contour_tree.dot

graph contour_tree {
	layout="dot"
	rankdir=UD
	ranksep="0.02"
	graph [fontname="helvetica"];
	node  [fontname="helvetica"];
	edge  [fontname="helvetica"];
	s_3539 [label="108" fontcolor="#0CADBC" shape=none]
	s_3459 [label="163" fontcolor="#92BF72" shape=none]
	s_3460 [label="163" fontcolor="#92BF72" shape=none]
	s_3577 [label="163" fontcolor="#92BF72" shape=none]
	s_3580 [label="163" fontcolor="#92BF72" shape=none]
	s_3581 [label="163" fontcolor="#92BF72" shape=none]
	s_3584 [label="163" fontcolor="#92BF72" shape=none]
	s_122  [label="189" fontcolor="#CCBB5B" shape=none]
	s_183  [label="189" fontcolor="#CCBB5B" shape=none]
	s_1464 [label="191" fontcolor="#D0BB59" shape=none]
	s_3539 -- s_3459 -- s_3460 -- s_3577 -- s_3580 -- s_3581 -- s_3584 -- s_122  -- s_183  -- s_1464 [style=invis]
	v_3539[label="v3539" fontcolor="#0CADBC" color="#0CADBC" style="setlinewidth(2)"]
	v_3459[label="v3459" fontcolor="#92BF72" color="#92BF72" style="setlinewidth(2)"]
	v_3460[label="v3460" fontcolor="#92BF72" color="#92BF72" style="setlinewidth(2)"]
	v_3577[label="v3577" fontcolor="#92BF72" color="#92BF72" style="setlinewidth(2)"]
	v_3580[label="v3580" fontcolor="#92BF72" color="#92BF72" style="setlinewidth(2)"]
	v_3581[label="v3581" fontcolor="#92BF72" color="#92BF72" style="setlinewidth(2)"]
	v_3584[label="v3584" fontcolor="#92BF72" color="#92BF72" style="setlinewidth(2)"]
	v_122[label="v122" fontcolor="#CCBB5B" color="#CCBB5B" style="setlinewidth(2)"]
	v_183[label="v183" fontcolor="#CCBB5B" color="#CCBB5B" style="setlinewidth(2)"]
	v_1464[label="v1464" fontcolor="#D0BB59" color="#D0BB59" style="setlinewidth(2)"]
	v_3539 -- v_3459  -- v_3460  -- v_3577  -- v_3580  -- v_3581  -- v_3584  -- v_122   -- v_183   -- v_1464  [style=invis]
	v_3577 -- v_3580 [label=" a = 8 p = 0" fontcolor="#94BF72" color="#94BF72" style="setlinewidth(2)"]
	v_3581 -- v_3460 [label=" a = 2 p = 0" fontcolor="#94BF72" color="#94BF72" style="setlinewidth(2)"]
	v_1464 -- v_183  [label=" a = 55 p = 2" fontcolor="#D2BB59" color="#D2BB59" style="setlinewidth(2)"]
	v_122  -- v_183  [label=" a = 1 p = 0" fontcolor="#CEBB5A" color="#CEBB5A" style="setlinewidth(2)"]
	v_3539 -- v_3580 [label=" a = 2360 p = 55" fontcolor="#94BF72" color="#94BF72" style="setlinewidth(2)"]
	v_3584 -- v_3459 [label=" a = 6 p = 0" fontcolor="#94BF72" color="#94BF72" style="setlinewidth(2)"]
	v_183  -- v_3460 [label=" a = 1158 p = 26" fontcolor="#CEBB5A" color="#CEBB5A" style="setlinewidth(2)"]
	v_3580 -- v_3459 [label=" a = 4 p = 0" fontcolor="#94BF72" color="#94BF72" style="setlinewidth(2)"]
	v_3460 -- v_3459 [label=" a = 4 p = 0" fontcolor="#94BF72" color="#94BF72" style="setlinewidth(2)"]
	{ rank = same; s_3539; v_3539; }
	{ rank = same; s_3459; v_3459; }
	{ rank = same; s_3460; v_3460; }
	{ rank = same; s_3577; v_3577; }
	{ rank = same; s_3580; v_3580; }
	{ rank = same; s_3581; v_3581; }
	{ rank = same; s_3584; v_3584; }
	{ rank = same; s_122; v_122; }
	{ rank = same; s_183; v_183; }
	{ rank = same; s_1464; v_1464; }
}

