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/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#ifndef itkDiffusionTensor3D_h
#define itkDiffusionTensor3D_h
// Undefine an eventual DiffusionTensor3D macro
#ifdef DiffusionTensor3D
# undef DiffusionTensor3D
#endif
#include "itkSymmetricSecondRankTensor.h"
namespace itk
{
/** \class DiffusionTensor3D
* \brief Represent a diffusion tensor as used in DTI images.
*
* This class implements a 3D symmetric tensor as it is used for representing
* diffusion of water molecules in Diffusion Tensor Images.
*
* This class derives from the SymmetricSecondRankTensor, inheriting
* most of the Tensor-related behavior. At this level we add the methods that
* are specific to 3D and that are closely related to the concept of diffusion.
*
*
* \author Jeffrey Duda from School of Engineering at University of Pennsylvania
* \author Torsten Rohlfing from SRI International Neuroscience Program.
*
* This class was mostly based on files that Jeffrey Duda, Torsten Rohlfing and
* Martin Styner contributed to the ITK users list during a discussion on
* support for DiffusionTensorImages. A discussion on the design of this class
* can be found in the WIKI pages of NAMIC:
*
* https://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:ITK-DiffusionTensorPixelType
*
* \note This work is part of the National Alliance for Medical Image
* Computing (NAMIC), funded by the National Institutes of Health
* through the NIH Roadmap for Medical Research, Grant U54 EB005149.
* Information on the National Centers for Biomedical Computing
* can be obtained from http://commonfund.nih.gov/bioinformatics.
*
*
* \note Contributions by Torsten Rohlfing were funded by the following NIH grants
*
* Alcohol, HIV and the Brain,
* NIAAA AA12999, PI: A. Pfefferbaum
*
* Normal Aging of Brain Structure and Function
* NIA AG 17919, PI: E.V. Sullivan.
*
*
* \par References
* E. R. Melhem, S. Mori, G. Mukundan, M. A. Kraut, M. G. Pomper, and
* P. C. M. van Zijl, "Diffusion tensor MR imaging of the brain and white
* matter tractography," Am. J. Roentgenol., vol. 178, pp. 3-16, 2002.
*
* \sa SymmetricSecondRankTensor
*
* \ingroup ImageObjects TensorObjects Geometry
* \ingroup ITKCommon
*/
template <typename TComponent>
class ITK_TEMPLATE_EXPORT DiffusionTensor3D : public SymmetricSecondRankTensor<TComponent, 3>
{
public:
/** Standard class type aliases. */
using Self = DiffusionTensor3D;
using Superclass = SymmetricSecondRankTensor<TComponent, 3>;
/** Propagating some type alias from the superclass */
using typename Superclass::ValueType;
using typename Superclass::ComponentType;
using typename Superclass::ComponentArrayType;
using typename Superclass::AccumulateValueType;
using typename Superclass::RealValueType;
using typename Superclass::EigenValuesArrayType;
using typename Superclass::EigenVectorsMatrixType;
/** Default Constructor. */
DiffusionTensor3D() = default;
/** Constructor with initialization. */
DiffusionTensor3D(const Superclass & r);
DiffusionTensor3D(const ComponentType & r);
DiffusionTensor3D(const ComponentArrayType r);
/** Constructor to enable casting... */
template <typename TCoordRepB>
DiffusionTensor3D(const DiffusionTensor3D<TCoordRepB> & pa)
: SymmetricSecondRankTensor<TComponent, 3>(pa)
{}
/** Pass-through assignment operator for the Array base class. */
Self &
operator=(const Superclass & r);
Self &
operator=(const ComponentType & r);
Self &
operator=(const ComponentArrayType r);
/** Templated Pass-through assignment for the Array base class. */
template <typename TCoordRepB>
Self &
operator=(const DiffusionTensor3D<TCoordRepB> & pa)
{
// NOTE (this != &pa ) because they are different pointer types
// if this templated function is called
// ComponentType 'itk::DiffusionTensor3D<double> *'
// TCoordRepB 'const DiffusionTensor3D<float> *')
SymmetricSecondRankTensor<TComponent, 3>::operator=(pa);
return *this;
}
/** Get the trace value.
*
* Note that the indices are related to the fact
* that we store only the upper-right triangle of
* the matrix. Like
*
* | 0 1 2 |
* | X 3 4 |
* | X X 5 |
*
* The trace is therefore the sum of the components
* M[0], M[3] and M[5].
*
*/
AccumulateValueType
GetTrace() const;
/** Get the value of Fractional Anisotropy from the Tensor. */
RealValueType
GetFractionalAnisotropy() const;
/** Get the value of Relative Anisotropy from the Tensor. */
RealValueType
GetRelativeAnisotropy() const;
/** Get the inner scalar product from the Tensor. */
RealValueType
GetInnerScalarProduct() const;
};
template <typename T>
inline void
swap(DiffusionTensor3D<T> & a, DiffusionTensor3D<T> & b)
{
a.swap(b);
}
} // end namespace itk
#include "itkNumericTraitsDiffusionTensor3DPixel.h"
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkDiffusionTensor3D.hxx"
#endif
#endif
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