WiscPlan_v2/WiscPlanPhotonkV125/matlab_frontend/superpix_group.m

function superMask = superpix_group(mask, N_svox)
% this function contains supervoxel grouping

canvas2 = sqrt(bwdist(1-mask));
% orthoslice (canvas2)

% find box crop of ROI
ymin = 0;
ymax = 0;
for yi = 1:size(mask,1)
    data = mask(yi, :,:);
    if max(data(:)) >0
        if ymin == 0
            ymin = yi;
        end
        ymax = yi;
    end
end
xmin = 0;
xmax = 0;
for xi = 1:size(mask,2)
    data = mask(:,xi,:);
    if max(data(:)) >0
        if xmin == 0
            xmin = xi;
        end
        xmax = xi;
    end
end
zmin = 0;
zmax = 0;
for zi = 1:size(mask,3)
    data = mask(:,:,zi);
    if max(data(:)) >0
        if zmin == 0
            zmin = zi;
        end
        zmax = zi;
    end
end

canvas3 = canvas2(ymin:ymax, xmin:xmax, zmin:zmax);

[L,NumLabels] = superpixels3(canvas3,N_svox);

superMask = zeros(size(mask));
superMask(ymin:ymax, xmin:xmax, zmin:zmax) = L;
superMask(logical(1-mask)) = 0;

disp([num2str(numel(unique(superMask))-1) ' areas created.' ])

end