/*========================================================================= Program: vv http://www.creatis.insa-lyon.fr/rio/vv Authors belong to: - University of LYON http://www.universite-lyon.fr/ - Léon Bérard cancer center http://www.centreleonberard.fr - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the copyright notices for more information. It is distributed under dual licence - BSD See included LICENSE.txt file - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html ===========================================================================**/ /*========================================================================= Program: Insight Segmentation & Registration Toolkit Module: $RCSfile: itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h,v $ Language: C++ Date: $Date: 2010/06/14 17:32:07 $ Version: $Revision: 1.1 $ Copyright (c) Insight Software Consortium. All rights reserved. See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 __itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD_h #define __itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD_h // First make sure that the configuration is available. // This line can be removed once the optimized versions // gets integrated into the main directories. #include "itkConfigure.h" #ifdef ITK_USE_OPTIMIZED_REGISTRATION_METHODS #include "itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h" #else #include "itkImageToImageMetric.h" #include "itkCovariantVector.h" #include "itkPoint.h" #include "itkIndex.h" #include "itkBSplineKernelFunction.h" #include "itkBSplineDerivativeKernelFunction.h" #include "itkCentralDifferenceImageFunction.h" #include "itkBSplineInterpolateImageFunction.h" #if ITK_VERSION_MAJOR >= 4 #include "itkBSplineTransform.h" #else #include "itkBSplineDeformableTransform.h" #endif #include "itkArray2D.h" namespace itk { /** \class MattesMutualInformationImageToImageMetricFor3DBLUTFFD * \brief Computes the mutual information between two images to be * registered using the method of Mattes et al. * * MattesMutualInformationImageToImageMetricFor3DBLUTFFD computes the mutual * information between a fixed and moving image to be registered. * * This class is templated over the FixedImage type and the MovingImage * type. * * The fixed and moving images are set via methods SetFixedImage() and * SetMovingImage(). This metric makes use of user specified Transform and * Interpolator. The Transform is used to map points from the fixed image to * the moving image domain. The Interpolator is used to evaluate the image * intensity at user specified geometric points in the moving image. * The Transform and Interpolator are set via methods SetTransform() and * SetInterpolator(). * * If a BSplineInterpolationFunction is used, this class obtain * image derivatives from the BSpline interpolator. Otherwise, * image derivatives are computed using central differencing. * * \warning This metric assumes that the moving image has already been * connected to the interpolator outside of this class. * * The method GetValue() computes of the mutual information * while method GetValueAndDerivative() computes * both the mutual information and its derivatives with respect to the * transform parameters. * * The calculations are based on the method of Mattes et al [1,2] * where the probability density distribution are estimated using * Parzen histograms. Since the fixed image PDF does not contribute * to the derivatives, it does not need to be smooth. Hence, * a zero order (box car) BSpline kernel is used * for the fixed image intensity PDF. On the other hand, to ensure * smoothness a third order BSpline kernel is used for the * moving image intensity PDF. * * On Initialize(), the FixedImage is uniformly sampled within * the FixedImageRegion. The number of samples used can be set * via SetNumberOfSpatialSamples(). Typically, the number of * spatial samples used should increase with the image size. * * The option UseAllPixelOn() disables the random sampling and uses * all the pixels of the FixedImageRegion in order to estimate the * joint intensity PDF. * * During each call of GetValue(), GetDerivatives(), * GetValueAndDerivatives(), marginal and joint intensity PDF's * values are estimated at discrete position or bins. * The number of bins used can be set via SetNumberOfHistogramBins(). * To handle data with arbitray magnitude and dynamic range, * the image intensity is scale such that any contribution to the * histogram will fall into a valid bin. * * One the PDF's have been contructed, the mutual information * is obtained by doubling summing over the discrete PDF values. * * * Notes: * 1. This class returns the negative mutual information value. * 2. This class in not thread safe due the private data structures * used to the store the sampled points and the marginal and joint pdfs. * * References: * [1] "Nonrigid multimodality image registration" * D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank * Medical Imaging 2001: Image Processing, 2001, pp. 1609-1620. * [2] "PET-CT Image Registration in the Chest Using Free-form