diff options
Diffstat (limited to 'example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp')
| -rw-r--r-- | example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp | 52 |
1 files changed, 22 insertions, 30 deletions
diff --git a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp b/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp index 4c6656f5..9618f278 100644 --- a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp +++ b/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp @@ -4,8 +4,7 @@ * * Author(s): Clément Maria, Marc Glisse * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France), - * 2015 INRIA Saclay Île de France) + * 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 @@ -21,12 +20,12 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <gudhi/reader_utils.h> -#include <gudhi/graph_simplicial_complex.h> -#include <gudhi/distance_functions.h> #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> +#include <gudhi/Rips_complex.h> #include <gudhi/Hasse_complex.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/distance_functions.h> #include <boost/program_options.hpp> @@ -44,14 +43,16 @@ // // //////////////////////////////////////////////////////////////// -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; - -typedef int Vertex_handle; -typedef double Filtration_value; +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Point = std::vector<double>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; void program_options(int argc, char * argv[] - , std::string & filepoints + , std::string & off_file_points , std::string & filediag , Filtration_value & threshold , int & dim_max @@ -59,30 +60,21 @@ void program_options(int argc, char * argv[] , Filtration_value & min_persistence); int main(int argc, char * argv[]) { - std::string filepoints; + std::string off_file_points; std::string filediag; Filtration_value threshold; int dim_max; int p; Filtration_value min_persistence; - program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence); - - // Extract the points from the file filepoints - typedef std::vector<double> Point_t; - std::vector< Point_t > points; - read_points(filepoints, points); + program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence); - // Compute the proximity graph of the points - Graph_t prox_graph = compute_proximity_graph(points, threshold - , euclidean_distance<Point_t>); + Points_off_reader off_reader(off_file_points); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); // Construct the Rips complex in a Simplex Tree - Simplex_tree<>& st = *new Simplex_tree<>; - // insert the proximity graph in the simplex tree - st.insert_graph(prox_graph); - // expand the graph until dimension dim_max - st.expansion(dim_max); + Simplex_tree& st = *new Simplex_tree; + rips_complex_from_file.create_complex(st, dim_max); std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; std::cout << " and has dimension " << st.dimension() << " \n"; @@ -99,7 +91,7 @@ int main(int argc, char * argv[]) { st.assign_key(sh, count++); // Convert to a more convenient representation. - Hasse_complex<> hcpx(st); + Gudhi::Hasse_complex<> hcpx(st); #ifdef GUDHI_USE_TBB ts.terminate(); @@ -109,7 +101,7 @@ int main(int argc, char * argv[]) { delete &st; // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology< Hasse_complex<>, Field_Zp > pcoh(hcpx); + Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Hasse_complex<>, Field_Zp > pcoh(hcpx); // initializes the coefficient field for homology pcoh.init_coefficients(p); @@ -126,7 +118,7 @@ int main(int argc, char * argv[]) { } void program_options(int argc, char * argv[] - , std::string & filepoints + , std::string & off_file_points , std::string & filediag , Filtration_value & threshold , int & dim_max @@ -135,7 +127,7 @@ void program_options(int argc, char * argv[] namespace po = boost::program_options; po::options_description hidden("Hidden options"); hidden.add_options() - ("input-file", po::value<std::string>(&filepoints), + ("input-file", po::value<std::string>(&off_file_points), "Name of file containing a point set. Format is one point per line: X1 ... Xd "); po::options_description visible("Allowed options", 100); |