mitkConnectomicsNetworkCreator.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 mitkConnectomicsNetworkCreator_h
#define mitkConnectomicsNetworkCreator_h

#include <itkObject.h>
#include <itkObjectFactory.h>
#include <itkMacro.h>

#include "mitkCommon.h"
#include "mitkImage.h"

#include "mitkFiberBundle.h"
#include "mitkConnectomicsNetwork.h"

#include <MitkConnectomicsExports.h>

namespace mitk
{

  class MITKCONNECTOMICS_EXPORT ConnectomicsNetworkCreator : public itk::Object
  {
  public:

    enum MappingStrategy
    {
      EndElementPosition,
      EndElementPositionAvoidingWhiteMatter,
      JustEndPointVerticesNoLabel,
      PrecomputeAndDistance
    };

    mitkClassMacroItkParent(ConnectomicsNetworkCreator, itk::Object);
    itkFactorylessNewMacro(Self)
    itkCloneMacro(Self)


    typedef itk::Image<int, 3 > ITKImageType;

    typedef itk::Point<float,3>                                          PointType;
    typedef itk::VectorContainer<unsigned int, PointType>                TractType;
    typedef itk::VectorContainer< unsigned int, TractType::Pointer >     TractContainerType; //init via smartpointer


    typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexType;
    typedef mitk::ConnectomicsNetwork::EdgeDescriptorType EdgeType;
    typedef mitk::ConnectomicsNetwork::NetworkNode NetworkNode;
    typedef std::pair< VertexType, VertexType >       ConnectionType;

    typedef int                                             ImageLabelType;
    typedef std::pair< ImageLabelType, ImageLabelType >     ImageLabelPairType;

    void CreateNetworkFromFibersAndSegmentation();
    void SetFiberBundle(mitk::FiberBundle::Pointer fiberBundle);
    void SetSegmentation(mitk::Image::Pointer segmentation);

    mitk::ConnectomicsNetwork::Pointer GetNetwork();

    itkSetMacro(MappingStrategy, MappingStrategy);
    itkSetMacro(EndPointSearchRadius, double);
    itkSetMacro(ZeroLabelInvalid, bool);

    void CalculateCenterOfMass();

  protected:

    ConnectomicsNetworkCreator();
    ConnectomicsNetworkCreator( mitk::Image::Pointer segmentation, mitk::FiberBundle::Pointer fiberBundle );
    ~ConnectomicsNetworkCreator();

    void AddConnectionToNetwork(ConnectionType newConnection);

    VertexType ReturnAssociatedVertexForLabel( ImageLabelType label );

    ConnectionType ReturnAssociatedVertexPairForLabelPair( ImageLabelPairType labelpair );

    ImageLabelPairType ReturnLabelForFiberTract( TractType::Pointer singleTract, MappingStrategy strategy );

    void SupplyVertexWithInformation( ImageLabelType& label, VertexType& vertex );

    std::string LabelToString( ImageLabelType& label );

    bool IsNonWhiteMatterLabel( int labelInQuestion );

    bool IsBackgroundLabel( int labelInQuestion );

    void LinearExtensionUntilGreyMatter( std::vector<int> & indexVectorOfPointsToUse, TractType::Pointer singleTract,
      int & label, itk::Index<3> & mitkIndex );

    void RetractionUntilBrainMatter( bool retractFront, TractType::Pointer singleTract,
      int & label, itk::Index<3> & mitkIndex );

    std::vector< double > GetCenterOfMass( int label );

    itk::Point<float, 3> GetItkPoint(double point[3]);

    void CreateNewNode( int label, itk::Index<3>, bool useIndex );


    ImageLabelPairType EndElementPositionLabel( TractType::Pointer singleTract );

    ImageLabelPairType PrecomputeVertexLocationsBySegmentation( TractType::Pointer singleTract );

    ImageLabelPairType JustEndPointVerticesNoLabelTest( TractType::Pointer singleTract );

    ImageLabelPairType EndElementPositionLabelAvoidingWhiteMatter( TractType::Pointer singleTract );


    void FiberToSegmentationCoords( mitk::Point3D& fiberCoord, mitk::Point3D& segCoord );
    void SegmentationToFiberCoords( mitk::Point3D& segCoord, mitk::Point3D& fiberCoord );

    mitk::FiberBundle::Pointer m_FiberBundle;
    mitk::Image::Pointer m_Segmentation;
    ITKImageType::Pointer m_SegmentationItk;

    // the graph itself
    mitk::ConnectomicsNetwork::Pointer m_ConNetwork;

    // the id counter
    int idCounter;

    // the map mapping labels to vertices
    std::map< ImageLabelType, VertexType > m_LabelToVertexMap;

    // mapping labels to additional information
    std::map< ImageLabelType, NetworkNode > m_LabelToNodePropertyMap;

    // toggles whether edges between a node and itself can exist
    bool allowLoops;

    // toggles whether to use the center of mass coordinates
    bool m_UseCoMCoordinates;

    // stores the coordinates of labels
    std::map< int, std::vector< double> > m_LabelsToCoordinatesMap;

    // the straty to use for mapping
    MappingStrategy m_MappingStrategy;

    // search radius for finding a non white matter/background area. Should be in mm
    double m_EndPointSearchRadius;

    // toggles whether a node with the label 0 may be present
    bool m_ZeroLabelInvalid;

    // used internally to communicate a connection should not be added if the a problem
    // is encountered while adding it
    bool m_AbortConnection;


    // These IDs are the freesurfer ids used in parcellation

    static const int freesurfer_Left_Cerebral_White_Matter = 2;
    static const int freesurfer_Left_Cerebellum_White_Matter = 7;
    static const int freesurfer_Left_Cerebellum_Cortex = 8;
    static const int freesurfer_Brain_Stem = 16;
    static const int freesurfer_Right_Cerebral_White_Matter = 41;
    static const int freesurfer_Right_Cerebellum_White_Matter = 46;
    static const int freesurfer_Right_Cerebellum_Cortex = 47;


  };

}// end namespace mitk

#endif // _mitkConnectomicsNetworkCreator_H_INCLUDED