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#ifndef PCL_REGISTRATION_IMPL_GICP_HPP_
#define PCL_REGISTRATION_IMPL_GICP_HPP_

#include <pcl/registration/exceptions.h>

namespace pcl {

template <typename PointSource, typename PointTarget>
template <typename PointT>
void
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::computeCovariances(
    typename pcl::PointCloud<PointT>::ConstPtr cloud,
    const typename pcl::search::KdTree<PointT>::Ptr kdtree,
    MatricesVector& cloud_covariances)
{
  if (k_correspondences_ > int(cloud->size())) {
    PCL_ERROR("[pcl::GeneralizedIterativeClosestPoint::computeCovariances] Number or "
              "points in cloud (%lu) is less than k_correspondences_ (%lu)!\n",
              cloud->size(),
              k_correspondences_);
    return;
  }

  Eigen::Vector3d mean;
  pcl::Indices nn_indecies;
  nn_indecies.reserve(k_correspondences_);
  std::vector<float> nn_dist_sq;
  nn_dist_sq.reserve(k_correspondences_);

  // We should never get there but who knows
  if (cloud_covariances.size() < cloud->size())
    cloud_covariances.resize(cloud->size());

  MatricesVector::iterator matrices_iterator = cloud_covariances.begin();
  for (auto points_iterator = cloud->begin(); points_iterator != cloud->end();
       ++points_iterator, ++matrices_iterator) {
    const PointT& query_point = *points_iterator;
    Eigen::Matrix3d& cov = *matrices_iterator;
    // Zero out the cov and mean
    cov.setZero();
    mean.setZero();

    // Search for the K nearest neighbours
    kdtree->nearestKSearch(query_point, k_correspondences_, nn_indecies, nn_dist_sq);

    // Find the covariance matrix
    for (int j = 0; j < k_correspondences_; j++) {
      const PointT& pt = (*cloud)[nn_indecies[j]];

      mean[0] += pt.x;
      mean[1] += pt.y;
      mean[2] += pt.z;

      cov(0, 0) += pt.x * pt.x;

      cov(1, 0) += pt.y * pt.x;
      cov(1, 1) += pt.y * pt.y;

      cov(2, 0) += pt.z * pt.x;
      cov(2, 1) += pt.z * pt.y;
      cov(2, 2) += pt.z * pt.z;
    }

    mean /= static_cast<double>(k_correspondences_);
    // Get the actual covariance
    for (int k = 0; k < 3; k++)
      for (int l = 0; l <= k; l++) {
        cov(k, l) /= static_cast<double>(k_correspondences_);
        cov(k, l) -= mean[k] * mean[l];
        cov(l, k) = cov(k, l);
      }

    // Compute the SVD (covariance matrix is symmetric so U = V')
    Eigen::JacobiSVD<Eigen::Matrix3d> svd(cov, Eigen::ComputeFullU);
    cov.setZero();
    Eigen::Matrix3d U = svd.matrixU();
    // Reconstitute the covariance matrix with modified singular values using the column
    // // vectors in V.
    for (int k = 0; k < 3; k++) {
      Eigen::Vector3d col = U.col(k);
      double v = 1.; // biggest 2 singular values replaced by 1
      if (k == 2)    // smallest singular value replaced by gicp_epsilon
        v = gicp_epsilon_;
      cov += v * col * col.transpose();
    }
  }
}

template <typename PointSource, typename PointTarget>
void
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::computeRDerivative(
    const Vector6d& x, const Eigen::Matrix3d& R, Vector6d& g) const
{
  Eigen::Matrix3d dR_dPhi;
  Eigen::Matrix3d dR_dTheta;
  Eigen::Matrix3d dR_dPsi;

  double phi = x[3], theta = x[4], psi = x[5];

  double cphi = std::cos(phi), sphi = sin(phi);
  double ctheta = std::cos(theta), stheta = sin(theta);
  double cpsi = std::cos(psi), spsi = sin(psi);

  dR_dPhi(0, 0) = 0.;
  dR_dPhi(1, 0) = 0.;
  dR_dPhi(2, 0) = 0.;

  dR_dPhi(0, 1) = sphi * spsi + cphi * cpsi * stheta;
  dR_dPhi(1, 1) = -cpsi * sphi + cphi * spsi * stheta;
  dR_dPhi(2, 1) = cphi * ctheta;

