From 3cf8477c5b259cd83ee869cb2b0913c31566aeda Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 16 Oct 2018 14:09:33 +0000 Subject: Remove Filtered_toplex_map and its derivative git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/toplex_map@3958 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2833261794ce5bda7a0e120cde6a7851553bd00c --- src/Toplex_map/example/Fake_simplex_tree.h | 188 ------------------ src/Toplex_map/example/Simple_toplex_map.cpp | 218 --------------------- .../example/Toplex_map_from_cliques_of_graph.cpp | 93 --------- src/Toplex_map/include/gudhi/Filtered_toplex_map.h | 75 ------- 4 files changed, 574 deletions(-) delete mode 100644 src/Toplex_map/example/Fake_simplex_tree.h delete mode 100644 src/Toplex_map/example/Simple_toplex_map.cpp delete mode 100644 src/Toplex_map/example/Toplex_map_from_cliques_of_graph.cpp delete mode 100644 src/Toplex_map/include/gudhi/Filtered_toplex_map.h (limited to 'src/Toplex_map') diff --git a/src/Toplex_map/example/Fake_simplex_tree.h b/src/Toplex_map/example/Fake_simplex_tree.h deleted file mode 100644 index 6a7e7bdc..00000000 --- a/src/Toplex_map/example/Fake_simplex_tree.h +++ /dev/null @@ -1,188 +0,0 @@ -#ifndef FAKE_SIMPLEX_TREE_H -#define FAKE_SIMPLEX_TREE_H - -#include - -#include -#include - -#include -#include - -namespace Gudhi { - -struct Visitor { - Toplex_map* tm; - - Visitor(Toplex_map* tm) - :tm(tm) - {} - - template - void clique(const Clique& c, const Graph& g) - { - tm->insert_simplex(c); - } -}; - -/** Fake_simplex_tree is a wrapper for Filtered_toplex_map which has the interface of the Simplex_tree. - * Mostly for retro-compatibility purpose. If you use a function that output non maximal simplices, it will be non efficient. - * \ingroup toplex_map */ -class Fake_simplex_tree : public Filtered_toplex_map { - -public: - - /** Handle type to a vertex contained in the simplicial complex. - * \ingroup toplex_map */ - typedef Toplex_map::Vertex Vertex_handle; - - /** Handle type to a simplex contained in the simplicial complex. - * \ingroup toplex_map */ - typedef Toplex_map::Simplex Simplex_handle; - - typedef void Insertion_result_type; - - /** Inserts the flag complex of a given range `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` - * in the simplicial complex. - * \ingroup toplex_map */ - template - void insert_graph(const OneSkeletonGraph& skel_graph); - - /** Do actually nothing. - * \ingroup toplex_map */ - void expansion(int max_dim); - - /** Returns the number of vertices stored i.e. the number of max simplices - * \ingroup toplex_map */ - std::size_t num_vertices() const; - - /** Returns the dimension of the complex. - * \ingroup toplex_map */ - std::size_t dimension() const; - - /** Returns the dimension of a given simplex in the complex. - * \ingroup toplex_map */ - std::size_t dimension(Simplex_ptr& sptr) const; - - /** Returns the number of simplices stored i.e. the number of maximal simplices. - * \ingroup toplex_map */ - std::size_t num_simplices() const; - - /** Returns a range over the vertices of a simplex. - * \ingroup toplex_map */ - Toplex_map::Simplex simplex_vertex_range(const Simplex& s) const; - - /** Returns a set of all maximal (critical if there is filtration values) simplices. - * \ingroup toplex_map */ - std::vector max_simplices() const; - - /** Returns all the simplices, of max dimension d if a parameter d is given. - * \ingroup toplex_map */ - std::vector filtration_simplex_range(int d=std::numeric_limits::max()) const; - - /** Returns all the