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#ifndef PCL_REGISTRATION_SAMPLE_CONSENSUS_PREREJECTIVE_HPP_
#define PCL_REGISTRATION_SAMPLE_CONSENSUS_PREREJECTIVE_HPP_

///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template <typename PointSource, typename PointTarget, typename FeatureT> void 
pcl::SampleConsensusPrerejective<PointSource, PointTarget, FeatureT>::setSourceFeatures (const FeatureCloudConstPtr &features)
{
  if (features == NULL || features->empty ())
  {
    PCL_ERROR ("[pcl::%s::setSourceFeatures] Invalid or empty point cloud dataset given!\n", getClassName ().c_str ());
    return;
  }
  input_features_ = features;
}

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template <typename PointSource, typename PointTarget, typename FeatureT> void 
pcl::SampleConsensusPrerejective<PointSource, PointTarget, FeatureT>::setTargetFeatures (const FeatureCloudConstPtr &features)
{
  if (features == NULL || features->empty ())
  {
    PCL_ERROR ("[pcl::%s::setTargetFeatures] Invalid or empty point cloud dataset given!\n", getClassName ().c_str ());
    return;
  }
  target_features_ = features;
  feature_tree_->setInputCloud (target_features_);
}

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template <typename PointSource, typename PointTarget, typename FeatureT> void 
pcl::SampleConsensusPrerejective<PointSource, PointTarget, FeatureT>::selectSamples (
    const PointCloudSource &cloud, int nr_samples, std::vector<int> &sample_indices)
{
  if (nr_samples > static_cast<int> (cloud.points.size ()))
  {
    PCL_ERROR ("[pcl::%s::selectSamples] ", getClassName ().c_str ());
    PCL_ERROR ("The number of samples (%d) must not be greater than the number of points (%lu)!\n",
               nr_samples, cloud.points.size ());
    return;
  }
  
  sample_indices.resize (nr_samples);
  int temp_sample;

  // Draw random samples until n samples is reached
  for (int i = 0; i < nr_samples; i++)
  {
    // Select a random number
    sample_indices[i] = getRandomIndex (static_cast<int> (cloud.points.size ()) - i);
      
    // Run trough list of numbers, starting at the lowest, to avoid duplicates
    for (int j = 0; j < i; j++)
    {
      // Move value up if it is higher than previous selections to ensure true randomness
      if (sample_indices[i] >= sample_indices[j])
      {
        sample_indices[i]++;
      }
      else
      {
        // The new number is lower, place it at the correct point and break for a sorted list
        temp_sample = sample_indices[i];
        for (int k = i; k > j; k--)
          sample_indices[k] = sample_indices[k - 1];
        
        sample_indices[j] = temp_sample;
        break;
      }
    }
  }
}

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template <typename PointSource, typename PointTarget, typename FeatureT> void 
pcl::SampleConsensusPrerejective<PointSource, PointTarget, FeatureT>::findSimilarFeatures (
        const std::vector<int> &sample_indices,
        std::vector<std::vector<int> >& similar_features,
        std::vector<int> &corresponding_indices)
{
  // Allocate results
  corresponding_indices.resize (sample_indices.size ());
  std::vector<float> nn_distances (k_correspondences_);
  
  // Loop over the sampled features
  for (size_t i = 0; i < sample_indices.size (); ++i)
  {
    // Current feature index
    const int idx = sample_indices[i];
    
    // Find the k nearest feature neighbors to the sampled input feature if they are not in the cache already
    if (similar_features[idx].empty ())
      feature_tree_->nearestKSearch (*input_features_, idx, k_correspondences_, similar_features[idx], nn_distances);

    // Select one at random and add it to corresponding_indices
    if (k_correspondences_ == 1)
      corresponding_indices[i] = similar_features[idx][0];
    else
      corresponding_indices[i] = similar_features[idx][getRandomIndex (k_correspondences_)];
  }
}

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template <typename PointSource, typename PointTarget, typename FeatureT> void 
pcl::SampleConsensusPrerejective<PointSource, PointTarget, FeatureT>::computeTransformation (PointCloudSource &output, const Eigen::Matrix4f& guess)
{
  // Some sanity checks first
  if (!input_features_)
  {
    PCL_ERROR ("[pcl::%s::computeTransformation] ", getClassName ().c_str ());
    PCL_ERROR ("No source features were given! Call setSourceFeatures before aligning.\n");
    return;
  }
  if (!target_features_)
  {
    PCL_ERROR ("[pcl::%s::computeTransformation] ", getClassName ().c_str ());
    PCL_ERROR ("No target features were given! Call setTargetFeatures before aligning.\n");
    return;
  }

  if (input_->size () != input_features_->size ())
  {
    PCL_ERROR ("[pcl::%s::computeTransformation] ", getClassName ().c_str ());
    PCL_ERROR ("The source points and source feature points need to be in a one-to-one relationship! Current input cloud sizes: %ld vs %ld.\n",
               input_->size (), input_features_->size ());
    return;
  }

  if (target_->size () != target_features_->size ())
  {
    PCL_ERROR ("[pcl::%s::computeTransformation] ", getClassName ().c_str ());
    PCL_ERROR ("The target points and target feature points need to be in a one-to-one relationship! Current input cloud sizes: %ld vs %ld.\n",
               target_->size (), target_features_->size ());
    return;
  }

