From 77e577eb28ca7622553cd0527db76d46b473c445 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 24 Mar 2021 15:27:11 +0100 Subject: Remove read_weights and depreciate off_file --- ...ex_diagram_persistence_from_off_file_example.py | 55 +++++------ .../alpha_rips_persistence_bottleneck_distance.py | 110 +++++++++------------ src/python/example/plot_alpha_complex.py | 5 +- 3 files changed, 74 insertions(+), 96 deletions(-) (limited to 'src/python/example') diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py index fe03be31..c96121a6 100755 --- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -1,9 +1,7 @@ #!/usr/bin/env python import argparse -import errno -import os -import gudhi +import gudhi as gd """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. @@ -41,33 +39,24 @@ parser.add_argument( 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"): - print("##############################################################") - print("AlphaComplex creation from points read in a OFF file") - - alpha_complex = gudhi.AlphaComplex(off_file=args.file) - if args.max_alpha_square is not None: - print("with max_edge_length=", args.max_alpha_square) - simplex_tree = alpha_complex.create_simplex_tree( - max_alpha_square=args.max_alpha_square - ) - else: - simplex_tree = alpha_complex.create_simplex_tree() - - print("Number of simplices=", simplex_tree.num_simplices()) - - diag = simplex_tree.persistence() - - print("betti_numbers()=", simplex_tree.betti_numbers()) - - if args.no_diagram == False: - import matplotlib.pyplot as plot - gudhi.plot_persistence_diagram(diag, band=args.band) - plot.show() - else: - raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), - args.file) - - f.close() +print("##############################################################") +print("AlphaComplex creation from points read in a OFF file") + +points = gd.read_points_from_off_file(off_file = args.file) +alpha_complex = gd.AlphaComplex(points = points) +if args.max_alpha_square is not None: + print("with max_edge_length=", args.max_alpha_square) + simplex_tree = alpha_complex.create_simplex_tree( + max_alpha_square=args.max_alpha_square + ) +else: + simplex_tree = alpha_complex.create_simplex_tree() + +print("Number of simplices=", simplex_tree.num_simplices()) + +diag = simplex_tree.persistence() +print("betti_numbers()=", simplex_tree.betti_numbers()) +if args.no_diagram == False: + import matplotlib.pyplot as plot + gd.plot_persistence_diagram(diag, band=args.band) + plot.show() diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py index 3e12b0d5..6b97fb3b 100755 --- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py @@ -1,10 +1,8 @@ #!/usr/bin/env python -import gudhi +import gudhi as gd import argparse import math -import errno -import os import numpy as np """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - @@ -37,70 +35,60 @@ 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_points_from_off_file(off_file=args.file) - print("##############################################################") - print("RipsComplex creation from points read in a OFF file") +point_cloud = gd.read_points_from_off_file(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) +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_stree.compute_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) +rips_complex = gd.RipsComplex( + points=point_cloud, max_edge_length=args.threshold +) - alpha_stree.compute_persistence() +rips_stree = rips_complex.create_simplex_tree( + max_dimension=args.max_dimension) - 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 - alpha_intervals = np.sqrt(alpha_stree.persistence_intervals_in_dimension(dim)) +message = "Number of simplices=" + repr(rips_stree.num_simplices()) +print(message) - 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) +rips_stree.compute_persistence() - print("==============================================================") - message = "Bottleneck distance is " + repr(max_b_distance) - print(message) +print("##############################################################") +print("AlphaComplex creation from points read in a OFF file") - else: - raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), - args.file) +message = "AlphaComplex with max_edge_length=" + repr(args.threshold) +print(message) +alpha_complex = gd.AlphaComplex(points=point_cloud) +alpha_stree = alpha_complex.create_simplex_tree( + max_alpha_square=(args.threshold * args.threshold) +) - f.close() +message = "Number of simplices=" + repr(alpha_stree.num_simplices()) +print(message) + +alpha_stree.compute_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 + alpha_intervals = np.sqrt(alpha_stree.persistence_intervals_in_dimension(dim)) + + rips_intervals = rips_stree.persistence_intervals_in_dimension(dim) + bottleneck_distance = gd.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) diff --git a/src/python/example/plot_alpha_complex.py b/src/python/example/plot_alpha_complex.py index 99c18a7c..0924619b 100755 --- a/src/python/example/plot_alpha_complex.py +++ b/src/python/example/plot_alpha_complex.py @@ -1,8 +1,9 @@ #!/usr/bin/env python import numpy as np -import gudhi -ac = gudhi.AlphaComplex(off_file='../../data/points/tore3D_1307.off') +import gudhi as gd +points = gd.read_points_from_off_file(off_file = '../../data/points/tore3D_1307.off') +ac = gd.AlphaComplex(points = points) st = ac.create_simplex_tree() points = np.array([ac.get_point(i) for i in range(st.num_vertices())]) # We want to plot the alpha-complex with alpha=0.1. -- cgit v1.2.3