diff options
Diffstat (limited to 'src/Persistent_cohomology/example/custom_persistence_sort.cpp')
-rw-r--r-- | src/Persistent_cohomology/example/custom_persistence_sort.cpp | 89 |
1 files changed, 55 insertions, 34 deletions
diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp index 9af38611..64f2a4dc 100644 --- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp +++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp @@ -27,6 +27,8 @@ #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> @@ -38,6 +40,9 @@ 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 @@ -60,7 +65,7 @@ std::vector<Point> random_points() { * Compare two intervals by dimension, then by length. */ struct cmp_intervals_by_dim_then_length { - explicit cmp_intervals_by_dim_then_length(Alpha_complex * sc) + explicit cmp_intervals_by_dim_then_length(Simplex_tree * sc) : sc_(sc) { } template<typename Persistent_interval> @@ -71,46 +76,62 @@ struct cmp_intervals_by_dim_then_length { else return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2))); } - Alpha_complex* sc_; + 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, 0.6); - - using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< Alpha_complex, - Gudhi::persistent_cohomology::Field_Zp >; - Persistent_cohomology pcoh(alpha_complex_from_points); - - // 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(&alpha_complex_from_points); - 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 << alpha_complex_from_points.dimension(get<0>(pair)) << " " - << alpha_complex_from_points.filtration(get<0>(pair)) << " " - << alpha_complex_from_points.filtration(get<1>(pair)) << std::endl; + 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; } - - // Persistent Betti numbers - std::cout << "The persistent Betti numbers in interval [0.40, 0.41] are : "; - for (int dim = 0; dim < alpha_complex_from_points.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; } |