#include <boost/program_options.hpp>

#include <CGAL/Epick_d.h>

#include <gudhi/Alpha_complex.h>
#include <gudhi/Persistent_cohomology.h>
// to construct a simplex_tree from alpha complex
#include <gudhi/Simplex_tree.h>

#include <iostream>
#include <string>
#include <limits>  // for numeric_limits

using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;

void program_options(int argc, char * argv[]
                     , std::string & off_file_points
                     , std::string & output_file_diag
                     , Filtration_value & alpha_square_max_value
                     , int & coeff_field_characteristic
                     , Filtration_value & min_persistence);

int main(int argc, char **argv) {
  std::string off_file_points;
  std::string output_file_diag;
  Filtration_value alpha_square_max_value;
  int coeff_field_characteristic;
  Filtration_value min_persistence;

  program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value,
                  coeff_field_characteristic, min_persistence);

  // ----------------------------------------------------------------------------
  // Init of an alpha complex from an OFF file
  // ----------------------------------------------------------------------------
  using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);

  Simplex_tree simplex;
  if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
    // ----------------------------------------------------------------------------
    // Display information about the alpha complex
    // ----------------------------------------------------------------------------
    std::cout << "Simplicial complex is of dimension " << simplex.dimension() <<
        " - " << simplex.num_simplices() << " simplices - " <<
        simplex.num_vertices() << " vertices." << std::endl;

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

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

    pcoh.compute_persistent_cohomology(min_persistence);

    // Output the diagram in filediag
    if (output_file_diag.empty()) {
      pcoh.output_diagram();
    } else {
      std::cout << "Result in file: " << output_file_diag << std::endl;
      std::ofstream out(output_file_diag);
      pcoh.output_diagram(out);
      out.close();
    }
  }

  return 0;
}

void program_options(int argc, char * argv[]
                     , std::string & off_file_points
                     , std::string & output_file_diag
                     , Filtration_value & alpha_square_max_value
                     , int & coeff_field_characteristic
                     , Filtration_value & min_persistence) {
  namespace po = boost::program_options;
  po::options_description hidden("Hidden options");
  hidden.add_options()
      ("input-file", po::value<std::string>(&off_file_points),
       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");

  po::options_description visible("Allowed options", 100);
  visible.add_options()
      ("help,h", "produce help message")
      ("output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
       "Name of file in which the persistence diagram is written. Default print in std::cout")
      ("max-alpha-square-value,r",
      po::value<Filtration_value>(&alpha_square_max_value)->default_value(std::numeric_limits<Filtration_value>::infinity()),
       "Maximal alpha square value for the Alpha complex construction.")
      ("field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
       "Characteristic p of the coefficient field Z/pZ for computing homology.")
      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");

  po::positional_options_description pos;
  pos.add("input-file", 1);

  po::options_description all;
  all.add(visible).add(hidden);

  po::variables_map vm;
  po::store(po::command_line_parser(argc, argv).
            options(all).positional(pos).run(), vm);
  po::notify(vm);

  if (vm.count("help") || !vm.count("input-file")) {
    std::cout << std::endl;
    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
    std::cout << "of an Alpha complex defined on a set of input points.\n \n";
    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
    std::cout << "   p   dim b d \n";
    std::cout << "where dim is the dimension of the homological feature,\n";
    std::cout << "b and d are respectively the birth and death of the feature and \n";
    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;

    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
    std::cout << visible << std::endl;
    std::abort();
  }
}