From 5b6bebd9a8072d8998b0c741e5b40de0cfe5dc8e Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 12 Aug 2016 15:29:48 +0000 Subject: Move cython/src/* in cython/ git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1436 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8f971ef16ef6df597d5d3667db0eecbca94233b2 --- src/cython/include/Alpha_complex_interface.h | 142 ++++++++++++++++ src/cython/include/Cubical_complex_interface.h | 58 +++++++ .../include/Persistent_cohomology_interface.h | 90 ++++++++++ src/cython/include/Simplex_tree_interface.h | 132 +++++++++++++++ src/cython/include/Witness_complex_interface.h | 187 +++++++++++++++++++++ 5 files changed, 609 insertions(+) create mode 100644 src/cython/include/Alpha_complex_interface.h create mode 100644 src/cython/include/Cubical_complex_interface.h create mode 100644 src/cython/include/Persistent_cohomology_interface.h create mode 100644 src/cython/include/Simplex_tree_interface.h create mode 100644 src/cython/include/Witness_complex_interface.h (limited to 'src/cython/include') diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h new file mode 100644 index 00000000..e2e6d100 --- /dev/null +++ b/src/cython/include/Alpha_complex_interface.h @@ -0,0 +1,142 @@ +/* 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): Vincent Rouvreau + * + * 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 + * 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 . + */ + +#ifndef ALPHA_COMPLEX_INTERFACE_H +#define ALPHA_COMPLEX_INTERFACE_H + +#include +#include + +#include +#include // std::pair +#include + +namespace Gudhi { + +namespace alpha_complex { + +class Alpha_complex_interface : public Alpha_complex< CGAL::Epick_d< CGAL::Dynamic_dimension_tag > > { + using Alpha_complex = Alpha_complex< CGAL::Epick_d< CGAL::Dynamic_dimension_tag > > ; + typedef typename Alpha_complex::Simplex_handle Simplex_handle; + typedef typename std::pair Insertion_result; + using Simplex = std::vector; + using Filtered_complex = std::pair; + using Complex_tree = std::vector; + using Point_d = Alpha_complex::Point_d; + + public: + + Alpha_complex_interface(std::vector>&points, double max_alpha_square) + : Alpha_complex(points, max_alpha_square) { + } + + // bool from_file is a workaround fro cython to find the correct signature + Alpha_complex_interface(const std::string& off_file, double max_alpha_square, bool from_file) + : Alpha_complex(off_file, max_alpha_square) { + } + + bool find_simplex(const Simplex& vh) { + return (Alpha_complex::find(vh) != Alpha_complex::null_simplex()); + } + + bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) { + Insertion_result result = Alpha_complex::insert_simplex_and_subfaces(complex, filtration); + return (result.second); + } + + Filtration_value simplex_filtration(const Simplex& complex) { + return Alpha_complex::filtration(Alpha_complex::find(complex)); + } + + void remove_maximal_simplex(const Simplex& complex) { + return Alpha_complex::remove_maximal_simplex(Alpha_complex::find(complex)); + } + + Complex_tree get_filtered_tree() { + Complex_tree filtered_tree; + for (auto f_simplex : Alpha_complex::filtration_simplex_range()) { + Simplex simplex; + for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + filtered_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex))); + } + return filtered_tree; + + } + + Complex_tree get_skeleton_tree(int dimension) { + Complex_tree skeleton_tree; + for (auto f_simplex : Alpha_complex::skeleton_simplex_range(dimension)) { + Simplex simplex; + for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + skeleton_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex))); + } + return skeleton_tree; + } + + Complex_tree get_star_tree(const Simplex& complex) { + Complex_tree star_tree; + for (auto f_simplex : Alpha_complex::star_simplex_range(Alpha_complex::find(complex))) { + Simplex simplex; + for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + star_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex))); + } + return star_tree; + } + + Complex_tree get_coface_tree(const Simplex& complex, int dimension) { + Complex_tree