author Dmitriy Morozov <dmitriy@mrzv.org>
Mon, 27 Nov 2017 10:26:59 -0800
changeset 293 bc7bd0ac9af6
parent 181 1ee6edc17cb6
permissions -rw-r--r--
Add CGAL pre-4.11 support back to e/a/alphashapes3d-periodic

#/usr/bin/env python

from    dionysus    import Rips, PairwiseDistances, StaticPersistence, Filtration, points_file, \
                           ExplicitDistances, data_dim_cmp
from    sys         import argv, exit
import  time

def main(filename, skeleton, max):
    points = [p for p in points_file(filename)]
    distances = PairwiseDistances(points)
    # distances = ExplicitDistances(distances)           # speeds up generation of the Rips complex at the expense of memory usage
    rips = Rips(distances)
    print time.asctime(), "Rips initialized"

    simplices = Filtration()
    rips.generate(skeleton, max, simplices.append)
    print time.asctime(), "Generated complex: %d simplices" % len(simplices)

    # While this step is unnecessary (Filtration below can be passed rips.cmp), 
    # it greatly speeds up the running times
    for s in simplices: s.data = rips.eval(s)
    print time.asctime(), simplices[0], '...', simplices[-1]

    simplices.sort(data_dim_cmp)             # could be rips.cmp if s.data for s in simplices is not set
    print time.asctime(), "Set up filtration"

    p = StaticPersistence(simplices)
    print time.asctime(), "Initialized StaticPersistence"

    print time.asctime(), "Simplices paired"

    print "Outputting persistence diagram"
    smap = p.make_simplex_map(simplices)
    for i in p:
        if i.sign():
            b = smap[i]

            if b.dimension() >= skeleton: continue

            if i.unpaired():
                print b.dimension(), b.data, "inf"

            d = smap[i.pair()]
            print b.dimension(), b.data, d.data

if __name__ == '__main__':
    if len(argv) < 4:
        print "Usage: %s POINTS SKELETON MAX" % argv[0]

    filename = argv[1]
    skeleton = int(argv[2])
    max = float(argv[3])

    main(filename, skeleton, max)