diff options
Diffstat (limited to 'example/Witness_complex')
| -rw-r--r-- | example/Witness_complex/CMakeLists.txt | 54 | ||||
| -rw-r--r-- | example/Witness_complex/example_nearest_landmark_table.cpp | 69 | ||||
| -rw-r--r-- | example/Witness_complex/example_strong_witness_complex_off.cpp | 79 | ||||
| -rw-r--r-- | example/Witness_complex/example_strong_witness_persistence.cpp | 171 | ||||
| -rw-r--r-- | example/Witness_complex/example_witness_complex_off.cpp | 60 | ||||
| -rw-r--r-- | example/Witness_complex/example_witness_complex_persistence.cpp | 171 | ||||
| -rw-r--r-- | example/Witness_complex/example_witness_complex_sphere.cpp (renamed from example/Witness_complex/witness_complex_sphere.cpp) | 34 | ||||
| -rw-r--r-- | example/Witness_complex/generators.h | 31 | ||||
| -rw-r--r-- | example/Witness_complex/witness_complex_from_file.cpp | 100 |
9 files changed, 635 insertions, 134 deletions
diff --git a/example/Witness_complex/CMakeLists.txt b/example/Witness_complex/CMakeLists.txt index 4d67e0d0..670651ce 100644 --- a/example/Witness_complex/CMakeLists.txt +++ b/example/Witness_complex/CMakeLists.txt @@ -1,16 +1,46 @@ cmake_minimum_required(VERSION 2.6) project(Witness_complex_examples) -# A simple example - add_executable( witness_complex_from_file witness_complex_from_file.cpp ) - add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100) - -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - if (EIGEN3_FOUND) - add_executable ( witness_complex_sphere witness_complex_sphere.cpp ) - target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) - add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10) - endif(EIGEN3_FOUND) - endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) +add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp ) +target_link_libraries(Witness_complex_example_nearest_landmark_table ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES}) endif() +add_test(NAME Witness_complex_example_nearest_landmark_table + COMMAND $<TARGET_FILE:Witness_complex_example_nearest_landmark_table>) + +# CGAL and Eigen3 are required for Euclidean version of Witness +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_off ${Boost_SYSTEM_LIBRARY}) + add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_strong_off ${Boost_SYSTEM_LIBRARY}) + add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) + target_link_libraries(Witness_complex_example_sphere ${Boost_SYSTEM_LIBRARY}) + + add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) + target_link_libraries(Witness_complex_example_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES}) + endif() + + add_test(NAME Witness_complex_example_off_test_torus + COMMAND $<TARGET_FILE:Witness_complex_example_off> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") + add_test(NAME Witness_complex_example_strong_off_test_torus + COMMAND $<TARGET_FILE:Witness_complex_example_strong_off> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") + add_test(NAME Witness_complex_example_test_sphere_10 + COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10") + add_test(NAME Witness_complex_example_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_example_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + add_test(NAME Witness_complex_example_strong_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/example/Witness_complex/example_nearest_landmark_table.cpp b/example/Witness_complex/example_nearest_landmark_table.cpp new file mode 100644 index 00000000..b8594212 --- /dev/null +++ b/example/Witness_complex/example_nearest_landmark_table.cpp @@ -0,0 +1,69 @@ +/* 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 (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/>. + */ + +#define BOOST_PARAMETER_MAX_ARITY 12 + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Witness_complex.h> +#include <gudhi/Persistent_cohomology.h> + +#include <iostream> +#include <fstream> +#include <utility> +#include <string> +#include <vector> + +int main(int argc, char * const argv[]) { + using Nearest_landmark_range = std::vector<std::pair<std::size_t, double>>; + using Nearest_landmark_table = std::vector<Nearest_landmark_range>; + using Witness_complex = Gudhi::witness_complex::Witness_complex<Nearest_landmark_table>; + using Simplex_tree = Gudhi::Simplex_tree<>; + using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; + using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; + + Simplex_tree simplex_tree; + Nearest_landmark_table nlt; + + // Example contains 5 witnesses and 5 landmarks + Nearest_landmark_range w0 = {std::make_pair(0, 0), std::make_pair(1, 1), std::make_pair(2, 2), + std::make_pair(3, 3), std::make_pair(4, 4)}; nlt.push_back(w0); + Nearest_landmark_range w1 = {std::make_pair(1, 0), std::make_pair(2, 1), std::make_pair(3, 2), + std::make_pair(4, 