/*
 * normal_estimator.h
 *
 *  Created on: Mar 22, 2012
 *      Author: aitor
 */

#pragma once

#include <pcl/common/time.h>
#include <pcl/features/integral_image_normal.h>
#include <pcl/features/normal_3d.h>
#include <pcl/filters/radius_outlier_removal.h>
#include <pcl/filters/voxel_grid.h>
#include <pcl/memory.h> // for pcl::make_shared
#include <pcl/types.h>  // for pcl::index_t

namespace pcl {
namespace rec_3d_framework {

template <typename PointInT, typename PointOutT>
class PreProcessorAndNormalEstimator {

  using PointInTPtr = typename pcl::PointCloud<PointInT>::Ptr;

  float
  computeMeshResolution(PointInTPtr& input)
  {
    using KdTreeInPtr = typename pcl::KdTree<PointInT>::Ptr;
    KdTreeInPtr tree = pcl::make_shared<pcl::KdTreeFLANN<PointInT>>(false);
    tree->setInputCloud(input);

    pcl::Indices nn_indices(9);
    std::vector<float> nn_distances(9);

    float sum_distances = 0.0;
    std::vector<float> avg_distances(input->size());
    // Iterate through the source data set
    for (std::size_t i = 0; i < input->size(); ++i) {
      tree->nearestKSearch((*input)[i], 9, nn_indices, nn_distances);

      float avg_dist_neighbours = 0.0;
      for (std::size_t j = 1; j < nn_indices.size(); j++)
        avg_dist_neighbours += std::sqrt(nn_distances[j]);

      avg_dist_neighbours /= static_cast<float>(nn_indices.size());

      avg_distances[i] = avg_dist_neighbours;
      sum_distances += avg_dist_neighbours;
    }

    std::sort(avg_distances.begin(), avg_distances.end());
    float avg = avg_distances[static_cast<int>(avg_distances.size()) / 2 + 1];
    return avg;
  }

public:
  bool compute_mesh_resolution_;
  bool do_voxel_grid_;
  bool remove_outliers_;

  // this values are used when CMR=false
  float grid_resolution_;
  float normal_radius_;

  // this are used when CMR=true
  float factor_normals_;
  float factor_voxel_grid_;
  float mesh_resolution_;

  PreProcessorAndNormalEstimator()
  {
    remove_outliers_ = do_voxel_grid_ = compute_mesh_resolution_ = false;
  }

  void
  setFactorsForCMR(float f1, float f2)
  {
    factor_voxel_grid_ = f1;
    factor_normals_ = f2;
  }

  void
  setValuesForCMRFalse(float f1, float f2)
  {
    grid_resolution_ = f1;
    normal_radius_ = f2;
  }

  void
  setDoVoxelGrid(bool b)
  {
    do_voxel_grid_ = b;
  }

  void
  setRemoveOutliers(bool b)
  {
    remove_outliers_ = b;
  }

  void
  setCMR(bool b)
  {
    compute_mesh_resolution_ = b;
  }

  void
  estimate(PointInTPtr& in,
           PointInTPtr& out,
           pcl::PointCloud<pcl::Normal>::Ptr& normals)
  {
    if (compute_mesh_resolution_) {
      mesh_resolution_ = computeMeshResolution(in);
      std::cout << "compute mesh resolution:" << mesh_resolution_ << std::endl;
    }

    if (do_voxel_grid_) {
      pcl::ScopeTime t("Voxel grid...");
      float voxel_grid_size = grid_resolution_;
      if (compute_mesh_resolution_) {
        voxel_grid_size = mesh_resolution_ * factor_voxel_grid_;
      }

      pcl::VoxelGrid<PointInT> grid_;
      grid_.setInputCloud(in);
      grid_.setLeafSize(voxel_grid_size, voxel_grid_size, voxel_grid_size);
      grid_.setDownsampleAllData(true);
      grid_.filter(*out);
    }
    else {
      out = in;
    }

