diff options
Diffstat (limited to 'src/Persistent_cohomology/example')
3 files changed, 93 insertions, 67 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index d97d1b63..758bd6b1 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -30,10 +30,10 @@ endif() add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology) add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0) -add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100) -add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100) -add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0) -add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) +add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100) +add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100) +add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0) +add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100) if(GMP_FOUND) if(GMPXX_FOUND) diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp index cb181936..2412569a 100644 --- a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp @@ -4,6 +4,8 @@ #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 <string> @@ -30,35 +32,38 @@ int main(int argc, char **argv) { // Init of an alpha complex from an OFF file // ---------------------------------------------------------------------------- using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; - Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value); - - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << - " - " << alpha_complex_from_file.num_simplices() << " simplices - " << - alpha_complex_from_file.num_vertices() << " vertices." << std::endl; - - // Sort the simplices in the order of the filtration - alpha_complex_from_file.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl; - // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alpha_complex::Alpha_complex<Kernel>, - Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (output_file_diag.empty()) { - pcoh.output_diagram(); - } else { - std::cout << "Result in file: " << output_file_diag << std::endl; - std::ofstream out(output_file_diag); - pcoh.output_diagram(out); - out.close(); + Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + // ---------------------------------------------------------------------------- + // 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; + // Compute the persistence diagram of the complex + Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>, + Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (output_file_diag.empty()) { + pcoh.output_diagram(); + } else { + std::cout << "Result in file: " << output_file_diag << std::endl; + std::ofstream out(output_file_diag); + pcoh.output_diagram(out); + out.close(); + } } return 0; 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; } |