NICE_SemSeg/semseg/SemSegContextTree3D.h

/**
* @file SemSegContextTree3D.h
* @brief Context Trees -> Combination of decision tree and context information
* @author Björn Fröhlich, Sven Sickert
* @date 29.11.2011

*/
#ifndef SemSegContextTree3DINCLUDE
#define SemSegContextTree3DINCLUDE

// nice-core includes
#include <core/vector/VVector.h>

// nice-vislearning includes
#include <vislearning/classifier/fpclassifier/gphik/FPCGPHIK.h>

// nice-segmentation includes
#include <segmentation/RegionSegmentationMethod.h>

// nice-semseg includes
#include "SemanticSegmentation.h"
#include "operations/SimpleOperationPool.h"
#include "operations/RegionOperationPool.h"
#include "operations/RectangleOperationPool.h"

namespace OBJREC
{

/** Localization system */

class SemSegContextTree3D : public SemanticSegmentation
{
private:
  /** Segmentation Method */
  RegionSegmentationMethod *segmentation;

  /** tree -> saved as vector of nodes */
  std::vector<std::vector<TreeNode> > forest;

  /** whether to use a particular feature type or not */
  bool useFeat0, useFeat1, useFeat2, useFeat3, useFeat4;

  /** array of usable feature types*/
  std::vector<int> featTypes;

  /** Number of trees used for the forest */
  int nbTrees;

  /** maximum samples for tree  */
  int maxSamples;

  /** size for neighbourhood */
  int windowSize;

  /** how many feats should be considered for a split */
  int featsPerSplit;

  /** count samples per label */
  //std::map<int, int> labelcounter;

  /** map of labels */
  std::map<int, int> labelmap;

  /** map of labels inverse*/
  std::map<int, int> labelmapback;

  /** scalefactor for balancing for each class */
  std::vector<double> a;

  /** the minimum number of features allowed in a leaf */
  int minFeats;

  /** maximal depth of tree */
  int maxDepth;

  /** current depth for training */
  int depth;

  /** how many splittests */
  int randomTests;

  int labelIncrement;

  /** prototype operations for features */
  std::vector<OperationPool*> ops;

  /** use alternative calculation for information gain */
  bool useShannonEntropy;

  /** Classnames */
  ClassNames classnames;

  /** train selection */
  std::set<int> forbidden_classes;

  /** Configfile */
  const NICE::Config *conf;

  /** use pixelwise labeling or regionlabeling with additional segmenation */
  bool pixelWiseLabeling;

  /** whether to use alternative tristimulus for CIE_Lab that matches openCV or not */
  bool useAltTristimulus;

  /** use Gradient image or not */
  bool useGradient;

  /** use additional input layers or not */
  bool useAdditionalLayer;

  /** how many additional input layers */
  int numAdditionalLayer;

  /** use external image categorization to avoid some classes */
  bool useCategorization;

  /** categorization information for external categorization */
  std::string cndir;

  /** list of channels per feature type */
  std::vector<std::vector<int> > channelsPerType;
  
  /** save / load trained icf classifier */
  bool saveLoadData;

  /** file location of trained icf classifier */
  std::string fileLocation;

  /** first iteration or not */
  bool firstiteration;

  /** amount of grayvalue Channels */
  int rawChannels;

  /** classifier for categorization */
  OBJREC::FPCGPHIK *fasthik;

  /** unique numbers for nodes */
  int uniquenumber;
  
  /**
   * @brief initOperations initialize the operation types
   */
  void initOperations();

  /**
   * @brief updateProbabilityMaps computes probability maps for context features
   * @param nodeIndices matrix with current node for each feature
   * @param feats output MCI3D (must be initilized)
   * @param firstChannel index of the first channel
   */
  void updateProbabilityMaps ( const NICE::MultiChannelImage3DT<unsigned short int> &nodeIndices, NICE::MultiChannelImage3DT<double> &feats, int firstChannel );

  /**
   * @brief computeRayFeatImage computes ray feature images using canny filter
   * @param feats output MCI3D (must be initilized)
   * @param firstChannel index of the first channel
   */
  void computeRayFeatImage ( NICE::MultiChannelImage3DT<double> &feats, int firstChannel );

  /**
   * @brief addFeatureMaps initializes the selected feature channels
   * @param imgData output MCI3D (must be initilized)
   * @param filelist a list of image file names representing slices of a stack
   * @param amountRegions the amount of regions created by the segmentation
   **/
  void addFeatureMaps ( NICE::MultiChannelImage3DT<double> &imgData, const std::vector<std::string> &filelist, int &amountRegions );

  /**
   * @brief compute best split for current settings
   * @param feats features
   * @param nodeIndices matrix with current node for each feature
   * @param labels labels for each feature
   * @param node current node
   * @param splitfeat output selected feature dimension
   * @param splitval output threshold for selected feature
   * @return double best information gain value
   */
  double getBestSplit ( std::vector<NICE::MultiChannelImage3DT<double> > &feats, std::vector<NICE::MultiChannelImage3DT<unsigned short int> > &nodeIndices, const std::vector<NICE::MultiChannelImageT<int> > &labels, int node, Operation3D *&splitop, double &splitval, const int &tree, std::vector<std::vector<std::vector<double> > > &regionProbs );

  /**
   * @brief computes the mean probability for a given class over all trees
   * @param x x position
   * @param y y position
   * @param z z position
   * @param channel current class
   * @param nodeIndices matrix with current node for each feature
   * @return double mean value
   **/
  inline double getMeanProb ( const int &x, const int &y, const int &z, const int &channel, const NICE::MultiChannelImage3DT<unsigned short int> &nodeIndices );

public:
  /** simple constructor */
  SemSegContextTree3D ();

  /** constructor */
  SemSegContextTree3D ( const NICE::Config *conf,
                        const ClassNames *classNames );

  /** simple destructor */
  virtual ~SemSegContextTree3D();

  /**
   * classify each voxel of a 3D image (image stack)
   * @param filelist filename list of images that represent slices of a stack
   * @param segresult segmentation results (output)
   * @param probabilities probabilities for each pixel (output)
   */
  void classify ( const std::vector<std::string> & filelist,
                  NICE::MultiChannelImageT<int> & segresult,
                  NICE::MultiChannelImage3DT<double> & probabilities );

  /**
   * @brief train the actual training method
   * @param trainp pointer to training data
   */
  void train ( const LabeledSet * trainp );

  /**
   * the training method with checking for already existing trained classifier from file
   * @param md training data
   */
  void train ( const MultiDataset *md );

  // deprecated stuff
  void semanticseg ( CachedExample *ce,
                     NICE::ImageT<int> & segresult,
                     NICE::MultiChannelImageT<double> & probabilities )
  {}

  void semanticseg ( CachedExample *ce,
                     NICE::MultiChannelImageT<int> & segresult,
                     NICE::MultiChannelImage3DT<double> & probabilities )
  {}

  void printFeatureStatistics();
  
  bool active3DMode ()
  {
    return run3Dseg;
  }

  /**
   * @brief load all data to is stream
   *
   * @param is input stream
   * @param format has no influence
   * @return void
   **/
  virtual void restore ( std::istream & is, int format = 0 );

  /**
   * @brief save all data to is stream
   *
   * @param os output stream
   * @param format has no influence
   * @return void
   **/
  virtual void store ( std::ostream & os, int format = 0 ) const;

  /**
   * @brief clean up
   *
   * @return void
   **/
  virtual void clear () {}

};

} // namespace

#endif