3), std::make_pair(0, 4)}; nlt.push_back(w1); + Nearest_landmark_range w2 = {std::make_pair(2, 0), std::make_pair(3, 1), std::make_pair(4, 2), + std::make_pair(0, 3), std::make_pair(1, 4)}; nlt.push_back(w2); + Nearest_landmark_range w3 = {std::make_pair(3, 0), std::make_pair(4, 1), std::make_pair(0, 2), + std::make_pair(1, 3), std::make_pair(2, 4)}; nlt.push_back(w3); + Nearest_landmark_range w4 = {std::make_pair(4, 0), std::make_pair(0, 1), std::make_pair(1, 2), + std::make_pair(2, 3), std::make_pair(3, 4)}; nlt.push_back(w4); + + Witness_complex witness_complex(nlt); + witness_complex.create_complex(simplex_tree, 4.1); + + std::cout << "Number of simplices: " << simplex_tree.num_simplices() << std::endl; + + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(11); + + pcoh.compute_persistent_cohomology(-0.1); + pcoh.output_diagram(); +} diff --git a/example/Witness_complex/example_strong_witness_complex_off.cpp b/example/Witness_complex/example_strong_witness_complex_off.cpp new file mode 100644 index 00000000..0ee9ee90 --- /dev/null +++ b/example/Witness_complex/example_strong_witness_complex_off.cpp @@ -0,0 +1,79 @@ +/* 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 (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/Euclidean_strong_witness_complex.h> +#include <gudhi/pick_n_random_points.h> +#include <gudhi/Points_off_io.h> + +#include <CGAL/Epick_d.h> + +#include <iostream> +#include <fstream> +#include <ctime> +#include <string> +#include <vector> + +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = typename K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>; +using Point_vector = std::vector<Point_d>; + +int main(int argc, char * const argv[]) { + if (argc != 5) { + std::cerr << "Usage: " << argv[0] + << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; + return 0; + } + + std::string file_name = argv[1]; + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); + double alpha2 = atof(argv[3]); + clock_t start, end; + Gudhi::Simplex_tree<> simplex_tree; + + // Read the point file + Point_vector point_vector, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + point_vector = Point_vector(off_reader.get_point_cloud()); + + std::cout << "Successfully read " << point_vector.size() << " points.\n"; + std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; + + // Choose landmarks + Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + start = clock(); + Witness_complex witness_complex(landmarks, + point_vector); + + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); + end = clock(); + std::cout << "Strong witness complex took " + << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; + std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; +} diff --git a/example/Witness_complex/example_strong_witness_persistence.cpp b/example/Witness_complex/example_strong_witness_persistence.cpp new file mode 100644 index 00000000..f786fe7b --- /dev/null +++ b/example/Witness_complex/example_strong_witness_persistence.cpp @@ -0,0 +1,171 @@ +/* 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 (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/Euclidean_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 K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = K::Point_d; + +using Point_vector = std::vector<Point_d>; +using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>; +using SimplexTree = Gudhi::Simplex_tree<>; + +using Filtration_value = SimplexTree::Filtration_value; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , 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, lim_d; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, 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, + witnesses); + + strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); + + 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 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 + , int & dim_max + , 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); + Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity(); + 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(default_alpha), + "Maximal squared relaxation parameter.") + ("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") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()), + "Maximal dimension of the strong witness complex we want to compute."); + + 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/example/Witness_complex/example_witness_complex_off.cpp b/example/Witness_complex/example_witness_complex_off.cpp new file mode 100644 index 00000000..b36dac0d --- /dev/null +++ b/example/Witness_complex/example_witness_complex_off.cpp @@ -0,0 +1,60 @@ +#include <sys/types.h> +#include <sys/stat.h> + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_witness_complex.h> +#include <gudhi/pick_n_random_points.h> +#include <gudhi/Points_off_io.h> + +#include <CGAL/Epick_d.h> + +#include <iostream> +#include <fstream> +#include <ctime> +#include <string> +#include <vector> + +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>; +using Point_vector = std::vector< Point_d >; + +int main(int argc, char * const argv[]) { + if (argc != 5) { + std::cerr << "Usage: " << argv[0] + << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; + return 0; + } + + std::string file_name = argv[1]; + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); + double alpha2 = atof(argv[3]); + clock_t start, end; + Gudhi::Simplex_tree<> simplex_tree; + + // Read the point file + Point_vector point_vector, 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); // ----- >> + } + point_vector = Point_vector(off_reader.get_point_cloud()); + + std::cout << "Successfully read " << point_vector.size() << " points.\n"; + std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; + + // Choose landmarks + Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + start = clock(); + Witness_complex witness_complex(landmarks, + point_vector); + + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); + end = clock(); + std::cout << "Witness complex took " + << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; + std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; +} diff --git a/example/Witness_complex/example_witness_complex_persistence.cpp b/example/Witness_complex/example_witness_complex_persistence.cpp new file mode 100644 index 00000000..a1146922 --- /dev/null +++ b/example/Witness_complex/example_witness_complex_persistence.cpp @@ -0,0 +1,171 @@ +/* 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 (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/Euclidean_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 K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = K::Point_d; + +using Point_vector = std::vector<Point_d>; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>; +using SimplexTree = Gudhi::Simplex_tree<>; + +using Filtration_value = SimplexTree::Filtration_value; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , 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, lim_d; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, 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, + witnesses); + + witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); + + 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 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 + , int & dim_max + , 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."); + + Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity(); + 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(default_alpha), + "Maximal squared relaxation parameter.") + ("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") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()), + "Maximal dimension of the weak witness complex we want to compute."); + + 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/example/Witness_complex/witness_complex_sphere.cpp b/example/Witness_complex/example_witness_complex_sphere.cpp index b26c9f36..124fd99b 100644 --- a/example/Witness_complex/witness_complex_sphere.cpp +++ b/example/Witness_complex/example_witness_complex_sphere.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2016 INRIA (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 @@ -19,17 +19,16 @@ * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#define BOOST_PARAMETER_MAX_ARITY 12 - -#include <sys/types.h> -#include <sys/stat.h> +#define BOOST_PARAMETER_MAX_ARITY 12 #include <gudhi/Simplex_tree.h> -#include <gudhi/Witness_complex.h> -#include <gudhi/Landmark_choice_by_random_point.h> +#include <gudhi/Euclidean_witness_complex.h> +#include <gudhi/pick_n_random_points.h> #include <gudhi/reader_utils.h> +#include <CGAL/Epick_d.h> + #include <iostream> #include <fstream> #include <ctime> @@ -51,6 +50,9 @@ void write_data(Data_range & data, std::string filename) { } int main(int argc, char * const argv[]) { + using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; + using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<Kernel>; + if (argc != 2) { std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n"; @@ -58,27 +60,27 @@ int main(int argc, char * const argv[]) { } int number_of_landmarks = atoi(argv[1]); - clock_t start, end; - - // Construct the Simplex Tree - Gudhi::Simplex_tree<> simplex_tree; std::vector< std::pair<int, double> > l_time; - // Read the point file + // Generate points for (int nbP = 500; nbP < 10000; nbP += 500) { - Point_Vector point_vector; + clock_t start, end; + // Construct the Simplex Tree + Gudhi::Simplex_tree<> simplex_tree; + Point_Vector point_vector, landmarks; generate_points_sphere(point_vector, nbP, 4); std::cout << "Successfully generated " << point_vector.size() << " points.