  dR_dPhi(0, 2) = cphi * spsi - cpsi * sphi * stheta;
  dR_dPhi(1, 2) = -cphi * cpsi - sphi * spsi * stheta;
  dR_dPhi(2, 2) = -ctheta * sphi;

  dR_dTheta(0, 0) = -cpsi * stheta;
  dR_dTheta(1, 0) = -spsi * stheta;
  dR_dTheta(2, 0) = -ctheta;

  dR_dTheta(0, 1) = cpsi * ctheta * sphi;
  dR_dTheta(1, 1) = ctheta * sphi * spsi;
  dR_dTheta(2, 1) = -sphi * stheta;

  dR_dTheta(0, 2) = cphi * cpsi * ctheta;
  dR_dTheta(1, 2) = cphi * ctheta * spsi;
  dR_dTheta(2, 2) = -cphi * stheta;

  dR_dPsi(0, 0) = -ctheta * spsi;
  dR_dPsi(1, 0) = cpsi * ctheta;
  dR_dPsi(2, 0) = 0.;

  dR_dPsi(0, 1) = -cphi * cpsi - sphi * spsi * stheta;
  dR_dPsi(1, 1) = -cphi * spsi + cpsi * sphi * stheta;
  dR_dPsi(2, 1) = 0.;

  dR_dPsi(0, 2) = cpsi * sphi - cphi * spsi * stheta;
  dR_dPsi(1, 2) = sphi * spsi + cphi * cpsi * stheta;
  dR_dPsi(2, 2) = 0.;

  g[3] = matricesInnerProd(dR_dPhi, R);
  g[4] = matricesInnerProd(dR_dTheta, R);
  g[5] = matricesInnerProd(dR_dPsi, R);
}

template <typename PointSource, typename PointTarget>
void
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::
    estimateRigidTransformationBFGS(const PointCloudSource& cloud_src,
                                    const pcl::Indices& indices_src,
                                    const PointCloudTarget& cloud_tgt,
                                    const pcl::Indices& indices_tgt,
                                    Eigen::Matrix4f& transformation_matrix)
{
  if (indices_src.size() < 4) // need at least 4 samples
  {
    PCL_THROW_EXCEPTION(
        NotEnoughPointsException,
        "[pcl::GeneralizedIterativeClosestPoint::estimateRigidTransformationBFGS] Need "
        "at least 4 points to estimate a transform! Source and target have "
            << indices_src.size() << " points!");
    return;
  }
  // Set the initial solution
  Vector6d x = Vector6d::Zero();
  // translation part
  x[0] = transformation_matrix(0, 3);
  x[1] = transformation_matrix(1, 3);
  x[2] = transformation_matrix(2, 3);
  // rotation part (Z Y X euler angles convention)
  // see: https://en.wikipedia.org/wiki/Rotation_matrix#General_rotations
  x[3] = std::atan2(transformation_matrix(2, 1), transformation_matrix(2, 2));
  x[4] = asin(-transformation_matrix(2, 0));
  x[5] = std::atan2(transformation_matrix(1, 0), transformation_matrix(0, 0));

  // Set temporary pointers
  tmp_src_ = &cloud_src;
  tmp_tgt_ = &cloud_tgt;
  tmp_idx_src_ = &indices_src;
  tmp_idx_tgt_ = &indices_tgt;

  // Optimize using forward-difference approximation LM
  OptimizationFunctorWithIndices functor(this);
  BFGS<OptimizationFunctorWithIndices> bfgs(functor);
  bfgs.parameters.sigma = 0.01;
  bfgs.parameters.rho = 0.01;
  bfgs.parameters.tau1 = 9;
  bfgs.parameters.tau2 = 0.05;
  bfgs.parameters.tau3 = 0.5;
  bfgs.parameters.order = 3;

  int inner_iterations_ = 0;
  int result = bfgs.minimizeInit(x);
  result = BFGSSpace::Running;
  do {
    inner_iterations_++;
    result = bfgs.minimizeOneStep(x);
    if (result) {
      break;
    }
    result = bfgs.testGradient();
  } while (result == BFGSSpace::Running && inner_iterations_ < max_inner_iterations_);
  if (result == BFGSSpace::NoProgress || result == BFGSSpace::Success ||
      inner_iterations_ == max_inner_iterations_) {
    PCL_DEBUG("[pcl::registration::TransformationEstimationBFGS::"
              "estimateRigidTransformation]");
    PCL_DEBUG("BFGS solver finished with exit code %i \n", result);
    transformation_matrix.setIdentity();
    applyState(transformation_matrix, x);
  }
  else
    PCL_THROW_EXCEPTION(
        SolverDidntConvergeException,
        "[pcl::" << getClassName()
                 << "::TransformationEstimationBFGS::estimateRigidTransformation] BFGS "
                    "solver didn't converge!");
}

