simplex_tree.h

/******************************************************************************
* Author:           Julián Burella Pérez
* Description:      gudhi's simplex tree interfacing with pybind11
* License:          TBD
*****************************************************************************/

#ifndef INCLUDE_SIMPLEX_TREE_INTERFACE_H_
#define INCLUDE_SIMPLEX_TREE_INTERFACE_H_

#include <gudhi/Points_off_io.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/distance_functions.h>
#include <gudhi/graph_simplicial_complex.h>

#include <iostream>
#include <utility>
#include <vector>

#include "persistent_cohomology.h"

namespace Gudhi {

template <typename SimplexTreeOptions = Simplex_tree_options_full_featured>
class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
public:
  using Base = Simplex_tree<SimplexTreeOptions>;
  using Filtration_value = typename Base::Filtration_value;
  using Vertex_handle = typename Base::Vertex_handle;
  using Simplex_handle = typename Base::Simplex_handle;
  using Insertion_result = typename std::pair<Simplex_handle, bool>;
  using Simplex = std::vector<Vertex_handle>;
  using Filtered_simplices = std::vector<std::pair<Simplex, Filtration_value>>;

public:
  bool find_simplex(const Simplex &vh) {
    return (Base::find(vh) != Base::null_simplex());
  }

  void assign_simplex_filtration(const Simplex &vh,
                                 Filtration_value filtration) {
    Base::assign_filtration(Base::find(vh), filtration);
  }

  bool insert(const Simplex &simplex, Filtration_value filtration = 0) {
    Insertion_result result =
        Base::insert_simplex_and_subfaces(simplex, filtration);
    return (result.second);
  }

  // Do not interface this function, only used in alpha complex interface for
  // complex creation
  bool insert_simplex(const Simplex &simplex, Filtration_value filtration = 0) {
    Insertion_result result = Base::insert_simplex(simplex, filtration);
    return (result.second);
  }

  // Do not interface this function, only used in interface for complex creation
  bool insert_simplex_and_subfaces(const Simplex &simplex,
                                   Filtration_value filtration = 0) {
    Insertion_result result =
        Base::insert_simplex_and_subfaces(simplex, filtration);
    return (result.second);
  }

  // Do not interface this function, only used in strong witness interface for
  // complex creation
  bool insert_simplex(const std::vector<std::size_t> &simplex,
                      Filtration_value filtration = 0) {
    Insertion_result result = Base::insert_simplex(simplex, filtration);
    return (result.second);
  }

  // Do not interface this function, only used in strong witness interface for
  // complex creation
  bool insert_simplex_and_subfaces(const std::vector<std::size_t> &simplex,
                                   Filtration_value filtration = 0) {
    Insertion_result result =
        Base::insert_simplex_and_subfaces(simplex, filtration);
    return (result.second);
  }

  Filtration_value simplex_filtration(const Simplex &simplex) {
    return Base::filtration(Base::find(simplex));
  }

  void remove_maximal_simplex(const Simplex &simplex) {
    Base::remove_maximal_simplex(Base::find(simplex));
    Base::initialize_filtration();
  }

  Filtered_simplices get_filtration() {
    Base::initialize_filtration();
    Filtered_simplices filtrations;
    for (auto f_simplex : Base::filtration_simplex_range()) {
      Simplex simplex;
      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
        simplex.insert(simplex.begin(), vertex);
      }
      filtrations.push_back(
          std::make_pair(simplex, Base::filtration(f_simplex)));
    }
    return filtrations;
  }

  Filtered_simplices get_skeleton(int dimension) {
    Filtered_simplices skeletons;
    for (auto f_simplex : Base::skeleton_simplex_range(dimension)) {
      Simplex simplex;
      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
        simplex.insert(simplex.begin(), vertex);
      }
      skeletons.push_back(std::make_pair(simplex, Base::filtration(f_simplex)));
    }
    return skeletons;
  }

  Filtered_simplices get_star(const Simplex &simplex) {
    Filtered_simplices star;
    for (auto f_simplex : Base::star_simplex_range(Base::find(simplex))) {
      Simplex simplex_star;
      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
        simplex_star.insert(simplex_star.begin(), vertex);
      }
      star.push_back(std::make_pair(simplex_star, Base::filtration(f_simplex)));
    }
    return star;
  }

  Filtered_simplices get_cofaces(const Simplex &simplex, int dimension) {
    Filtered_simplices cofaces;
    for (auto f_simplex :
         Base::cofaces_simplex_range(Base::find(simplex), dimension)) {
      Simplex simplex_coface;
      for (auto vertex : Base::simplex_vertex_range(f_simplex)) {
        simplex_coface.insert(simplex_coface.begin(), vertex);
      }
      cofaces.push_back(
          std::make_pair(simplex_coface, Base::filtration(f_simplex)));
    }
    return cofaces;
  }

  void create_persistence(Gudhi::Persistent_cohomology_interface<Base> *pcoh) {
    Base::initialize_filtration();
    pcoh = new Gudhi::Persistent_cohomology_interface<Base>(*this);
  }
};

} // namespace Gudhi

#endif