#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>

#include <CGAL/Point_set_3.h>
#include <CGAL/Point_set_3/IO.h>

#include <CGAL/remove_outliers.h>
#include <CGAL/grid_simplify_point_set.h>
#include <CGAL/jet_smooth_point_set.h>
#include <CGAL/jet_estimate_normals.h>
#include <CGAL/mst_orient_normals.h>

#include <CGAL/poisson_surface_reconstruction.h>
#include <CGAL/Advancing_front_surface_reconstruction.h>
#include <CGAL/Scale_space_surface_reconstruction_3.h>
#include <CGAL/Scale_space_reconstruction_3/Jet_smoother.h>
#include <CGAL/Scale_space_reconstruction_3/Advancing_front_mesher.h>

#include <CGAL/Surface_mesh.h>
#include <CGAL/Polygon_mesh_processing/polygon_soup_to_polygon_mesh.h>

#include <cstdlib>
#include <vector>
#include <fstream>

// types
typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
typedef Kernel::FT FT;
typedef Kernel::Point_3 Point_3;
typedef Kernel::Vector_3 Vector_3;
typedef Kernel::Sphere_3 Sphere_3;
typedef CGAL::Point_set_3<Point_3, Vector_3> Point_set;

int main(int argc, char*argv[])
{
  ///////////////////////////////////////////////////////////////////
  //! [Reading input]

  Point_set points;

  std::string fname = argc==1?CGAL::data_file_path("points_3/kitten.xyz") : argv[1];
  if (argc < 2)
  {
    std::cerr << "Usage: " << argv[0] << " [input.xyz/off/ply/las]" << std::endl;
    std::cerr <<"Running " << argv[0] << " data/kitten.xyz -1\n";
  }

  std::ifstream stream (fname, std::ios_base::binary);
  if (!stream)
  {
    std::cerr << "Error: cannot read file " << fname << std::endl;
    return EXIT_FAILURE;
  }

  stream >> points;

  std::cout << "Read " << points.size () << " point(s)" << std::endl;
  if (points.empty())
    return EXIT_FAILURE;

  //! [Reading input]
  ///////////////////////////////////////////////////////////////////

  ///////////////////////////////////////////////////////////////////
  //! [Outlier removal]

  typename Point_set::iterator rout_it = CGAL::remove_outliers<CGAL::Sequential_tag>
    (points,
     24, // Number of neighbors considered for evaluation
     points.parameters().threshold_percent (5.0)); // Percentage of points to remove
  points.remove(rout_it, points.end());

  std::cout << points.number_of_removed_points()
            << " point(s) are outliers." << std::endl;

  // Applying point set processing algorithm to a CGAL::Point_set_3
  // object does not erase the points from memory but place them in
  // the garbage of the object: memory can be freed by the user.
  points.collect_garbage();

  //! [Outlier removal]
  ///////////////////////////////////////////////////////////////////

  ///////////////////////////////////////////////////////////////////
  //! [Simplification]

  // Compute average spacing using neighborhood of 6 points
  double spacing = CGAL::compute_average_spacing<CGAL::Sequential_tag> (points, 6);

  // Simplify using a grid of size 2 * average spacing
  typename Point_set::iterator gsim_it = CGAL::grid_simplify_point_set (points, 2. * spacing);
  points.remove(gsim_it, points.end());

  std::cout << points.number_of_removed_points()
            << " point(s) removed after simplification." << std::endl;

  points.collect_garbage();

  //! [Simplification]
  ///////////////////////////////////////////////////////////////////

  ///////////////////////////////////////////////////////////////////
  //! [Smoothing]

  CGAL::jet_smooth_point_set<CGAL::Sequential_tag> (points, 24);

  //! [Smoothing]
  ///////////////////////////////////////////////////////////////////

  int reconstruction_choice
    = argc==1? -1 : (argc < 3 ? 0 : atoi(argv[2]));

  if (reconstruction_choice == 0 || reconstruction_choice==-1) // Poisson
  {
    ///////////////////////////////////////////////////////////////////
    //! [Normal estimation]