\n"; std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n"; // Choose landmarks start = clock(); - std::vector<std::vector< int > > knn; - Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, number_of_landmarks, knn); + Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks)); // Compute witness complex - Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree); + Witness_complex witness_complex(landmarks, + point_vector); + witness_complex.create_complex(simplex_tree, 0); end = clock(); double time = static_cast<double>(end - start) / CLOCKS_PER_SEC; std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " diff --git a/example/Witness_complex/generators.h b/example/Witness_complex/generators.h index ac445261..7df43db5 100644 --- a/example/Witness_complex/generators.h +++ b/example/Witness_complex/generators.h @@ -25,17 +25,19 @@ #include <CGAL/Epick_d.h> #include <CGAL/point_generators_d.h> +#include <CGAL/Random.h> #include <fstream> #include <string> #include <vector> +#include <cmath> -typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K; -typedef K::FT FT; -typedef K::Point_d Point_d; -typedef std::vector<Point_d> Point_Vector; -typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator; -typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator; +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using FT = K::FT; +using Point_d = K::Point_d; +using Point_Vector = std::vector<Point_d>; +using Random_cube_iterator = CGAL::Random_points_in_cube_d<Point_d>; +using Random_point_iterator = CGAL::Random_points_in_ball_d<Point_d>; /** * \brief Rock age method of reading off file @@ -144,4 +146,21 @@ void generate_points_sphere(Point_Vector& W, int nbP, int dim) { W.push_back(*rp++); } +/** \brief Generate nbP points on a (flat) d-torus embedded in R^{2d} + * + */ +void generate_points_torus(Point_Vector& W, int nbP, int dim) { + CGAL::Random rand; + const double pi = std::acos(-1); + for (int i = 0; i < nbP; i++) { + std::vector<FT> point; + for (int j = 0; j < dim; j++) { + double alpha = rand.uniform_real(static_cast<double>(0), 2*pi); + point.push_back(sin(alpha)); + point.push_back(cos(alpha)); + } + W.push_back(Point_d(point)); + } +} + #endif // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ diff --git a/example/Witness_complex/witness_complex_from_file.cpp b/example/Witness_complex/witness_complex_from_file.cpp deleted file mode 100644 index 53207ad2..00000000 --- a/example/Witness_complex/witness_complex_from_file.cpp +++ /dev/null @@ -1,100 +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): Siargey Kachanovich - * - * Copyright (C) 2015 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 <sys/types.h> -#include <sys/stat.h> - -#include <gudhi/Simplex_tree.h> -#include <gudhi/Witness_complex.h> -#include <gudhi/Landmark_choice_by_random_point.h> -#include <gudhi/reader_utils.h> - -#include <iostream> -#include <fstream> -#include <ctime> -#include <string> -#include <vector> - -typedef std::vector< Vertex_handle > typeVectorVertex; -typedef std::vector< std::vector <double> > Point_Vector; - -/** - * \brief Customized version of read_points - * which takes into account a possible nbP first line - * - */ -inline void -read_points_cust(std::string file_name, std::vector< std::vector< double > > & points) { - std::ifstream in_file(file_name.c_str(), std::ios::in); - if (!in_file.is_open()) { - std::cerr << "Unable to open file " << file_name << std::endl; - return; - } - std::string line; - double x; - while (getline(in_file, line)) { - std::vector< double > point; - std::istringstream iss(line); - while (iss >> x) { - point.push_back(x); - } - if (point.size() != 1) - points.push_back(point); - } - in_file.close(); -} - -int main(int argc, char * const argv[]) { - if (argc != 3) { - std::cerr << "Usage: " << argv[0] - << " path_to_point_file nbL \n"; - return 0; - } - - std::string file_name = argv[1]; - int nbL = atoi(argv[2]); - clock_t start, end; - - // Construct the Simplex Tree - Gudhi::Simplex_tree<> simplex_tree; - - // Read the point file - Point_Vector point_vector; - read_points_cust(file_name, point_vector); - std::cout << "Successfully read " << point_vector.size() << " points.\n"; - std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n"; - - // Choose landmarks - start = clock(); - std::vector<std::vector< int > > knn; - Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, knn); - end = clock(); - std::cout << "Landmark choice for " << nbL << " landmarks took " - << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; - - // Compute witness complex - start = clock(); - Gudhi::witness_complex::witness_complex(knn, nbL, point_vector[0].size(), simplex_tree); - end = clock(); - std::cout << "Witness complex took " - << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; -} |