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 * Author : jpapon@gmail.com
 * Email  : jpapon@gmail.com
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#ifndef PCL_SEGMENTATION_SUPERVOXEL_CLUSTERING_H_
#define PCL_SEGMENTATION_SUPERVOXEL_CLUSTERING_H_

#include <pcl/features/normal_3d.h>
#include <pcl/pcl_base.h>
#include <pcl/point_cloud.h>
#include <pcl/point_types.h>
#include <pcl/octree/octree.h>
#include <pcl/octree/octree_pointcloud_adjacency.h>
#include <pcl/search/search.h>
#include <pcl/segmentation/boost.h>



//DEBUG TODO REMOVE
#include <pcl/common/time.h>


namespace pcl
{
  /** \brief Supervoxel container class - stores a cluster extracted using supervoxel clustering 
   */
  template <typename PointT>
  class Supervoxel
  {
    public:
      Supervoxel () :
        voxels_ (new pcl::PointCloud<PointT> ()),
        normals_ (new pcl::PointCloud<Normal> ())
        {  } 
      
      typedef boost::shared_ptr<Supervoxel<PointT> > Ptr;
      typedef boost::shared_ptr<const Supervoxel<PointT> > ConstPtr;

      /** \brief Gets the centroid of the supervoxel
       *  \param[out] centroid_arg centroid of the supervoxel
       */ 
      void
      getCentroidPoint (PointXYZRGBA &centroid_arg)
      {
        centroid_arg = centroid_;
      }
      
      /** \brief Gets the point normal for the supervoxel 
       * \param[out] normal_arg Point normal of the supervoxel
       * \note This isn't an average, it is a normal computed using all of the voxels in the supervoxel as support
       */ 
      void
      getCentroidPointNormal (PointNormal &normal_arg)
      {
        normal_arg.x = centroid_.x;
        normal_arg.y = centroid_.y;
        normal_arg.z = centroid_.z;
        normal_arg.normal_x = normal_.normal_x;
        normal_arg.normal_y = normal_.normal_y;
        normal_arg.normal_z = normal_.normal_z;
        normal_arg.curvature = normal_.curvature;
      }
      
      /** \brief The normal calculated for the voxels contained in the supervoxel */
      pcl::Normal normal_;
      /** \brief The centroid of the supervoxel - average voxel */
      pcl::PointXYZRGBA centroid_;
      /** \brief A Pointcloud of the voxels in the supervoxel */
      typename pcl::PointCloud<PointT>::Ptr voxels_;
      /** \brief A Pointcloud of the normals for the points in the supervoxel */
      typename pcl::PointCloud<Normal>::Ptr normals_;
                
    public:
      EIGEN_MAKE_ALIGNED_OPERATOR_NEW  
  };
  
  /** \brief Implements a supervoxel algorithm based on voxel structure, normals, and rgb values
   *   \note Supervoxels are oversegmented volumetric patches (usually surfaces) 
   *   \note Usually, color isn't needed (and can be detrimental)- spatial structure is mainly used
    * - J. Papon, A. Abramov, M. Schoeler, F. Woergoetter
    *   Voxel Cloud Connectivity Segmentation - Supervoxels from PointClouds
    *   In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 2013 
    *  \author Jeremie Papon (jpapon@gmail.com)
    */
  template <typename PointT>
  class PCL_EXPORTS SupervoxelClustering : public pcl::PCLBase<PointT>
  {
    //Forward declaration of friended helper class
    class SupervoxelHelper;
    friend class SupervoxelHelper;
    public:
      /** \brief VoxelData is a structure used for storing data within a pcl::octree::OctreePointCloudAdjacencyContainer
       *  \note It stores xyz, rgb, normal, distance, an index, and an owner.
       */
      class VoxelData
      {
        public:
          VoxelData ():
            xyz_ (0.0f, 0.0f, 0.0f),
            rgb_ (0.0f, 0.0f, 0.0f),
            normal_ (0.0f, 0.0f, 0.0f, 0.0f),
            curvature_ (0.0f),
            owner_ (0)
            {}
            
          /** \brief Gets the data of in the form of a point
           *  \param[out] point_arg Will contain the point value of the voxeldata
           */  
          void
          getPoint (PointT &point_arg) const;
          
          /** \brief Gets the data of in the form of a normal
           *  \param[out] normal_arg Will contain the normal value of the voxeldata
           */            
          void
          getNormal (Normal &normal_arg) const;
          
