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Diffstat (limited to 'src/Cech_complex/include/gudhi')
| -rw-r--r-- | src/Cech_complex/include/gudhi/Cech_complex.h | 126 | ||||
| -rw-r--r-- | src/Cech_complex/include/gudhi/Cech_complex_blocker.h | 85 |
2 files changed, 211 insertions, 0 deletions
diff --git a/src/Cech_complex/include/gudhi/Cech_complex.h b/src/Cech_complex/include/gudhi/Cech_complex.h new file mode 100644 index 00000000..3a0d828a --- /dev/null +++ b/src/Cech_complex/include/gudhi/Cech_complex.h @@ -0,0 +1,126 @@ +/* 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) 2018 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef CECH_COMPLEX_H_ +#define CECH_COMPLEX_H_ + +#include <gudhi/graph_simplicial_complex.h> // for Gudhi::Proximity_graph +#include <gudhi/Debug_utils.h> // for GUDHI_CHECK +#include <gudhi/Cech_complex_blocker.h> // for Gudhi::cech_complex::Cech_blocker + +#include <iostream> +#include <vector> +#include <cstddef> +#include <iterator> // for std::size + +namespace Gudhi { + +namespace cech_complex { + +/** + * \class Cech_complex + * \brief Cech complex data structure. + * + * \ingroup Cech_complex + * + * \details + * The data structure is a one skeleton graph, or Rips graph, containing edges when the edge length is less or equal + * to a given threshold. Edge length is computed from a user given point cloud with a given distance function, or a + * distance matrix. + * + * \tparam Filtration_value is the type used to store the filtration values of the simplicial complex. + */ +template<typename SimplicialComplexForCechComplex, typename ForwardPointRange> +class Cech_complex { + private: + using Vertex_handle = typename SimplicialComplexForCechComplex::Vertex_handle; + using Filtration_value = typename SimplicialComplexForCechComplex::Filtration_value; + using Proximity_graph = Gudhi::Proximity_graph<SimplicialComplexForCechComplex>; + + public: + /** \brief Cech_complex constructor from a list of points. + * + * @param[in] points Range of points. + * @param[in] threshold Rips value. + * @param[in] distance distance function that returns a `Filtration_value` from 2 given points. + * + * \tparam ForwardPointRange must be a range for which `std::begin` and `std::end` return input iterators on a + * point. + * + * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where + * `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`. + */ + template<typename Distance > + Cech_complex(const ForwardPointRange& points, Filtration_value threshold, Distance distance) + : threshold_(threshold), + point_cloud_(points) { + GUDHI_CHECK(std::size(points) > 0, + std::invalid_argument("Cech_complex::create_complex - point cloud is empty")); + dimension_ = points[0].size(); + cech_skeleton_graph_ = Gudhi::compute_proximity_graph<SimplicialComplexForCechComplex>(point_cloud_, threshold_, distance); + } + + /** \brief Initializes the simplicial complex from the Rips graph and expands it until a given maximal + * dimension. + * + * @param[in] complex SimplicialComplexForCech to be created. + * @param[in] dim_max graph expansion for Rips until this given maximal dimension. + * @exception std::invalid_argument In debug mode, if `complex.num_vertices()` does not return 0. + * + */ + void create_complex(SimplicialComplexForCechComplex& complex, int dim_max) { + GUDHI_CHECK(complex.num_vertices() == 0, + std::invalid_argument("Cech_complex::create_complex - simplicial complex is not empty")); + + // insert the proximity graph in the simplicial complex + complex.insert_graph(cech_skeleton_graph_); + // expand the graph until dimension dim_max + complex.expansion_with_blockers(dim_max, + Cech_blocker<SimplicialComplexForCechComplex, ForwardPointRange>(complex, this)); + } + + Filtration_value threshold() const { + return threshold_; + } + + std::size_t dimension() const { + return dimension_; + } + + auto point(std::size_t vertex) const -> decltype(point_cloud_.begin() + vertex) { + GUDHI_CHECK((point_cloud_.begin() + vertex) < point_cloud_.end(), + std::invalid_argument("Cech_complex::point - simplicial complex is not empty")); + return (point_cloud_.begin() + vertex); + } + + private: + Proximity_graph cech_skeleton_graph_; + Filtration_value threshold_; + ForwardPointRange point_cloud_; + std::size_t dimension_; +}; + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // CECH_COMPLEX_H_ diff --git a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h new file mode 100644 index 00000000..647bf0b7 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h @@ -0,0 +1,85 @@ +/* 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) 2018 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef CECH_COMPLEX_BLOCKER_H_ +#define CECH_COMPLEX_BLOCKER_H_ + +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Cech_complex.h> + +#include <Miniball/Miniball.hpp> + +#include <iostream> +#include <vector> +#include <cmath> // for std::sqrt + +namespace Gudhi { + +namespace cech_complex { + +// Just declaring Cech_complex class because used and not yet defined. +template<typename SimplicialComplexForCechComplex, typename ForwardPointRange> +class Cech_complex; + +template <typename SimplicialComplexForCech, typename ForwardPointRange> +class Cech_blocker { + private: + using Point = std::vector<double>; + using Point_cloud = std::vector<Point>; + using Point_iterator = Point_cloud::const_iterator; + using Coordinate_iterator = Point::const_iterator; + using Min_sphere = Miniball::Miniball<Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + using Simplex_handle = typename SimplicialComplexForCech::Simplex_handle; + using Filtration_value = typename SimplicialComplexForCech::Filtration_value; + using Cech_complex = Gudhi::cech_complex::Cech_complex<SimplicialComplexForCech, ForwardPointRange>; + + public: + bool operator()(Simplex_handle sh) { + Point_cloud points; + for (auto vertex : simplicial_complex_.simplex_vertex_range(sh)) { + points.push_back(cc_ptr_->point(vertex)); +#ifdef DEBUG_TRACES + std::cout << "#(" << vertex << ")#"; +#endif // DEBUG_TRACES + } + Min_sphere ms(cc_ptr_->dimension(), points.begin(),points.end()); + Filtration_value radius = std::sqrt(ms.squared_radius()); +#ifdef DEBUG_TRACES + std::cout << "radius = " << radius << " - " << (radius > cc_ptr_->threshold()) << std::endl; +#endif // DEBUG_TRACES + simplicial_complex_.assign_filtration(sh, radius); + return (radius > cc_ptr_->threshold()); + } + Cech_blocker(SimplicialComplexForCech& simplicial_complex, Cech_complex* cc_ptr) + : simplicial_complex_(simplicial_complex), + cc_ptr_(cc_ptr) { + } + private: + SimplicialComplexForCech simplicial_complex_; + Cech_complex* cc_ptr_; +}; + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // CECH_COMPLEX_BLOCKER_H_ |