#include <iostream>
#include <string>
#include <algorithm>

#include <CGAL/array.h>
#include <CGAL/Bbox_3.h>
#include <CGAL/Polygon_mesh_processing/polygon_soup_to_polygon_mesh.h>
#include <CGAL/Polygon_mesh_processing/orient_polygon_soup.h>
#include <CGAL/Polygon_mesh_processing/repair.h>

#include <CGAL/Polygon_mesh_processing/internal/named_function_params.h>
#include <CGAL/Polygon_mesh_processing/internal/named_params_helper.h>

//a material is composed of an material Id and a material name.
typedef std::pair<int, std::string> material;

struct MaterialData
{
  material innerRegion;
  material outerRegion;
};

std::string to_lower_case(const std::string& str)
{
  std::string r = str;
  std::transform(r.begin(), r.end(), r.begin(), ::tolower);
  return r;
}

bool get_material_metadata(std::istream& input,
                           std::string& line,
                           material& _material)
{
  std::istringstream iss;
  iss.str(line);

  iss >> _material.second;//name

  static int material_id = 0;
  while (std::getline(input, line))
  {
    std::string prop; //property
    iss.clear();
    iss.str(line);
    iss >> prop;

    if (prop.compare("Id") == 0)
    {
      int tmp_id;
      iss >> tmp_id;
      _material.first = material_id++;

      if ((0 == to_lower_case(_material.second).compare("exterior"))
          && _material.first != 0)
      {
        std::cerr << "Exterior should have index 0. ";
        std::cerr << "In this file it has index " << _material.first << "." << std::endl;
        std::cerr << "Reader failed, because Meshing will fail to terminate." << std::endl;
        return false;
      }
    }
    else if (prop.compare("}") == 0)
      return true; //end of this material
  }
  return false;
}

bool line_starts_with(const std::string& line, const char* cstr)
{
  const std::size_t fnws = line.find_first_not_of(" \t");
  if (fnws != std::string::npos)
    return (line.compare(fnws, strlen(cstr), cstr) == 0);
  return false;
}

/*!
 * read_surf reads a file which extension is .surf and fills `output` with one `Mesh` per patch.
 * Mesh is a model of FaceListGraph.
 */
template<class Mesh, typename DuplicatedPointsOutIterator, class NamedParameters>
bool read_surf(std::istream& input, std::vector<Mesh>& output,
    std::vector<MaterialData>& metadata,
    CGAL::Bbox_3& grid_box,
    CGAL::cpp11::array<unsigned int, 3>& grid_size,
    DuplicatedPointsOutIterator out,
    const NamedParameters&)
{
  typedef typename CGAL::GetGeomTraits<Mesh,
      NamedParameters>::type Kernel;
  typedef typename Kernel::Point_3 Point_3;
  std::vector<Point_3> points;
  std::string line;
  std::istringstream iss;
  std::size_t nb_vertices(0);
  std::vector<material> materials;
  //ignore header
  while(std::getline(input, line))
  {
    if (line_starts_with(line, "Materials"))
    {
      while(std::getline(input, line))
      {
        if(line_starts_with(line, "}"))
          break;
        else
        {
          material _material;
          if (!get_material_metadata(input, line, _material))
            return false;
          materials.push_back(_material);
        }
      }
      break;
    }
  }

  //get grid box
  while (std::getline(input, line))
  {
    if (line_starts_with(line, "GridBox"))
    {
      iss.clear();
      iss.str(line);
      std::string dump;
      double xmin, xmax, ymin, ymax, zmin, zmax;
      iss >> dump >> xmin >> xmax >> ymin >> ymax >> zmin >> zmax;
      grid_box = CGAL::Bbox_3(xmin, ymin, zmin, xmax, ymax, zmax);
      break;
    }
  }

  //get grid size
  while (std::getline(input, line))
  {
    if (line_starts_with(line, "GridSize"))
    {
      iss.clear();
      iss.str(line);
      std::string dump;
      iss >> dump >> grid_size[0] >> grid_size[1] >> grid_size[2];
      break;
    }
  }

