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/*=========================================================================
Program: Advanced Normalization Tools
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
https://github.com/stnava/ANTs/blob/master/ANTSCopyright.txt for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkPreservationOfPrincipalDirectionTensorReorientationImageFilter_h
#define __itkPreservationOfPrincipalDirectionTensorReorientationImageFilter_h
#include "itkImageToImageFilter.h"
#include "itkVectorInterpolateImageFunction.h"
#include "itkImage.h"
#include "itkMatrix.h"
#include "itkNumericTraits.h"
#include "itkVector.h"
#include "itkSymmetricSecondRankTensor.h"
#include "itkDisplacementFieldTransform.h"
namespace itk
{
/** \class PreservationOfPrincipalDirectionImageFilter
* \brief Applies an averaging filter to an image
*
* Computes an image where a given pixel is the mean value of the
* the pixels in a neighborhood about the corresponding input pixel.
*
* A mean filter is one of the family of linear filters.
*
* \sa Image
* \sa Neighborhood
* \sa NeighborhoodOperator
* \sa NeighborhoodIterator
*
* \ingroup IntensityImageFilters
*/
template <typename TTensorImage, typename TVectorImage>
class PreservationOfPrincipalDirectionTensorReorientationImageFilter final
: public ImageToImageFilter<TTensorImage, TTensorImage>
{
public:
typedef TTensorImage InputImageType;
typedef TTensorImage OutputImageType;
typedef TVectorImage DisplacementFieldType;
typedef typename DisplacementFieldType::Pointer DisplacementFieldPointer;
typedef typename DisplacementFieldType::PixelType VectorType;
typedef typename VectorType::RealValueType RealType;
typedef itk::DisplacementFieldTransform<double, 3> DisplacementFieldTransformType;
typedef typename DisplacementFieldTransformType::Pointer DisplacementFieldTransformPointer;
typedef Matrix<RealType, 3, 3> MatrixType;
// typedef Vector<RealType, 3> VectorType;
typedef VariableSizeMatrix<RealType> VariableMatrixType;
itkStaticConstMacro(ImageDimension, unsigned int, TTensorImage::ImageDimension);
typedef itk::Image<RealType, ImageDimension> RealTypeImageType;
typedef itk::MatrixOffsetTransformBase<RealType, ImageDimension, ImageDimension> AffineTransformType;
typedef typename AffineTransformType::Pointer AffineTransformPointer;
typedef typename AffineTransformType::InputVectorType TransformInputVectorType;
typedef typename AffineTransformType::OutputVectorType TransformOutputVectorType;
typedef typename AffineTransformType::InverseTransformBaseType InverseTransformType;
typedef typename InverseTransformType::Pointer InverseTransformPointer;
// typedef Vector<RealType, 6> TensorType;
// typedef itk::SymmetricSecondRankTensor< RealType, 3 > TensorType;
// typedef Image<TensorType, ImageDimension> TensorImageType;
// typedef typename TensorImageType::Pointer TensorImagePointer;
typedef typename InputImageType::PixelType InputImagePixelType;
typedef InputImagePixelType TensorType;
typedef vnl_matrix<RealType> VnlMatrixType;
typedef vnl_vector<RealType> VnlVectorType;
typedef vnl_vector<RealType> vvec;
/** Standard class typedefs. */
typedef PreservationOfPrincipalDirectionTensorReorientationImageFilter Self;
typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
itkSetMacro(DisplacementField, DisplacementFieldPointer);
itkGetMacro(DisplacementField, DisplacementFieldPointer);
void
SetAffineTransform(AffineTransformPointer aff)
{
this->m_AffineTransform = aff;
this->m_UseAffine = true;
}
itkGetMacro(AffineTransform, AffineTransformPointer);
itkSetMacro(UseImageDirection, bool);
itkGetMacro(UseImageDirection, bool);
/** Run-time type information (and related methods). */
itkTypeMacro(PreservationOfPrincipalDirectionTensorReorientationImageFilter, ImageToImageFilter);
/** Image typedef support. */
typedef typename InputImageType::ConstPointer InputImagePointer;
typedef typename OutputImageType::Pointer OutputImagePointer;
typedef typename InputImageType::PixelType InputPixelType;
typedef typename OutputImageType::PixelType OutputPixelType;
typedef typename InputPixelType::ValueType InputRealType;
typedef typename InputImageType::RegionType InputImageRegionType;
typedef typename OutputImageType::RegionType OutputImageRegionType;
typedef typename InputImageType::SizeType InputSizeType;
typedef typename OutputImageType::SizeType OutputSizeType;
typedef typename InputImageType::IndexType InputIndexType;
typedef typename OutputImageType::IndexType OutputIndexType;
protected:
PreservationOfPrincipalDirectionTensorReorientationImageFilter();
~PreservationOfPrincipalDirectionTensorReorientationImageFilter() override = default;
void
PrintSelf(std::ostream & os, Indent indent) const override;
/** PreservationOfPrincipalDirectionTensorReorientationImageFilter can be implemented as a multithreaded filter.
* Therefore, this implementation provides a ThreadedGenerateData()
* routine which is called for each processing thread. The output
* image data is allocated automatically by the superclass prior to
* calling ThreadedGenerateData(). ThreadedGenerateData can only
* write to the portion of the output image specified by the
* parameter "outputRegionForThread"
*
* \sa ImageToImageFilter::ThreadedGenerateData(),
* ImageToImageFilter::GenerateData() */
void
GenerateData() override;
typename DisplacementFieldType::PixelType
TransformVectorByDirection(typename DisplacementFieldType::PixelType cpix)
{
typedef itk::Vector<double, ImageDimension> locVectorType;
if (this->m_UseImageDirection)
{
locVectorType outpix;
for (unsigned int d = 0; d < ImageDimension; d++)
{
outpix[d] = cpix[d];
}
outpix = m_DirectionTransform->TransformVector(outpix);
for (unsigned int d = 0; d < ImageDimension; d++)
{
cpix[d] = outpix[d];
}
}
return cpix;
}
private:
PreservationOfPrincipalDirectionTensorReorientationImageFilter(const Self &) = delete;
void
operator=(const Self &) = delete;
AffineTransformPointer GetLocalDeformation(DisplacementFieldPointer, typename DisplacementFieldType::IndexType);
TensorType ApplyReorientation(InverseTransformPointer, TensorType);
void DirectionCorrectTransform(AffineTransformPointer, AffineTransformPointer);
DisplacementFieldPointer m_DisplacementField;
DisplacementFieldTransformPointer m_DisplacementTransform;
AffineTransformPointer m_DirectionTransform;
AffineTransformPointer m_AffineTransform;
InverseTransformPointer m_InverseAffineTransform;
bool m_UseAffine;
bool m_UseImageDirection;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkPreservationOfPrincipalDirectionTensorReorientationImageFilter.cxx"
#endif
#endif
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