diff options
Diffstat (limited to 'src/cython/example/alpha_rips_persistence_bottleneck_distance.py')
-rwxr-xr-x | src/cython/example/alpha_rips_persistence_bottleneck_distance.py | 76 |
1 files changed, 40 insertions, 36 deletions
diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py index b51fa7a8..086307ee 100755 --- a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py @@ -4,47 +4,37 @@ import gudhi import argparse import math -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. +""" 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 - Author(s): Vincent Rouvreau + Copyright (C) 2016 Inria - Copyright (C) 2016 Inria - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. + Modification(s): + - YYYY/MM Author: Description of the modification """ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" -__license__ = "GPL v3" - -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') +__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: +with open(args.file, "r") as f: first_line = f.readline() - if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): + 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") @@ -52,8 +42,9 @@ with open(args.file, 'r') as f: message = "RipsComplex with max_edge_length=" + repr(args.threshold) print(message) - rips_complex = gudhi.RipsComplex(points=point_cloud, - max_edge_length=args.threshold) + rips_complex = gudhi.RipsComplex( + points=point_cloud, max_edge_length=args.threshold + ) rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) @@ -69,7 +60,9 @@ with open(args.file, 'r') as f: print(message) alpha_complex = gudhi.AlphaComplex(points=point_cloud) - alpha_stree = alpha_complex.create_simplex_tree(max_alpha_square=(args.threshold * args.threshold)) + 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) @@ -83,15 +76,26 @@ with open(args.file, 'r') as f: 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)) + 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) + 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("================================================================================") + print( + "================================================================================" + ) message = "Bottleneck distance is " + repr(max_b_distance) print(message) |