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/*=========================================================================
*
* Copyright UMC Utrecht and contributors
*
* 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
*
* http://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 itkPCAMetric2_h
#define itkPCAMetric2_h
#include "itkAdvancedImageToImageMetric.h"
#include "itkSmoothingRecursiveGaussianImageFilter.h"
#include "itkImageRandomCoordinateSampler.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkExtractImageFilter.h"
namespace itk
{
template <class TFixedImage, class TMovingImage>
class ITK_TEMPLATE_EXPORT PCAMetric2 : public AdvancedImageToImageMetric<TFixedImage, TMovingImage>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(PCAMetric2);
/** Standard class typedefs. */
using Self = PCAMetric2;
using Superclass = AdvancedImageToImageMetric<TFixedImage, TMovingImage>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
using typename Superclass::FixedImageRegionType;
using FixedImageSizeType = typename FixedImageRegionType::SizeType;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(PCAMetric2, AdvancedImageToImageMetric);
/** Set functions. */
itkSetMacro(NumAdditionalSamplesFixed, unsigned int);
itkSetMacro(ReducedDimensionIndex, unsigned int);
itkSetMacro(UseZeroAverageDisplacementConstraint, bool);
itkSetMacro(GridSize, FixedImageSizeType);
itkSetMacro(TransformIsStackTransform, bool);
/** Typedefs from the superclass. */
using typename Superclass::CoordinateRepresentationType;
using typename Superclass::MovingImageType;
using typename Superclass::MovingImagePixelType;
using typename Superclass::MovingImageConstPointer;
using typename Superclass::FixedImageType;
using typename Superclass::FixedImageConstPointer;
using typename Superclass::TransformType;
using typename Superclass::TransformPointer;
using typename Superclass::InputPointType;
using typename Superclass::OutputPointType;
using typename Superclass::TransformParametersType;
using typename Superclass::TransformJacobianType;
using typename Superclass::InterpolatorType;
using typename Superclass::InterpolatorPointer;
using typename Superclass::RealType;
using typename Superclass::GradientPixelType;
using typename Superclass::GradientImageType;
using typename Superclass::GradientImagePointer;
using typename Superclass::FixedImageMaskType;
using typename Superclass::FixedImageMaskPointer;
using typename Superclass::MovingImageMaskType;
using typename Superclass::MovingImageMaskPointer;
using typename Superclass::MeasureType;
using typename Superclass::DerivativeType;
using typename Superclass::ParametersType;
using typename Superclass::FixedImagePixelType;
using typename Superclass::MovingImageRegionType;
using typename Superclass::ImageSamplerType;
using typename Superclass::ImageSamplerPointer;
using typename Superclass::ImageSampleContainerType;
using typename Superclass::ImageSampleContainerPointer;
using typename Superclass::FixedImageLimiterType;
using typename Superclass::MovingImageLimiterType;
using typename Superclass::FixedImageLimiterOutputType;
using typename Superclass::MovingImageLimiterOutputType;
using typename Superclass::MovingImageDerivativeScalesType;
using typename Superclass::DerivativeValueType;
/** The fixed image dimension. */
itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
/** The moving image dimension. */
itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);
/** Get the value for single valued optimizers. */
MeasureType
GetValue(const TransformParametersType & parameters) const override;
/** Get the derivatives of the match measure. */
void
GetDerivative(const TransformParametersType & parameters, DerivativeType & derivative) const override;
/** Get value and derivatives for multiple valued optimizers. */
void
GetValueAndDerivative(const TransformParametersType & parameters,
MeasureType & Value,
DerivativeType & Derivative) const override;
/** Initialize the Metric by making sure that all the components
* are present and plugged together correctly.
* \li Call the superclass' implementation.
*/
void
Initialize() override;
protected:
PCAMetric2();
~PCAMetric2() override = default;
void
PrintSelf(std::ostream & os, Indent indent) const override;
/** Protected Typedefs ******************/
/** Typedefs inherited from superclass */
using typename Superclass::FixedImageIndexType;
using typename Superclass::FixedImageIndexValueType;
using typename Superclass::MovingImageIndexType;
using typename Superclass::FixedImagePointType;
using FixedImageContinuousIndexType =
typename itk::ContinuousIndex<CoordinateRepresentationType, FixedImageDimension>;
using typename Superclass::MovingImagePointType;
using typename Superclass::MovingImageContinuousIndexType;
using typename Superclass::BSplineInterpolatorType;
using typename Superclass::MovingImageDerivativeType;
using typename Superclass::NonZeroJacobianIndicesType;
/** Computes the innerproduct of transform Jacobian with moving image gradient.
* The results are stored in imageJacobian, which is supposed
* to have the right size (same length as Jacobian's number of columns).
*/
void
EvaluateTransformJacobianInnerProduct(const TransformJacobianType & jacobian,
const MovingImageDerivativeType & movingImageDerivative,
DerivativeType & imageJacobian) const override;
private:
/** Sample n random numbers from 0..m and add them to the vector. */
void
SampleRandom(const int n, const int m, std::vector<int> & numbers) const;
/** Variables to control random sampling in last dimension. */
unsigned int m_NumAdditionalSamplesFixed{};
unsigned int m_ReducedDimensionIndex{};
/** Bool to determine if we want to subtract the mean derivate from the derivative elements. */
bool m_UseZeroAverageDisplacementConstraint{ true };
/** GridSize of B-spline transform. */
FixedImageSizeType m_GridSize{};
/** Bool to indicate if the transform used is a stacktransform. Set by elx files. */
bool m_TransformIsStackTransform{ false };
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
# include "itkPCAMetric2.hxx"
#endif
#endif // end #ifndef itkPCAMetric2_h
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