simplices of max dimension d - * \ingroup toplex_map */ - std::vector skeleton_simplex_range(int d) const; - - Toplex_map::Vertex contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y); - - -protected: - - /** \internal Does all the facets of the given simplex belong to the complex ? - * \ingroup toplex_map */ - template - bool all_facets_inside(const Input_vertex_range &vertex_range) const; - -}; - -template -void Fake_simplex_tree::insert_graph(const OneSkeletonGraph& skel_graph){ - toplex_maps.emplace(nan(""), new Toplex_map()); - using vertex_iterator = typename boost::graph_traits::vertex_iterator; - vertex_iterator vi, vi_end; - for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi) { - Simplex s; s.insert(*vi); - insert_simplex_and_subfaces(s); - } - bron_kerbosch_all_cliques(skel_graph, Visitor(this->toplex_maps.at(nan("")))); -} - -void Fake_simplex_tree::expansion(int max_dim){} - -template -bool Fake_simplex_tree::all_facets_inside(const Input_vertex_range &vertex_range) const{ - Simplex sigma(vertex_range); - for(const Simplex& s : facets(sigma)) - if(!membership(s)) return false; - return true; -} - -std::size_t Fake_simplex_tree::dimension() const { - std::size_t max = 0; - for(const Simplex& s : max_simplices()) - max = std::max(max, s.size()); - return max-1; -} - -std::size_t Fake_simplex_tree::dimension(Simplex_ptr& sptr) const{ - return sptr->size(); -} - -std::size_t Fake_simplex_tree::num_simplices() const { - return max_simplices().size(); -} - -std::size_t Fake_simplex_tree::num_vertices() const { - std::unordered_set vertices; - for(const Toplex_map::Simplex& s : max_simplices()) - for (Toplex_map::Vertex v : s) - vertices.emplace(v); - return vertices.size(); -} - -Toplex_map::Simplex Fake_simplex_tree::simplex_vertex_range(const Simplex& s) const { - return s; -} - -std::vector Fake_simplex_tree::max_simplices() const{ - std::vector max_s; - for(auto kv : toplex_maps) - for(const Toplex_map::Simplex_ptr& sptr : kv.second->maximal_cofaces(Simplex())) - max_s.emplace_back(*sptr); - return max_s; -} - -std::vector Fake_simplex_tree::filtration_simplex_range(int d) const{ - std::vector m = max_simplices(); - std::vector range; - Toplex_map::Simplex_ptr_set seen; - while(m.begin()!=m.end()){ - Toplex_map::Simplex s(m.back()); - m.pop_back(); - if(seen.find(get_key(s))==seen.end()){ - if((int) s.size()-1 <=d) - range.emplace_back(s); - seen.emplace(get_key(s)); - if(s.size()>0) - for(Simplex& sigma : facets(s)) - m.emplace_back(sigma); - } - } - return range; -} - -std::vector Fake_simplex_tree::skeleton_simplex_range(int d) const{ - return filtration_simplex_range(d); -} - -Toplex_map::Vertex Fake_simplex_tree::contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y){ - for(auto kv : toplex_maps) - kv.second->contraction(x,y); - return y; -} - -} //namespace Gudhi - -#endif /* FAKE_SIMPLEX_TREE_H */ - diff --git a/src/Toplex_map/example/Simple_toplex_map.cpp b/src/Toplex_map/example/Simple_toplex_map.cpp deleted file mode 100644 index d383e84b..00000000 --- a/src/Toplex_map/example/Simple_toplex_map.cpp +++ /dev/null @@ -1,218 +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) 2017 - * - * 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 . - */ - -#include -#include "Fake_simplex_tree.h" - -#include -#include // for pair -#include - -using Toplex_map = Gudhi::Fake_simplex_tree; -using typeVectorVertex = std::vector< Toplex_map::Vertex_handle >; -using typePairSimplexBool = std::pair< Toplex_map::Simplex_handle, bool >; - -int