mitkConnectomicsNetwork.h

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/*===================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.

This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.

See LICENSE.txt or http://www.mitk.org for details.

===================================================================*/


#ifndef _MITK_ConnectomicsNetwork_H
#define _MITK_ConnectomicsNetwork_H

#include <MitkConnectomicsExports.h>

#include "mitkBaseData.h"

#ifndef Q_MOC_RUN
#include <boost/graph/adjacency_list.hpp>
#endif

namespace mitk {

  class MITKCONNECTOMICS_EXPORT ConnectomicsNetwork : public BaseData
  {
  public:
    struct NetworkNode
    {
      int id;
      std::string label;
      std::vector< float > coordinates;
    };

    struct NetworkEdge
    {
      int sourceId;
      int targetId;
      int weight; // For now the number of times it was present
      double edge_weight; // For boost, currently set to 1 by default for unweighted calculations
    };

    //typedef boost::adjacency_list< boost::listS, boost::listS, boost::undirectedS, NetworkNode, NetworkEdge > NetworkType;
    typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, NetworkNode, NetworkEdge > NetworkType;
    typedef boost::graph_traits<NetworkType>::vertex_descriptor VertexDescriptorType;
    typedef boost::graph_traits<NetworkType>::edge_descriptor EdgeDescriptorType;

    // virtual methods that need to be implemented
    virtual void UpdateOutputInformation() override;
    virtual void SetRequestedRegionToLargestPossibleRegion() override;
    virtual bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
    virtual bool VerifyRequestedRegion() override;
    virtual void SetRequestedRegion(const itk::DataObject * ) override;


    // Macros
    mitkClassMacro( ConnectomicsNetwork, BaseData );
    itkFactorylessNewMacro(Self)
    itkCloneMacro(Self)


    bool EdgeExists( VertexDescriptorType vertexA, VertexDescriptorType vertexB ) const;

    void IncreaseEdgeWeight( VertexDescriptorType vertexA, VertexDescriptorType vertexB );

    void AddEdge( VertexDescriptorType vertexA, VertexDescriptorType vertexB);

    void AddEdge( VertexDescriptorType vertexA, VertexDescriptorType vertexB, int sourceID, int targetID, int weight = 1, double edge_weight = 1.0 );

    VertexDescriptorType AddVertex( int id);

    void SetLabel( VertexDescriptorType vertex, std::string inLabel );

    void SetCoordinates( VertexDescriptorType vertex, std::vector< float > inCoordinates );

    void clear();

    NetworkNode GetNode( VertexDescriptorType vertex ) const;

    NetworkEdge GetEdge( VertexDescriptorType vertexA, VertexDescriptorType vertexB ) const;

    std::vector< NetworkNode > GetVectorOfAllNodes() const;

    std::vector< VertexDescriptorType > GetVectorOfAllVertexDescriptors() const;

    std::vector< VertexDescriptorType > GetVectorOfAdjacentNodes( VertexDescriptorType vertex ) const;

    std::vector< std::pair< std::pair< NetworkNode, NetworkNode > , NetworkEdge > > GetVectorOfAllEdges() const;

    int GetNumberOfVertices() const;

    int GetNumberOfEdges() const;

    int GetNumberOfSelfLoops();

    double GetAverageDegree();

    double GetConnectionDensity();

    int GetMaximumWeight() const;

    std::vector< int > GetDegreeOfNodes( ) const;

    int GetMaximumDegree() const;

    std::vector< double > GetLocalClusteringCoefficients( ) const;

    std::vector< double > GetClusteringCoefficientsByDegree( );

    double GetGlobalClusteringCoefficient( );

    std::vector< double > GetNodeBetweennessVector() const;

    std::vector< double > GetEdgeBetweennessVector() const;

    bool CheckForLabel( std::string targetLabel ) const;

    std::vector< double > GetShortestDistanceVectorFromLabel( std::string targetLabel ) const;

    NetworkType* GetBoostGraph();

    void SetBoostGraph( NetworkType* newGraph );

    void ImportNetwort( mitk::ConnectomicsNetwork::Pointer source );

    bool GetIsModified() const;

    void SetIsModified( bool );

    void UpdateBounds( );

    void PruneUnconnectedSingleNodes();

    void UpdateIDs();

  protected:
    ConnectomicsNetwork();
    virtual ~ConnectomicsNetwork();

    NetworkType m_Network;


    bool m_IsModified;

  private:

  };

  MITKCONNECTOMICS_EXPORT bool Equal( mitk::ConnectomicsNetwork* leftHandSide, mitk::ConnectomicsNetwork* rightHandSide, mitk::ScalarType eps, bool verbose);

} // namespace mitk

#endif /*  _MITK_ConnectomicsNetwork_H */