WiscPlan_v2/WiscPlanPhotonkV125/matlab_frontend/superpix_group.m

function superMask = superpix_group(mask, N_svox_in, orthoPlot)
% this function contains supervoxel grouping
fprintf(['\n' 'Creating ' num2str(N_svox_in) ' SupVox:\n' ])
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);

N_svox = N_svox_in; % number of supervoxels to give as param to parse
converge_factor = 1;
while true
    [L,NumLabels] = superpixels3(canvas3,N_svox);

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

    numSupVox = numel(unique(superMask))-1; % number of created supervoxels
    fprintf([num2str(numSupVox) ' areas created' ])
    
    if abs(numSupVox-N_svox_in)/N_svox_in < 0.2/sqrt(converge_factor)
        
        switch orthoPlot
            case 'yes'
                orthoslice(superMask)
            case 'no'
                fprintf('\n supervoxel volume created! (orthoslice skipped)')
        end
        break
    end
    N_svox2 = N_svox * N_svox_in/numSupVox;
    N_svox = round(converge_factor * N_svox2 + (1-converge_factor)*N_svox);
    converge_factor = converge_factor * 0.95;
    fprintf([' - not ok. ' num2str(numSupVox/N_svox_in) ' of target. New start size: ' num2str(N_svox) '\n'])
    
    if converge_factor < 0.01
%         orthoslice(superMask)
        break
    end
end 
fprintf([' -  ok.\n'])

end