itkPCAMetric.h

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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
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 *  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.
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#ifndef __itkPCAMetric_h
#define __itkPCAMetric_h
 
#include "itkAdvancedImageToImageMetric.h"
 
#include "itkSmoothingRecursiveGaussianImageFilter.h"
#include "itkImageRandomCoordinateSampler.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkExtractImageFilter.h"
 
using namespace std;
 
namespace itk
{
template< class TFixedImage, class TMovingImage >
class PCAMetric :
  public AdvancedImageToImageMetric< TFixedImage, TMovingImage >
{
public:
 
  typedef PCAMetric                   Self;
  typedef AdvancedImageToImageMetric<
    TFixedImage, TMovingImage >       Superclass;
  typedef SmartPointer< Self >        Pointer;
  typedef SmartPointer< const Self >  ConstPointer;
 
  typedef typename Superclass::FixedImageRegionType FixedImageRegionType;
  typedef typename FixedImageRegionType::SizeType   FixedImageSizeType;
 
  itkNewMacro( Self );
 
  itkTypeMacro( PCAMetric, AdvancedImageToImageMetric );
 
  itkSetMacro( SampleLastDimensionRandomly, bool );
  itkSetMacro( NumSamplesLastDimension, unsigned int );
  itkSetMacro( NumAdditionalSamplesFixed, unsigned int );
  itkSetMacro( ReducedDimensionIndex, unsigned int );
  itkSetMacro( SubtractMean, bool );
  itkSetMacro( GridSize, FixedImageSizeType );
  itkSetMacro( TransformIsStackTransform, bool );
  itkSetMacro( NumEigenValues, unsigned int );
  itkSetMacro( UseDerivativeOfMean, bool );
  itkSetMacro( DeNoise, bool );
  itkSetMacro( VarNoise, double );
 
  itkGetConstMacro( SampleLastDimensionRandomly, bool );
  itkGetConstMacro( NumSamplesLastDimension, int );
 
  typedef typename
    Superclass::CoordinateRepresentationType              CoordinateRepresentationType;
  typedef typename Superclass::MovingImageType            MovingImageType;
  typedef typename Superclass::MovingImagePixelType       MovingImagePixelType;
  typedef typename Superclass::MovingImageConstPointer    MovingImageConstPointer;
  typedef typename Superclass::FixedImageType             FixedImageType;
  typedef typename Superclass::FixedImageConstPointer     FixedImageConstPointer;
  typedef typename Superclass::TransformType              TransformType;
  typedef typename Superclass::TransformPointer           TransformPointer;
  typedef typename Superclass::InputPointType             InputPointType;
  typedef typename Superclass::OutputPointType            OutputPointType;
  typedef typename Superclass::TransformParametersType    TransformParametersType;
  typedef typename Superclass::TransformJacobianType      TransformJacobianType;
  typedef typename Superclass::InterpolatorType           InterpolatorType;
  typedef typename Superclass::InterpolatorPointer        InterpolatorPointer;
  typedef typename Superclass::RealType                   RealType;
  typedef typename Superclass::GradientPixelType          GradientPixelType;
  typedef typename Superclass::GradientImageType          GradientImageType;
  typedef typename Superclass::GradientImagePointer       GradientImagePointer;
  typedef typename Superclass::GradientImageFilterType    GradientImageFilterType;
  typedef typename Superclass::GradientImageFilterPointer GradientImageFilterPointer;
  typedef typename Superclass::FixedImageMaskType         FixedImageMaskType;
  typedef typename Superclass::FixedImageMaskPointer      FixedImageMaskPointer;
  typedef typename Superclass::MovingImageMaskType        MovingImageMaskType;
  typedef typename Superclass::MovingImageMaskPointer     MovingImageMaskPointer;
  typedef typename Superclass::MeasureType                MeasureType;
  typedef typename Superclass::DerivativeType             DerivativeType;
  typedef typename Superclass::ParametersType             ParametersType;
  typedef typename Superclass::FixedImagePixelType        FixedImagePixelType;
  typedef typename Superclass::MovingImageRegionType      MovingImageRegionType;
  typedef typename Superclass::ImageSamplerType           ImageSamplerType;
  typedef typename Superclass::ImageSamplerPointer        ImageSamplerPointer;
  typedef typename Superclass::ImageSampleContainerType   ImageSampleContainerType;
  typedef typename
    Superclass::ImageSampleContainerPointer               ImageSampleContainerPointer;
  typedef typename Superclass::FixedImageLimiterType      FixedImageLimiterType;
  typedef typename Superclass::MovingImageLimiterType     MovingImageLimiterType;
  typedef typename
    Superclass::FixedImageLimiterOutputType               FixedImageLimiterOutputType;
 typedef typename
    Superclass::MovingImageLimiterOutputType              MovingImageLimiterOutputType;
  typedef typename
    Superclass::MovingImageDerivativeScalesType           MovingImageDerivativeScalesType;
 