          Eigen::Vector3f xyz_;
          Eigen::Vector3f rgb_;
          Eigen::Vector4f normal_;
          float curvature_;
          float distance_;
          int idx_;
          SupervoxelHelper* owner_;
          
        public:
          EIGEN_MAKE_ALIGNED_OPERATOR_NEW
      };
      
      typedef pcl::octree::OctreePointCloudAdjacencyContainer<PointT, VoxelData> LeafContainerT;
      typedef std::vector <LeafContainerT*> LeafVectorT;
      
      typedef typename pcl::PointCloud<PointT> PointCloudT;
      typedef typename pcl::PointCloud<Normal> NormalCloudT;
      typedef typename pcl::octree::OctreePointCloudAdjacency<PointT, LeafContainerT> OctreeAdjacencyT;
      typedef typename pcl::octree::OctreePointCloudSearch <PointT> OctreeSearchT;
      typedef typename pcl::search::KdTree<PointT> KdTreeT;
      typedef boost::shared_ptr<std::vector<int> > IndicesPtr;
           
      using PCLBase <PointT>::initCompute;
      using PCLBase <PointT>::deinitCompute;
      using PCLBase <PointT>::input_;
      
      typedef boost::adjacency_list<boost::setS, boost::setS, boost::undirectedS, uint32_t, float> VoxelAdjacencyList;
      typedef VoxelAdjacencyList::vertex_descriptor VoxelID;
      typedef VoxelAdjacencyList::edge_descriptor EdgeID;
      
      
    public:

      /** \brief Constructor that sets default values for member variables. 
       *  \param[in] voxel_resolution The resolution (in meters) of voxels used
       *  \param[in] seed_resolution The average size (in meters) of resulting supervoxels
       *  \param[in] use_single_camera_transform Set to true if point density in cloud falls off with distance from origin (such as with a cloud coming from one stationary camera), set false if input cloud is from multiple captures from multiple locations.
       */
      SupervoxelClustering (float voxel_resolution, float seed_resolution, bool use_single_camera_transform = true);

      /** \brief This destructor destroys the cloud, normals and search method used for
        * finding neighbors. In other words it frees memory.
        */
      virtual
      ~SupervoxelClustering ();

      /** \brief Set the resolution of the octree voxels */
      void
      setVoxelResolution (float resolution);
      
      /** \brief Get the resolution of the octree voxels */
      float 
      getVoxelResolution () const;
      
      /** \brief Set the resolution of the octree seed voxels */
      void
      setSeedResolution (float seed_resolution);
      
      /** \brief Get the resolution of the octree seed voxels */
      float 
      getSeedResolution () const;
        
      /** \brief Set the importance of color for supervoxels */
      void
      setColorImportance (float val);
      
      /** \brief Set the importance of spatial distance for supervoxels */
      void
      setSpatialImportance (float val);
            
      /** \brief Set the importance of scalar normal product for supervoxels */
      void
      setNormalImportance (float val);
      
      /** \brief This method launches the segmentation algorithm and returns the supervoxels that were
       * obtained during the segmentation.
       * \param[out] supervoxel_clusters A map of labels to pointers to supervoxel structures
       */
      virtual void
      extract (std::map<uint32_t,typename Supervoxel<PointT>::Ptr > &supervoxel_clusters);

      /** \brief This method sets the cloud to be supervoxelized
       * \param[in] cloud The cloud to be supervoxelize
       */
      virtual void
      setInputCloud (typename pcl::PointCloud<PointT>::ConstPtr cloud);
      
      /** \brief This method sets the normals to be used for supervoxels (should be same size as input cloud)
      * \param[in] cloud The input normals                         
      */
      virtual void
      setNormalCloud (typename NormalCloudT::ConstPtr normal_cloud);
      
      /** \brief This method refines the calculated supervoxels - may only be called after extract
       * \param[in] num_itr The number of iterations of refinement to be done (2 or 3 is usually sufficient)
       * \param[out] supervoxel_clusters The resulting refined supervoxels
       */
      virtual void
      refineSupervoxels (int num_itr, std::map<uint32_t,typename Supervoxel<PointT>::Ptr > &supervoxel_clusters);
      
