WHierarchicalTreeFibers.h

//---------------------------------------------------------------------------
//
// Project: OpenWalnut ( http://www.openwalnut.org )
//
// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
// For more information see http://www.openwalnut.org/copying
//
// This file is part of OpenWalnut.
//
// OpenWalnut is free software: you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// OpenWalnut is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
//
//---------------------------------------------------------------------------
 
#ifndef WHIERARCHICALTREEFIBERS_H
#define WHIERARCHICALTREEFIBERS_H
 
#include <list>
#include <memory>
#include <queue>
#include <utility>
#include <vector>
 
 
#include "WColor.h"
#include "WHierarchicalTree.h"
 
 
/**
 * Class implements a hierarchical tree and provides helper functions for selection and navigation
 */
class WHierarchicalTreeFibers : public WHierarchicalTree
{
public:
    /**
     * standard constructor
     */
    WHierarchicalTreeFibers();
 
    /**
     * destructor
     */
    ~WHierarchicalTreeFibers();
 
    /**
     * A leaf is at the very bottom of the tree, it represents a single fiber or voxel, for several purposes
     * a leaf also counts as a cluster
     */
    void addLeaf();
 
    /**
     * adds a cluster to the set, it combines 2 already existing clusters
     *
     * \param cluster1 first cluster to add
     * \param cluster2 second cluster to add
     * \param level level of the new cluster
     * \param leafes vector of leafes the new cluster contains
     * \param customData some arbitrary data stored with the cluster
     */
    void addCluster( size_t cluster1, size_t cluster2, size_t level, std::vector<size_t> leafes, float customData );
 
    /**
     * generates a bitfield where for every leaf in the selected cluster the value is true, false otherwise
     *
     * \param cluster
     * \return shared pointer to the bitfield
     */
    std::shared_ptr< std::vector<bool> >getOutputBitfield( size_t cluster );
 
    /**
     * generates a bitfield where for every leaf in the selected cluster the value is true, false otherwise
     *
     * \param clusters
     * \return shared pointer to the bitfield
     */
    std::shared_ptr< std::vector<bool> >getOutputBitfield( std::vector<size_t>clusters );
 
    /**
     * finds clusters that match a given ROI up to a certain percentage
     *
     * \param ratio value of [0,1] of how many leafs have to be in the ROI to activate the cluster
     * \param number number of clusters to select, if more than given number matches the ratio criterion only the
     * biggest clusters are returned
     *
     * \return The indices of the chosen clusters.
     */
    std::vector<size_t> getBestClustersFittingRoi( float ratio = 0.9, size_t number = 1 );
 
    /**
     * calculates the ratio of fibers in the roi for a given cluster
     * \param cluster
     * \return ratio
     */
    float getRatio( size_t cluster );
 
    /**
     * setter
     * \param bitfield
     */
    void setRoiBitField( std::shared_ptr< std::vector<bool> > bitfield );
 
protected:
private:
    /**
     * stores a pointer to the bitfield by the current roi setting
     */
    std::shared_ptr< std::vector<bool> > m_roiSelection;
};
 
 
inline void WHierarchicalTreeFibers::setRoiBitField( std::shared_ptr< std::vector<bool> > bitfield )
{
    m_roiSelection = bitfield;
}
 
#endif  // WHIERARCHICALTREEFIBERS_H