template <typename PointSource, typename PointTarget>
inline double
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::
    OptimizationFunctorWithIndices::operator()(const Vector6d& x)
{
  Eigen::Matrix4f transformation_matrix = gicp_->base_transformation_;
  gicp_->applyState(transformation_matrix, x);
  double f = 0;
  int m = static_cast<int>(gicp_->tmp_idx_src_->size());
  for (int i = 0; i < m; ++i) {
    // The last coordinate, p_src[3] is guaranteed to be set to 1.0 in registration.hpp
    Vector4fMapConst p_src =
        (*gicp_->tmp_src_)[(*gicp_->tmp_idx_src_)[i]].getVector4fMap();
    // The last coordinate, p_tgt[3] is guaranteed to be set to 1.0 in registration.hpp
    Vector4fMapConst p_tgt =
        (*gicp_->tmp_tgt_)[(*gicp_->tmp_idx_tgt_)[i]].getVector4fMap();
    Eigen::Vector4f pp(transformation_matrix * p_src);
    // Estimate the distance (cost function)
    // The last coordinate is still guaranteed to be set to 1.0
    Eigen::Vector3d res(pp[0] - p_tgt[0], pp[1] - p_tgt[1], pp[2] - p_tgt[2]);
    Eigen::Vector3d temp(gicp_->mahalanobis((*gicp_->tmp_idx_src_)[i]) * res);
    // increment= res'*temp/num_matches = temp'*M*temp/num_matches (we postpone
    // 1/num_matches after the loop closes)
    f += double(res.transpose() * temp);
  }
  return f / m;
}

template <typename PointSource, typename PointTarget>
inline void
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::
    OptimizationFunctorWithIndices::df(const Vector6d& x, Vector6d& g)
{
  Eigen::Matrix4f transformation_matrix = gicp_->base_transformation_;
  gicp_->applyState(transformation_matrix, x);
  // Zero out g
  g.setZero();
  // Eigen::Vector3d g_t = g.head<3> ();
  Eigen::Matrix3d R = Eigen::Matrix3d::Zero();
  int m = static_cast<int>(gicp_->tmp_idx_src_->size());
  for (int i = 0; i < m; ++i) {
    // The last coordinate, p_src[3] is guaranteed to be set to 1.0 in registration.hpp
    Vector4fMapConst p_src =
        (*gicp_->tmp_src_)[(*gicp_->tmp_idx_src_)[i]].getVector4fMap();
    // The last coordinate, p_tgt[3] is guaranteed to be set to 1.0 in registration.hpp
    Vector4fMapConst p_tgt =
        (*gicp_->tmp_tgt_)[(*gicp_->tmp_idx_tgt_)[i]].getVector4fMap();

    Eigen::Vector4f pp(transformation_matrix * p_src);
    // The last coordinate is still guaranteed to be set to 1.0
    Eigen::Vector3d res(pp[0] - p_tgt[0], pp[1] - p_tgt[1], pp[2] - p_tgt[2]);
    // temp = M*res
    Eigen::Vector3d temp(gicp_->mahalanobis((*gicp_->tmp_idx_src_)[i]) * res);
    // Increment translation gradient
    // g.head<3> ()+= 2*M*res/num_matches (we postpone 2/num_matches after the loop
    // closes)
    g.head<3>() += temp;
    // Increment rotation gradient
    pp = gicp_->base_transformation_ * p_src;
    Eigen::Vector3d p_src3(pp[0], pp[1], pp[2]);
    R += p_src3 * temp.transpose();
  }
  g.head<3>() *= 2.0 / m;
  R *= 2.0 / m;
  gicp_->computeRDerivative(x, R, g);
}

