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

4 files changed, 0 insertions, 574 deletions

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 <cmath>
-
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Filtered_toplex_map.h>
-
-#include <boost/graph/adjacency_list.hpp>
-#include <boost/graph/bron_kerbosch_all_cliques.hpp>
-
-namespace Gudhi {
-
-struct Visitor {
-    Toplex_map* tm;
-
-    Visitor(Toplex_map* tm)
-        :tm(tm)
-    {}
-
-    template <typename Clique, typename Graph>
-    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<class OneSkeletonGraph>
-    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<Toplex_map::Simplex> max_simplices() const;
-
-    /** Returns all the simplices, of max dimension d if a parameter d is given.
-      * \ingroup toplex_map   */
-    std::vector<Toplex_map::Simplex> filtration_simplex_range(int d=std::numeric_limits<int>::max()) const;
-
-    /** Returns all the simplices of max dimension d
-      * \ingroup toplex_map   */
-    std::vector<Toplex_map::Simplex> 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 <typename Input_vertex_range>
-    bool all_facets_inside(const Input_vertex_range &vertex_range) const;
-
-};
-
-template<class OneSkeletonGraph>
-void Fake_simplex_tree::insert_graph(const OneSkeletonGraph& skel_graph){
-    toplex_maps.emplace(nan(""), new Toplex_map());
-    using vertex_iterator = typename boost::graph_traits<OneSkeletonGraph>::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 <typename Input_vertex_range>
-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<Toplex_map::Vertex> 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<Toplex_map::Simplex> Fake_simplex_tree::max_simplices() const{
-    std::vector<Toplex_map::Simplex> 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<Toplex_map::Simplex> Fake_simplex_tree::filtration_simplex_range(int d) const{
-    std::vector<Toplex_map::Simplex> m = max_simplices();
-    std::vector<Toplex_map::Simplex> 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<Toplex_map::Simplex> 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 <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/graph_simplicial_complex.h>
-#include "Fake_simplex_tree.h"
-
-#include <iostream>
-#include <utility>  // for pair
-#include <vector>
-
-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 <http://www.gnu.org/licenses/>.
- */
-
-#include <gudhi/reader_utils.h>
-#include "Fake_simplex_tree.h"
-
-#include <iostream>
-#include <ctime>
-#include <string>
-#include <utility>  // 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<Graph_t, Filtration_value, Vertex_handle>(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<double>(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<double>(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 <gudhi/Toplex_map.h>
-#include <map>
-#include <limits>
-
-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 <typename Input_vertex_range>
-    std::pair<Simplex, bool> insert_simplex_and_subfaces(const Input_vertex_range &vertex_range, Filtration_value f = std::numeric_limits<double>::quiet_NaN());
-
-    /** Gives the filtration of the input simplex. */
-    template <typename Input_vertex_range>
-    Filtration_value filtration(const Input_vertex_range &vertex_range) const;
-
-    /** Is the input simplex member of the complex ? */
-    template <typename Input_vertex_range>
-    bool membership(const Input_vertex_range &vertex_range) const;
-
-protected:
-    std::map<Filtration_value, Toplex_map*> toplex_maps;
-};
-
-template <typename Input_vertex_range>
-std::pair<Toplex_map::Simplex, bool> 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 <typename Input_vertex_range>
-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<double>::quiet_NaN() ;
-}
-
-template <typename Input_vertex_range>
-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 */