diff options
Diffstat (limited to 'src')
5 files changed, 16 insertions, 10 deletions
diff --git a/src/Collapse/doc/intro_edge_collapse.h b/src/Collapse/doc/intro_edge_collapse.h index 0691ccf6..5c126d29 100644 --- a/src/Collapse/doc/intro_edge_collapse.h +++ b/src/Collapse/doc/intro_edge_collapse.h @@ -2,7 +2,7 @@ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. * Author(s): Siddharth Pritam * - * Copyright (C) 2019 Inria + * Copyright (C) 2020 Inria * * Modification(s): * - YYYY/MM Author: Description of the modification diff --git a/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h b/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h index 49c28f63..6fa4438c 100644 --- a/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h +++ b/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h @@ -2,7 +2,7 @@ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. * Author(s): Siddharth Pritam * - * Copyright (C) 2018 Inria + * Copyright (C) 2020 Inria * * Modification(s): * - 2020/03 Vincent Rouvreau: integration to the gudhi library @@ -44,8 +44,8 @@ namespace collapse { * \ingroup collapse * * \details - * A class to store the vertices v/s MaxSimplices Sparse Matrix and to perform collapse operations using the N^2() - * Algorithm. + * This class stores a <a target="_blank" href="https://en.wikipedia.org/wiki/Clique_complex">Flag complex</a> + * in an <a target="_blank" href="https://eigen.tuxfamily.org/dox/group__TutorialSparse.html">Eigen sparse matrix</a>. * * \tparam Vertex type must be a signed integer type. It admits a total order <. * \tparam Filtration type for the value of the filtration function. Must be comparable with <. @@ -73,7 +73,7 @@ class Flag_complex_sparse_matrix { using Row_indices_vector = std::vector<Row_index>; public: - /** \brief A Filtered_edge is a std::pair<std::pair<`Vertex_handle`, `Vertex_handle`>, `Filtration_value`>. */ + /** \brief Filtered_edge is a type to store an edge with its filtration value. */ using Filtered_edge = std::pair<Edge, Filtration_value>; /** \brief Proximity_graph is a type that can be used to construct easily a Flag_complex_sparse_matrix. */ using Proximity_graph = Gudhi::Proximity_graph<Flag_complex_sparse_matrix>; @@ -358,7 +358,7 @@ class Flag_complex_sparse_matrix { } } - /** \brief Performs edge collapse in a decreasing sequence of the filtration value. + /** \brief Performs edge collapse in a increasing sequence of the filtration value. * * \tparam FilteredEdgeInsertion is an output iterator that furnishes * `({Vertex_handle u, Vertex_handle v}, Filtration_value f)` that will fill the user defined data structure. diff --git a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp index f4a460ab..f39e9764 100644 --- a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp +++ b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp @@ -79,9 +79,7 @@ int main(int argc, char* argv[]) { program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); - Distance_matrix distances; - - distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); std::cout << "Read the distance matrix succesfully, of size: " << distances.size() << std::endl; Proximity_graph proximity_graph = Gudhi::compute_proximity_graph<Simplex_tree>(boost::irange((size_t)0, diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index cdea3d94..85b39be9 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -242,7 +242,7 @@ </tr> </table> -#### Strong collapse +#### Edge collapse <table> <tr> diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index b8508697..3e7720d7 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -19,6 +19,9 @@ #include <tuple> // for std::tie namespace Gudhi { +/** @file + * @brief Graph simplicial complex methods + */ /* Edge tag for Boost PropertyGraph. */ struct edge_filtration_t { @@ -43,9 +46,14 @@ using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vec /** \brief Computes the proximity graph of the points. * + * \fn Gudhi::Proximity_graph<SimplicialComplexForProximityGraph> compute_proximity_graph(const ForwardPointRange& + * points, typename SimplicialComplexForProximityGraph::Filtration_value threshold, Distance distance) + * * If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the * distance function between points u and v is smaller than threshold. * + * \tparam SimplicialComplexForProximityGraph furnishes `Filtration_value` and `Vertex_handle` type definitions. + * * \tparam ForwardPointRange furnishes `.begin()` and `.end()` methods. * * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where |