Deformations" * D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank * IEEE Transactions in Medical Imaging. Vol.22, No.1, January 2003. pp.120-128. * [3] "Optimization of Mutual Information for MultiResolution Image * Registration" * P. Thevenaz and M. Unser * IEEE Transactions in Image Processing, 9(12) December 2000. * * \ingroup RegistrationMetrics * \ingroup ThreadUnSafe */ template class ITK_EXPORT MattesMutualInformationImageToImageMetricFor3DBLUTFFD : public ImageToImageMetric< TFixedImage, TMovingImage > { public: /** Standard class typedefs. */ typedef MattesMutualInformationImageToImageMetricFor3DBLUTFFD Self; typedef ImageToImageMetric< TFixedImage, TMovingImage > Superclass; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(MattesMutualInformationImageToImageMetricFor3DBLUTFFD, ImageToImageMetric); /** Types inherited from Superclass. */ typedef typename Superclass::TransformType TransformType; typedef typename Superclass::TransformPointer TransformPointer; typedef typename Superclass::TransformJacobianType TransformJacobianType; typedef typename Superclass::InterpolatorType InterpolatorType; typedef typename Superclass::MeasureType MeasureType; typedef typename Superclass::DerivativeType DerivativeType; typedef typename Superclass::ParametersType ParametersType; typedef typename Superclass::FixedImageType FixedImageType; typedef typename Superclass::MovingImageType MovingImageType; typedef typename Superclass::FixedImageConstPointer FixedImageConstPointer; typedef typename Superclass::MovingImageConstPointer MovingImageCosntPointer; typedef typename Superclass::InputPointType InputPointType; typedef typename Superclass::OutputPointType OutputPointType; typedef typename Superclass::CoordinateRepresentationType CoordinateRepresentationType; /** Index and Point typedef support. */ typedef typename FixedImageType::IndexType FixedImageIndexType; typedef typename FixedImageIndexType::IndexValueType FixedImageIndexValueType; typedef typename MovingImageType::IndexType MovingImageIndexType; typedef typename TransformType::InputPointType FixedImagePointType; typedef typename TransformType::OutputPointType MovingImagePointType; /** The moving image dimension. */ itkStaticConstMacro( MovingImageDimension, unsigned int, MovingImageType::ImageDimension ); /** * Initialize the Metric by * (1) making sure that all the components are present and plugged * together correctly, * (2) uniformly select NumberOfSpatialSamples within * the FixedImageRegion, and * (3) allocate memory for pdf data structures. */ virtual void Initialize(void) throw ( ExceptionObject ); /** Get the derivatives of the match measure. */ void GetDerivative( const ParametersType& parameters, DerivativeType & Derivative ) const; /** Get the value. */ MeasureType GetValue( const ParametersType& parameters ) const; /** Get the value and derivatives for single valued optimizers. */ void GetValueAndDerivative( const ParametersType& parameters, MeasureType& Value, DerivativeType& Derivative ) const; /** Number of spatial samples to used to compute metric */ itkSetClampMacro( NumberOfSpatialSamples, unsigned long, 1, NumericTraits::max() ); itkGetConstReferenceMacro( NumberOfSpatialSamples, unsigned long); /** Number of bins to used in the histogram. Typical value is 50. */ itkSetClampMacro( NumberOfHistogramBins, unsigned long, 1, NumericTraits::max() ); itkGetConstReferenceMacro( NumberOfHistogramBins, unsigned long); /** Reinitialize the seed of the random number generator that selects the * sample of pixels used for estimating the image histograms and the joint * histogram. By nature, this metric is not deterministic, since at each run * it may select a different set of pixels. By initializing the random number * generator seed to the same value you can restore determinism. On the other * hand, calling the method ReinitializeSeed() without arguments will use the * clock from your machine in order to have a very random initialization of * the seed. This will indeed increase the non-deterministic behavior of the * metric. */ void ReinitializeSeed(); void ReinitializeSeed(int); /** Select whether the metric will be computed using all the pixels on the * fixed image region, or only using a set of randomly selected pixels. */ itkSetMacro(UseAllPixels,bool); itkGetConstReferenceMacro(UseAllPixels,bool); itkBooleanMacro(UseAllPixels); /** This variable selects the method to be used for computing the Metric * derivatives with respect to the Transform parameters. Two modes of * computation are available. The choice between one and the other is a * trade-off between computation speed and memory allocations. The two modes * are described in detail below: * * UseExplicitPDFDerivatives = True * will compute the Metric derivative by first calculating the derivatives of * each one of the Joint PDF bins with respect to each one of the Transform * parameters and then accumulating these contributions in the final metric * derivative array by using a bin-specific weight. The memory required for * storing the intermediate derivatives is a 3D array of doubles with size * equals to the product of (number of histogram bins)^2 times number of * transform parameters. This method is well suited for Transform with a small * number of parameters. * * UseExplicitPDFDerivatives = False will compute the Metric derivative by * first computing the weights for each one of the Joint PDF bins and caching * them into an array. Then it will revisit each one of the PDF bins for * computing its weighted contribution to the full derivative array. In this * method an extra 2D array is used for storing the weights of each one of * the PDF bins. This is an array of doubles with size equals to (number of * histogram bins)^2. This method is well suited for Transforms with a large * number of parameters, such as, BSplineDeformableTransforms. */ itkSetMacro(UseExplicitPDFDerivatives,bool); itkGetConstReferenceMacro(UseExplicitPDFDerivatives,bool); itkBooleanMacro(UseExplicitPDFDerivatives); /** This boolean flag is only relevant when this metric is used along * with a BSplineDeformableTransform. The flag enables/disables the * caching of values computed when a physical point is mapped through * the BSplineDeformableTransform. In particular it will cache the * values of the BSpline weights for that points, and the indexes * indicating what BSpline-grid nodes are relevant for that specific * point. This caching is made optional due to the fact that the * memory arrays used for the caching can reach large sizes even for * moderate image size problems. For example, for a 3D image of * 256^3, using 20% of pixels, these arrays will take about 1 * Gigabyte of RAM for storage. The ratio of computing time between * using the cache or not using the cache can reach 1:5, meaning that * using the caching can provide a five times speed up. It is * therefore, interesting to enable the caching, if enough memory is * available for it. The caching is enabled by default, in order to * preserve backward compatibility with previous versions of ITK. */ itkSetMacro(UseCachingOfBSplineWeights,bool); itkGetConstReferenceMacro(UseCachingOfBSplineWeights,bool); itkBooleanMacro(UseCachingOfBSplineWeights); protected: MattesMutualInformationImageToImageMetricFor3DBLUTFFD(); virtual ~MattesMutualInformationImageToImageMetricFor3DBLUTFFD() {}; void PrintSelf(std::ostream& os, Indent indent) const; /** \class FixedImageSpatialSample * A fixed image spatial sample consists of the fixed domain point * and the fixed image value at that point. */ /// @cond class FixedImageSpatialSample { public: FixedImageSpatialSample():FixedImageValue(0.0) { FixedImagePointValue.Fill(0.0); } ~FixedImageSpatialSample() {}; FixedImagePointType FixedImagePointValue; double FixedImageValue; unsigned int FixedImageParzenWindowIndex; }; /// @endcond /** FixedImageSpatialSample typedef support. */ typedef std::vector FixedImageSpatialSampleContainer; /** Container to store a set of points and fixed image values. */ FixedImageSpatialSampleContainer m_FixedImageSamples; /** Uniformly select a sample set from the fixed image domain. */ virtual void SampleFixedImageDomain( FixedImageSpatialSampleContainer& samples); /** Gather all the pixels from the fixed image domain. */ virtual void SampleFullFixedImageDomain( FixedImageSpatialSampleContainer& samples); /** Transform a point from FixedImage domain to MovingImage domain. * This function also checks if mapped point is within support region. */ virtual void TransformPoint( unsigned int sampleNumber, const ParametersType& parameters, MovingImagePointType& mappedPoint, bool& sampleWithinSupportRegion, double& movingImageValue ) const; private: //purposely not implemented MattesMutualInformationImageToImageMetricFor3DBLUTFFD(const Self&); //purposely not implemented void operator=(const Self&); /** The marginal PDFs are stored as std::vector. */ typedef float PDFValueType; typedef std::vector MarginalPDFType; /** The fixed image marginal PDF. */ mutable MarginalPDFType m_FixedImageMarginalPDF; /** The moving image marginal PDF. */ mutable MarginalPDFType m_MovingImageMarginalPDF; /** Helper array for storing the values of the JointPDF ratios. */ typedef double PRatioType; typedef Array2D< PRatioType > PRatioArrayType; mutable PRatioArrayType m_PRatioArray; /** Helper variable for accumulating the derivative of the metric. */ mutable DerivativeType m_MetricDerivative; /** Typedef for the joint PDF and PDF derivatives are stored as ITK Images. */ typedef Image JointPDFType; typedef JointPDFType::IndexType JointPDFIndexType; typedef JointPDFType::PixelType JointPDFValueType; typedef JointPDFType::RegionType JointPDFRegionType; typedef JointPDFType::SizeType JointPDFSizeType; typedef Image JointPDFDerivativesType; typedef JointPDFDerivativesType::IndexType JointPDFDerivativesIndexType; typedef JointPDFDerivativesType::PixelType JointPDFDerivativesValueType; typedef JointPDFDerivativesType::RegionType JointPDFDerivativesRegionType; typedef JointPDFDerivativesType::SizeType JointPDFDerivativesSizeType; /** The joint PDF and PDF derivatives. */ typename JointPDFType::Pointer m_JointPDF; typename JointPDFDerivativesType::Pointer m_JointPDFDerivatives; unsigned