main(int argc, char * const argv[]) { - - // TEST OF INSERTION - std::cout << "********************************************************************" << std::endl; - std::cout << "EXAMPLE OF SIMPLE INSERTION" << std::endl; - // Construct the Toplex_map - Toplex_map t_map; - - /* Simplex to be inserted: */ - /* 1 */ - /* o */ - /* /X\ */ - /* o---o---o */ - /* 2 0 3 */ - - // ++ FIRST - std::cout << " * INSERT 0" << std::endl; - typeVectorVertex firstSimplexVector = { 0 }; - typePairSimplexBool returnValue = t_map.insert_simplex_and_subfaces(firstSimplexVector, 0.1); - - if (returnValue.second == true) { - std::cout << " + 0 INSERTED" << std::endl; - } else { - std::cout << " - 0 NOT INSERTED" << std::endl; - } - - // ++ SECOND - std::cout << " * INSERT 1" << std::endl; - typeVectorVertex secondSimplexVector = { 1 }; - returnValue = t_map.insert_simplex_and_subfaces(secondSimplexVector, 0.1); - - if (returnValue.second == true) { - std::cout << " + 1 INSERTED" << std::endl; - } else { - std::cout << " - 1 NOT INSERTED" << std::endl; - } - - // ++ THIRD - std::cout << " * INSERT (0,1)" << std::endl; - typeVectorVertex thirdSimplexVector = { 0, 1 }; - returnValue = - t_map.insert_simplex_and_subfaces(thirdSimplexVector, 0.2); - - if (returnValue.second == true) { - std::cout << " + (0,1) INSERTED" << std::endl; - } else { - std::cout << " - (0,1) NOT INSERTED" << std::endl; - } - - // ++ FOURTH - std::cout << " * INSERT 2" << std::endl; - typeVectorVertex fourthSimplexVector = { 2 }; - returnValue = - t_map.insert_simplex_and_subfaces(fourthSimplexVector, 0.1); - - if (returnValue.second == true) { - std::cout << " + 2 INSERTED" << std::endl; - } else { - std::cout << " - 2 NOT INSERTED" << std::endl; - } - - // ++ FIFTH - std::cout << " * INSERT (2,0)" << std::endl; - typeVectorVertex fifthSimplexVector = { 2, 0 }; - returnValue = - t_map.insert_simplex_and_subfaces(fifthSimplexVector, 0.2); - - if (returnValue.second == true) { - std::cout << " + (2,0) INSERTED" << std::endl; - } else { - std::cout << " - (2,0) NOT INSERTED" << std::endl; - } - - // ++ SIXTH - std::cout << " * INSERT (2,1)" << std::endl; - typeVectorVertex sixthSimplexVector = { 2, 1 }; - returnValue = - t_map.insert_simplex_and_subfaces(sixthSimplexVector, 0.2); - - if (returnValue.second == true) { - std::cout << " + (2,1) INSERTED" << std::endl; - } else { - std::cout << " - (2,1) NOT INSERTED" << std::endl; - } - - // ++ SEVENTH - std::cout << " * INSERT (2,1,0)" << std::endl; - typeVectorVertex seventhSimplexVector = { 2, 1, 0 }; - returnValue = - t_map.insert_simplex_and_subfaces(seventhSimplexVector, 0.3); - - if (returnValue.second == true) { - std::cout << " + (2,1,0) INSERTED" << std::endl; - } else { - std::cout << " - (2,1,0) NOT INSERTED" << std::endl; - } - - // ++ EIGHTH - std::cout << " * INSERT 3" << std::endl; - typeVectorVertex eighthSimplexVector = { 3 }; - returnValue = - t_map.insert_simplex_and_subfaces(eighthSimplexVector, 0.1); - - if (returnValue.second == true) { - std::cout << " + 3 INSERTED" << std::endl; - } else { - std::cout << " - 3 NOT INSERTED" << std::endl; - } - - // ++ NINETH - std::cout << " * INSERT (3,0)" << std::endl; - typeVectorVertex ninethSimplexVector = { 3, 0 }; - returnValue = - t_map.insert_simplex_and_subfaces(ninethSimplexVector, 0.2); - - if (returnValue.second == true) { - std::cout << " + (3,0) INSERTED" << std::endl; - } else { - std::cout << " - (3,0) NOT INSERTED" << std::endl; - } - - // ++ TENTH - std::cout << " * INSERT 0 (already