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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 elxStatisticalShapePenalty_h
#define elxStatisticalShapePenalty_h
#include "elxIncludes.h" // include first to avoid MSVS warning
#include "itkStatisticalShapePointPenalty.h"
#include <vnl/vnl_matrix.h>
#include <vnl/vnl_vector.h>
namespace elastix
{
using namespace itk;
/**
* \class StatisticalShapePenalty
* \brief An metric based on the itk::StatisticalShapePointPenalty.
*
* The parameters used in this class are:
* \parameter Metric: Select this metric as follows:\n
* <tt>(Metric "StatisticalShapePenalty")</tt>
* \parameter ShrinkageIntensity: The mixing ratio ($\beta$) of the provided
* covariance matrix and an identity matrix.
* $\Sigma' = (1-\beta)\Sigma + \beta \sigma_0^2 I$
* Can be defined for each resolution\n
* example: <tt>(ShrinkageIntensity 0.2)</tt>
* \parameter BaseVariance: The width ($\sigma_0^2$) of the non-informative prior.
* Can be defined for each resolution\n
* example: <tt>(BaseVariance 1000.0)</tt>
*
* \author F.F. Berendsen, Image Sciences Institute, UMC Utrecht, The Netherlands
* \note This work was funded by the projects Care4Me and Mediate.
* \note If you use the StatisticalShapePenalty anywhere we would appreciate if you cite the following article:\n
* F.F. Berendsen et al., Free-form image registration regularized by a statistical shape model:
* application to organ segmentation in cervical MR, Comput. Vis. Image Understand. (2013),
* http://dx.doi.org/10.1016/j.cviu.2012.12.006
*
* \ingroup Metrics
*/
template <class TElastix>
class ITK_TEMPLATE_EXPORT StatisticalShapePenalty
: public StatisticalShapePointPenalty<typename MetricBase<TElastix>::FixedPointSetType,
typename MetricBase<TElastix>::MovingPointSetType>
, public MetricBase<TElastix>
{
public:
ITK_DISALLOW_COPY_AND_MOVE(StatisticalShapePenalty);
/** Standard ITK-stuff. */
using Self = StatisticalShapePenalty;
using Superclass1 = StatisticalShapePointPenalty<typename MetricBase<TElastix>::FixedPointSetType,
typename MetricBase<TElastix>::MovingPointSetType>;
using Superclass2 = MetricBase<TElastix>;
using Pointer = SmartPointer<Self>;
using ConstPointer = SmartPointer<const Self>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(StatisticalShapePenalty, StatisticalShapePointPenalty);
/** Name of this class.
* Use this name in the parameter file to select this specific metric. \n
* example: <tt>(Metric "StatisticalShapePenalty")</tt>\n
*/
elxClassNameMacro("StatisticalShapePenalty");
/** Typedefs from the superclass. */
using typename Superclass1::CoordinateRepresentationType;
using typename Superclass1::FixedPointSetType;
using typename Superclass1::FixedPointSetConstPointer;
using typename Superclass1::MovingPointSetType;
using typename Superclass1::MovingPointSetConstPointer;
// using typename Superclass1::FixedImageRegionType;
using typename Superclass1::TransformType;
using typename Superclass1::TransformPointer;
using typename Superclass1::InputPointType;
using typename Superclass1::OutputPointType;
using typename Superclass1::TransformParametersType;
using typename Superclass1::TransformJacobianType;
// using typename Superclass1::RealType;
using typename Superclass1::FixedImageMaskType;
using typename Superclass1::FixedImageMaskPointer;
using typename Superclass1::MovingImageMaskType;
using typename Superclass1::MovingImageMaskPointer;
using typename Superclass1::MeasureType;
using typename Superclass1::DerivativeType;
using typename Superclass1::ParametersType;
using CoordRepType = typename OutputPointType::CoordRepType;
using VnlVectorType = vnl_vector<CoordRepType>;
/** Other typedef's. */
/*typedef itk::AdvancedTransform<
CoordRepType,
itkGetStaticConstMacro( FixedImageDimension ),
itkGetStaticConstMacro( MovingImageDimension ) > ITKBaseType;
*/
using CombinationTransformType = itk::AdvancedCombinationTransform<CoordRepType, Self::FixedImageDimension>;
using InitialTransformType = typename CombinationTransformType::InitialTransformType;
/** Typedefs inherited from elastix. */
using typename Superclass2::ElastixType;
using typename Superclass2::RegistrationType;
using ITKBaseType = typename Superclass2::ITKBaseType;
using typename Superclass2::FixedImageType;
using typename Superclass2::MovingImageType;
/** The fixed image dimension. */
itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
/** The moving image dimension. */
itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);
/** Assuming fixed and moving pointsets are of equal type, which implicitly
* assumes that the fixed and moving image are of the same type.
*/
using PointSetType = FixedPointSetType;
using ImageType = FixedImageType;
/** Sets up a timer to measure the initialization time and calls the
* Superclass' implementation.
*/
void
Initialize() override;
/**
* Do some things before registration:
* \li Load and set the pointsets.
*/
void
BeforeRegistration() override;
void
BeforeEachResolution() override;
/** Function to read the corresponding points. */
unsigned int
ReadLandmarks(const std::string & landmarkFileName,
typename PointSetType::Pointer & pointSet,
const typename ImageType::ConstPointer image);
unsigned int
ReadShape(const std::string & ShapeFileName, typename PointSetType::Pointer & pointSet);
/** Overwrite to silence warning. */
void
SelectNewSamples() override
{}
protected:
/** The constructor. */
StatisticalShapePenalty() = default;
/** The destructor. */
~StatisticalShapePenalty() override = default;
private:
elxOverrideGetSelfMacro;
};
} // end namespace elastix
#ifndef ITK_MANUAL_INSTANTIATION
# include "elxStatisticalShapePenalty.hxx"
#endif
#endif // end #ifndef elxStatisticalShapePenalty_h
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