    CGAL::jet_estimate_normals<CGAL::Sequential_tag>
      (points, 24); // Use 24 neighbors

    // Orientation of normals, returns iterator to first unoriented point
    typename Point_set::iterator unoriented_points_begin =
      CGAL::mst_orient_normals(points, 24); // Use 24 neighbors

    points.remove (unoriented_points_begin, points.end());

    //! [Normal estimation]
    ///////////////////////////////////////////////////////////////////

    ///////////////////////////////////////////////////////////////////
    //! [Poisson reconstruction]

    CGAL::Surface_mesh<Point_3> output_mesh;
    CGAL::poisson_surface_reconstruction_delaunay
      (points.begin(), points.end(),
       points.point_map(), points.normal_map(),
       output_mesh, spacing);

    //! [Poisson reconstruction]
    ///////////////////////////////////////////////////////////////////

    ///////////////////////////////////////////////////////////////////
    //! [Output poisson]

    std::ofstream f ("out_poisson.ply", std::ios_base::binary);
    CGAL::IO::set_binary_mode (f);
    CGAL::IO::write_PLY(f, output_mesh);
    f.close ();

    //! [Output poisson]
    ///////////////////////////////////////////////////////////////////
  }
  if (reconstruction_choice == 1 || reconstruction_choice==-1) // Advancing front
  {
    ///////////////////////////////////////////////////////////////////
    //! [Advancing front reconstruction]

    typedef std::array<std::size_t, 3> Facet; // Triple of indices

    std::vector<Facet> facets;

    // The function is called using directly the points raw iterators
    CGAL::advancing_front_surface_reconstruction(points.points().begin(),
                                                 points.points().end(),
                                                 std::back_inserter(facets));
    std::cout << facets.size ()
              << " facet(s) generated by reconstruction." << std::endl;

    //! [Advancing front reconstruction]
    ///////////////////////////////////////////////////////////////////

    ///////////////////////////////////////////////////////////////////
    //! [Output advancing front]

    // copy points for random access
    std::vector<Point_3> vertices;
    vertices.reserve (points.size());
    std::copy (points.points().begin(), points.points().end(), std::back_inserter (vertices));

    CGAL::Surface_mesh<Point_3> output_mesh;
    CGAL::Polygon_mesh_processing::polygon_soup_to_polygon_mesh (vertices, facets, output_mesh);
    std::ofstream f ("out_af.off");
    f << output_mesh;
    f.close ();

    //! [Output advancing front]
    ///////////////////////////////////////////////////////////////////
  }
  if (reconstruction_choice == 2 || reconstruction_choice==-1) // Scale space
  {
    ///////////////////////////////////////////////////////////////////
    //! [Scale space reconstruction]

    CGAL::Scale_space_surface_reconstruction_3<Kernel> reconstruct
      (points.points().begin(), points.points().end());

    // Smooth using 4 iterations of Jet Smoothing
    reconstruct.increase_scale (4, CGAL::Scale_space_reconstruction_3::Jet_smoother<Kernel>());
    // Mesh with the Advancing Front mesher with a maximum facet length of 0.5
    reconstruct.reconstruct_surface (CGAL::Scale_space_reconstruction_3::Advancing_front_mesher<Kernel>(0.5));

    //! [Scale space reconstruction]
    ///////////////////////////////////////////////////////////////////

    ///////////////////////////////////////////////////////////////////
    //! [Output scale space]

    std::ofstream f ("out_sp.off");
    f << "OFF" << std::endl << points.size () << " "
      << reconstruct.number_of_facets() << " 0" << std::endl;
    for (Point_set::Index idx : points)
      f << points.point (idx) << std::endl;
    for (const auto& facet : CGAL::make_range (reconstruct.facets_begin(), reconstruct.facets_end()))
      f << "3 "<< facet[0] << " " << facet[1] << " " << facet[2] << std::endl;
    f.close ();

    //! [Output scale space]
    ///////////////////////////////////////////////////////////////////
  }
  else // Handle error
  {
    std::cerr << "Error: invalid reconstruction id: " << reconstruction_choice << std::endl;
    return EXIT_FAILURE;
  }

  return EXIT_SUCCESS;
}