contour_tree.m

img = double(rgb2gray(imread('test2.bmp')));

[ct, ct_img] = ContourTree(img);

% For an n x 2 matrix of edge end nodes, ct(n,2) 
% and an image ct_img(w,h) where each pixels value 
% is the endpoint of the superarc containing it.

% Unique vertices (critical points)
vs = unique([ct(:,1), ct(:,2)]);
fs = [];
for i = 1:numel(vs)
    [x,y] = ind2sub(size(img), vs(i));
    fs = [fs, int32(img(x,y))];
end

% Sort critical points by height function
[~, fsidx] = sort(fs);
vs = vs(fsidx);

cmap = parula(256);

fid = fopen('ct.dot','wt');
fprintf(fid, 'graph contour_tree {\n');
fprintf(fid, '\tlayout="dot"\n');
fprintf(fid, '\trankdir=UD\n');
fprintf(fid, '\tranksep="0.02"\n');
fprintf(fid, '\tgraph [fontname="helvetica"];\n');
fprintf(fid, '\tnode  [fontname="helvetica"];\n');
fprintf(fid, '\tedge  [fontname="helvetica"];\n');

% Create support graph
for i = 1:numel(vs)
    [x,y] = ind2sub(size(img), vs(i));
    f = int32(img(x,y));
    fprintf(fid, '\ts_%-4d [label="%d" fontcolor="%s" shape=none]\n', vs(i), f, rgb2hex(cmap(f,:)));
end

% Support edges
fprintf(fid, '\ts_%-4d', vs(1));
for i = 2:numel(vs)
    fprintf(fid, ' -- s_%-4d', vs(i));
end
fprintf(fid, ' [style=invis]\n');

% Critical points
for i = 1:numel(vs)
    [x,y] = ind2sub(size(img), vs(i));
    f = int32(img(x,y));
    fprintf(fid, '\tv_%d[label="v%d" fontcolor="%s" color="%s" style="setlinewidth(2)"]\n', vs(i), vs(i), rgb2hex(cmap(f,:)), rgb2hex(cmap(f,:)));
end

% Critical support edges
fprintf(fid, '\tv_%-4d', vs(1));
for i = 2:numel(vs)
    fprintf(fid, ' -- v_%-4d ', vs(i));
end
fprintf(fid, ' [style=invis]\n');

% Super Arcs
for i = 1:size(ct(:,1))
    if (ct(i,1) ~= ct(i,2))
        [x,y] = ind2sub(size(img), ct(i,1));
        f = img(x,y);
        p = f;
        [x,y] = ind2sub(size(img), ct(i,2));
        f = int32(max(img(x,y), f)) + 1;
        p = int32(abs(p - img(x,y)));
        fprintf(fid, '\tv_%-4d -- v_%-4d [label=" a = %d p = %d" fontcolor="%s" color="%s" style="setlinewidth(2)"]\n', ct(i,1), ct(i,2), numel(ct_img(ct_img == ct(i,1))), p, rgb2hex(cmap(f,:)), rgb2hex(cmap(f,:)));
    end
end

% Link Critical points to support structure
for i = 1:numel(vs)
    fprintf(fid, '\t{ rank = same; s_%d; v_%d; }\n', vs(i), vs(i));
end

fprintf(fid, '}\n');
fclose(fid);
system(sprintf('dot -Teps "ct.dot" > "ct.eps"');