Find cycles in an undirected graph

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Sim
Sim on 7 Oct 2019
Commented: Sim on 16 Jun 2022
Hi, I need to find cycles in a graph, exactly as it was asked here (and apparently without fully clear/working solutions!):
Here my example/code:
clear all; clc; close all;
figure('Color',[1 1 1]);
s = [1 1 1 2 3 3 4 4 5 6 7 6 8 9 10 10 12 12 13 14 15 16 17 17 18 19 20 21 20 25];
t = [2 8 18 3 4 23 5 21 6 7 8 11 9 10 11 12 14 13 15 18 16 17 18 25 19 20 1 22 24 26];
G = graph(s,t);
x = [0.5 0 0 0 0.5 1 1.5 2 3 3 3 5.5 6 4 6 6 4 3 2 0.5 -1 -2 -1 1.5 4.5 4.5];
y = [0 0.5 1 1.5 2 2 1.5 1 1 1.5 2 1 0.5 0.5 0 -1 -1 -0.5 -1 -1 1 0.5 0.5 -0.5 -0.5 0];
h = plot(G,'XData',x,'YData',y,'linewidth',2,'MarkerSize',7);
nl = h.NodeLabel;
h.NodeLabel = '';
xd = get(h, 'XData');
yd = get(h, 'YData');
text(xd, yd, nl, 'FontSize',17, 'FontWeight','bold', ...
'HorizontalAlignment','left', 'VerticalAlignment','top')
set(gca,'Fontsize',15,'FontWeight','Bold','LineWidth',2, 'box','on')
% Remove "branches"
xy = [x' y'];
while ~isempty(find(degree(G)==1))
degreeone = find(degree(G)==1);
G = rmnode(G,degreeone);
xy(degreeone,:) = [];
end
Here the corresponding Figure (after removal of "branches"):
My goal would be to find the following 5 cycles as output (i.e. lists of nodes composing each cycle):
  • 1-2-3-4-5-6-7-8-1
  • 6-7-8-9-10-11-6
  • 1-8-9-10-12-14-18-1
  • 1-18-19-20-1
  • 12-13-15-16-17-18-14-12
Note 1:
This method is partially working for my purposes.
Unfortunately, the 2nd and 4th cycles are not what I needed/expected.
% Sergii Iglin
% https://iglin.org/All/GrMatlab/grCycleBasis.html
E = table2array(G.Edges);
Output_SI = grCycleBasis(E);
% [my part] From the Sergii Iglin's output to cycles nodes
for i = 1 : size(Output_SI,2)
w = [];
u = E(find(Output_SI(:,i)),:); % edges list
w(1) = u(1,1);
w(2) = u(1,2);
u(1,:) = [];
j = 2;
while ~isempty(u)
[ind,~] = find(u==w(j));
[~,ind2] = ismember(u, u(ind,:), 'rows');
g = u( ind2==1 ,:) ~= w(j);
w(j+1) = u( ind2==1 , g);
u( ind2==1 ,:) = [];
j = j + 1;
end
cycles_SI{i} = w;
end
% Sergii Iglin's results
>> cycles_SI{:}
1 2 3 4 5 6 7 8 1
1 2 3 4 5 6 11 10 9 8 1
1 8 9 10 12 14 18 1
1 8 9 10 12 13 15 16 17 18 1
1 18 19 20 1
Note 2:
This method is partially working for my purposes.
Unfortunately, the 2nd and 4th cycles are not what I needed/expected.
% Christine Tobler
% https://ch.mathworks.com/matlabcentral/answers/353565-are-there-matlab-codes-to-compute-cycle-spaces-of-graphs
t = minspantree(G, 'Type', 'forest');
% highlight(h,t)
nonTreeEdges = setdiff(G.Edges.EndNodes, t.Edges.EndNodes, 'rows');
cycles_CT = cell(size(nonTreeEdges, 1), 1);
for i = 1 : length(cycles_CT)
src = nonTreeEdges(i, 1);
tgt = nonTreeEdges(i, 2);
cycles_CT{i} = [tgt shortestpath(t, src, tgt)];
end
% Christine Tobler's results
>> cycles_CT{:}
8 7 6 5 4 3 2 1 8
11 10 9 8 1 2 3 4 5 6 11
18 14 12 10 9 8 1 18
18 17 16 15 13 12 10 9 8 1 18
20 19 18 1 20
Note 3:
Methods from Sergii Iglin and Christine Tobler give the same result!
Note 4:
The ideas / FileExchange submissions
  • Count all cycles in simple undirected graph version 1.2.0.0 (5.43 KB) by Jeff Howbert
  • Count Loops in a Graph version 1.1.0.0 (167 KB) by Joseph Kirk
kindly suggested here
are not working for my case...
Any further idea / suggestion ?
Thanks a lot!
  6 Comments
Sim
Sim on 27 Dec 2020
Hi Can, sorry I have just noticed your post! I am available for answering your questions. How can I contact you directly?

