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Diffstat (limited to 'concept')
20 files changed, 0 insertions, 1221 deletions
diff --git a/concept/Alpha_complex/SimplicialComplexForAlpha.h b/concept/Alpha_complex/SimplicialComplexForAlpha.h deleted file mode 100644 index a51df127..00000000 --- a/concept/Alpha_complex/SimplicialComplexForAlpha.h +++ /dev/null @@ -1,89 +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) 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ -#define CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ - -namespace Gudhi { - -namespace alpha_complex { - -/** \brief The concept SimplicialComplexForAlpha describes the requirements for a type to implement a simplicial - * complex, that can be created from a `Alpha_complex`. - */ -struct SimplicialComplexForAlpha { - /** Handle to specify a simplex. */ - typedef unspecified Simplex_handle; - /** 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(); - - /** Sets the simplicial complex dimension. */ - void set_dimension(int dimension); - - /** Gets the 'simplex' dimension. */ - int dimension(Simplex_handle simplex); - - /** Assigns the 'simplex' with the given 'filtration' value. */ - int assign_filtration(Simplex_handle simplex, Filtration_value filtration); - - /** \brief Inserts a simplex with vertices from a given simplex (represented by a vector of Vertex_handle) in the - * simplicial complex with the given 'filtration' value. */ - void insert_simplex_and_subfaces(std::vector<Vertex_handle> 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); - - /** \brief Iterator over vertices of a simplex. - * - * 'value type' must be 'Vertex_handle'.*/ - typedef unspecified Simplex_vertex_range; - - /** \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. - * - * 'value_type' must be 'Simplex_handle'.*/ - typedef unspecified Boundary_simplex_range; - - /** \brief Returns a range over boundaries of a given simplex. */ - Boundary_simplex_range boundary_simplex_range(Simplex_handle const & simplex); - - /** \brief Return type of an insertion of a simplex - */ - typedef unspecified Insertion_result_type; -}; - -} // namespace alpha_complex - -} // namespace Gudhi - -#endif // CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ diff --git a/concept/Bottleneck_distance/Persistence_diagram.h b/concept/Bottleneck_distance/Persistence_diagram.h deleted file mode 100644 index d016faf4..00000000 --- a/concept/Bottleneck_distance/Persistence_diagram.h +++ /dev/null @@ -1,50 +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: François Godi - * - * 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 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 CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ -#define CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ - -namespace Gudhi { - -namespace persistence_diagram { - -/** \brief Concept of point in a persistence diagram. std::get<0>(point) must return the birth of the corresponding component and std::get<1>(point) its death. - * Both should be convertible to `double`. - * A valid implementation of this concept is std::pair<double,double>. - * Death should be larger than birth, death can be std::numeric_limits<double>::infinity() for components which stay alive. - * - * \ingroup bottleneck_distance - */ -struct DiagramPoint{}; - -/** \brief Concept of persistence diagram. It is a range of `DiagramPoint`. - * std::begin(diagram) and std::end(diagram) must return corresponding iterators. - * - * \ingroup bottleneck_distance - */ -struct PersistenceDiagram{}; - -} // namespace persistence_diagram - -} // namespace Gudhi - -#endif // CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ diff --git a/concept/Cech_complex/SimplicialComplexForCech.h b/concept/Cech_complex/SimplicialComplexForCech.h deleted file mode 100644 index 89231eec..00000000 --- a/concept/Cech_complex/SimplicialComplexForCech.h +++ /dev/null @@ -1,66 +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) 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 CONCEPT_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_ -#define CONCEPT_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_ - -namespace Gudhi { - -namespace cech_complex { - -/** \brief The concept SimplicialComplexForCech describes the requirements for a type to implement a simplicial - * complex, that can be created from a `Cech_complex`. - */ -struct SimplicialComplexForCech { - /** Handle to specify a simplex. */ - typedef unspecified Simplex_handle; - /** 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; - - /** Assigns the 'simplex' with the given 'filtration' value. */ - int assign_filtration(Simplex_handle simplex, Filtration_value filtration); - - /** \brief Returns a range over vertices of a given - * simplex. */ - Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex); - - /** \brief Inserts a given `Gudhi::ProximityGraph` in the simplicial complex. */ - template<class ProximityGraph> - void insert_graph(const ProximityGraph& proximity_graph); - - /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension. - * expansion can be blocked by the blocker oracle. */ - template< typename Blocker > - void expansion_with_blockers(int max_dim, Blocker block_simplex); - - /** Returns the number of vertices in the simplicial complex. */ - std::size_t num_vertices(); - -}; - -} // namespace alpha_complex - -} // namespace Gudhi - -#endif // CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ diff --git a/concept/Persistence_representations/Real_valued_topological_data.h b/concept/Persistence_representations/Real_valued_topological_data.h deleted file mode 100644 index 22ef6d72..00000000 --- a/concept/Persistence_representations/Real_valued_topological_data.h +++ /dev/null @@ -1,51 +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): Pawel Dlotko - * - * 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONCEPT_REAL_VALUED_TOPOLOGICAL_DATA_H_ -#define CONCEPT_REAL_VALUED_TOPOLOGICAL_DATA_H_ - -namespace Gudhi { - -namespace Persistence_representations { - -/** \brief The concept Real_valued_topological_data describes the requirements - * for a type to implement a container that allows computations of its projections to R. - */ -class Real_valued_topological_data { - public: - /** -* Typically there are various ways data can be projected to R. This function gives us the number of functions for -* vectorization provided by a given class. - **/ - size_t number_of_projections_to_R(); - /** -* This is a function to compute the projection from this container to reals. The parameter of a function have to -* be between 0 and the value returned by number_of_projections_to_R(). -**/ - double project_to_R(size_t number_of_projection); -}; - -} // namespace Persistence_representations - -} // namespace Gudhi - -#endif // CONCEPT_REAL_VALUED_TOPOLOGICAL_DATA_H_ diff --git a/concept/Persistence_representations/Topological_data_with_averages.h b/concept/Persistence_representations/Topological_data_with_averages.h deleted file mode 100644 index aa64467f..00000000 --- a/concept/Persistence_representations/Topological_data_with_averages.h +++ /dev/null @@ -1,44 +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): Pawel Dlotko - * - * 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONCEPT_TOPOLOGICAL_DATA_WITH_AVERAGES_H_ -#define CONCEPT_TOPOLOGICAL_DATA_WITH_AVERAGES_H_ - -namespace Gudhi { - -namespace Persistence_representations { - -/** \brief The concept Topological_data_with_averages describes the requirements - * for a type to implement a container that allows computations of averages. - * Note that the average object after being computed is stored in *this. - */ -class Topological_data_with_averages { - public: - void compute_average(const std::vector<Topological_data_with_averages*>& to_average); -}; - -} // namespace Persistence_representations - -} // namespace Gudhi - -#endif // CONCEPT_TOPOLOGICAL_DATA_WITH_AVERAGES_H_ diff --git a/concept/Persistence_representations/Topological_data_with_distances.h b/concept/Persistence_representations/Topological_data_with_distances.h deleted file mode 100644 index c8eb2b34..00000000 --- a/concept/Persistence_representations/Topological_data_with_distances.h +++ /dev/null @@ -1,49 +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): Pawel Dlotko - * - * 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONCEPT_TOPOLOGICAL_DATA_WITH_DISTANCES_H_ -#define CONCEPT_TOPOLOGICAL_DATA_WITH_DISTANCES_H_ - -namespace Gudhi { - -namespace Persistence_representations { - -/** \brief The concept Topological_data_with_distances describes the requirements - * for a type to implement a container that allows computations of distance to another contained of that type. - * \details - * The second parameter of the distance function allow to declare power of a distance. The exact meaning of that - * number will be different for different distances. A few examples are given below: - * In case of p-Wasserstein distance, the power is equal to p. power = std::limit<double>::max() for bottleneck - * distance. - * - * In case of L^p landscape distance, the power is equal to p. s - */ -class Topological_data_with_distances { - public: - double distance(const Topological_data_with_distances& second, double power = 1); -}; - -} // namespace Persistence_representations - -} // namespace Gudhi - -#endif // CONCEPT_TOPOLOGICAL_DATA_WITH_DISTANCES_H_ diff --git a/concept/Persistence_representations/Topological_data_with_scalar_product.h b/concept/Persistence_representations/Topological_data_with_scalar_product.h deleted file mode 100644 index 0f08b8c6..00000000 --- a/concept/Persistence_representations/Topological_data_with_scalar_product.h +++ /dev/null @@ -1,42 +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): Pawel Dlotko - * - * 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONCEPT_TOPOLOGICAL_DATA_WITH_SCALAR_PRODUCT_H_ -#define CONCEPT_TOPOLOGICAL_DATA_WITH_SCALAR_PRODUCT_H_ - -namespace Gudhi { - -namespace Persistence_representations { - -/** \brief The concept Topological_data_with_scalar_product describes the requirements - * for a type to implement a container that allows computations of scalar products. - */ -class Topological_data_with_scalar_product { - public: - double compute_scalar_product(const Topological_data_with_scalar_product& second); -}; - -} // namespace Persistence_representations - -} // namespace Gudhi - -#endif // CONCEPT_TOPOLOGICAL_DATA_WITH_SCALAR_PRODUCT_H_ diff --git a/concept/Persistence_representations/Vectorized_topological_data.h b/concept/Persistence_representations/Vectorized_topological_data.h deleted file mode 100644 index 365105d6..00000000 --- a/concept/Persistence_representations/Vectorized_topological_data.h +++ /dev/null @@ -1,51 +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): Pawel Dlotko - * - * 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONCEPT_VECTORIZED_TOPOLOGICAL_DATA_H_ -#define CONCEPT_VECTORIZED_TOPOLOGICAL_DATA_H_ - -namespace Gudhi { - -namespace Persistence_representations { - -/** \brief The concept Vectorized_topological_data describes the requirements - * for a type to implement a container that allows vectorization. - */ -class Vectorized_topological_data { - public: - /** - * There are various ways data can be vectorized. This function give us the number of functions for vectorization - *provided by a given class. - **/ - size_t number_of_vectorize_functions(); - /** - * This is a function to vectorize given container. The parameter of a function have to be between 0 and the value - *returned by number_of_vectorize_functions(). - **/ - std::vector<double> vectorize(int number_of_function); -}; - -} // namespace Persistence_representations - -} // namespace Gudhi - -#endif // CONCEPT_VECTORIZED_TOPOLOGICAL_DATA_H_ diff --git a/concept/Persistent_cohomology/CoefficientField.h b/concept/Persistent_cohomology/CoefficientField.h deleted file mode 100644 index 9d066cca..00000000 --- a/concept/Persistent_cohomology/CoefficientField.h +++ /dev/null @@ -1,52 +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): Clément Maria - * - * 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 - * 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/>. - */ - -/** \brief Concept describing the requirements for a class to represent - * a field of coefficients to compute persistent homology. - */ -struct CoefficientField { - -/** \brief Type of element of the field. - * - * Must be Assignable. */ - typedef unspecified Element; - -/** Default constructible. */ - CoefficientField(); - - void init(Element charac); - void init(Element charac_min, Element charac_max); - -/** Return the characteristic of the field. */ - Element characteristic(); -/** Return the element 1 of the field. */ - Element multiplicative_identity(); -/** Return the element 0 of the field. */ - Element additive_identity(); - -/** Assign: x <- x + y */ - void plus_equal(Element x, Element y); - -/** */ -//... inverse() - - };
\ No newline at end of file diff --git a/concept/Persistent_cohomology/FilteredComplex.h b/concept/Persistent_cohomology/FilteredComplex.h deleted file mode 100644 index 62b9002f..00000000 --- a/concept/Persistent_cohomology/FilteredComplex.h +++ /dev/null @@ -1,150 +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): Clément Maria - * - * 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 - * 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/>. - */ - -/** \brief The concept FilteredComplex describes the requirements - * for a type to implement a filtered cell complex, from which - * one can compute persistent homology via a model of the concept - * PersistentHomology. - */ -struct FilteredComplex -{ -/** Handle to specify a simplex. */ - typedef unspecified Simplex_handle; -/** \brief Type for the value of the filtration function. - * - * Must be comparable with <. */ - typedef unspecified Filtration_value; - -/** \brief Specifies the nature of the indexing scheme. - * - * is model of IndexingTag. */ - typedef unspecified Indexing_tag; - -/** Returns a Simplex_handle that is different from all simplex handles - * of the simplices. */ - Simplex_handle null_simplex(); -/** \brief Returns the number of simplices in the complex. - * - * Does not count the empty simplex. */ - size_t num_simplices(); -/** \brief Returns the dimension of a simplex. */ - int dimension(Simplex_handle sh); -/** \brief Returns