long m_NumberOfSpatialSamples; unsigned long m_NumberOfParameters; /** Variables to define the marginal and joint histograms. */ unsigned long m_NumberOfHistogramBins; double m_MovingImageNormalizedMin; double m_FixedImageNormalizedMin; double m_MovingImageTrueMin; double m_MovingImageTrueMax; double m_FixedImageBinSize; double m_MovingImageBinSize; /** Typedefs for BSpline kernel and derivative functions. */ typedef BSplineKernelFunction<3> CubicBSplineFunctionType; typedef BSplineDerivativeKernelFunction<3> CubicBSplineDerivativeFunctionType; /** Cubic BSpline kernel for computing Parzen histograms. */ typename CubicBSplineFunctionType::Pointer m_CubicBSplineKernel; typename CubicBSplineDerivativeFunctionType::Pointer m_CubicBSplineDerivativeKernel; /** Precompute fixed image parzen window indices. */ virtual void ComputeFixedImageParzenWindowIndices( FixedImageSpatialSampleContainer& samples ); /** * Types and variables related to image derivative calculations. * If a BSplineInterpolationFunction is used, this class obtain * image derivatives from the BSpline interpolator. Otherwise, * image derivatives are computed using central differencing. */ typedef CovariantVector< double, itkGetStaticConstMacro(MovingImageDimension) > ImageDerivativesType; /** Compute image derivatives at a point. */ virtual void ComputeImageDerivatives( const MovingImagePointType& mappedPoint, ImageDerivativesType& gradient ) const; /** Boolean to indicate if the interpolator BSpline. */ bool m_InterpolatorIsBSpline; /** Typedefs for using BSpline interpolator. */ typedef BSplineInterpolateImageFunction BSplineInterpolatorType; /** Pointer to BSplineInterpolator. */ typename BSplineInterpolatorType::Pointer m_BSplineInterpolator; /** Typedefs for using central difference calculator. */ typedef CentralDifferenceImageFunction DerivativeFunctionType; /** Pointer to central difference calculator. */ typename DerivativeFunctionType::Pointer m_DerivativeCalculator; /** Compute PDF derivative contribution for each parameter. */ virtual void ComputePDFDerivatives( unsigned int sampleNumber, int movingImageParzenWindowIndex, const ImageDerivativesType& movingImageGradientValue, double cubicBSplineDerivativeValue ) const; /** * Types and variables related to BSpline deformable transforms. * If the transform is of type third order BSplineDeformableTransform, * then we can speed up the metric derivative calculation by * only inspecting the parameters within the support region * of a mapped point. */ /** Boolean to indicate if the transform is BSpline deformable. */ bool m_TransformIsBSpline; /** The number of BSpline parameters per image dimension. */ long m_NumParametersPerDim; /** * The number of BSpline transform weights is the number of * of parameter in the support region (per dimension ). */ unsigned long m_NumBSplineWeights; /** The fixed image dimension. */ itkStaticConstMacro( FixedImageDimension, unsigned int, FixedImageType::ImageDimension ); /** * Enum of the deformabtion field spline order. */ enum { DeformationSplineOrder = 3 }; /** * Typedefs for the BSplineDeformableTransform. */ #if ITK_VERSION_MAJOR >= 4 typedef BSplineTransform< CoordinateRepresentationType, ::itk::GetImageDimension::ImageDimension, DeformationSplineOrder> BSplineTransformType; #else typedef BSplineDeformableTransform< CoordinateRepresentationType, ::itk::GetImageDimension::ImageDimension, DeformationSplineOrder> BSplineTransformType; #endif typedef typename BSplineTransformType::WeightsType BSplineTransformWeightsType; typedef typename BSplineTransformType::ParameterIndexArrayType BSplineTransformIndexArrayType; /** * Variables used when transform is of type BSpline deformable. */ typename BSplineTransformType::Pointer m_BSplineTransform; /** * Cache pre-transformed points, weights, indices and * within support region flag. */ typedef typename BSplineTransformWeightsType::ValueType WeightsValueType; typedef Array2D BSplineTransformWeightsArrayType; typedef typename BSplineTransformIndexArrayType::ValueType IndexValueType; typedef Array2D BSplineTransformIndicesArrayType; typedef std::vector MovingImagePointArrayType; typedef std::vector BooleanArrayType; BSplineTransformWeightsArrayType m_BSplineTransformWeightsArray; BSplineTransformIndicesArrayType m_BSplineTransformIndicesArray; MovingImagePointArrayType m_PreTransformPointsArray; BooleanArrayType m_WithinSupportRegionArray; typedef FixedArray::ImageDimension> ParametersOffsetType; ParametersOffsetType m_ParametersOffset; bool m_UseAllPixels; virtual void PreComputeTransformValues(); bool m_ReseedIterator; int m_RandomSeed; // Selection of explicit or implicit computation of PDF derivatives // with respect to Transform parameters. bool m_UseExplicitPDFDerivatives; // Variables needed for optionally caching values when using a BSpline transform. bool m_UseCachingOfBSplineWeights; mutable BSplineTransformWeightsType m_Weights; mutable BSplineTransformIndexArrayType m_Indices; }; } // end namespace itk #ifndef ITK_MANUAL_INSTANTIATION #include "itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx" #endif #endif #endif