/*    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) 2014  INRIA Saclay (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 <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Delaunay_triangulation_3.h>
#include <CGAL/Alpha_shape_3.h>
#include <CGAL/iterator.h>

#include <fstream>
#include <cmath>

#include "gudhi/graph_simplicial_complex.h"
#include "gudhi/Simplex_tree.h"
#include "gudhi/Persistent_cohomology.h"
#include <boost/variant.hpp>

using namespace Gudhi;
using namespace Gudhi::persistent_cohomology;

// Alpha_shape_3 templates type definitions
typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
typedef CGAL::Alpha_shape_vertex_base_3<Kernel>             Vb;
typedef CGAL::Alpha_shape_cell_base_3<Kernel>               Fb;
typedef CGAL::Triangulation_data_structure_3<Vb,Fb>         Tds;
typedef CGAL::Delaunay_triangulation_3<Kernel,Tds>          Triangulation_3;
typedef CGAL::Alpha_shape_3<Triangulation_3>                Alpha_shape_3;

// From file type definition
typedef Kernel::Point_3                                     Point;

// filtration with alpha values needed type definition
typedef Alpha_shape_3::FT Alpha_value_type;
typedef CGAL::Object      Object;
typedef CGAL::Dispatch_output_iterator<
  CGAL::cpp11::tuple<Object, Alpha_value_type>,
  CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, std::back_insert_iterator< std::vector<Alpha_value_type> >
                     > > Dispatch;
typedef Alpha_shape_3::Cell_handle   Cell_handle;
typedef Alpha_shape_3::Facet         Facet;
typedef Alpha_shape_3::Edge          Edge;
typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;

// gudhi type definition
typedef Simplex_tree<>::Vertex_handle Simplex_tree_vertex;
typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;

//#define DEBUG_TRACES

Vertex_list from (const Cell_handle& ch)
{
  Vertex_list the_list;
  for (auto i = 0; i < 4; i++)
  {
#ifdef DEBUG_TRACES
    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
#endif // DEBUG_TRACES
    the_list.push_back(ch->vertex(i));
  }
  return the_list;
}
Vertex_list from (const Facet& fct)
{
  Vertex_list the_list;
  for (auto i = 0; i < 4; i++)
  {
    if (fct.second != i)
    {
#ifdef DEBUG_TRACES
      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
#endif // DEBUG_TRACES
      the_list.push_back(fct.first->vertex(i));
    }
  }
  return the_list;
}
Vertex_list from (const Edge& edg)
{
  Vertex_list the_list;
  for (auto i = 0; i < 4; i++)
  {
    if ((edg.second == i) ||(edg.third == i))
    {
#ifdef DEBUG_TRACES
      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
#endif // DEBUG_TRACES
      the_list.push_back(edg.first->vertex(i));
    }
  }
  return the_list;
}
Vertex_list from (const Alpha_shape_3::Vertex_handle& vh)
{
  Vertex_list the_list;
#ifdef DEBUG_TRACES
  std::cout << "from vertex=" << vh->point() << std::endl;
#endif // DEBUG_TRACES
  the_list.push_back(vh);
  return the_list;
}

void usage(char * const progName)
{
  std::cerr << "Usage: " << progName << " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
  exit(-1); // ----- >>
}

int main (int argc, char * const argv[])
{

  int coeff_field_characteristic=0;
  int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
    std::cerr << "Error: " << argv[2] << " is not correct\n";
    usage(argv[0]);
  }

  float min_persistence = 0.0;
  returnedScanValue = sscanf(argv[3], "%f", &min_persistence);
  if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
    std::cerr << "Error: " << argv[3] << " is not correct\n";
    usage(argv[0]);
  }
  //Filtration_value min_persistence = (Filtration_value)min_persist_int;

  // program args management
  if (argc != 4) {
    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
    usage(argv[0]);
  }

  // Read points from file
  std::string filegraph   = argv[1];
  std::list<Point> lp;
  std::ifstream is(filegraph.c_str());
  int n;
  is >> n;
#ifdef DEBUG_TRACES
  std::cout << "Reading " << n << " points " << std::endl;
#endif // DEBUG_TRACES
  Point p;
  for( ; n>0 ; n--)    {
    is >> p;
    lp.push_back(p);
  }

