diff options
6 files changed, 361 insertions, 7 deletions
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 469c9aac..38cfa821 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -7,7 +7,12 @@ if(CGAL_FOUND) if (EIGEN3_FOUND) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) - #add_executable ( relaxed_witness_persistence relaxed_witness_persistence.cpp ) + add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) + target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_test(Witness_complex_test_torus_persistence src/Witness_complex/example/Witness_complex_example_witncess_complex_persistence ../data/points/tore3D_1307.off -l 20 -a 0.5) + add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_test(Witness_complex_test_torus_persistence src/Witness_complex/example/Witness_complex_example_strong_witness_persistence ../data/points/tore3D_1307.off -l 20 -a 0.5) endif(EIGEN3_FOUND) endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) endif() diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp new file mode 100644 index 00000000..bf6b4011 --- /dev/null +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -0,0 +1,172 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) + * + * 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 <gudhi/Simplex_tree.h> +#include <gudhi/Strong_witness_complex.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/pick_n_random_points.h> + +#include <boost/program_options.hpp> + +#include <CGAL/Epick_d.h> + +#include <string> +#include <vector> +#include <limits> // infinity + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K; +typedef typename K::Point_d Point_d; + +typedef typename std::vector<Point_d> Point_vector; +typedef typename Gudhi::witness_complex::Strong_witness_complex<K> Strong_witness_complex; +typedef Gudhi::Simplex_tree<> SimplexTree; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string file_name; + std::string filediag; + Filtration_value max_squared_alpha; + int p, nbL; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + witnesses = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << witnesses.size() << " points.\n"; + std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; + + // Choose landmarks from witnesses + Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Strong_witness_complex strong_witness_complex(landmarks.begin(), + landmarks.end(), + witnesses.begin(), + witnesses.end()); + + strong_witness_complex.create_complex(simplex_tree, max_squared_alpha); + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp > pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , Filtration_value & min_persistence) { + + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&file_name), + "Name of file containing a point set in off format."); + + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value<int>(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + po::variables_map vm; + + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Strong witness complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} + diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 6b0060d9..849a0a40 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -53,8 +53,6 @@ int main(int argc, char * const argv[]) { int nbL = atoi(argv[2]); double alpha2 = atof(argv[3]); clock_t start, end; - - // Construct the Simplex Tree Gudhi::Simplex_tree<> simplex_tree; // Read the point file @@ -78,6 +76,7 @@ int main(int argc, char * const argv[]) { landmarks.end(), point_vector.begin(), point_vector.end()); + witness_complex.create_complex(simplex_tree, alpha2); end = clock(); std::cout << "Witness complex took " diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp new file mode 100644 index 00000000..9b06b504 --- /dev/null +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -0,0 +1,172 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) + * + * 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 <gudhi/Simplex_tree.h> +#include <gudhi/Witness_complex.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/pick_n_random_points.h> + +#include <boost/program_options.hpp> + +#include <CGAL/Epick_d.h> + +#include <string> +#include <vector> +#include <limits> // infinity + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K; +typedef typename K::Point_d Point_d; + +typedef typename std::vector<Point_d> Point_vector; +typedef typename Gudhi::witness_complex::Witness_complex<K> Witness_complex; +typedef Gudhi::Simplex_tree<> SimplexTree; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string file_name; + std::string filediag; + Filtration_value max_squared_alpha; + int p, nbL; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + witnesses = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << witnesses.size() << " points.\n"; + std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; + + // Choose landmarks from witnesses + Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Witness_complex witness_complex(landmarks.begin(), + landmarks.end(), + witnesses.begin(), + witnesses.end()); + + witness_complex.create_complex(simplex_tree, max_squared_alpha); + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp > pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , Filtration_value & min_persistence) { + + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&file_name), + "Name of file containing a point set in off format."); + + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value<int>(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + po::variables_map vm; + + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Weak witness complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} + diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index f5633a98..3a862d71 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -27,9 +27,6 @@ #include <boost/iterator/transform_iterator.hpp> #include <algorithm> #include <utility> -#include "gudhi/reader_utils.h" -#include "gudhi/distance_functions.h" -#include "gudhi/Simplex_tree.h" #include <vector> #include <list> #include <set> @@ -39,6 +36,11 @@ #include <ctime> #include <iostream> +#include "Active_witness/Active_witness.h" +#include <gudhi/Simplex_tree.h> +#include <gudhi/Kd_tree_search.h> + + // Needed for nearest neighbours #include <CGAL/Cartesian_d.h> #include <CGAL/Search_traits.h> @@ -142,6 +144,7 @@ private: FT max_alpha_square) { unsigned nbL = landmarks_.size(); + unsigned complex_dim = 0; if (complex.num_vertices() > 0) { std::cerr << "Witness complex cannot create complex - complex is not empty.\n"; return false; @@ -168,7 +171,10 @@ private: complex.insert_simplex_and_subfaces(simplex, aw_it->second - aw.begin()->second); aw_it++; } + if (simplex.size() - 1 > complex_dim) + complex_dim = simplex.size() - 1; } + complex.set_dimension(complex_dim); return true; } diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index a16f9270..7d8fce86 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -31,7 +31,6 @@ #include <boost/range/size.hpp> #include "Active_witness/Active_witness.h" -#include <gudhi/distance_functions.h> #include <gudhi/Kd_tree_search.h> #include <algorithm> @@ -175,6 +174,7 @@ private: } k++; } + complex.set_dimension(k-1); return true; } |