animaDTIProbabilisticTractographyImageFilter.h

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#pragma once

#include <itkVectorImage.h>
#include <animaBaseProbabilisticTractographyImageFilter.h>

#include <random>

#include "AnimaTractographyExport.h"

namespace anima
{

class ANIMATRACTOGRAPHY_EXPORT DTIProbabilisticTractographyImageFilter : public BaseProbabilisticTractographyImageFilter < itk::VectorImage <double, 3> >
{
public:
    typedef DTIProbabilisticTractographyImageFilter Self;
    typedef BaseProbabilisticTractographyImageFilter < itk::VectorImage <double, 3> > Superclass;

    typedef itk::SmartPointer<Self> Pointer;
    typedef itk::SmartPointer<const Self> ConstPointer;

    itkNewMacro(Self)
    itkTypeMacro(DTIProbabilisticTractographyImageFilter,BaseProbabilisticTractographyImageFilter)

    void SetKappaPolynomialCoefficients(std::vector <double> &coefs);

    itkSetMacro(FAThreshold,double)
    itkSetMacro(ThresholdForProlateTensor,double)

protected:
    DTIProbabilisticTractographyImageFilter();
    virtual ~DTIProbabilisticTractographyImageFilter();

    double GetKappaFromFA(double FA);
    void GetDTIPrincipalDirection(const VectorType &modelValue, Vector3DType &resVec, bool is2d);
    void GetDTIMinorDirection(VectorType &modelValue, Vector3DType &resVec);

    virtual Vector3DType ProposeNewDirection(Vector3DType &oldDirection, VectorType &modelValue,
                                             Vector3DType &sampling_direction, double &log_prior,
                                             double &log_proposal, std::mt19937 &random_generator,
                                             unsigned int threadId) ITK_OVERRIDE;

    virtual double ComputeLogWeightUpdate(double b0Value, double noiseValue, Vector3DType &newDirection, VectorType &modelValue,
                                          double &log_prior, double &log_proposal, unsigned int threadId) ITK_OVERRIDE;

    virtual void ComputeModelValue(InterpolatorPointer &modelInterpolator, ContinuousIndexType &index, VectorType &modelValue) ITK_OVERRIDE;

    virtual Vector3DType InitializeFirstIterationFromModel(Vector3DType &colinearDir,
                                                           VectorType &modelValue, unsigned int threadId) ITK_OVERRIDE;
    virtual bool CheckModelProperties(double estimatedB0Value, double estimatedNoiseValue,
                                      VectorType &modelValue, unsigned int threadId) ITK_OVERRIDE;

    double GetLinearCoefficient(VectorType &modelValue);
    double GetFractionalAnisotropy(VectorType &modelValue);
    void GetEigenValueCombinations(VectorType &modelValue, double &meanLambda, double &perpLambda);

    void ComputeAdditionalScalarMaps() ITK_OVERRIDE;

private:
    ITK_DISALLOW_COPY_AND_ASSIGN(DTIProbabilisticTractographyImageFilter);

    double m_ThresholdForProlateTensor;
    double m_FAThreshold;

    std::vector <double> m_KappaPolynomialCoefficients;
};

} // end of namespace anima