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author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-09-09 16:03:40 +0200 |
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committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-09-09 16:03:40 +0200 |
commit | 68753b3c28321e28eedd5829c94234da84e25c8d (patch) | |
tree | 36003a30309b3203b41092ad4d7ee8fa78551452 /src/python/example/alpha_rips_persistence_bottleneck_distance.py | |
parent | dcbdaa0dc00eb069d1a13575f22c0a2f7d63dcc8 (diff) |
Code review: rename cython as python (make target and directory
Diffstat (limited to 'src/python/example/alpha_rips_persistence_bottleneck_distance.py')
-rwxr-xr-x | src/python/example/alpha_rips_persistence_bottleneck_distance.py | 105 |
1 files changed, 105 insertions, 0 deletions
diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py new file mode 100755 index 00000000..086307ee --- /dev/null +++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py @@ -0,0 +1,105 @@ +#!/usr/bin/env python + +import gudhi +import argparse +import math + +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Vincent Rouvreau + + Copyright (C) 2016 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "MIT" + +parser = argparse.ArgumentParser( + description="AlphaComplex and RipsComplex " + "persistence creation from points read in " + "a OFF file. Bottleneck distance computation" + " on each dimension", + epilog="Example: " + "example/alpha_rips_persistence_bottleneck_distance.py " + "-f ../data/points/tore3D_1307.off -t 0.15 -d 3", +) +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-t", "--threshold", type=float, default=0.5) +parser.add_argument("-d", "--max_dimension", type=int, default=1) + +args = parser.parse_args() +with open(args.file, "r") as f: + first_line = f.readline() + if (first_line == "OFF\n") or (first_line == "nOFF\n"): + point_cloud = gudhi.read_off(off_file=args.file) + print("#####################################################################") + print("RipsComplex creation from points read in a OFF file") + + message = "RipsComplex with max_edge_length=" + repr(args.threshold) + print(message) + + rips_complex = gudhi.RipsComplex( + points=point_cloud, max_edge_length=args.threshold + ) + + rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) + + message = "Number of simplices=" + repr(rips_stree.num_simplices()) + print(message) + + rips_diag = rips_stree.persistence() + + print("#####################################################################") + print("AlphaComplex creation from points read in a OFF file") + + message = "AlphaComplex with max_edge_length=" + repr(args.threshold) + print(message) + + alpha_complex = gudhi.AlphaComplex(points=point_cloud) + alpha_stree = alpha_complex.create_simplex_tree( + max_alpha_square=(args.threshold * args.threshold) + ) + + message = "Number of simplices=" + repr(alpha_stree.num_simplices()) + print(message) + + alpha_diag = alpha_stree.persistence() + + max_b_distance = 0.0 + for dim in range(args.max_dimension): + # Alpha persistence values needs to be transform because filtration + # values are alpha square values + funcs = [math.sqrt, math.sqrt] + alpha_intervals = [] + for interval in alpha_stree.persistence_intervals_in_dimension(dim): + alpha_intervals.append( + map(lambda func, value: func(value), funcs, interval) + ) + + rips_intervals = rips_stree.persistence_intervals_in_dimension(dim) + bottleneck_distance = gudhi.bottleneck_distance( + rips_intervals, alpha_intervals + ) + message = ( + "In dimension " + + repr(dim) + + ", bottleneck distance = " + + repr(bottleneck_distance) + ) + print(message) + max_b_distance = max(bottleneck_distance, max_b_distance) + + print( + "================================================================================" + ) + message = "Bottleneck distance is " + repr(max_b_distance) + print(message) + + else: + print(args.file, "is not a valid OFF file") + + f.close() |