From d5b5de5aa50c2fdc73d00bbdcf295caf44237a34 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 4 Jul 2018 06:21:07 +0000 Subject: Fix SimplicialComplexForAlpha (dD version) Write SimplicialComplexForAlpha3d concept Add make_filtration_non_decreasing and prune_above_filtration mechanism for Alpha_complex_3d Write documentation for Alpha_complex_3d ( still missing the user version) Remove exact static bool from Alpha_complex_3d_options mechanism and add some comments on value_from_iterator functions Fix Alpha_complex/utilities/CMakeLists.txt warnings git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3667 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 32e15aaf98df14a43eaef4a4af00de2ec418924c --- .../concept/SimplicialComplexForAlpha.h | 14 ++++-- .../concept/SimplicialComplexForAlpha3d.h | 58 ++++++++++++++++++++++ src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 29 +++++++++-- .../include/gudhi/Alpha_complex_3d_options.h | 9 ++-- src/Alpha_complex/utilities/CMakeLists.txt | 2 +- 5 files changed, 97 insertions(+), 15 deletions(-) create mode 100644 src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h (limited to 'src') diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h index a51df127..ba97c802 100644 --- a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h +++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h @@ -41,9 +41,6 @@ struct SimplicialComplexForAlpha { /** Returns the number of vertices in the simplicial complex. */ std::size_t num_vertices(); - /** Sets the simplicial complex dimension. */ - void set_dimension(int dimension); - /** Gets the 'simplex' dimension. */ int dimension(Simplex_handle simplex); @@ -65,8 +62,7 @@ struct SimplicialComplexForAlpha { * 'value type' must be 'Vertex_handle'.*/ typedef unspecified Simplex_vertex_range; - /** \brief Returns a range over vertices of a given - * simplex. */ + /** \brief Returns a range over vertices of a given simplex. */ Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex); /** \brief Iterator over the boundaries of the complex, in an arbitrary order. @@ -77,6 +73,14 @@ struct SimplicialComplexForAlpha { /** \brief Returns a range over boundaries of a given simplex. */ Boundary_simplex_range boundary_simplex_range(Simplex_handle const & simplex); + /** \brief Iterator over the simplices of the skeleton of the complex, for a given dimension. + * + * 'value_type' must be 'Simplex_handle'. */ + typedef unspecified Skeleton_simplex_range; + /** \brief Returns a range over the simplices of the skeleton of the simplicial complex, for a given + * dimension. */ + Skeleton_simplex_range skeleton_simplex_range; + /** \brief Return type of an insertion of a simplex */ typedef unspecified Insertion_result_type; diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h new file mode 100644 index 00000000..f6085a26 --- /dev/null +++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.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) 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 . + */ + +#ifndef CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_3D_H_ +#define CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_3D_H_ + +namespace Gudhi { + +namespace alpha_complex { + +/** \brief The concept SimplicialComplexForAlpha3d describes the requirements for a type to implement a simplicial + * complex, that can be created from a `Alpha_complex_3d`. + */ +struct SimplicialComplexForAlpha3d { + /** Handle to specify a vertex. Must be a non-negative integer. */ + typedef unspecified Vertex_handle; + /** Handle to specify the simplex filtration value. */ + typedef unspecified Filtration_value; + + /** Returns the number of vertices in the simplicial complex. */ + std::size_t num_vertices(); + + /** \brief Inserts a simplex from a given simplex (represented by a vector of Vertex_handle) in the + * simplicial complex with the given 'filtration' value. */ + void insert_simplex(std::vector const & vertex_range, Filtration_value filtration); + + /** Browses the simplicial complex to make the filtration non-decreasing. */ + void make_filtration_non_decreasing(); + + /** Prune the simplicial complex above 'filtration' value given as parameter. */ + void prune_above_filtration(Filtration_value filtration); + +}; + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_3D_H_ diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 1d171f7d..f37c0816 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -56,19 +56,23 @@ namespace Gudhi { namespace alpha_complex { /** - * \class Alpha_complex_3d Alpha_complex_3d.h gudhi/Alpha_complex_3d.h + * \class Alpha_complex_3d * \brief Alpha complex data structure for 3d specific case. * * \ingroup