  //get number of vertices
  while(std::getline(input, line))
  {
    if (line_starts_with(line, "Vertices"))
    {
      iss.clear();
      iss.str(line);
      std::string dump;
      iss >> dump >> nb_vertices;
      points.reserve(nb_vertices);
      break;
    }
  }
  //get vertices
  while(std::getline(input, line))
  {
    if (line_starts_with(line, "NBranchingPoints"))
      break;
    double x(0),y(0),z(0);
    iss.clear();
    iss.str(line);
    iss >> CGAL::iformat(x) >> CGAL::iformat(y) >> CGAL::iformat(z);
    points.push_back(Point_3(x,y,z));
  }
  std::cout<<nb_vertices<<" vertices"<<std::endl;
  int nb_patches = 0;
  //get number of patches
  while(std::getline(input, line))
  {
    if (line_starts_with(line, "Patches"))
    {
      iss.clear();
      iss.str(line);
      std::string dump;
      iss >> dump >> nb_patches;
      break;
    }
  }
  std::cout<<nb_patches<<" patch(es)"<<std::endl;
  metadata.resize(nb_patches);
  output.resize(nb_patches);

  for(int i=0; i < nb_patches; ++i)
  {
    //get metada
    while(std::getline(input, line))
    {
      if (line_starts_with(line, "InnerRegion"))
      {
        std::string name;
        iss.clear();
        iss.str(line);
        std::string dump;
        iss >> dump >> name;
        for(std::size_t j=0; j<materials.size(); ++j)
        {
          if(materials[j].second.compare(name) == 0)
          {
            metadata[i].innerRegion=materials[j];
            break;
          }
        }
        std::getline(input, line);
        iss.clear();
        iss.str(line);
        iss >> dump >> name;
        for(std::size_t j=0; j<materials.size(); ++j)
        {
          if(materials[j].second.compare(name) == 0)
          {
            metadata[i].outerRegion=materials[j];
            break;
          }
        }
        break;
      }
    }

    std::size_t nb_triangles(0);
    while(std::getline(input, line))
    {
      if (line_starts_with(line, "Triangles"))
      {
        iss.clear();
        iss.str(line);
        std::string dump;
        iss >> dump >> nb_triangles;
        break;
      }
    }

    //connect triangles
    typedef CGAL::cpp11::array<std::size_t, 3> Triangle_ind;
    std::vector<Triangle_ind> polygons;
    polygons.reserve(nb_triangles);
    while(std::getline(input, line))
    {
      std::size_t fnws=line.find_first_not_of(" \t");
      if(fnws != std::string::npos)
        line.erase(0, fnws);
      std::size_t index[3];
      if(line.compare(0, 1, "}") == 0)
      {
        break;
      }
      iss.clear();
      iss.str(line);
      iss >> index[0] >> index[1] >> index[2];

      Triangle_ind polygon;
      polygon[0] = index[0] - 1;
      polygon[1] = index[1] - 1;
      polygon[2] = index[2] - 1;
      polygons.push_back(polygon);
    }
    CGAL_assertion(nb_triangles == polygons.size());

    //build patch
    namespace PMP = CGAL::Polygon_mesh_processing;
    if (!PMP::is_polygon_soup_a_polygon_mesh(polygons))
    {
      std::cout << "Orientation of patch #" << (i + 1) << "...";
      std::cout.flush();

      const std::size_t nbp_init = points.size();
      bool no_duplicates =
      PMP::orient_polygon_soup(points, polygons);//returns false if some points
                                                 //were duplicated

      std::cout << "\rOrientation of patch #" << (i + 1) << " done";

      if(!no_duplicates) //collect duplicates
      { 
        for (std::size_t i = nbp_init; i < points.size(); ++i)
          *out++ = points[i];
        std::cout << " (non manifold -> "
                  << (points.size() - nbp_init) << " duplicated vertices)";
      }
      std::cout << "." << std::endl;
    }

    Mesh& mesh = output[i];

    PMP::internal::Polygon_soup_to_polygon_mesh<Mesh, Point_3, Triangle_ind>
      converter(points, polygons);
    converter(mesh, false/*insert_isolated_vertices*/);

    CGAL_assertion(PMP::remove_isolated_vertices(mesh) == 0);
    CGAL_assertion(is_valid(mesh));
  } // end loop on patches

  return true;
}

template<class Mesh, typename DuplicatedPointsOutIterator>
bool read_surf(std::istream& input, std::vector<Mesh>& output,
  std::vector<MaterialData>& metadata,
  CGAL::Bbox_3& grid_box,
  CGAL::cpp11::array<unsigned int, 3>& grid_size,
  DuplicatedPointsOutIterator out)
{
  return read_surf(input, output, metadata, grid_box, grid_size, out,
    CGAL::Polygon_mesh_processing::parameters::all_default());
}

