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Diffstat (limited to 'example/Persistent_cohomology/custom_persistence_sort.cpp')
-rw-r--r-- | example/Persistent_cohomology/custom_persistence_sort.cpp | 137 |
1 files changed, 0 insertions, 137 deletions
diff --git a/example/Persistent_cohomology/custom_persistence_sort.cpp b/example/Persistent_cohomology/custom_persistence_sort.cpp deleted file mode 100644 index 35366144..00000000 --- a/example/Persistent_cohomology/custom_persistence_sort.cpp +++ /dev/null @@ -1,137 +0,0 @@ -/* 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) 2014 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/>. - */ - -#include <CGAL/Epick_d.h> -#include <CGAL/point_generators_d.h> -#include <CGAL/algorithm.h> -#include <CGAL/assertions.h> - -#include <gudhi/Alpha_complex.h> -#include <gudhi/Persistent_cohomology.h> -// to construct a simplex_tree from alpha complex -#include <gudhi/Simplex_tree.h> - -#include <iostream> -#include <iterator> -#include <vector> -#include <fstream> // for std::ofstream -#include <algorithm> // for std::sort - - -using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >; -using Point = Kernel::Point_d; -using Alpha_complex = Gudhi::alpha_complex::Alpha_complex<Kernel>; -using Simplex_tree = Gudhi::Simplex_tree<>; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree, - Gudhi::persistent_cohomology::Field_Zp >; - -std::vector<Point> random_points() { - // Instanciate a random point generator - CGAL::Random rng(0); - - // Generate "points_number" random points in a vector - std::vector<Point> points; - - // Generates 1000 random 3D points on a sphere of radius 4.0 - CGAL::Random_points_on_sphere_d<Point> rand_outside(3, 4.0, rng); - CGAL::cpp11::copy_n(rand_outside, 1000, std::back_inserter(points)); - // Generates 2000 random 3D points in a sphere of radius 3.0 - CGAL::Random_points_in_ball_d<Point> rand_inside(3, 3.0, rng); - CGAL::cpp11::copy_n(rand_inside, 2000, std::back_inserter(points)); - - return points; -} - -/* - * Compare two intervals by dimension, then by length. - */ -struct cmp_intervals_by_dim_then_length { - explicit cmp_intervals_by_dim_then_length(Simplex_tree * sc) - : sc_(sc) { } - - template<typename Persistent_interval> - bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) { - if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2))) - return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1)) - > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2))); - else - return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2))); - } - Simplex_tree* sc_; -}; - -int main(int argc, char **argv) { - std::vector<Point> points = random_points(); - - std::cout << "Points size=" << points.size() << std::endl; - // Alpha complex persistence computation from generated points - Alpha_complex alpha_complex_from_points(points); - std::cout << "alpha_complex_from_points" << std::endl; - - Simplex_tree simplex; - std::cout << "simplex" << std::endl; - if (alpha_complex_from_points.create_complex(simplex, 0.6)) { - std::cout << "simplex" << std::endl; - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - std::cout << "Simplicial complex is of dimension " << simplex.dimension() << - " - " << simplex.num_simplices() << " simplices - " << - simplex.num_vertices() << " vertices." << std::endl; - - // Sort the simplices in the order of the filtration - simplex.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; - - Persistent_cohomology pcoh(simplex); - - // initializes the coefficient field for homology - Z/3Z - pcoh.init_coefficients(3); - pcoh.compute_persistent_cohomology(0.2); - - // Custom sort and output persistence - cmp_intervals_by_dim_then_length cmp(&simplex); - auto persistent_pairs = pcoh.get_persistent_pairs(); - std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp); - for (auto pair : persistent_pairs) { - std::cout << simplex.dimension(get<0>(pair)) << " " - << simplex.filtration(get<0>(pair)) << " " - << simplex.filtration(get<1>(pair)) << std::endl; - } - - // Persistent Betti numbers - std::cout << "The persistent Betti numbers in interval [0.40, 0.41] are : "; - for (int dim = 0; dim < simplex.dimension(); dim++) - std::cout << "b" << dim << " = " << pcoh.persistent_betti_number(dim, 0.40, 0.41) << " ; "; - std::cout << std::endl; - - // Betti numbers - std::vector<int> betti_numbers = pcoh.betti_numbers(); - std::cout << "The Betti numbers are : "; - for (std::size_t i = 0; i < betti_numbers.size(); i++) - std::cout << "b" << i << " = " << betti_numbers[i] << " ; "; - std::cout << std::endl; - } - return 0; -} - |