alpha_complex * * \details - * The data structure is constructing 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/) from a - * range of points or from an OFF file (cf. Points_off_reader). + * The data structure is constructing a CGAL 3D Alpha + * Shapes from a range of points (can be read from an OFF file, cf. Points_off_reader). + * + * \tparam AlphaComplex3dOptions can be `Gudhi::alpha_complex::Alpha_shapes_3d`, + * `Gudhi::alpha_complex::Exact_alpha_shapes_3d`, `Gudhi::alpha_complex::Weighted_alpha_shapes_3d`, + * `Gudhi::alpha_complex::Periodic_alpha_shapes_3d` or `Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d`. * * Please refer to \ref alpha_complex for examples. * - * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. + * \remark When Alpha_complex_3d is constructed with an infinite value of alpha (default value), the complex is a + * Delaunay complex. * */ template @@ -100,6 +104,9 @@ public: * * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 * + * @pre Available if AlphaComplex3dOptions is `Gudhi::alpha_complex::Alpha_shapes_3d` or + * `Gudhi::alpha_complex::Exact_alpha_shapes_3d`. + * * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a AlphaComplex3dOptions::Point_3. */ @@ -135,6 +142,8 @@ public: * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 * @param[in] weights Range of weights on points. Points must be in AlphaComplex3dOptions::Point_3 * + * @pre Available if AlphaComplex3dOptions is `Weighted_alpha_shapes_3d`. + * * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a AlphaComplex3dOptions::Point_3. * The type WeightRange must be a range for which std::begin and @@ -192,6 +201,8 @@ public: * @param[in] y_max Iso-oriented cuboid y_max. * @param[in] z_max Iso-oriented cuboid z_max. * + * @pre Available if AlphaComplex3dOptions is `Periodic_alpha_shapes_3d`. + * * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a AlphaComplex3dOptions::Point_3. * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. @@ -265,6 +276,8 @@ public: * @param[in] y_max Iso-oriented cuboid y_max. * @param[in] z_max Iso-oriented cuboid z_max. * + * @pre Available if AlphaComplex3dOptions is `Weighted_periodic_alpha_shapes_3d`. + * * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a AlphaComplex3dOptions::Point_3. * The type WeightRange must be a range for which std::begin and @@ -461,6 +474,12 @@ public: std::cout << "facets \t\t" << count_facets << std::endl; std::cout << "cells \t\t" << count_cells << std::endl; #endif // DEBUG_TRACES + // -------------------------------------------------------------------------------------------- + // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension + complex.make_filtration_non_decreasing(); + // Remove all simplices that have a filtration value greater than max_alpha_square + complex.prune_above_filtration(max_alpha_square); + // -------------------------------------------------------------------------------------------- return true; } diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h index e1b246c5..567b19cb 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h @@ -55,6 +55,7 @@ public: static const bool weighted = false; static const bool periodic = false; + // Default value_from_iterator as Alpha_shape_3 is not exact template static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; @@ -77,8 +78,8 @@ public: static const bool weighted = false; static const bool periodic = false; - static const bool exact = true; + // value_from_iterator needs to compute filtration value as Alpha_shape_3 is exact template static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ CGAL::to_double(avi->exact()); @@ -103,8 +104,8 @@ public: static const bool weighted = true; static const bool periodic = false; - static const bool exact = false; + // Default value_from_iterator as Alpha_shape_3 is not exact template static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; @@ -134,8 +135,8 @@ public: static const bool weighted = false; static const bool periodic = true; - static const bool exact = false; + // Default value_from_iterator as Alpha_shape_3 is not exact template static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; @@ -163,8 +164,8 @@ public: static const bool weighted = true; static const bool periodic = true; - static const bool exact = false; + // Default value_from_iterator as Alpha_shape_3 is not exact template static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 86e761ef..13476ba5 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -53,6 +53,6 @@ if(CGAL_FOUND) install(TARGETS alpha_complex_3d_persistence DESTINATION bin) - endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) endif(CGAL_FOUND) -- cgit v1.2.3