      ////////////////////////////////////////////////////////////
      /** \brief Returns an RGB colorized cloud showing superpixels
        * Otherwise it returns an empty pointer.
        * Points that belong to the same supervoxel have the same color.
        * But this function doesn't guarantee that different segments will have different
        * color(it's random). Points that are unlabeled will be black
        * \note This will expand the label_colors_ vector so that it can accomodate all labels
        */
      typename pcl::PointCloud<PointXYZRGBA>::Ptr
      getColoredCloud () const;
      
      /** \brief Returns a deep copy of the voxel centroid cloud */
      typename pcl::PointCloud<PointT>::Ptr
      getVoxelCentroidCloud () const;
      
      /** \brief Returns labeled cloud
        * Points that belong to the same supervoxel have the same label.
        * Labels for segments start from 1, unlabled points have label 0
        */
      typename pcl::PointCloud<PointXYZL>::Ptr
      getLabeledCloud () const;
      
      /** \brief Returns an RGB colorized voxelized cloud showing superpixels
       * Otherwise it returns an empty pointer.
       * Points that belong to the same supervoxel have the same color.
       * But this function doesn't guarantee that different segments will have different
       * color(it's random). Points that are unlabeled will be black
       * \note This will expand the label_colors_ vector so that it can accomodate all labels
       */
      pcl::PointCloud<pcl::PointXYZRGBA>::Ptr
      getColoredVoxelCloud () const;
      
      /** \brief Returns labeled voxelized cloud
       * Points that belong to the same supervoxel have the same label.
       * Labels for segments start from 1, unlabled points have label 0
       */      
      pcl::PointCloud<pcl::PointXYZL>::Ptr
      getLabeledVoxelCloud () const;

      /** \brief Gets the adjacency list (Boost Graph library) which gives connections between supervoxels
       *  \param[out] adjacency_list_arg BGL graph where supervoxel labels are vertices, edges are touching relationships
       */
      void
      getSupervoxelAdjacencyList (VoxelAdjacencyList &adjacency_list_arg) const;
      
      /** \brief Get a multimap which gives supervoxel adjacency
       *  \param[out] label_adjacency Multi-Map which maps a supervoxel label to all adjacent supervoxel labels
       */
      void 
      getSupervoxelAdjacency (std::multimap<uint32_t, uint32_t> &label_adjacency) const;
            
      /** \brief Static helper function which returns a pointcloud of normals for the input supervoxels 
       *  \param[in] supervoxel_clusters Supervoxel cluster map coming from this class
       *  \returns Cloud of PointNormals of the supervoxels
       * 
       */
      static pcl::PointCloud<pcl::PointNormal>::Ptr
      makeSupervoxelNormalCloud (std::map<uint32_t,typename Supervoxel<PointT>::Ptr > &supervoxel_clusters);
      
      /** \brief Returns the current maximum (highest) label */
      int
      getMaxLabel () const;
      
    private:
      
      /** \brief This method initializes the label_colors_ vector (assigns random colors to labels)
       * \note Checks to see if it is already big enough - if so, does not reinitialize it
       */
      void
      initializeLabelColors ();
      
      /** \brief This method simply checks if it is possible to execute the segmentation algorithm with
        * the current settings. If it is possible then it returns true.
        */
      virtual bool
      prepareForSegmentation ();

      /** \brief This selects points to use as initial supervoxel centroids
       *  \param[out] seed_points The selected points
       */
      void
      selectInitialSupervoxelSeeds (std::vector<PointT, Eigen::aligned_allocator<PointT> > &seed_points);
      
      /** \brief This method creates the internal supervoxel helpers based on the provided seed points
       *  \param[in] seed_points The selected points
       */
      void
      createSupervoxelHelpers (std::vector<PointT, Eigen::aligned_allocator<PointT> > &seed_points);
      
      /** \brief This performs the superpixel evolution */
      void
      expandSupervoxels (int depth);

      /** \brief This sets the data of the voxels in the tree */
      void 
      computeVoxelData ();
     
      /** \brief Reseeds the supervoxels by finding the voxel closest to current centroid */
      void
      reseedSupervoxels ();
      
      /** \brief Constructs the map of supervoxel clusters from the internal supervoxel helpers */
      void
      makeSupervoxels (std::map<uint32_t,typename Supervoxel<PointT>::Ptr > &supervoxel_clusters);
      
      /** \brief Stores the resolution used in the octree */
      float resolution_;
    