coface_tree; + for (auto f_simplex : Alpha_complex::cofaces_simplex_range(Alpha_complex::find(complex), dimension)) { + Simplex simplex; + for (auto vertex : Alpha_complex::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + coface_tree.push_back(std::make_pair(simplex, Alpha_complex::filtration(f_simplex))); + } + return coface_tree; + } + + std::vector get_point(int vh) { + std::vector vd; + try { + Point_d ph = Alpha_complex::get_point(vh); + for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++) + vd.push_back(*coord); + } catch (std::out_of_range outofrange) { + // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown + } + return vd; + } + +}; + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // ALPHA_COMPLEX_INTERFACE_H + diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h new file mode 100644 index 00000000..5d17ff6b --- /dev/null +++ b/src/cython/include/Cubical_complex_interface.h @@ -0,0 +1,58 @@ +/* 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): Vincent Rouvreau + * + * 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 + * 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 . + */ + +#ifndef CUBICAL_COMPLEX_INTERFACE_H +#define CUBICAL_COMPLEX_INTERFACE_H + +#include +#include +#include + +#include +#include // std::pair +#include + +namespace Gudhi { + +namespace cubical_complex { + +template> +class Cubical_complex_interface : public Bitmap_cubical_complex { + public: + + Cubical_complex_interface(const std::vector& dimensions, + const std::vector& top_dimensional_cells) + : Bitmap_cubical_complex(dimensions, top_dimensional_cells) { + } + + Cubical_complex_interface(const std::string& perseus_file) + : Bitmap_cubical_complex(perseus_file.c_str()) { + } + +}; + +} // namespace cubical_complex + +} // namespace Gudhi + +#endif // CUBICAL_COMPLEX_INTERFACE_H + diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h new file mode 100644 index 00000000..58421799 --- /dev/null +++ b/src/cython/include/Persistent_cohomology_interface.h @@ -0,0 +1,90 @@ +/* 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): Vincent Rouvreau + * + * 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 + * 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 . + */ + +#ifndef PERSISTENT_COHOMOLOGY_INTERFACE_H +#define PERSISTENT_COHOMOLOGY_INTERFACE_H + +#include + +#include +#include // for std::pair + +namespace Gudhi { + +template +class Persistent_cohomology_interface : public +persistent_cohomology::Persistent_cohomology { + private: + /* + * Compare two intervals by dimension, then by length. + */ + struct cmp_intervals_by_dim_then_length { + + explicit cmp_intervals_by_dim_then_length(FilteredComplex * sc) + : sc_(sc) { } + + template + bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) { + if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2))) + return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1)) + > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2))); + else + return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2))); + } + FilteredComplex* sc_; + }; + + public: + + Persistent_cohomology_interface(FilteredComplex* stptr) + : persistent_cohomology::Persistent_cohomology(*stptr), + stptr_(stptr) { } + + std::vector>> get_persistence(int homology_coeff_field, double min_persistence) { + persistent_cohomology::Persistent_cohomology::init_coefficients(homology_coeff_field); + persistent_cohomology::Persistent_cohomology::compute_persistent_cohomology(min_persistence); + + // Custom sort and output persistence + cmp_intervals_by_dim_then_length cmp(stptr_); + auto persistent_pairs = persistent_cohomology::Persistent_cohomology::get_persistent_pairs(); + std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp); + + std::vector>> persistence; + for (auto pair : persistent_pairs) { + persistence.push_back(std::make_pair(stptr_->dimension(get<0>(pair)), + std::make_pair(stptr_->filtration(get<0>(pair)), + stptr_->filtration(get<1>(pair))))); + } + return persistence; + + } + + private: + // A copy + FilteredComplex* stptr_; + +}; + +} // namespace Gudhi + +#endif // PERSISTENT_COHOMOLOGY_INTERFACE_H + diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h new file mode 100644 index 00000000..9aee630b --- /dev/null +++ b/src/cython/include/Simplex_tree_interface.h @@ -0,0 +1,132 @@ +/* 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): Vincent Rouvreau + * + * 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 + * 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 . + */ + +#ifndef SIMPLEX_TREE_INTERFACE_H +#define SIMPLEX_TREE_INTERFACE_H + +#include +#include +#include + +#include +#include // std::pair +#include + +namespace Gudhi { + +template +class Simplex_tree_interface : public Simplex_tree { + typedef typename Simplex_tree::Simplex_handle Simplex_handle; + typedef typename std::pair Insertion_result; + using Simplex = std::vector; + using Filtered_complex = std::pair; + using Complex_tree = std::vector; + + public: + + bool find_simplex(const Simplex& vh) { + return (Simplex_tree::find(vh) != Simplex_tree::null_simplex()); + } + + bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) { + Insertion_result result = Simplex_tree::insert_simplex_and_subfaces(complex, filtration); + return (result.second); + } + + Filtration_value simplex_filtration(const Simplex& complex) { + return Simplex_tree::filtration(Simplex_tree::find(complex)); + } + + void remove_maximal_simplex(const Simplex& complex) { + return Simplex_tree::remove_maximal_simplex(Simplex_tree::find(complex)); + } + + Complex_tree get_filtered_tree() { + Complex_tree filtered_tree; + for (auto f_simplex : Simplex_tree::filtration_simplex_range()) { + Simplex simplex; + for (auto vertex : Simplex_tree::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + filtered_tree.push_back(std::make_pair(simplex, Simplex_tree::filtration(f_simplex))); + } + return filtered_tree; + + } + + Complex_tree get_skeleton_tree(int dimension) { + Complex_tree skeleton_tree; + for (auto f_simplex : Simplex_tree::skeleton_simplex_range(dimension)) { + Simplex simplex; + for (auto vertex : Simplex_tree::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + skeleton_tree.push_back(std::make_pair(simplex, Simplex_tree::filtration(f_simplex))); + } + return skeleton_tree; + } + + Complex_tree get_star_tree(const Simplex& complex) { + Complex_tree star_tree; + for (auto f_simplex : Simplex_tree::star_simplex_range(Simplex_tree::find(complex))) { + Simplex simplex; + for (auto vertex : Simplex_tree::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + star_tree.push_back(std::make_pair(simplex, Simplex_tree::filtration(f_simplex))); + } + return star_tree; + } + + Complex_tree get_coface_tree(const Simplex& complex, int dimension) { + Complex_tree coface_tree; + for (auto f_simplex : Simplex_tree::cofaces_simplex_range(Simplex_tree::find(complex), dimension)) { + Simplex simplex; + for (auto vertex : Simplex_tree::simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + coface_tree.push_back(std::make_pair(simplex, Simplex_tree::filtration(f_simplex))); + } + return coface_tree; + } + + void graph_expansion(std::vector>&points, int max_dimension, double max_edge_length) { + Graph_t prox_graph = compute_proximity_graph(points, max_edge_length, euclidean_distance>); + Simplex_tree::insert_graph(prox_graph); + Simplex_tree::expansion(max_dimension); + Simplex_tree::initialize_filtration(); + } + +}; + +struct Simplex_tree_options_mini : Simplex_tree_options_full_featured { + // Not doing persistence, so we don't need those + static const bool store_key = true; + static const bool store_filtration = false; + // I have few vertices + typedef short Vertex_handle; +}; + +} // namespace Gudhi + +#endif // SIMPLEX_TREE_INTERFACE_H + diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h new file mode 100644 index 00000000..bdfea91f --- /dev/null +++ b/src/cython/include/Witness_complex_interface.h @@ -0,0 +1,187 @@ +/* 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): Vincent Rouvreau + * + * 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 + * 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 . + */ + +#ifndef