the filtration value of a simplex. - * - * If sh is null_simplex(), returns the maximal value of the - * filtration function on the complex. */ - Filtration_value filtration(Simplex_handle sh); - -/** \brief Returns the simplex that has index idx in the filtration. - * - * This is only called on valid indices. */ - Simplex_handle simplex ( size_t idx ); -/** \brief Iterator on the simplices belonging to the - * boundary of a simplex. - * - * <CODE>value_type</CODE> must be 'Simplex_handle'. - */ -typedef unspecified Boundary_simplex_iterator; -/** \brief Range giving access to the simplices in the boundary of - * a simplex. - * - * .begin() and .end() return type Boundary_simplex_iterator. - */ -typedef unspecified Boundary_simplex_range; - -/** \brief Returns a range giving access to all simplices of the - * boundary of a simplex, i.e. - * the set of codimension 1 subsimplices of the Simplex. - * - * If the simplex is \f$[v_0, \cdots ,v_d]\f$, with canonical orientation - * induced by \f$ v_0 < \cdots < v_d \f$, the iterator enumerates the - * simplices of the boundary in the order: - * \f$[v_0,\cdots,\widehat{v_i},\cdots,v_d]\f$ for \f$i\f$ from 0 to d - * - * We note that the alternate sum of the simplices given by the iterator - * gives the chains corresponding to the boundary of the simplex.*/ -Boundary_simplex_range boundary_simplex_range(Simplex_handle sh); - -/** \brief Iterator over all simplices of the complex - * in the order of the indexing scheme. - * - * 'value_type' must be 'Simplex_handle'. - */ -typedef unspecified Filtration_simplex_iterator; -/** \brief Range over the simplices of the complex - * in the order of the filtration. - * - * .begin() and .end() return type Filtration_simplex_iterator.*/ -typedef unspecified Filtration_simplex_range; -/** \brief Returns a range over the simplices of the complex - * in the order of the filtration. - * - * .begin() and .end() return type Filtration_simplex_iterator.*/ -Filtration_simplex_range filtration_simplex_range(); - -/** \name Map interface - * Conceptually a `std::unordered_map<Simplex_handle,std::size_t>`. - * @{ */ -/** \brief Data stored for each simplex. - * - * Must be an integer type. */ - typedef unspecified Simplex_key; -/** \brief Returns a constant dummy number that is either negative, - * or at least as large as `num_simplices()`. Suggested value: -1. */ - Simplex_key null_key (); -/** \brief Returns the number stored for a simplex by `assign_key`. - * - * This is never called on null_simplex(). */ - Simplex_key key ( Simplex_handle sh ); -/** \brief Store a number for a simplex, which can later be retrieved with `key(sh)`. - * - * This is never called on null_simplex(). */ - void assign_key(Simplex_handle sh, Simplex_key n); -/** @} */ - - -/* \brief Iterator over the simplices of the complex, - * in an arbitrary order. - * - * 'value_type' must be 'Simplex_handle'.*/ -//typedef unspecified Complex_simplex_iterator; -//typedef unspecified Complex_simplex_range; - -/* -* Returns a range over all the simplices of a -* complex. -*/ -//Complex_simplex_range complex_simplex_range(); - -/*************************************************/ /** -* @details Compares the filtration values of simplices s and t -* -* @return -1 if s comes before t in the filtration, +1 -* if it comes later, and 0 if they come at the same time -* -* @note OPTIONAL -* @todo use an enum? Just a bool? -*/ -//int is_before_in_filtration(Simplex_handle s, Simplex_handle t); -/*************************************************/ - -}; diff --git a/concept/Persistent_cohomology/PersistentHomology.h b/concept/Persistent_cohomology/PersistentHomology.h deleted file mode 100644 index f9a78763..00000000 --- a/concept/Persistent_cohomology/PersistentHomology.h +++ /dev/null @@ -1,41 +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): Clément Maria - * - * 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 - * 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/>. - */ - -/** \brief Concept describing the requirements for a class to compute - * persistent homology. */ -struct PersistentHomology { - -/** \brief Type of filtered cell complex on which persistent homology - * is computed. - * - * Must be a model of concept FilteredComplex. - */ - typedef unspecified Filtered_complex; - -/** \brief Type of coefficients to be used for computing persistent - * homology. - * - * Must be a model of concept CoefficientField. - */ - typedef unspecified Coefficient_field; - - }; diff --git a/concept/Rips_complex/SimplicialComplexForRips.h b/concept/Rips_complex/SimplicialComplexForRips.h deleted file mode 100644 index 3c5acecf..00000000 --- a/concept/Rips_complex/SimplicialComplexForRips.h +++ /dev/null @@ -1,54 +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) 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 <http://www.gnu.org/licenses/>. - */ - -#ifndef CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_ -#define CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_ - -namespace Gudhi { - -namespace rips_complex { - -/** \brief The concept SimplicialComplexForRips describes the requirements for a type to implement a simplicial - * complex, that can be created from a `Rips_complex`. The only available model for the moment is the `Simplex_tree`. - */ -struct SimplicialComplexForRips { - /** \brief Type used to store the filtration values of the simplicial complex. */ - typedef unspecified Filtration_value; - - /** \brief Inserts a given `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` in the simplicial complex. */ - template<class OneSkeletonGraph> - void insert_graph(const OneSkeletonGraph& skel_graph); - - /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension as - * explained in \ref ripsdefinition. */ - void expansion(int max_dim); - - /** \brief Returns the number of vertices in the simplicial complex. */ - std::size_t num_vertices(); - -}; - -} // namespace rips_complex - -} // namespace Gudhi - -#endif // CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_ diff --git a/concept/Simplex_tree/FiltrationValue.h b/concept/Simplex_tree/FiltrationValue.h deleted file mode 100644 index f4dcf985..00000000 --- a/concept/Simplex_tree/FiltrationValue.h +++ /dev/null @@ -1,35 +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): Clément Maria - * - * 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 - * 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/>. - */ - -/** \brief Value type for a filtration function on a cell complex. - * - * A <EM>filtration</EM> of a cell complex (see FilteredComplex) is - * a function \f$f:\mathbf{K} \rightarrow \mathbb{R}\f$ satisfying \f$f(\tau)\leq - * f(\sigma)\f$ whenever \f$\tau \subseteq \sigma\f$. Ordering the simplices - * by increasing filtration values (breaking ties so as a simplex appears after - * its subsimplices of same filtration value) provides an indexing scheme - * (see IndexingTag). - */ - struct FiltrationValue { - /** \brief Operator < is a StrictWeakOrdering. */ - bool operator<(FiltrationValue f1, FiltrationValue f2); - }; diff --git a/concept/Simplex_tree/IndexingTag.h b/concept/Simplex_tree/IndexingTag.h deleted file mode 100644 index 37e7e294..00000000 --- a/concept/Simplex_tree/IndexingTag.h +++ /dev/null @@ -1,30 +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): Clément Maria - * - * 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 - * 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/>. - */ - -/** \brief Concept describing an indexing scheme (see FilteredComplex) - * for applying - * continuous maps to a cell complex, and compute its persistent - * homology. - * - * Must be `Gudhi::linear_indexing_tag`. - */ -struct IndexingTag {}; diff --git a/concept/Simplex_tree/SimplexKey.h b/concept/Simplex_tree/SimplexKey.h deleted file mode 100644 index c03f7da1..00000000 --- a/concept/Simplex_tree/SimplexKey.h +++ /dev/null @@ -1,28 +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): Clément Maria - * - * 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 - * 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/>. - */ - - /** \brief Key type used as simplex identifier. - * - * Must be an integer type. - */ - struct SimplexKey {}; - diff --git a/concept/Simplex_tree/SimplexTreeOptions.h b/concept/Simplex_tree/SimplexTreeOptions.h deleted file mode 100644 index 6638da26..00000000 --- a/concept/Simplex_tree/SimplexTreeOptions.h +++ /dev/null @@ -1,43 +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): Marc Glisse - * - * 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 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/>. - */ - -/** \brief Concept of the template parameter for the class `Gudhi::Simplex_tree<SimplexTreeOptions>`. - * - * One model for this is `Gudhi::Simplex_tree_options_full_featured`. If you want to provide your own, it is recommended that you derive from it and override some parts instead of writing a class from scratch. - */ -struct SimplexTreeOptions { - /// Forced for now. - typedef IndexingTag Indexing_tag; - /// Must be a signed integer type. It admits a total order <. - typedef VertexHandle Vertex_handle; - /// Must be comparable with operator<. - typedef FiltrationValue Filtration_value; - /// Must be an integer type. - typedef SimplexKey Simplex_key; - /// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`. - static const bool store_key; - /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology. - static const bool store_filtration; - /// If true, the list of vertices present in the complex must always be 0, ..., num_vertices-1, without any hole. - static