template <typename PointSource, typename PointTarget>
inline void
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::
    OptimizationFunctorWithIndices::fdf(const Vector6d& x, double& f, Vector6d& g)
{
  Eigen::Matrix4f transformation_matrix = gicp_->base_transformation_;
  gicp_->applyState(transformation_matrix, x);
  f = 0;
  g.setZero();
  Eigen::Matrix3d R = Eigen::Matrix3d::Zero();
  const int m = static_cast<int>(gicp_->tmp_idx_src_->size());
  for (int i = 0; i < m; ++i) {
    // The last coordinate, p_src[3] is guaranteed to be set to 1.0 in registration.hpp
    Vector4fMapConst p_src =
        (*gicp_->tmp_src_)[(*gicp_->tmp_idx_src_)[i]].getVector4fMap();
    // The last coordinate, p_tgt[3] is guaranteed to be set to 1.0 in registration.hpp
    Vector4fMapConst p_tgt =
        (*gicp_->tmp_tgt_)[(*gicp_->tmp_idx_tgt_)[i]].getVector4fMap();
    Eigen::Vector4f pp(transformation_matrix * p_src);
    // The last coordinate is still guaranteed to be set to 1.0
    Eigen::Vector3d res(pp[0] - p_tgt[0], pp[1] - p_tgt[1], pp[2] - p_tgt[2]);
    // temp = M*res
    Eigen::Vector3d temp(gicp_->mahalanobis((*gicp_->tmp_idx_src_)[i]) * res);
    // Increment total error
    f += double(res.transpose() * temp);
    // Increment translation gradient
    // g.head<3> ()+= 2*M*res/num_matches (we postpone 2/num_matches after the loop
    // closes)
    g.head<3>() += temp;
    pp = gicp_->base_transformation_ * p_src;
    Eigen::Vector3d p_src3(pp[0], pp[1], pp[2]);
    // Increment rotation gradient
    R += p_src3 * temp.transpose();
  }
  f /= double(m);
  g.head<3>() *= double(2.0 / m);
  R *= 2.0 / m;
  gicp_->computeRDerivative(x, R, g);
}

template <typename PointSource, typename PointTarget>
inline BFGSSpace::Status
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::
    OptimizationFunctorWithIndices::checkGradient(const Vector6d& g)
{
  auto translation_epsilon = gicp_->translation_gradient_tolerance_;
  auto rotation_epsilon = gicp_->rotation_gradient_tolerance_;

  if ((translation_epsilon < 0.) || (rotation_epsilon < 0.))
    return BFGSSpace::NegativeGradientEpsilon;

  // express translation gradient as norm of translation parameters
  auto translation_grad = g.head<3>().norm();

  // express rotation gradient as a norm of rotation parameters
  auto rotation_grad = g.tail<3>().norm();

  if ((translation_grad < translation_epsilon) && (rotation_grad < rotation_epsilon))
    return BFGSSpace::Success;

  return BFGSSpace::Running;
}

template <typename PointSource, typename PointTarget>
inline void
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::computeTransformation(
    PointCloudSource& output, const Eigen::Matrix4f& guess)
{
  pcl::IterativeClosestPoint<PointSource, PointTarget>::initComputeReciprocal();
  // Difference between consecutive transforms
  double delta = 0;
  // Get the size of the target
  const std::size_t N = indices_->size();
  // Set the mahalanobis matrices to identity
  mahalanobis_.resize(N, Eigen::Matrix3d::Identity());
  // Compute target cloud covariance matrices
  if ((!target_covariances_) || (target_covariances_->empty())) {
    target_covariances_.reset(new MatricesVector);
    computeCovariances<PointTarget>(target_, tree_, *target_covariances_);
  }
  // Compute input cloud covariance matrices
  if ((!input_covariances_) || (input_covariances_->empty())) {
    input_covariances_.reset(new MatricesVector);
    computeCovariances<PointSource>(input_, tree_reciprocal_, *input_covariances_);
  }

  base_transformation_ = Eigen::Matrix4f::Identity();
  nr_iterations_ = 0;
  converged_ = false;
  double dist_threshold = corr_dist_threshold_ * corr_dist_threshold_;
  pcl::Indices nn_indices(1);
  std::vector<float> nn_dists(1);

  pcl::transformPointCloud(output, output, guess);

  while (!converged_) {
    std::size_t cnt = 0;
    pcl::Indices source_indices(indices_->size());
    pcl::Indices target_indices(indices_->size());

    // guess corresponds to base_t and transformation_ to t
    Eigen::Matrix4d transform_R = Eigen::Matrix4d::Zero();
    for (std::size_t i = 0; i < 4; i++)
      for (std::size_t j = 0; j < 4; j++)
        for (std::size_t k = 0; k < 4; k++)
          transform_R(i, j) += double(transformation_(i, k)) * double(guess(k, j));

