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diff --git a/include/gudhi/Alpha_complex.h~ b/include/gudhi/Alpha_complex.h~ deleted file mode 100644 index a1900cb9..00000000 --- a/include/gudhi/Alpha_complex.h~ +++ /dev/null @@ -1,417 +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): Vincent Rouvreau - * - * Copyright (C) 2015 INRIA Saclay (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/>. - */ - -#ifndef ALPHA_COMPLEX_H_ -#define ALPHA_COMPLEX_H_ - -// to construct a simplex_tree from Delaunay_triangulation -#include <gudhi/graph_simplicial_complex.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Debug_utils.h> -// to construct Alpha_complex from a OFF file of points -#include <gudhi/Points_off_io.h> - -#include <stdlib.h> -#include <math.h> // isnan, fmax - -#include <CGAL/Delaunay_triangulation.h> -#include <CGAL/Epick_d.h> -#include <CGAL/Spatial_sort_traits_adapter_d.h> - -#include <iostream> -#include <vector> -#include <string> -#include <limits> // NaN -#include <map> -#include <utility> // std::pair -#include <stdexcept> -#include <numeric> // for std::iota - -namespace Gudhi { - -namespace alphacomplex { - -/** - * \class Alpha_complex Alpha_complex.h gudhi/Alpha_complex.h - * \brief Alpha complex data structure. - * - * \ingroup alpha_complex - * - * \details - * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay - * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from - * an OFF file (cf. Points_off_reader). - * - * Please refer to \ref alpha_complex for examples. - * - * The complex is a template class requiring an Epick_d <a target="_blank" - * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a> - * \cite cgal:s-gkd-15b from CGAL as template, default value is <a target="_blank" - * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> - * < <a target="_blank" href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dynamic__dimension__tag.html"> - * CGAL::Dynamic_dimension_tag </a> > - * - * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. - * - */ -template<class Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>> -class Alpha_complex : public Simplex_tree<> { - public: - // Add an int in TDS to save point index in the structure - typedef CGAL::Triangulation_data_structure<typename Kernel::Dimension, - CGAL::Triangulation_vertex<Kernel, std::ptrdiff_t>, - CGAL::Triangulation_full_cell<Kernel> > TDS; - /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ - typedef CGAL::Delaunay_triangulation<Kernel, TDS> Delaunay_triangulation; - - /** \brief A point in Euclidean space.*/ - typedef typename Kernel::Point_d Point_d; - /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay - * triangulations.*/ - typedef Kernel Geom_traits; - - private: - // From Simplex_tree - // Type required to insert into a simplex_tree (with or without subfaces). - typedef std::vector<Vertex_handle> Vector_vertex; - - // Simplex_result is the type returned from simplex_tree insert function. - typedef typename std::pair<Simplex_handle, bool> Simplex_result; - - typedef typename Kernel::Compute_squared_radius_d Squared_Radius; - typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel; - typedef typename Kernel::Point_dimension_d Point_Dimension; - - // Type required to compute squared radius, or side of bounded sphere on a vector of points. - typedef typename std::vector<Point_d> Vector_of_CGAL_points; - - // Vertex_iterator type from CGAL. - typedef typename Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator; - - // size_type type from CGAL. - typedef typename Delaunay_triangulation::size_type size_type; - - // Map type to switch from simplex tree vertex handle to CGAL vertex iterator. - typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Vector_vertex_iterator; - - private: - /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator. - * Vertex handles are inserted sequentially, starting at 0.*/ - Vector_vertex_iterator vertex_handle_to_iterator_; - /** \brief Pointer on the CGAL Delaunay triangulation.*/ - Delaunay_triangulation* triangulation_; - /** \brief Kernel for triangulation_ functions access.*/ - Kernel kernel_; - - public: - /** \brief Alpha_complex constructor from an OFF file name. - * Uses the Delaunay_triangulation_off_reader to construct the Delaunay triangulation required to initialize - * the Alpha_complex. - * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. - * - * @param[in] off_file_name OFF file [path and] name. - * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. - */ - Alpha_complex(const std::string& off_file_name, - Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) - : triangulation_(nullptr) { - Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); - if (!off_reader.is_valid()) { - std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n"; - exit(-1); // ----- >> - } - - init_from_range(off_reader.get_point_cloud(), max_alpha_square); - } - - /** \brief Alpha_complex constructor from a list of points. - * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. - * - * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d - * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. - * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a Kernel::Point_d. - * - * @post Compare num_simplices with InputPointRange points number (not the same in case of duplicate points). - */ - template<typename InputPointRange > - Alpha_complex(const InputPointRange& points, - Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) - : triangulation_(nullptr) { - init_from_range(points, max_alpha_square); - } - - /** \brief Alpha_complex destructor. - * - * @warning Deletes the Delaunay triangulation. - */ - ~Alpha_complex() { - delete triangulation_; - } - - // Forbid copy/move constructor/assignment operator - Alpha_complex(const Alpha_complex& other) = delete; - Alpha_complex& operator= (const Alpha_complex& other) = delete; - Alpha_complex (Alpha_complex&& other) = delete; - Alpha_complex& operator= (Alpha_complex&& other) = delete; - - /** \brief get_point returns the point corresponding to the vertex given as parameter. - * - * @param[in] vertex Vertex handle of the point to retrieve. - * @return The point found. - * @exception std::out_of_range In case vertex is not found (cf. std::vector::at). - */ - Point_d get_point(Vertex_handle vertex) const { - return vertex_handle_to_iterator_.at(vertex)->point(); - } - - private: - template<typename InputPointRange > - void init_from_range(const InputPointRange& points, Filtration_value max_alpha_square) { - auto first = std::begin(points); - auto last = std::end(points); - if (first != last) { - // point_dimension function initialization - Point_Dimension point_dimension = kernel_.point_dimension_d_object(); - - // Delaunay triangulation is point dimension. - triangulation_ = new Delaunay_triangulation(point_dimension(*first)); - - std::vector<Point_d> points(first, last); - - // Creates a vector {0, 1, ..., N-1} - std::vector<std::ptrdiff_t> indices(boost::counting_iterator<std::ptrdiff_t>(0), - boost::counting_iterator<std::ptrdiff_t>(points.size())); - - // Sort indices considering CGAL spatial sort - typedef CGAL::Spatial_sort_traits_adapter_d<Kernel, Point_d*> Search_traits_d; - spatial_sort(indices.begin(), indices.end(), Search_traits_d(&(points[0]))); - - typename Delaunay_triangulation::Full_cell_handle hint; - for (auto index : indices) { - typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(points[index], hint); - // Save index value as data to retrieve it after insertion - pos->data() = index; - hint = pos->full_cell(); - } - init(max_alpha_square); - } - } - - /** \brief Initialize the Alpha_complex from the Delaunay triangulation. - * - * @param[in] max_alpha_square maximum for alpha square value. - * - * @warning Delaunay triangulation must be already constructed with at least one vertex and dimension must be more - * than 0. - * - * Initialization can be launched once. - */ - void init(Filtration_value max_alpha_square) { - if (triangulation_ == nullptr) { - std::cerr << "Alpha_complex init - Cannot init from a NULL triangulation\n"; - return; // ----- >> - } - if (triangulation_->number_of_vertices() < 1) { - std::cerr << "Alpha_complex init - Cannot init from a triangulation without vertices\n"; - return; // ----- >> - } - if (triangulation_->maximal_dimension() < 1) { - std::cerr << "Alpha_complex init - Cannot init from a zero-dimension triangulation\n"; - return; // ----- >> - } - if (num_vertices() > 0) { - std::cerr << "Alpha_complex init - Cannot init twice\n"; - return; // ----- >> - } - - set_dimension(triangulation_->maximal_dimension()); - - // -------------------------------------------------------------------------------------------- - // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa - // Loop on triangulation vertices list - for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) { - if (!triangulation_->is_infinite(*vit)) { -#ifdef DEBUG_TRACES - std::cout << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl; -#endif // DEBUG_TRACES - vertex_handle_to_iterator_.emplace(vit->data(), vit); - } - } - // -------------------------------------------------------------------------------------------- - - // -------------------------------------------------------------------------------------------- - // Simplex_tree construction from loop on triangulation finite full cells list - for (auto cit = triangulation_->finite_full_cells_begin(); cit != triangulation_->finite_full_cells_end(); ++cit) { - Vector_vertex vertexVector; -#ifdef DEBUG_TRACES - std::cout << "Simplex_tree insertion "; -#endif // DEBUG_TRACES - for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { - if (*vit != nullptr) { -#ifdef DEBUG_TRACES - std::cout << " " << (*vit)->data(); -#endif // DEBUG_TRACES - // Vector of vertex construction for simplex_tree structure - vertexVector.push_back((*vit)->data()); - } - } -#ifdef DEBUG_TRACES - std::cout << std::endl; -#endif // DEBUG_TRACES - // Insert each simplex and its subfaces in the simplex tree - filtration is NaN - insert_simplex_and_subfaces(vertexVector, std::numeric_limits<double>::quiet_NaN()); - } - // -------------------------------------------------------------------------------------------- - - // -------------------------------------------------------------------------------------------- - // Will be re-used many times - Vector_of_CGAL_points pointVector; - // ### For i : d -> 0 - for (int decr_dim = dimension(); decr_dim >= 0; decr_dim--) { - // ### Foreach Sigma of dim i - for (auto f_simplex : skeleton_simplex_range(decr_dim)) { - int f_simplex_dim = dimension(f_simplex); - if (decr_dim == f_simplex_dim) { - pointVector.clear(); -#ifdef DEBUG_TRACES - std::cout << "Sigma of dim " << decr_dim << " is"; -#endif // DEBUG_TRACES - for (auto vertex : simplex_vertex_range(f_simplex)) { - pointVector.push_back(get_point(vertex)); -#ifdef DEBUG_TRACES - std::cout << " " << vertex; -#endif // DEBUG_TRACES - } -#ifdef DEBUG_TRACES - std::cout << std::endl; -#endif // DEBUG_TRACES - // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma) - if (isnan(filtration(f_simplex))) { - Filtration_value alpha_complex_filtration = 0.0; - // No need to compute squared_radius on a single point - alpha is 0.0 - if (f_simplex_dim > 0) { - // squared_radius function initialization - Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object(); - - alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end()); - } - assign_filtration(f_simplex, alpha_complex_filtration); -#ifdef DEBUG_TRACES - std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << filtration(f_simplex) << std::endl; -#endif // DEBUG_TRACES - } - propagate_alpha_filtration(f_simplex, decr_dim); - } - } - } - // -------------------------------------------------------------------------------------------- - - // -------------------------------------------------------------------------------------------- - // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension - bool modified_filt = make_filtration_non_decreasing(); - // Remove all simplices that have a filtration value greater than max_alpha_square - // Remark: prune_above_filtration does not require initialize_filtration to be done before. - modified_filt |= prune_above_filtration(max_alpha_square); - if (modified_filt) { - initialize_filtration(); - } - // -------------------------------------------------------------------------------------------- - } - - template<typename Simplex_handle> - void propagate_alpha_filtration(Simplex_handle f_simplex, int decr_dim) { - // ### Foreach Tau face of Sigma - for (auto f_boundary : boundary_simplex_range(f_simplex)) { -#ifdef DEBUG_TRACES - std::cout << " | --------------------------------------------------\n"; - std::cout << " | Tau "; - for (auto vertex : simplex_vertex_range(f_boundary)) { - std::cout << vertex << " "; - } - std::cout << "is a face of Sigma\n"; - std::cout << " | isnan(filtration(Tau)=" << isnan(filtration(f_boundary)) << std::endl; -#endif // DEBUG_TRACES - // ### If filt(Tau) is not NaN - if (!isnan(filtration(f_boundary))) { - // ### filt(Tau) = fmin(filt(Tau), filt(Sigma)) - Filtration_value alpha_complex_filtration = fmin(filtration(f_boundary), filtration(f_simplex)); - assign_filtration(f_boundary, alpha_complex_filtration); -#ifdef DEBUG_TRACES - std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << filtration(f_boundary) << std::endl; -#endif // DEBUG_TRACES - // ### Else - } else { - // No need to compute is_gabriel for dimension <= 2 - // i.e. : Sigma = (3,1) => Tau = 1 - if (decr_dim > 1) { - // insert the Tau points in a vector for is_gabriel function - Vector_of_CGAL_points pointVector; -#ifdef DEBUG_TRACES - Vertex_handle vertexForGabriel = Vertex_handle(); -#endif // DEBUG_TRACES - for (auto vertex : simplex_vertex_range(f_boundary)) { - pointVector.push_back(get_point(vertex)); - } - // Retrieve the Sigma point that is not part of Tau - parameter for is_gabriel function - Point_d point_for_gabriel; - for (auto vertex : simplex_vertex_range(f_simplex)) { - point_for_gabriel = get_point(vertex); - if (std::find(pointVector.begin(), pointVector.end(), point_for_gabriel) == pointVector.end()) { -#ifdef DEBUG_TRACES - // vertex is not found in Tau - vertexForGabriel = vertex; -#endif // DEBUG_TRACES - // No need to continue loop - break; - } - } - // is_gabriel function initialization - Is_Gabriel is_gabriel = kernel_.side_of_bounded_sphere_d_object(); - bool is_gab = is_gabriel(pointVector.begin(), pointVector.end(), point_for_gabriel) - != CGAL::ON_BOUNDED_SIDE; -#ifdef DEBUG_TRACES - std::cout << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << vertexForGabriel << std::endl; -#endif // DEBUG_TRACES - // ### If Tau is not Gabriel of Sigma - if (false == is_gab) { - // ### filt(Tau) = filt(Sigma) - Filtration_value alpha_complex_filtration = filtration(f_simplex); - assign_filtration(f_boundary, alpha_complex_filtration); -#ifdef DEBUG_TRACES - std::cout << " | filt(Tau) = filt(Sigma) = " << filtration(f_boundary) << std::endl; -#endif // DEBUG_TRACES - } - } - } - } - } -}; - -} // namespace alphacomplex - -} // namespace Gudhi - -#endif // ALPHA_COMPLEX_H_ |