constexpr bool contiguous_vertices; -}; - diff --git a/concept/Simplex_tree/VertexHandle.h b/concept/Simplex_tree/VertexHandle.h deleted file mode 100644 index 9d0642c3..00000000 --- a/concept/Simplex_tree/VertexHandle.h +++ /dev/null @@ -1,27 +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): Clément Maria - * - * 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 - * 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/>. - */ - -/** \brief Handle type for the vertices of a cell complex. - * - * Must be a signed integer type. <code>operator<</code> defines a total order on it. - */ -struct VertexHandle {}; diff --git a/concept/Skeleton_blocker/SkeletonBlockerDS.h b/concept/Skeleton_blocker/SkeletonBlockerDS.h deleted file mode 100644 index fd806ff1..00000000 --- a/concept/Skeleton_blocker/SkeletonBlockerDS.h +++ /dev/null @@ -1,129 +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): David Salinas - * - * 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 - * 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 CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERDS_H_ -#define CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERDS_H_ - -namespace Gudhi { - -namespace skeleton_blocker { - -/** \brief Concept for the template class passed for Skeleton_blocker_complex. - * Most importantly, it contains the nodes for vertices and edges - * (Graph_vertex and Graph_edge) that are stored in the simplicial - * complex. The user can redefine these classes to attach - * additional information to vertices and edges. - */ -struct SkeletonBlockerDS { - /** - * @brief index that allows to find the vertex in the boost graph - */ - typedef int boost_vertex_handle; - - /** - * @brief Root_vertex_handle and Vertex_handle are similar to global and local vertex descriptor - * used in <a href="http://www.boost.org/doc/libs/1_38_0/libs/graph/doc/subgraph.html">boost subgraphs</a> - * and allow to localize a vertex of a subcomplex on its parent root complex. - * - * In gross, vertices are stored in a vector - * and the Root_vertex_handle and Vertex_handle store indices of a vertex in this vector. - * - * For the root simplicial complex, the Root_vertex_handle and Vertex_handle of a vertex - * are the same. - * - * - * For a subcomplex L of a simplicial complex K, the local descriptor, ie the Vertex_handle, of a - * vertex v (that belongs to L) is its position in the vector of vertices - * of the subcomplex L whereas its Root_vertex_handle (global descriptor) is the position of v in the vector of the - * vertices of the root simplicial complex K. - */ - struct Root_vertex_handle { - boost_vertex_handle vertex; - - friend ostream& operator<<(ostream& o, const Root_vertex_handle & v); - }; - - /** - * A Vertex_handle must be Default Constructible, Assignable and Equality Comparable. - */ - struct Vertex_handle { - boost_vertex_handle vertex; - - friend ostream& operator<<(ostream& o, const Vertex_handle & v); - }; - - /** - * \brief The type of vertices that are stored the boost graph. - * A Vertex must be Default Constructible and Equality Comparable. - * - */ - struct Graph_vertex { - /** \brief Used to deactivate a vertex for example when contracting an edge. - * It allows in some cases to remove the vertex at low cost. - */ - void deactivate(); - - /** \brief Used to activate a vertex. - */ - void activate(); - - /** \brief Tells if the vertex is active. - */ - bool is_active() const; - - void set_id(Root_vertex_handle i); - Root_vertex_handle get_id() const; - virtual string to_string() const; - friend ostream& operator<<(ostream& o, const Graph_vertex & v); - }; - - /** - * \brief The type of edges that are stored the boost graph. - * An Edge must be Default Constructible and Equality Comparable. - */ - struct Graph_edge { - /** - * @brief Allows to modify vertices of the edge. - */ - void setId(Root_vertex_handle a, Root_vertex_handle b); - - /** - * @brief Returns the first vertex of the edge. - */ - Root_vertex_handle first() const; - - /** - * @brief Returns the second vertex of the edge. - */ - Root_vertex_handle second() const; - - friend ostream& operator<<(ostream& o, const Simple_edge & v); - }; -}; - -} // namespace skeleton_blocker - -namespace skbl = skeleton_blocker; - -} // namespace Gudhi - -#endif // CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERDS_H_ diff --git a/concept/Skeleton_blocker/SkeletonBlockerGeometricDS.h b/concept/Skeleton_blocker/SkeletonBlockerGeometricDS.h deleted file mode 100644 index d8521343..00000000 --- a/concept/Skeleton_blocker/SkeletonBlockerGeometricDS.h +++ /dev/null @@ -1,90 +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): David Salinas - * - * 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 - * 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 CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERGEOMETRICDS_H_ -#define CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERGEOMETRICDS_H_ - -namespace Gudhi { -namespace skeleton_blocker { - -/** - * \brief Concept for template class of Skeleton_blocker_geometric_complex . - * It must specify a GeometryTrait which contains a Point definition. - * - * Graph_vertex must specify how to access to a point. - * Graph_edge must specify how to access to an index. - * - */ -// TODO(DS): the index is just for contraction, to remove - -template<typename GeometryTrait> -struct SkeletonBlockerGeometricDS : public SkeletonBlockerDS { - /** - * Geometry information. - */ - typedef GeometryTrait GT; - - /** - * Type of point (should be the same as GT::Point). - */ - typedef typename GeometryTrait::Point Point; - - /** - * @brief Vertex that stores a point. - */ - class Graph_vertex : public SkeletonBlockerDS::Graph_vertex { - public: - /** - * @brief Access to the point. - */ - Point& point(); - /** - * @brief Access to the point. - */ - const Point& point(); - }; - - /** - * @brief Edge that allows to access to an index. - * The indices of the edges are used to store heap information - * in the edge contraction algorithm. - */ - class Graph_Edge : public SkeletonBlockerDS::Graph_edge { - public: - /** - * @brief Access to the index. - */ - int& index(); - /** - * @brief Access to the index. - */ - int index(); - }; -}; - -} // namespace skeleton_blocker - -namespace skbl = skeleton_blocker; - -} // namespace Gudhi - -#endif // CONCEPT_SKELETON_BLOCKER_SKELETONBLOCKERGEOMETRICDS_H_ diff --git a/concept/Witness_complex/SimplicialComplexForWitness.h b/concept/Witness_complex/SimplicialComplexForWitness.h deleted file mode 100644 index 8b85f4e4..00000000 --- a/concept/Witness_complex/SimplicialComplexForWitness.h +++ /dev/null @@ -1,100 +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) 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 - * 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 CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_WITNESS_H_ -#define CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_WITNESS_H_ - -namespace Gudhi { - -namespace witness_complex { - -/** \brief The concept SimplicialComplexForWitness describes the requirements - * for a type to implement a simplicial complex, - * used for example to build a Witness_complex or Strong_witness_complex. - */ -struct SimplicialComplexForWitness { - /** Handle to specify a simplex. */ - typedef unspecified Simplex_handle; - // /** Handle to specify a vertex. Must be a non-negative integer. */ - // typedef unspecified Vertex_handle; - - /** \brief Returns a Simplex_hanlde that is different from all simplex handles - * of the simplices. */ - Simplex_handle null_simplex(); - - /** Returns the number of vertices in the simplicial complex - */ - std::size_t num_vertices(); - - /** \brief Return type of an insertion of a simplex - */ - typedef unspecified Insertion_result_type; - - /** \brief Inserts a simplex with vertices from a given range - * 'vertex_range' in the simplicial complex. - * The function is only used in Witness_complex class - * and by construction, it is not necessary to check if - * the faces are in the simplicial complex before insertion. - * The simplex is given the filtration value 'filtration'. - * Filtration_value should be convertible from double. - * The return type is not used. - * */ - template< typedef Input_vertex_range > - Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range, Filtration_value filtration); - - /** \brief Inserts a simplex and all its faces - * with vertices from a given range - * 'vertex_range' in the simplicial complex. - * The function is only used in Strong_witness_complex class. - * All inserted simplices are given the filtration - * value 'filtration'. - * Filtration_value should be convertible from double. - * The return type is not used. - */ - - template< typedef Input_vertex_range, - typedef Filtration_value> - Insertion_result_type insert_simplex_and_subfaces(Input_vertex_range const & vertex_range, Filtration_value filtration); - - /** \brief Finds a simplex with vertices given by a range - * - * If a simplex exists, its Simplex_handle is returned. - * Otherwise null_simplex() is returned. */ - template< typedef Input_vertex_range > - Simplex_handle find(Input_vertex_range const & vertex_range); - - /** \brief Sets the dimension of the simplicial complex to - * 'dimension'. - */ - void set_dimension(int dimension); - - /** \brief Returns the filtration of the simplex given by - * the simplex handle 'sh'. - */ - double filtration(Simplex_handle sh); -}; - -} // namespace witness_complex - -} // namespace Gudhi - -#endif // CONCEPT_WITNESS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_WITNESS_H_ |