self loops in graphs - Githubissues

I worked on some graphs problems using persistence diagram as a feature. If the graph has self-loops, we will have simplices like [1,1] and [2,2]. This will cause some runtime error when calling d.homology_persistence(f). A small example is given. Running it on Linux throws RuntimeError: Trying to access non-existent cell: <313215472>. This is not very informative and takes me quite a while to figure out where the bug is.

If [1,1] and [2,2] are commented out, I can run the code without a problem.

def dionysus_test():
    import dionysus as d
    simplices = [([0, 6], 0.0035655512881059928),
                 ([0, 5], 0.004388370816130452),
                 ([0, 4], 0.024136039488717488),
                 ([0, 3], 0.035381239705051776),
                 ([3, 5], 0.035381239705051776),
                 ([0, 1], 0.9824465164612051),
                 ([1, 1], 0.9824465164612051),
                 ([1, 3], 0.9824465164612051),
                 ([1, 4], 0.9824465164612051),
                 ([1, 5], 0.9824465164612051),
                 ([1, 6], 0.9824465164612051),
                 ([0, 2], 0.9999999997257268),
                 ([1, 2], 0.9999999997257268),
                 ([2, 2], 0.9999999997257268),
                 ([2, 3], 0.9999999997257268),
                 ([2, 4], 0.9999999997257268),
                 ([2, 5], 0.9999999997257268),
                 ([2, 6], 0.9999999997257268),
                 ([0], 0.0016456390560489196),
                 ([6], 0.0035655512881059928),
                 ([5], 0.004388370816130452),
                 ([4], 0.024136039488717488),
                 ([3], 0.035381239705051776),
                 ([1], 0.9824465164612051),
                 ([2], 0.9999999997257268)]
    f = d.Filtration()
    for vertices, time in simplices:
        f.append(d.Simplex(vertices, time))
    f.sort()
    m = d.homology_persistence(f)
    for i, c in enumerate(m):
        print(i, c)
dionysus_test()

mrzv / dionysus

self loops in graphs #35