:6
        nextidx = idx + offs(k);
        % find all 1-valued voxels that are located within the domain
        goodidx = find(nextidx > 0 & nextidx < fulllen);
        % for all neighboring voxels, add a fraction from the non-0 voxels
        % problematic when running in parallel (racing)
        len = length(goodidx);
        % control granualarity with step
        if (len > step)
            for j = 1:step:len - step
                vol(nextidx(goodidx(j:j + step - 1))) = vol(nextidx(goodidx(j:j + step - 1))) + weight * val(goodidx(j:j + step - 1));
            end
            vol(nextidx(goodidx(j + step:end))) = vol(nextidx(goodidx(j + step:end))) + weight * val(goodidx(j + step:end));
        else
            vol(nextidx(goodidx)) = vol(nextidx(goodidx)) + weight * val(goodidx);
        end
        % the above line may change the values of the non-zero voxels, recover
        % them
    end
    vol(idx) = val;
end