/*    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 Saclay - Ile-de-France (France)
 *
 *    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/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>

#include <iostream>
#include <vector>

using namespace Gudhi;

/* We could perfectly well use the default Simplex_tree<> (which uses
 * Simplex_tree_options_full_featured), the following simply demonstrates
 * how to save on storage by not storing a filtration value.  */

struct MyOptions : Simplex_tree_options_full_featured {
  // Implicitly use 0 as filtration value for all simplices
  static const bool store_filtration = false;
  // The persistence algorithm needs this
  static const bool store_key = true;
  // I have few vertices
  typedef short Vertex_handle;
};
typedef Simplex_tree<MyOptions> ST;

  /*
   * Compare two intervals by dimension, then by length.
   */
  struct cmp_intervals_by_dim_then_length {
    explicit cmp_intervals_by_dim_then_length(ST * sc)
        : sc_(sc) {
    }
    template<typename Persistent_interval>
    bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) {
      if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2)))
        return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1))
            > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2)));
      else
        return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2)));
    }
    ST* sc_;
  };

int main() {
  ST st;

  /* Complex to build. */
  /*    1   3          */
  /*    o---o          */
  /*   /X\ /           */
  /*  o---o   o        */
  /*  2   0   4        */

  const short triangle012[] = {0, 1, 2};
  const short edge03[] = {0, 3};
  const short edge13[] = {1, 3};
  const short vertex4[] = {4};
  st.insert_simplex_and_subfaces(triangle012);
  st.insert_simplex_and_subfaces(edge03);
  st.insert_simplex(edge13);
  st.insert_simplex(vertex4);
  // FIXME: Remove this line
  st.set_dimension(2);

  // Sort the simplices in the order of the filtration
  st.initialize_filtration();

  // Class for homology computation
  persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st);

  // Initialize the coefficient field Z/2Z for homology
  pcoh.init_coefficients(2);

  // Compute the persistence diagram of the complex
  pcoh.compute_persistent_cohomology();

  // Print the result. The format is, on each line: 2 dim 0 inf
  // where 2 represents the field, dim the dimension of the feature.
  // 2  0 0 inf 
  // 2  0 0 inf 
  // 2  1 0 inf 
  // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.
  pcoh.output_diagram();
  
  
  // ********************************************************
  // get_persistence
  // ********************************************************
  std::cout << std::endl;
  std::cout << std::endl;

  // First version
  std::vector<int> betti_numbers = pcoh.betti_numbers();
  std::cout << "The Betti numbers are : ";
  for (std::size_t i = 0; i < betti_numbers.size(); i++)
    std::cout << "b" << i << " = " << betti_numbers[i] << " ; ";
  std::cout << std::endl;

  // Second version
  std::cout << "The Betti numbers are : ";
  for (int i = 0; i < st.dimension(); i++)
    std::cout << "b" << i << " = " << pcoh.betti_number(i) << " ; ";
  std::cout << std::endl;
  
  // Get persistence
  cmp_intervals_by_dim_then_length cmp(&st);
  auto persistent_pairs = pcoh.get_persistent_pairs();
  std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
  for (auto pair : persistent_pairs) {
    std::cout << st.dimension(get<0>(pair)) << " "
          << st.filtration(get<0>(pair)) << " "
          << st.filtration(get<1>(pair)) << std::endl;
  }


}