Atlas merge code

merge_manifold.m

function [atlas] = merge_manifold()
% merge atlas2 into atlas, return a new atlas
% this code performs a "Brute force" merge where all the charts of the second
% atlas are checked for nearness to the first atlas, and then merged in 
atlas1 = coco_bd_read('cylinder1', 'atlas');
atlas2 = coco_bd_read('cylinder2', 'atlas');
atlas2charts = atlas2.charts{1:5};
atlas = atlas1;
for i = 1:numel(atlas2charts)
    chart        = atlas2.charts{i};
    nbfunc       = @(x) atlas.isclose(chart, x);
    bd_charts    = atlas.charts(atlas.boundary);
    idx          = cellfun(nbfunc, bd_charts);
    close_charts = atlas.boundary(idx);
    checked      = [0, chart.id];
    while ~isempty(close_charts)
      [atlas chart checked] = ...
        atlas.merge_recursive(chart, close_charts(1), checked);
      close_charts = setdiff(close_charts, checked);
    end
    atlas.charts   = [atlas.charts, {chart}];
    atlas.boundary = [atlas.boundary, chart.id];
    bd_charts      = atlas.charts(atlas.boundary);
    idx            = cellfun(@(x) ~isempty(x.bv), bd_charts);
    atlas.boundary = atlas.boundary(idx);
end
% plot the results
plot_charts(atlas.charts, 1, 2, 3);
axis equal
axis tight
view(60,30)
drawnow
end