  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
  Alpha_shape_3 as(lp.begin(),lp.end(),0,Alpha_shape_3::GENERAL);
#ifdef DEBUG_TRACES
  std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
#endif // DEBUG_TRACES

  // filtration with alpha values from alpha shape
  std::vector<Object> the_objects;
  std::vector<Alpha_value_type> the_alpha_values;

  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>( std::back_inserter(the_objects), std::back_inserter(the_alpha_values));

  as.filtration_with_alpha_values(disp);
#ifdef DEBUG_TRACES
  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
#endif // DEBUG_TRACES

  Alpha_shape_3::size_type count_vertices = 0;
  Alpha_shape_3::size_type count_edges    = 0;
  Alpha_shape_3::size_type count_facets   = 0;
  Alpha_shape_3::size_type count_cells    = 0;

  // Loop on objects vector
  Vertex_list vertex_list;
  Simplex_tree<> simplex_tree;
  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
  int dim_max=0;
  Filtration_value filtration_max=0.0;
  for(auto object_iterator: the_objects)
  {
    // Retrieve Alpha shape vertex list from object
    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator))
    {
      vertex_list = from(*cell);
      count_cells++;
      if (dim_max < 3) {
        dim_max=3; // Cell is of dim 3
      }
    }
    else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator))
    {
      vertex_list = from(*facet);
      count_facets++;
      if (dim_max < 2) {
        dim_max=2; // Facet is of dim 2
      }
    }
    else if (const Edge* edge = CGAL::object_cast<Edge>(&object_iterator))
    {
      vertex_list = from(*edge);
      count_edges++;
      if (dim_max < 1) {
        dim_max=1; // Edge is of dim 1
      }
    }
    else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator))
    {
      count_vertices++;
      vertex_list = from(*vertex);
    }
    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
    Simplex_tree_vector_vertex the_simplex_tree;
    for (auto the_alpha_shape_vertex:vertex_list)
    {
      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
      if (the_map_iterator == map_cgal_simplex_tree.end())
      {
        // alpha shape not found
        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
#ifdef DEBUG_TRACES
        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
        the_simplex_tree.push_back(vertex);
        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex,vertex));
      } else
      {
        // alpha shape found
        Simplex_tree_vertex vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
        the_simplex_tree.push_back(vertex);
      }
    }
    // Construction of the simplex_tree
    Filtration_value filtr = std::sqrt(*the_alpha_value_iterator);
#ifdef DEBUG_TRACES
    std::cout << "filtration = " << filtr << std::endl;
#endif // DEBUG_TRACES
    if (filtr > filtration_max) {
      filtration_max = filtr;
    }
    simplex_tree.insert(the_simplex_tree, filtr);
    if (the_alpha_value_iterator != the_alpha_values.end())
      ++the_alpha_value_iterator;
    else
      std::cout << "This shall not happen" << std::endl;
  }
  simplex_tree.set_filtration(filtration_max);
  simplex_tree.set_num_simplices(count_vertices + count_edges + count_facets + count_cells);
  simplex_tree.set_dimension(dim_max);

#ifdef DEBUG_TRACES
  std::cout << "vertices \t\t" << count_vertices << std::endl;
  std::cout << "edges \t\t"    << count_edges << std::endl;
  std::cout << "facets \t\t"   << count_facets << std::endl;
  std::cout << "cells \t\t"    << count_cells << std::endl;


  std::cout << "Information of the Simplex Tree: " << std::endl;
  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
#endif // DEBUG_TRACES

#ifdef DEBUG_TRACES
  std::cout << "Iterator on vertices: " << std::endl;
  for( auto vertex : simplex_tree.complex_vertex_range() )
  { std::cout << vertex << " "; }
#endif // DEBUG_TRACES

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

  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
  // Compute the persistence diagram of the complex
  Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree );
  pcoh.init_coefficients( coeff_field_characteristic ); //initializes the coefficient field for homology

  pcoh.compute_persistent_cohomology( (Filtration_value)min_persistence );

  pcoh.output_diagram();

  return 0;
}