// Copyright (C) 2006 Johan Hoffman
//
// This file is part of DOLFIN.
//
// DOLFIN is free software: you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// DOLFIN 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 Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
//
// Modified by Anders Logg, 2009-2011.
// Modified by Garth N. Wells, 2010-2011.
// Modified by Marie E. Rognes, 2011.
//
// First added:  2006-11-01
// Last changed: 2011-04-07

#include <memory>
#include <dolfin/log/dolfin_log.h>
#include <dolfin/mesh/Mesh.h>
#include <dolfin/mesh/Facet.h>
#include <dolfin/mesh/Cell.h>
#include <dolfin/mesh/MeshFunction.h>
#include "RivaraRefinement.h"
#include "BisectionRefinement.h"

using namespace dolfin;

//-----------------------------------------------------------------------------
void BisectionRefinement::refine_by_recursive_bisection(Mesh& refined_mesh,
                        const Mesh& mesh, const MeshFunction<bool>& cell_marker)
{
  not_working_in_parallel("BisectionRefinement::refine");

  // Transformation maps
  MeshFunction<std::size_t> cell_map;
  std::vector<int> facet_map;

  // Call Rivara refinement
  RivaraRefinement::refine(refined_mesh, mesh, cell_marker, cell_map,
                           facet_map);

  // Store child->parent cell and facet information as mesh data
  const std::size_t D = refined_mesh.topology().dim();
  std::vector<std::size_t>& cf
    = refined_mesh.data().create_array("parent_cell", D);
  cf.resize(refined_mesh.num_cells());
  for(std::size_t i = 0; i < refined_mesh.num_cells(); i++)
    cf[i] = cell_map[i];

  // Create mesh function in refined mesh encoding parent facet maps
  refined_mesh.init(D - 1);
  std::vector<std::size_t>& ff
    = refined_mesh.data().create_array("parent_facet", D - 1);
  ff.resize(refined_mesh.num_facets());

  // Fill ff from facet_map
  mesh.init(D, D - 1);
  refined_mesh.init(D - 1, D);
  const std::size_t orphan = mesh.num_facets() + 1;
  for (FacetIterator facet(refined_mesh); !facet.end(); ++facet)
  {
    // Extract (arbitrary) cell that this facet belongs to
    Cell cell(refined_mesh, facet->entities(D)[0]);

    // Extract local facet number of this facet with that cell
    const std::size_t local_facet = cell.index(*facet);

    // Extract local facet index of parent cell (using facet_map)
    const std::size_t index = cell.index()*(D + 1) + local_facet;
    const int parent_local_facet_index = facet_map[index];

    // Ignore if orphaned facet
    if (parent_local_facet_index == -1)
    {
      ff[facet->index()] = orphan;
      continue;
    }

    // Get parent cell
    Cell parent_cell(mesh, cf[cell.index()]);

    // Figure out global facet number of local facet number of parent
    const std::size_t parent_facet_index
      = parent_cell.entities(D - 1)[parent_local_facet_index];

    // Assign parent facet index to this facet
    ff[facet->index()] = parent_facet_index;
  }
}
/*
//-----------------------------------------------------------------------------
void BisectionRefinement::transform_data(Mesh& newmesh, const Mesh& oldmesh,
                                         const MeshFunction<std::size_t>& cell_map,
                                         const std::vector<int>& facet_map)
{
  newmesh.data().clear();

  // Rewrite materials
  if (oldmesh.data().mesh_function("material_indicators"))
  {
    std::shared_ptr<MeshFunction<std::size_t> > mat;
    mat = newmesh.data().create_mesh_function("material_indicators", newmesh.type().dim());

    for(std::size_t i=0; i < newmesh.num_cells(); i++)
      (*mat)[i] = (*oldmesh.data().mesh_function("material_indicators"))[cell_map[i]];

    log(TRACE, "MeshData MeshFunction \"material_indicators\" transformed.");
  }

  // Rewrite boundary indicators
  if (oldmesh.data().array("boundary facet cells")
        && oldmesh.data().array("boundary facet numbers")
        && oldmesh.data().array("boundary indicators"))
  {

    std::size_t num_ent = oldmesh.type().num_entities(0);
    std::vector<std::size_t>*  bfc = oldmesh.data().array("boundary facet cells");
    std::vector<std::size_t>*  bfn = oldmesh.data().array("boundary facet numbers");
    std::vector<std::size_t>*  bi  = oldmesh.data().array("boundary indicators");
    std::size_t bi_table_size = oldmesh.num_cells()*num_ent;
    std::vector<int> bi_table;
    bi_table.resize(bi_table_size);

    for(std::size_t i= 0 ; i< bi_table_size; i++)
      bi_table[i] = -1;

    for(std::size_t i = 0; i < bi->size(); i++)
      bi_table[(*bfc)[i]*num_ent+(*bfn)[i]] = (*bi)[i];

    // Empty loop to count elements
    std::size_t bi_size = 0;
    for(std::size_t c = 0; c < newmesh.num_cells(); c++)
    {
      for(std::size_t f = 0; f < num_ent; f++)
      {
        if (facet_map[c*num_ent+f] != -1)
        {
          std::size_t table_map = cell_map[c]*num_ent + facet_map[c*num_ent+f];
          if (bi_table[table_map] != -1)
            bi_size++;
        }
      }
    }

    // Create new MeshData std::vectors for boundary indicators
    std::vector<std::size_t>* bfc_new = newmesh.data().create_array("boundary facet cells", bi_size);
    std::vector<std::size_t>* bfn_new = newmesh.data().create_array("boundary facet numbers", bi_size);
    std::vector<std::size_t>* bi_new  = newmesh.data().create_array("boundary indicators", bi_size);

    // Main transformation loop
    std::size_t number_bi = 0;
    for(std::size_t c = 0; c < newmesh.num_cells(); c++)
    {
      for(std::size_t f = 0; f < num_ent; f++)
      {
        if (facet_map[c*num_ent+f] != -1)
        {
          std::size_t table_map = cell_map[c]*num_ent + facet_map[c*num_ent+f];
          if (bi_table[table_map] != -1)
          {
            (*bfc_new)[number_bi] = c;
            (*bfn_new)[number_bi] = f;
            (*bi_new)[number_bi] = bi_table[table_map];
            number_bi++;
          }
        }
      }
    }
    log(TRACE, "MeshData \"boundary indicators\" transformed.");
  }
}
//-----------------------------------------------------------------------------
*/