    if (out->points.empty()) {
      PCL_WARN("NORMAL estimator: Cloud has no points after voxel grid, "
               "won't be able to compute normals!\n");
      return;
    }

    if (remove_outliers_) {
      pcl::ScopeTime t("remove_outliers_...");
      PointInTPtr out2(new pcl::PointCloud<PointInT>());
      float radius = normal_radius_;
      if (compute_mesh_resolution_) {
        radius = mesh_resolution_ * factor_normals_;
        if (do_voxel_grid_)
          radius *= factor_voxel_grid_;
      }

      // in synthetic views the render grazes some parts of the objects
      // thus creating a very sparse set of points that causes the normals to be very
      // noisy remove these points
      pcl::RadiusOutlierRemoval<PointInT> sor;
      sor.setInputCloud(out);
      sor.setRadiusSearch(radius);
      sor.setMinNeighborsInRadius(16);
      sor.filter(*out2);
      out = out2;
    }

    if (out->points.empty()) {
      PCL_WARN("NORMAL estimator: Cloud has no points after removing outliers...!\n");
      return;
    }

    float radius = normal_radius_;
    if (compute_mesh_resolution_) {
      radius = mesh_resolution_ * factor_normals_;
      if (do_voxel_grid_)
        radius *= factor_voxel_grid_;
    }

    if (out->isOrganized()) {
      pcl::IntegralImageNormalEstimation<PointInT, pcl::Normal> n3d;
      n3d.setNormalEstimationMethod(n3d.COVARIANCE_MATRIX);
      n3d.setInputCloud(out);
      n3d.setRadiusSearch(radius);
      n3d.setKSearch(0);
      {
        pcl::ScopeTime t("compute normals...");
        n3d.compute(*normals);
      }
    }
    else {

      // check nans before computing normals
      {
        pcl::ScopeTime t("check nans...");
        pcl::index_t j = 0;
        for (const auto& point : *out) {
          if (!isXYZFinite(point))
            continue;

          (*out)[j] = point;
          j++;
        }

        if (j != static_cast<pcl::index_t>(out->size())) {
          PCL_ERROR("Contain nans...\n");
        }

        out->points.resize(j);
        out->width = j;
        out->height = 1;
      }

      pcl::NormalEstimation<PointInT, pcl::Normal> n3d;
      typename pcl::search::KdTree<PointInT>::Ptr normals_tree(
          new pcl::search::KdTree<PointInT>);
      normals_tree->setInputCloud(out);
      n3d.setRadiusSearch(radius);
      n3d.setSearchMethod(normals_tree);
      n3d.setInputCloud(out);
      {
        pcl::ScopeTime t("compute normals not organized...");
        n3d.compute(*normals);
      }
    }

    // check nans...
    if (!out->isOrganized()) {
      pcl::ScopeTime t("check nans...");
      int j = 0;
      for (std::size_t i = 0; i < normals->size(); ++i) {
        if (!isNormalFinite((*normals)[i]))
          continue;

        (*normals)[j] = (*normals)[i];
        (*out)[j] = (*out)[i];
        j++;
      }

      normals->points.resize(j);
      normals->width = j;
      normals->height = 1;

      out->points.resize(j);
      out->width = j;
      out->height = 1;
    }
    else {
      // is is organized, we set the xyz points to NaN
      pcl::ScopeTime t("check nans organized...");
      bool NaNs = false;
      for (std::size_t i = 0; i < normals->size(); ++i) {
        if (!isNormalFinite((*normals)[i]))
          continue;

        NaNs = true;

        (*out)[i].x = (*out)[i].y = (*out)[i].z =
            std::numeric_limits<float>::quiet_NaN();
      }

      if (NaNs) {
        PCL_WARN("normals contain NaNs\n");
        out->is_dense = false;
      }
    }
  }
};

} // namespace rec_3d_framework
} // namespace pcl