    Eigen::Matrix3d R = transform_R.topLeftCorner<3, 3>();

    for (std::size_t i = 0; i < N; i++) {
      PointSource query = output[i];
      query.getVector4fMap() = transformation_ * query.getVector4fMap();

      if (!searchForNeighbors(query, nn_indices, nn_dists)) {
        PCL_ERROR("[pcl::%s::computeTransformation] Unable to find a nearest neighbor "
                  "in the target dataset for point %d in the source!\n",
                  getClassName().c_str(),
                  (*indices_)[i]);
        return;
      }

      // Check if the distance to the nearest neighbor is smaller than the user imposed
      // threshold
      if (nn_dists[0] < dist_threshold) {
        Eigen::Matrix3d& C1 = (*input_covariances_)[i];
        Eigen::Matrix3d& C2 = (*target_covariances_)[nn_indices[0]];
        Eigen::Matrix3d& M = mahalanobis_[i];
        // M = R*C1
        M = R * C1;
        // temp = M*R' + C2 = R*C1*R' + C2
        Eigen::Matrix3d temp = M * R.transpose();
        temp += C2;
        // M = temp^-1
        M = temp.inverse();
        source_indices[cnt] = static_cast<int>(i);
        target_indices[cnt] = nn_indices[0];
        cnt++;
      }
    }
    // Resize to the actual number of valid correspondences
    source_indices.resize(cnt);
    target_indices.resize(cnt);
    /* optimize transformation using the current assignment and Mahalanobis metrics*/
    previous_transformation_ = transformation_;
    // optimization right here
    try {
      rigid_transformation_estimation_(
          output, source_indices, *target_, target_indices, transformation_);
      /* compute the delta from this iteration */
      delta = 0.;
      for (int k = 0; k < 4; k++) {
        for (int l = 0; l < 4; l++) {
          double ratio = 1;
          if (k < 3 && l < 3) // rotation part of the transform
            ratio = 1. / rotation_epsilon_;
          else
            ratio = 1. / transformation_epsilon_;
          double c_delta =
              ratio * std::abs(previous_transformation_(k, l) - transformation_(k, l));
          if (c_delta > delta)
            delta = c_delta;
        }
      }
    } catch (PCLException& e) {
      PCL_DEBUG("[pcl::%s::computeTransformation] Optimization issue %s\n",
                getClassName().c_str(),
                e.what());
      break;
    }
    nr_iterations_++;
    // Check for convergence
    if (nr_iterations_ >= max_iterations_ || delta < 1) {
      converged_ = true;
      PCL_DEBUG("[pcl::%s::computeTransformation] Convergence reached. Number of "
                "iterations: %d out of %d. Transformation difference: %f\n",
                getClassName().c_str(),
                nr_iterations_,
                max_iterations_,
                (transformation_ - previous_transformation_).array().abs().sum());
      previous_transformation_ = transformation_;
    }
    else
      PCL_DEBUG("[pcl::%s::computeTransformation] Convergence failed\n",
                getClassName().c_str());
  }
  final_transformation_ = previous_transformation_ * guess;

  // Transform the point cloud
  pcl::transformPointCloud(*input_, output, final_transformation_);
}

template <typename PointSource, typename PointTarget>
void
GeneralizedIterativeClosestPoint<PointSource, PointTarget>::applyState(
    Eigen::Matrix4f& t, const Vector6d& x) const
{
  // Z Y X euler angles convention
  Eigen::Matrix3f R;
  R = Eigen::AngleAxisf(static_cast<float>(x[5]), Eigen::Vector3f::UnitZ()) *
      Eigen::AngleAxisf(static_cast<float>(x[4]), Eigen::Vector3f::UnitY()) *
      Eigen::AngleAxisf(static_cast<float>(x[3]), Eigen::Vector3f::UnitX());
  t.topLeftCorner<3, 3>().matrix() = R * t.topLeftCorner<3, 3>().matrix();
  Eigen::Vector4f T(static_cast<float>(x[0]),
                    static_cast<float>(x[1]),
                    static_cast<float>(x[2]),
                    0.0f);
  t.col(3) += T;
}

} // namespace pcl

#endif // PCL_REGISTRATION_IMPL_GICP_HPP_