From af46c40bec8ae03cdf5a1e5a37ede198f910e3ea Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 14 Mar 2017 22:08:43 +0000 Subject: Add Windows and CGAL_HEADER_ONLY cythonization support Add OFF reader interfaces (required by Euclidean witness complex) Add Euclidean_witness_complex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2186 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4d780f05c3409bea47a81e4377dbaf509b9e718c --- ...ex_diagram_persistence_from_off_file_example.py | 78 ++++++++++++++++++++++ .../example/witness_complex_from_file_example.py | 56 ---------------- 2 files changed, 78 insertions(+), 56 deletions(-) create mode 100755 src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py delete mode 100755 src/cython/example/witness_complex_from_file_example.py (limited to 'src/cython/example') diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py new file mode 100755 index 00000000..7f04a98e --- /dev/null +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -0,0 +1,78 @@ +#!/usr/bin/env python + +import gudhi +import argparse + +"""This file is part of the Gudhi Library. The Gudhi library + (Geometric Understanding in Higher Dimensions) is a generic C++ + library for computational topology. + + Author(s): Vincent Rouvreau + + 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 . +""" + +__author__ = "Vincent Rouvreau" +__copyright__ = "Copyright (C) 2016 INRIA" +__license__ = "GPL v3" + +parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from ' + 'points read in a OFF file.', + epilog='Example: ' + 'example/witness_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2' + '- Constructs a alpha complex with the ' + 'points from the given OFF file.') +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-a", "--max_alpha_square", type=float, required=True) +parser.add_argument("-n", "--number_of_landmarks", type=int, required=True) +parser.add_argument("-d", "--limit_dimension", type=int, required=True) +parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +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("EuclideanWitnessComplex creation from points read in a OFF file") + + witnesses = gudhi.read_off(off_file=args.file) + landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks) + + message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \ + " - Number of landmarks=" + repr(args.number_of_landmarks) + print(message) + + witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks) + simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square, + limit_dimension=args.limit_dimension) + + message = "Number of simplices=" + repr(simplex_tree.num_simplices()) + print(message) + + diag = simplex_tree.persistence() + + print("betti_numbers()=") + print(simplex_tree.betti_numbers()) + + if args.no_diagram == False: + gudhi.diagram_persistence(diag) + + else: + print(args.file, "is not a valid OFF file") + + f.close() diff --git a/src/cython/example/witness_complex_from_file_example.py b/src/cython/example/witness_complex_from_file_example.py deleted file mode 100755 index 82a5b49a..00000000 --- a/src/cython/example/witness_complex_from_file_example.py +++ /dev/null @@ -1,56 +0,0 @@ -#!/usr/bin/env python - -import gudhi -import pandas -import argparse - -"""This file is part of the Gudhi Library. The Gudhi library - (Geometric Understanding in Higher Dimensions) is a generic C++ - library for computational topology. - - Author(s): Vincent Rouvreau - - 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 . -""" - -__author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" -__license__ = "GPL v3" - -print("#####################################################################") -print("WitnessComplex creation from points read in a file") - -parser = argparse.ArgumentParser(description='WitnessComplex creation from ' - 'points read in a file.', - epilog='Example: ' - 'example/witness_complex_from_file_example.py' - ' data/2000_random_points_on_3D_Torus.csv ' - '- Constructs a witness complex with the ' - 'points from the given file. File format ' - 'is X1, X2, ..., Xn') -parser.add_argument('file', type=argparse.FileType('r')) -args = parser.parse_args() - -points = pandas.read_csv(args.file, header=None) - -print("WitnessComplex with number_of_landmarks=100") - -witness_complex = gudhi.WitnessComplex(points=points.values, - number_of_landmarks=100) - -witness_complex.initialize_filtration() - -print("filtered_tree=", witness_complex.get_filtered_tree()) -- cgit v1.2.3