inserted)" << std::endl; - typeVectorVertex tenthSimplexVector = { 0 }; - // With a different filtration value - returnValue = t_map.insert_simplex_and_subfaces(tenthSimplexVector, 0.4); - - if (returnValue.second == true) { - std::cout << " + 0 INSERTED" << std::endl; - } else { - std::cout << " - 0 NOT INSERTED" << std::endl; - } - - // ++ ELEVENTH - std::cout << " * INSERT (2,1,0) (already inserted)" << std::endl; - typeVectorVertex eleventhSimplexVector = { 2, 1, 0 }; - returnValue = - t_map.insert_simplex_and_subfaces(eleventhSimplexVector, 0.4); - - if (returnValue.second == true) { - std::cout << " + (2,1,0) INSERTED" << std::endl; - } else { - std::cout << " - (2,1,0) NOT INSERTED" << std::endl; - } - - // ++ GENERAL VARIABLE SET - - std::cout << "********************************************************************\n"; - // Display the Simplex_tree - Can not be done in the middle of 2 inserts - std::cout << "* The complex contains " << t_map.num_vertices() << " vertices and " << t_map.num_simplices() - << " simplices - dimension is " << t_map.dimension() << "\n"; - std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : t_map.filtration_simplex_range()) { - if (f_simplex.size() > 0) { - std::cout << " " << "[" << t_map.filtration(f_simplex) << "] "; - for (auto vertex : t_map.simplex_vertex_range(f_simplex)) - std::cout << "(" << vertex << ")"; - std::cout << std::endl; - } - } - // [0.1] 0 - // [0.1] 1 - // [0.1] 2 - // [0.1] 3 - // [0.2] 1 0 - // [0.2] 2 0 - // [0.2] 2 1 - // [0.2] 3 0 - // [0.3] 2 1 0 - - std::cout << std::endl << std::endl; - - std::cout << "Iterator on skeleton[1]:" << std::endl; - for (auto f_simplex : t_map.skeleton_simplex_range(1)) { - if (f_simplex.size() > 0) { - std::cout << " " << "[" << t_map.filtration(f_simplex) << "] "; - for (auto vertex : t_map.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; - } - std::cout << std::endl; - } - } - - return 0; -} diff --git a/src/Toplex_map/example/Toplex_map_from_cliques_of_graph.cpp b/src/Toplex_map/example/Toplex_map_from_cliques_of_graph.cpp deleted file mode 100644 index c43f1b69..00000000 --- a/src/Toplex_map/example/Toplex_map_from_cliques_of_graph.cpp +++ /dev/null @@ -1,93 +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) 2017 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 . - */ - -#include -#include "Fake_simplex_tree.h" - -#include -#include -#include -#include // for std::pair - -using Toplex_map = Gudhi::Fake_simplex_tree; -using Vertex_handle = Toplex_map::Vertex_handle; -using Filtration_value = Toplex_map::Filtration_value; - -typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS, - boost::property < vertex_filtration_t, Filtration_value >, - boost::property < edge_filtration_t, Filtration_value > > Graph_t; - -int main(int argc, char * const argv[]) { - if (argc != 3) { - std::cerr << "Usage: " << argv[0] - << " path_to_file_graph max_dim \n"; - return 0; - } - std::string filegraph = argv[1]; - int max_dim = atoi(argv[2]); - - clock_t start, end; - // Construct the Toplex Map - Toplex_map t_map; - - start = clock(); - auto g = Gudhi::read_graph(filegraph); - // insert the graph in the toplex map as 1-skeleton - t_map.insert_graph(g); - end = clock(); - std::cout << "Insert the 1-skeleton in the toplex map in " - << static_cast(end - start) / CLOCKS_PER_SEC << " s. \n"; - - start = clock(); - // expand the 1-skeleton until dimension max_dim - t_map.expansion(max_dim); - end = clock(); - std::cout << "max_dim = " << max_dim << "\n"; - std::cout << "Expand