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Accepted Answer

Matt J
Matt J on 8 Oct 2019
Edited: Matt J on 8 Oct 2019
Because this sounds like a generally useful thing, I cooked up the attached polyregions class to do the partitioning that you described. It uses graph theoretic functions only.
Here is its application to the data example that you provided. Each partitioned polygon is contained in the polyshape array, pgon.
s = [1 1 1 2 3 3 4 4 5 6 7 6 8 9 10 10 12 12 13 14 15 16 17 17 18 19 20 21 20 25];
t = [2 8 18 3 4 23 5 21 6 7 8 11 9 10 11 12 14 13 15 18 16 17 18 25 19 20 1 22 24 26];
G = graph(s,t);
x = [0.5 0 0 0 0.5 1 1.5 2 3 3 3 5.5 6 4 6 6 4 3 2 0.5 -1 -2 -1 1.5 4.5 4.5];
y = [0 0.5 1 1.5 2 2 1.5 1 1 1.5 2 1 0.5 0.5 0 -1 -1 -0.5 -1 -1 1 0.5 0.5 -0.5 -0.5 0];
obj=polyregions(G,x,y);
pgon=polyshape(obj);
plot(obj);
hold on
plot(pgon);
hold off
  43 Comments
NA
NA on 28 Feb 2022
What is the time complexity of this algorithm?

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More Answers (2)

darova
darova on 7 Oct 2019
Just use for loop and cells since you already know indices of each polygon
s = [1 1 1 2 3 3 4 4 5 6 6 6 8 9 10 10 12 12 13 14 15 16 17 17 18 19 20 21 20 25];
t = [2 8 18 3 4 23 5 21 6 7 8 11 9 10 11 12 14 13 15 18 16 17 18 25 19 20 1 22 24 26];
x = [0.5 0 0 0 0.5 1 1.5 2 3 3 3 5.5 6 4 6 6 4 3 2 0.5 -1 -2 -1 1.5 4.5 4.5];
y = [0 0.5 1 1.5 2 2 1.5 1 1 1.5 2 1 0.5 0.5 0 -1 -1 -0.5 -1 -1 1 0.5 0.5 -0.5 -0.5 0];
ind = {{1 2 3 4 5 6 7 8 1}
{6 7 8 9 10 11 6}
{1 8 9 10 12 14 18 1}
{1 18 19 20 1}
{12 13 15 16 17 18 14 12}};
cla
% plot([x(s);x(t)],[y(s);y(t)],'.b')
hold on
for i = 1:length(ind)
ix = cell2mat(ind{i});
plot(x(ix),y(ix),'color',rand(1,3))
end
hold off
axis equal
  5 Comments
Sim
Sim on 9 Oct 2019
Hi Darova, to remove branches I used this:
% Remove branches
xy = [x' y'];
while ~isempty(find(degree(G)==1))
degreeone = find(degree(G)==1);
G = rmnode(G,degreeone);
xy(degreeone,:) = [];
end
About your idea/proposal, it looks cool and promising! Also, a nice animation!
However, is there any way to extrapolate the nodes composing each "cycle"/"polygon" that you were able to isolate ?
Thanks a lot for your efforts!

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Sim
Sim on 15 Jun 2022
Edited: Sim on 15 Jun 2022
Hey @Matt J! hope this message finds you well! I am back to my post after a while :-)
... I have a quite silly question..... I was trying to use your function in a loop for, in order to get automatically the number of polygons / cycles.... However, sometimes, it happens that there are not polygons / cycles (i.e. there are only tree-like graphs) to detect, as in this example, which returns an error...
% (1) use the function "spatialgraph2D"
>> obj = spatialgraph2D(SG, SG.Nodes.X, SG.Nodes.Y)
obj =
spatialgraph2D with properties:
G: [1×1 graph]
x: [12×1 double]
y: [12×1 double]
labels: [1 2 3 4 5 6 7 8 9 10 11 12]
pruneType: 'basic'
% (2) plot the graph
>> plot(obj)
% (3) calculate "polyshape" of "obj"
>> pgon = polyshape(obj)
Index in position 1 exceeds array bounds.
Error in spatialgraph2D (line 70)
obj.tol=min(D(2,:))/1000;
Error in spatialgraph2D/pruneBranches (line 253)
obj=spatialgraph2D(Gp,xp,yp,lp);
Error in spatialgraph2D/polyshape (line 98)
obj=pruneBranches(obj);
Is there a way to workaround this error in spatialgraph2D ?
Maybe just giving an empty "pgon" or something, but not an error (otherwise the loop for breaks..) ?
All the best,
Sim
P.S.: Just for a sake of completness.... here following the edge list of my example:
>> obj.G.Edges(:,1)
ans =
11×1 table
EndNodes
________
1 6
2 3
2 9
3 8
4 7
5 6
5 7
7 11
9 10
10 11
11 12
  7 Comments
Sim
Sim on 16 Jun 2022
@Matt J, any idea on how to solve this small issue ? :)

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