  itkStaticConstMacro( FixedImageDimension, unsigned int,
    FixedImageType::ImageDimension );
 
  itkStaticConstMacro( MovingImageDimension, unsigned int,
    MovingImageType::ImageDimension );
 
  virtual MeasureType GetValue( const TransformParametersType & parameters ) const;
 
  virtual void GetDerivative( const TransformParametersType & parameters,
    DerivativeType & derivative ) const;
 
  virtual void GetValueAndDerivative( const TransformParametersType & parameters,
    MeasureType & Value, DerivativeType & Derivative ) const;
 
  virtual void Initialize( void );
 
protected:
 
  PCAMetric();
  virtual ~PCAMetric() {}
  void PrintSelf( std::ostream & os, Indent indent ) const;
 
  typedef typename Superclass::FixedImageIndexType                FixedImageIndexType;
  typedef typename Superclass::FixedImageIndexValueType           FixedImageIndexValueType;
  typedef typename Superclass::MovingImageIndexType               MovingImageIndexType;
  typedef typename Superclass::FixedImagePointType                FixedImagePointType;
  typedef typename itk::ContinuousIndex< CoordinateRepresentationType, FixedImageDimension >
                                                                  FixedImageContinuousIndexType;
  typedef typename Superclass::MovingImagePointType               MovingImagePointType;
  typedef typename Superclass::MovingImageContinuousIndexType     MovingImageContinuousIndexType;
  typedef typename Superclass::BSplineInterpolatorType            BSplineInterpolatorType;
  typedef typename Superclass::CentralDifferenceGradientFilterType CentralDifferenceGradientFilterType;
  typedef typename Superclass::MovingImageDerivativeType          MovingImageDerivativeType;
  typedef typename Superclass::NonZeroJacobianIndicesType         NonZeroJacobianIndicesType;
 
  void EvaluateTransformJacobianInnerProduct(
    const TransformJacobianType & jacobian,
    const MovingImageDerivativeType & movingImageDerivative,
    DerivativeType & imageJacobian ) const;
 
  mutable vnl_vector< double > m_firstEigenVector;
  mutable vnl_vector< double > m_secondEigenVector;
  mutable vnl_vector< double > m_thirdEigenVector;
  mutable vnl_vector< double > m_fourthEigenVector;
  mutable vnl_vector< double > m_fifthEigenVector;
  mutable vnl_vector< double > m_sixthEigenVector;
  mutable vnl_vector< double > m_seventhEigenVector;
  mutable vnl_vector< double > m_eigenValues;
  mutable vnl_vector< double > m_normdCdmu;
  mutable int                  m_NumberOfSamples;
 
private:
 
  PCAMetric( const Self & );      // purposely not implemented
  void operator=( const Self & ); // purposely not implemented
 
  void SampleRandom( const int n, const int m, std::vector< int > & numbers ) const;
 
  bool         m_SampleLastDimensionRandomly;
  unsigned int m_NumSamplesLastDimension;
  unsigned int m_NumAdditionalSamplesFixed;
  unsigned int m_ReducedDimensionIndex;
 
  bool m_DeNoise;
 
  double m_VarNoise;
 
  bool m_SubtractMean;
 
  FixedImageSizeType m_GridSize;
 
  bool m_TransformIsStackTransform;
 
  unsigned int m_NumEigenValues;
 
  bool m_UseDerivativeOfMean;
 
};
 
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkPCAMetric.hxx"
#endif
 
#endif // end #ifndef __itkPCAMetric_h