the toplex map in " - << static_cast(end - start) / CLOCKS_PER_SEC << " s. \n"; - - std::cout << "Information of the toplex map: " << std::endl; - std::cout << " Number of vertices = " << t_map.num_vertices() << " "; - std::cout << " Number of simplices = " << t_map.num_simplices() << std::endl; - std::cout << std::endl << std::endl; - - std::cout << "Iterator on Simplices in the filtration:" << std::endl; - for (auto f_simplex : t_map.filtration_simplex_range()) { - std::cout << " " << "[" << t_map.filtration(f_simplex) << "] "; - for (auto vertex : t_map.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; - } - std::cout << std::endl; - } - - std::cout << std::endl << std::endl; - - std::cout << "Iterator on skeleton:" << std::endl; - for (auto f_simplex : t_map.skeleton_simplex_range(max_dim)) { - std::cout << " " << "[" << t_map.filtration(f_simplex) << "] "; - for (auto vertex : t_map.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; - } - std::cout << std::endl; - } - return 0; -} diff --git a/src/Toplex_map/include/gudhi/Filtered_toplex_map.h b/src/Toplex_map/include/gudhi/Filtered_toplex_map.h deleted file mode 100644 index 9a35b8b7..00000000 --- a/src/Toplex_map/include/gudhi/Filtered_toplex_map.h +++ /dev/null @@ -1,75 +0,0 @@ - #ifndef FILTERED_TOPLEX_MAP_H -#define FILTERED_TOPLEX_MAP_H - -#include -#include -#include - -namespace Gudhi { - -/** A Filtered_toplex_map represents the simplicial complex with a filtration. - * A "toplex" is a critical simplex. */ -class Filtered_toplex_map { - -public: - /** Vertex is the type of vertices. */ - typedef Toplex_map::Vertex Vertex; - - /** Simplex is the type of simplices. */ - typedef Toplex_map::Simplex Simplex; - - /** The type of the pointers to maximal simplices. */ - typedef Toplex_map::Simplex_ptr Simplex_ptr; - - /** The type of the sets of Simplex_ptr. */ - typedef Toplex_map::Simplex_ptr_set Simplex_ptr_set; - - /** The type of the filtration values. */ - typedef double Filtration_value; - - /** Add a simplex and its subfaces with the given filtration value - * in the Filtered_toplex_map. */ - template - std::pair insert_simplex_and_subfaces(const Input_vertex_range &vertex_range, Filtration_value f = std::numeric_limits::quiet_NaN()); - - /** Gives the filtration of the input simplex. */ - template - Filtration_value filtration(const Input_vertex_range &vertex_range) const; - - /** Is the input simplex member of the complex ? */ - template - bool membership(const Input_vertex_range &vertex_range) const; - -protected: - std::map toplex_maps; -}; - -template -std::pair Filtered_toplex_map::insert_simplex_and_subfaces(const Input_vertex_range &vertex_range, Filtration_value f){ - Simplex s(vertex_range.begin(),vertex_range.end()); - if(membership(s)) return make_pair(s,false); - if(!toplex_maps.count(f)) toplex_maps.emplace(f,new Toplex_map()); - toplex_maps.at(f)->insert_simplex(vertex_range); - return make_pair(s,true); -} - - -template -Filtered_toplex_map::Filtration_value Filtered_toplex_map::filtration(const Input_vertex_range &vertex_range) const{ - for(auto kv : toplex_maps) - if(kv.second->membership(vertex_range)) - return kv.first; //min only because a map is ordered - return std::numeric_limits::quiet_NaN() ; -} - -template -bool Filtered_toplex_map::membership(const Input_vertex_range &vertex_range) const{ - for(auto kv : toplex_maps) - if(kv.second->membership(vertex_range)) - return true; - return false; -} - -} //namespace Gudhi - -#endif /* FILTERED_TOPLEX_MAP_H */ -- cgit v1.2.3