itkGibbsTrackingFilter.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 itkGibbsTrackingFilter_h
#define itkGibbsTrackingFilter_h

// MITK
#include <mitkSphereInterpolator.h>

// ITK
#include <itkProcessObject.h>
#include <itkImage.h>
#include <itkDiffusionTensor3D.h>
#include <itkMersenneTwisterRandomVariateGenerator.h>

// VTK
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkCellArray.h>
#include <vtkPoints.h>
#include <vtkPolyLine.h>

namespace itk{

template< class ItkQBallImageType >
class GibbsTrackingFilter : public ProcessObject
{
public:
    typedef GibbsTrackingFilter Self;
    typedef ProcessObject Superclass;
    typedef SmartPointer< Self > Pointer;
    typedef SmartPointer< const Self > ConstPointer;

    itkFactorylessNewMacro(Self)
    itkCloneMacro(Self)
    itkTypeMacro( GibbsTrackingFilter, ProcessObject )

    typedef Image< DiffusionTensor3D<float>, 3 >    ItkTensorImage;
    typedef typename ItkQBallImageType::Pointer     ItkQBallImageTypePointer;
    typedef Image< float, 3 >                       ItkFloatImageType;
    typedef vtkSmartPointer< vtkPolyData >          FiberPolyDataType;

    itkSetMacro( StartTemperature, float )          
    itkSetMacro( EndTemperature, float )            
    itkSetMacro( Iterations, double )        
    itkSetMacro( ParticleWeight, float )            
    itkSetMacro( ParticleWidth, float )             
    itkSetMacro( ParticleLength, float )
    itkSetMacro( ConnectionPotential, float )
    itkSetMacro( InexBalance, float )               
    itkSetMacro( ParticlePotential, float )
    itkSetMacro( MinFiberLength, int )              
    itkSetMacro( AbortTracking, bool )              
    itkSetMacro( CurvatureThreshold, float)         
    itkSetMacro( DuplicateImage, bool )             
    itkSetMacro( RandomSeed, int )                  
    itkSetMacro( LoadParameterFile, std::string )   
    itkSetMacro( SaveParameterFile, std::string )
    itkSetMacro( LutPath, std::string )             

    itkGetMacro( ParticleWeight, float )
    itkGetMacro( ParticleWidth, float )
    itkGetMacro( ParticleLength, float )
    itkGetMacro( NumParticles, int )
    itkGetMacro( NumConnections, int )
    itkGetMacro( NumAcceptedFibers, int )
    itkGetMacro( ProposalAcceptance, float )
    itkGetMacro( CurrentIteration, double)
    itkGetMacro( Iterations, double)
    itkGetMacro( IsInValidState, bool)
    FiberPolyDataType GetFiberBundle();             

    itkSetMacro(QBallImage, typename ItkQBallImageType::Pointer)
    itkSetMacro(MaskImage, ItkFloatImageType::Pointer)
    itkSetMacro(TensorImage, ItkTensorImage::Pointer)

    virtual void Update() override{
        this->GenerateData();
    }

protected:

    void GenerateData() override;

    GibbsTrackingFilter();
    virtual ~GibbsTrackingFilter();
    void EstimateParticleWeight();
    void PrepareMaskImage();
    bool LoadParameters();
    bool SaveParameters();

    // Input Images
    typename ItkQBallImageType::Pointer m_QBallImage;
    typename ItkFloatImageType::Pointer m_MaskImage;
    typename ItkTensorImage::Pointer    m_TensorImage;

    // Tracking parameters
    float           m_StartTemperature;     
    float           m_EndTemperature;       
    double          m_Iterations;           
    double          m_CurrentIteration;     
    unsigned long   m_CurrentStep;          
    float           m_ParticleWeight;       
    float           m_ParticleWidth;        
    float           m_ParticleLength;       
    float           m_ConnectionPotential;  
    float           m_InexBalance;          
    float           m_ParticlePotential;    
    int             m_MinFiberLength;       
    bool            m_AbortTracking;        
    int             m_NumAcceptedFibers;    
    volatile bool   m_BuildFibers;          
    float           m_ProposalAcceptance;   
    float           m_CurvatureThreshold;   
    bool            m_DuplicateImage;       
    int             m_NumParticles;         
    int             m_NumConnections;       
    int             m_RandomSeed;           
    std::string     m_LoadParameterFile;    
    std::string     m_SaveParameterFile;    
    std::string     m_LutPath;              
    bool            m_IsInValidState;       

    FiberPolyDataType m_FiberPolyData;      

    //Constant values
    static const int m_ParticleGridCellCapacity = 1024;
};
}

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkGibbsTrackingFilter.cpp"
#endif

#endif