  if (inlier_fraction_ < 0.0f || inlier_fraction_ > 1.0f)
  {
    PCL_ERROR ("[pcl::%s::computeTransformation] ", getClassName ().c_str ());
    PCL_ERROR ("Illegal inlier fraction %f, must be in [0,1]!\n",
               inlier_fraction_);
    return;
  }
  
  const float similarity_threshold = correspondence_rejector_poly_->getSimilarityThreshold ();
  if (similarity_threshold < 0.0f || similarity_threshold >= 1.0f)
  {
    PCL_ERROR ("[pcl::%s::computeTransformation] ", getClassName ().c_str ());
    PCL_ERROR ("Illegal prerejection similarity threshold %f, must be in [0,1[!\n",
               similarity_threshold);
    return;
  }
  
  if (k_correspondences_ <= 0)
  {
    PCL_ERROR ("[pcl::%s::computeTransformation] ", getClassName ().c_str ());
    PCL_ERROR ("Illegal correspondence randomness %d, must be > 0!\n",
            k_correspondences_);
    return;
  }
  
  // Initialize prerejector (similarity threshold already set to default value in constructor)
  correspondence_rejector_poly_->setInputSource (input_);
  correspondence_rejector_poly_->setInputTarget (target_);
  correspondence_rejector_poly_->setCardinality (nr_samples_);
  int num_rejections = 0; // For debugging
  
  // Initialize results
  final_transformation_ = guess;
  inliers_.clear ();
  float lowest_error = std::numeric_limits<float>::max ();
  converged_ = false;
  
  // Temporaries
  std::vector<int> inliers;
  float inlier_fraction;
  float error;
  
  // If guess is not the Identity matrix we check it
  if (!guess.isApprox (Eigen::Matrix4f::Identity (), 0.01f))
  {
    getFitness (inliers, error);
    inlier_fraction = static_cast<float> (inliers.size ()) / static_cast<float> (input_->size ());
    
    if (inlier_fraction >= inlier_fraction_ && error < lowest_error)
    {
      inliers_ = inliers;
      lowest_error = error;
      converged_ = true;
    }
  }
  
  // Feature correspondence cache
  std::vector<std::vector<int> > similar_features (input_->size ());
  
  // Start
  for (int i = 0; i < max_iterations_; ++i)
  {
    // Temporary containers
    std::vector<int> sample_indices;
    std::vector<int> corresponding_indices;
    
    // Draw nr_samples_ random samples
    selectSamples (*input_, nr_samples_, sample_indices);
    
    // Find corresponding features in the target cloud
    findSimilarFeatures (sample_indices, similar_features, corresponding_indices);
    
    // Apply prerejection
    if (!correspondence_rejector_poly_->thresholdPolygon (sample_indices, corresponding_indices))
    {
      ++num_rejections;
      continue;
    }

    // Estimate the transform from the correspondences, write to transformation_
    transformation_estimation_->estimateRigidTransformation (*input_, sample_indices, *target_, corresponding_indices, transformation_);
    
    // Take a backup of previous result
    const Matrix4 final_transformation_prev = final_transformation_;
    
    // Set final result to current transformation
    final_transformation_ = transformation_;
    
    // Transform the input and compute the error (uses input_ and final_transformation_)
    getFitness (inliers, error);
    
    // Restore previous result
    final_transformation_ = final_transformation_prev;

    // If the new fit is better, update results
    inlier_fraction = static_cast<float> (inliers.size ()) / static_cast<float> (input_->size ());

    // Update result if pose hypothesis is better
    if (inlier_fraction >= inlier_fraction_ && error < lowest_error)
    {
      inliers_ = inliers;
      lowest_error = error;
      converged_ = true;
      final_transformation_ = transformation_;
    }
  }

  // Apply the final transformation
  if (converged_)
    transformPointCloud (*input_, output, final_transformation_);
  
  // Debug output
  PCL_DEBUG("[pcl::%s::computeTransformation] Rejected %i out of %i generated pose hypotheses.\n",
            getClassName ().c_str (), num_rejections, max_iterations_);
}

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
template <typename PointSource, typename PointTarget, typename FeatureT> void 
pcl::SampleConsensusPrerejective<PointSource, PointTarget, FeatureT>::getFitness (std::vector<int>& inliers, float& fitness_score)
{
  // Initialize variables
  inliers.clear ();
  inliers.reserve (input_->size ());
  fitness_score = 0.0f;
  
  // Use squared distance for comparison with NN search results
  const float max_range = corr_dist_threshold_ * corr_dist_threshold_;

  // Transform the input dataset using the final transformation
  PointCloudSource input_transformed;
  input_transformed.resize (input_->size ());
  transformPointCloud (*input_, input_transformed, final_transformation_);
  
  // For each point in the source dataset
  for (size_t i = 0; i < input_transformed.points.size (); ++i)
  {
    // Find its nearest neighbor in the target
    std::vector<int> nn_indices (1);
    std::vector<float> nn_dists (1);
    tree_->nearestKSearch (input_transformed.points[i], 1, nn_indices, nn_dists);
    
    // Check if point is an inlier
    if (nn_dists[0] < max_range)
    {
      // Update inliers
      inliers.push_back (static_cast<int> (i));
      
      // Update fitness score
      fitness_score += nn_dists[0];
    }
  }

  // Calculate MSE
  if (inliers.size () > 0)
    fitness_score /= static_cast<float> (inliers.size ());
  else
    fitness_score = std::numeric_limits<float>::max ();
}

#endif

