diff options
Diffstat (limited to 'src/Witness_complex')
22 files changed, 223 insertions, 313 deletions
diff --git a/src/Witness_complex/concept/SimplicialComplexForWitness.h b/src/Witness_complex/concept/SimplicialComplexForWitness.h index d78cc83f..8b85f4e4 100644 --- a/src/Witness_complex/concept/SimplicialComplexForWitness.h +++ b/src/Witness_complex/concept/SimplicialComplexForWitness.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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 diff --git a/src/Witness_complex/doc/COPYRIGHT b/src/Witness_complex/doc/COPYRIGHT index 7d032c87..25a700cf 100644 --- a/src/Witness_complex/doc/COPYRIGHT +++ b/src/Witness_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Siargey Kachanovich -Copyright (C) 2015 INRIA +Copyright (C) 2015 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 the Free Software diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 171a185f..62203054 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -90,8 +90,9 @@ int main(int argc, char * const argv[]) { Gudhi::Points_off_reader<Point_d> off_reader(file_name); point_vector = Point_vector(off_reader.get_point_cloud()); - // Choose landmarks - Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + // Choose landmarks (one can choose either of the two methods below) + // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); // Compute witness complex Witness_complex witness_complex(landmarks, @@ -107,10 +108,14 @@ int main(int argc, char * const argv[]) { Here is an example of constructing a strong witness complex filtration and computing persistence on it: - \include Witness_complex/example_strong_witness_persistence.cpp + \include Witness_complex/strong_witness_persistence.cpp - \copyright GNU General Public License v3. + \section witnessexample3 Example3: Computing relaxed witness complex persistence from a distance matrix + In this example we compute the relaxed witness complex persistence from a given matrix of closest landmarks to each witness. + Each landmark is given as the couple (index, distance). + + \include Witness_complex/example_nearest_landmark_table.cpp */ diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 0f709409..3d838c0d 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_examples) add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp ) @@ -13,41 +12,23 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) # 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 ) - add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) -add_executable( Witness_complex_example_strong_fvecs example_strong_witness_complex_fvecs.cpp ) add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.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_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}) - - 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_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_strong_off) 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_test_sphere_10 + COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10") 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") - + install(TARGETS Witness_complex_example_off DESTINATION bin) - install(TARGETS Witness_complex_example_strong_off DESTINATION bin) - install(TARGETS Witness_complex_example_strong_fvecs DESTINATION bin) install(TARGETS Witness_complex_example_sphere DESTINATION bin) - install(TARGETS Witness_complex_example_witness_persistence DESTINATION bin) - install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_example_strong_off DESTINATION bin) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/example/example_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp index b8594212..acaf7c54 100644 --- a/src/Witness_complex/example/example_nearest_landmark_table.cpp +++ b/src/Witness_complex/example/example_nearest_landmark_table.cpp @@ -1,25 +1,3 @@ -/* 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> diff --git a/src/Witness_complex/example/example_strong_witness_complex_fvecs.cpp b/src/Witness_complex/example/example_strong_witness_complex_fvecs.cpp deleted file mode 100644 index 3e0efa15..00000000 --- a/src/Witness_complex/example/example_strong_witness_complex_fvecs.cpp +++ /dev/null @@ -1,81 +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) 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/Fake_simplex_tree.h> -//#include <gudhi/Sb_wrapper.h> -#include <gudhi/Euclidean_strong_witness_complex.h> -#include <gudhi/pick_n_random_points.h> -#include <gudhi/Points_fvecs_reader.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; - //Gudhi::Fake_simplex_tree simplex_tree; - //Gudhi::Sb_wrapper simplex_tree; - - // Read the point file - Point_vector point_vector, landmarks; - Gudhi::load_points_from_fvecs_file<K>(file_name, std::back_insert_iterator< Point_vector >(point_vector)); - - - 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() << std::endl; - // std::cout << "Max dimension is : " << simplex_tree.dimension() << std::endl; - -} diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp index f195953b..19f73836 100644 --- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -1,29 +1,7 @@ -/* 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/Fake_simplex_tree.h> #include <gudhi/Euclidean_strong_witness_complex.h> #include <gudhi/pick_n_random_points.h> +#include <gudhi/choose_n_farthest_points.h> #include <gudhi/Points_off_io.h> #include <CGAL/Epick_d.h> @@ -39,10 +17,9 @@ 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[]) { +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"; + std::cerr << "Usage: " << argv[0] << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; return 0; } @@ -51,31 +28,30 @@ int main(int argc, char * const argv[]) { double alpha2 = atof(argv[3]); clock_t