WITNESS_COMPLEX_INTERFACE_H +#define WITNESS_COMPLEX_INTERFACE_H + +#include +#include +#include + +#include "Persistent_cohomology_interface.h" + +#include +#include // std::pair +#include + +namespace Gudhi { + +namespace witness_complex { + +class Witness_complex_interface { + typedef typename Simplex_tree<>::Simplex_handle Simplex_handle; + typedef typename std::pair Insertion_result; + using Simplex = std::vector; + using Filtered_complex = std::pair; + using Complex_tree = std::vector; + + public: + Witness_complex_interface(std::vector>&points, int number_of_landmarks) + : pcoh_(nullptr) { + std::vector > knn; + + Gudhi::witness_complex::landmark_choice_by_furthest_point(points, number_of_landmarks, knn); + Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, points[0].size(), simplex_tree_); + + } + + bool find_simplex(const Simplex& vh) { + return (simplex_tree_.find(vh) != simplex_tree_.null_simplex()); + } + + bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) { + Insertion_result result = simplex_tree_.insert_simplex_and_subfaces(complex, filtration); + return (result.second); + } + + Filtration_value simplex_filtration(const Simplex& complex) { + return simplex_tree_.filtration(simplex_tree_.find(complex)); + } + + void remove_maximal_simplex(const Simplex& complex) { + return simplex_tree_.remove_maximal_simplex(simplex_tree_.find(complex)); + } + + Complex_tree get_filtered_tree() { + Complex_tree filtered_tree; + for (auto f_simplex : simplex_tree_.filtration_simplex_range()) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + filtered_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return filtered_tree; + + } + + Complex_tree get_skeleton_tree(int dimension) { + Complex_tree skeleton_tree; + for (auto f_simplex : simplex_tree_.skeleton_simplex_range(dimension)) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + skeleton_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return skeleton_tree; + } + + Complex_tree get_star_tree(const Simplex& complex) { + Complex_tree star_tree; + for (auto f_simplex : simplex_tree_.star_simplex_range(simplex_tree_.find(complex))) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + star_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return star_tree; + } + + Complex_tree get_coface_tree(const Simplex& complex, int dimension) { + Complex_tree coface_tree; + for (auto f_simplex : simplex_tree_.cofaces_simplex_range(simplex_tree_.find(complex), dimension)) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + coface_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return coface_tree; + } + + // Specific to Witness complex because no inheritance + Filtration_value filtration() const { + return simplex_tree_.filtration(); + } + + void set_filtration(Filtration_value fil) { + simplex_tree_.set_filtration(fil); + } + + void initialize_filtration() { + simplex_tree_.initialize_filtration(); + } + + size_t num_vertices() const { + return simplex_tree_.num_vertices(); + } + + size_t num_simplices() { + return simplex_tree_.num_simplices(); + } + + int dimension() const { + return simplex_tree_.dimension(); + } + + void set_dimension(int dimension) { + simplex_tree_.set_dimension(dimension); + } + + std::vector>> get_persistence(int homology_coeff_field, double min_persistence) { + if (pcoh_ != nullptr) { + delete pcoh_; + } + pcoh_ = new Persistent_cohomology_interface>(&simplex_tree_); + return pcoh_->get_persistence(homology_coeff_field, min_persistence); + } + + std::vector get_betti_numbers() const { + if (pcoh_ != nullptr) { + return pcoh_->betti_numbers(); + } + std::vector betti_numbers; + return betti_numbers; + } + + std::vector get_persistent_betti_numbers(Filtration_value from, Filtration_value to) const { + if (pcoh_ != nullptr) { + return pcoh_->persistent_betti_numbers(from, to); + } + std::vector persistent_betti_numbers; + return persistent_betti_numbers; + } + + private: + Simplex_tree<> simplex_tree_; + Persistent_cohomology_interface>* pcoh_; + +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif // WITNESS_COMPLEX_INTERFACE_H + -- cgit v1.2.3