      /** \brief Stores the resolution used to seed the superpixels */
      float seed_resolution_;
      
      /** \brief Distance function used for comparing voxelDatas */
      float
      voxelDataDistance (const VoxelData &v1, const VoxelData &v2) const;
      
      /** \brief Transform function used to normalize voxel density versus distance from camera */
      void
      transformFunction (PointT &p);
      
      /** \brief Contains a KDtree for the voxelized cloud */
      typename pcl::search::KdTree<PointT>::Ptr voxel_kdtree_;
      
      /** \brief Octree Adjacency structure with leaves at voxel resolution */
      typename OctreeAdjacencyT::Ptr adjacency_octree_;
      
      /** \brief Contains the Voxelized centroid Cloud */
      typename PointCloudT::Ptr voxel_centroid_cloud_;
      
      /** \brief Contains the Voxelized centroid Cloud */
      typename NormalCloudT::ConstPtr input_normals_;
      
      /** \brief Importance of color in clustering */
      float color_importance_;
      /** \brief Importance of distance from seed center in clustering */
      float spatial_importance_;
      /** \brief Importance of similarity in normals for clustering */
      float normal_importance_;
      
      /** \brief Stores the colors used for the superpixel labels*/
      std::vector<uint32_t> label_colors_;
      
      /** \brief Internal storage class for supervoxels 
       * \note Stores pointers to leaves of clustering internal octree, 
       * \note so should not be used outside of clustering class 
       */
      class SupervoxelHelper
      {
        public:
          SupervoxelHelper (uint32_t label, SupervoxelClustering* parent_arg):
            label_ (label),
            parent_ (parent_arg)
          { }
          
          void
          addLeaf (LeafContainerT* leaf_arg);
        
          void
          removeLeaf (LeafContainerT* leaf_arg);
        
          void
          removeAllLeaves ();
          
          void 
          expand ();
          
          void 
          refineNormals ();
          
          void 
          updateCentroid ();
          
          void 
          getVoxels (typename pcl::PointCloud<PointT>::Ptr &voxels) const;
          
          void 
          getNormals (typename pcl::PointCloud<Normal>::Ptr &normals) const;
          
          typedef float (SupervoxelClustering::*DistFuncPtr)(const VoxelData &v1, const VoxelData &v2);
          
          uint32_t
          getLabel () const 
          { return label_; }
          
          Eigen::Vector4f 
          getNormal () const 
          { return centroid_.normal_; }
          
          Eigen::Vector3f 
          getRGB () const 
          { return centroid_.rgb_; }
          
          Eigen::Vector3f
          getXYZ () const 
          { return centroid_.xyz_;}
          
          void
          getXYZ (float &x, float &y, float &z) const
          { x=centroid_.xyz_[0]; y=centroid_.xyz_[1]; z=centroid_.xyz_[2]; }
          
          void
          getRGB (uint32_t &rgba) const
          { 
            rgba = static_cast<uint32_t>(centroid_.rgb_[0]) << 16 | 
                   static_cast<uint32_t>(centroid_.rgb_[1]) << 8 | 
                   static_cast<uint32_t>(centroid_.rgb_[2]); 
          }
          
          void 
          getNormal (pcl::Normal &normal_arg) const 
          { 
            normal_arg.normal_x = centroid_.normal_[0];
            normal_arg.normal_y = centroid_.normal_[1];
            normal_arg.normal_z = centroid_.normal_[2];
            normal_arg.curvature = centroid_.curvature_;
          }
          
          void
          getNeighborLabels (std::set<uint32_t> &neighbor_labels) const;
          
          VoxelData
          getCentroid () const
          { return centroid_; }
            
          
          size_t
          size () const { return leaves_.size (); }
      private:
          //Stores leaves
          std::set<LeafContainerT*> leaves_;
          uint32_t label_;
          VoxelData centroid_;
          SupervoxelClustering* parent_;
          

      };
      
      typedef boost::ptr_list<SupervoxelHelper> HelperListT;
      HelperListT supervoxel_helpers_;
      
      //TODO DEBUG REMOVE
      StopWatch timer_;
    public:
      EIGEN_MAKE_ALIGNED_OPERATOR_NEW
      
     

  };

}

#ifdef PCL_NO_PRECOMPILE
#include <pcl/segmentation/impl/supervoxel_clustering.hpp>
#endif

#endif