start, end; Gudhi::Simplex_tree<> simplex_tree; - //Gudhi::Fake_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); // ----- >> - } + 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)); + // Choose landmarks (decomment one of the following two lines) + // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, + std::back_inserter(landmarks)); // Compute witness complex start = clock(); - Witness_complex witness_complex(landmarks, - point_vector); + 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 << "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/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index b36dac0d..be11c955 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -4,6 +4,7 @@ #include <gudhi/Simplex_tree.h> #include <gudhi/Euclidean_witness_complex.h> #include <gudhi/pick_n_random_points.h> +#include <gudhi/choose_n_farthest_points.h> #include <gudhi/Points_off_io.h> #include <CGAL/Epick_d.h> @@ -44,8 +45,9 @@ int main(int argc, char * const argv[]) { 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)); + // Choose landmarks (decomment one of the following two lines) + // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks)); // Compute witness complex start = clock(); diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index 124fd99b..9e3c972d 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -1,30 +1,9 @@ -/* 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/Euclidean_witness_complex.h> #include <gudhi/pick_n_random_points.h> +#include <gudhi/choose_n_farthest_points.h> #include <gudhi/reader_utils.h> #include <CGAL/Epick_d.h> @@ -41,27 +20,25 @@ /** Write a gnuplot readable file. * Data range is a random access range of pairs (arg, value) */ -template < typename Data_range > -void write_data(Data_range & data, std::string filename) { +template <typename Data_range> +void write_data(Data_range& data, std::string filename) { std::ofstream ofs(filename, std::ofstream::out); - for (auto entry : data) - ofs << entry.first << ", " << entry.second << "\n"; + for (auto entry : data) ofs << entry.first << ", " << entry.second << "\n"; ofs.close(); } -int main(int argc, char * const argv[]) { +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"; + std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n"; return 0; } int number_of_landmarks = atoi(argv[1]); - std::vector< std::pair<int, double> > l_time; + std::vector<std::pair<int, double> > l_time; // Generate points for (int nbP = 500; nbP < 10000; nbP += 500) { @@ -75,16 +52,17 @@ int main(int argc, char * const argv[]) { // Choose landmarks start = clock(); - Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks)); + // Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, number_of_landmarks, + Gudhi::subsampling::random_starting_point, + std::back_inserter(landmarks)); // Compute witness complex - Witness_complex witness_complex(landmarks, - point_vector); + 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 " - << time << " s. \n"; + std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " << time << " s. \n"; std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; l_time.push_back(std::make_pair(nbP, time)); } diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h index 7df43db5..4b755daa 100644 --- a/src/Witness_complex/example/generators.h +++ b/src/Witness_complex/example/generators.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 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 @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ -#define EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ +#ifndef GENERATORS_H_ +#define GENERATORS_H_ #include <CGAL/Epick_d.h> #include <CGAL/point_generators_d.h> @@ -163,4 +163,4 @@ void generate_points_torus(Point_Vector& W, int nbP, int dim) { } } -#endif // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_ +#endif // GENERATORS_H_ diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h index d41a6811..8cb8662b 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 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 diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h index 0a05173a..10d2ec52 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 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 diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h index 4f3cef4f..ea97cd3f 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h index ff8bb139..1dacefa5 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index c18335d3..fd6b3f38 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 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 @@ -34,7 +34,8 @@ namespace Gudhi { namespace witness_complex { -/* \private + /** + * \private * \class Strong_witness_complex * \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses. * \ingroup witness_complex @@ -130,6 +131,8 @@ class Strong_witness_complex { return true; } + //@} + private: /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness. * Iterator is needed to know until how far we can take landmarks to form simplexes. @@ -170,7 +173,6 @@ class Strong_witness_complex { simplex.pop_back(); } } - //@} }; } // namespace witness_complex diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 53c38520..67885258 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h index b68d75a1..c7b732b9 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h +++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt index 0b523eaf..58ac60c5 100644 --- a/src/Witness_complex/test/CMakeLists.txt +++ b/src/Witness_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_tests) include(GUDHI_test_coverage) diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..ce5e29f2 --- /dev/null +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -0,0 +1,27 @@ +project(Witness_complex_utilities) + +# 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_strong_witness_persistence strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) + target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) + endif() + + add_test(NAME Witness_complex_strong_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + add_test(NAME Witness_complex_weak_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + + install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) + +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp index f786fe7b..f386e992 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 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 @@ -25,6 +25,7 @@ #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_off_io.h> #include <gudhi/pick_n_random_points.h> +#include <gudhi/choose_n_farthest_points.h> #include <boost/program_options.hpp> @@ -46,16 +47,10 @@ 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); +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[]) { +int main(int argc, char* argv[]) { std::string file_name; std::string filediag; Filtration_value max_squared_alpha; @@ -69,19 +64,20 @@ int main(int argc, char * argv[]) { 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); // ----- >> + 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)); + // Choose landmarks (decomment one of the following two lines) + // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, + std::back_inserter(landmarks)); // Compute witness complex - Strong_witness_complex strong_witness_complex(landmarks, - witnesses); + Strong_witness_complex strong_witness_complex(landmarks, witnesses); strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); @@ -110,37 +106,28 @@ int main(int argc, char * argv[]) { 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) { +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."); + 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."); + 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); @@ -149,8 +136,7 @@ void program_options(int argc, char * argv[] all.add(visible).add(hidden); po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), 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")) { @@ -165,7 +151,6 @@ void program_options(int argc, char * argv[] std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; std::cout << visible << std::endl; - std::abort(); + exit(-1); } } - diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp index a1146922..ea00cfe7 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * Copyright (C) 2016 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 @@ -25,6 +25,7 @@ #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_off_io.h> #include <gudhi/pick_n_random_points.h> +#include <gudhi/choose_n_farthest_points.h> #include <boost/program_options.hpp> @@ -46,16 +47,10 @@ 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); +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[]) { +int main(int argc, char* argv[]) { std::string file_name; std::string filediag; Filtration_value max_squared_alpha; @@ -69,19 +64,20 @@ int main(int argc, char * argv[]) { 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); // ----- >> + 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)); + // Choose landmarks (decomment one of the following two lines) + // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, + std::back_inserter(landmarks)); // Compute witness complex - Witness_complex witness_complex(landmarks, - witnesses); + Witness_complex witness_complex(landmarks, witnesses); witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); @@ -110,38 +106,28 @@ int main(int argc, char * argv[]) { 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) { +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."); + 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."); + 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); @@ -150,8 +136,7 @@ void program_options(int argc, char * argv[] all.add(visible).add(hidden); po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), 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")) { @@ -166,6 +151,6 @@ void program_options(int argc, char * argv[] std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; std::cout << visible << std::endl; - std::abort(); + exit(-1); } } diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md new file mode 100644 index 00000000..7ea397b9 --- /dev/null +++ b/src/Witness_complex/utilities/witnesscomplex.md @@ -0,0 +1,73 @@ +---
+layout: page
+title: "Witness complex"
+meta_title: "Witness complex"
+teaser: ""
+permalink: /witnesscomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
+
+
+For more details about the witness complex, please read the [user manual of the package]({{ site.officialurl }}/doc/latest/group__witness__complex.html).
+
+## weak_witness_persistence ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points.
+The output diagram contains one bar per line, written with the convention:
+
+`p dim birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,
+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+**Usage**
+
+`weak_witness_persistence [options] <OFF input file>`
+
+**Allowed options**
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+**Example**
+
+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
+
+
+## strong_witness_persistence ##
+
+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points.
+The output diagram contains one bar per line, written with the convention:
+
+`p dim birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,
+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+**Usage**
+
+`strong_witness_persistence [options] <OFF input file>`
+
+**Allowed options**
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+**Example**
+
+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
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