/*========================================================================= * * Copyright Insight Software Consortium * * 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 itkMattesMutualInformationImageToImageMetric_h #define itkMattesMutualInformationImageToImageMetric_h #include "itkImageToImageMetric.h" #include "itkPoint.h" #include "itkIndex.h" #include "itkBSplineDerivativeKernelFunction.h" #include "itkArray2D.h" #include "itkSimpleFastMutexLock.h" namespace itk { /** \class MattesMutualInformationImageToImageMetric * \brief Computes the mutual information between two images to be * registered using the method of Mattes et al. * * MattesMutualInformationImageToImageMetric 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. * * 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 ITKRegistrationCommon */ template class ITK_TEMPLATE_EXPORT MattesMutualInformationImageToImageMetric: public ImageToImageMetric { public: /** Standard class typedefs. */ typedef MattesMutualInformationImageToImageMetric Self; typedef ImageToImageMetric Superclass; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(MattesMutualInformationImageToImageMetric, 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::MovingImagePointType MovingImagePointType; typedef typename Superclass::FixedImageConstPointer FixedImageConstPointer; typedef typename Superclass::MovingImageConstPointer MovingImageConstPointer; typedef typename Superclass::BSplineTransformWeightsType BSplineTransformWeightsType; typedef typename Superclass::BSplineTransformIndexArrayType BSplineTransformIndexArrayType; typedef typename Superclass::CoordinateRepresentationType CoordinateRepresentationType; typedef typename Superclass::FixedImageSampleContainer FixedImageSampleContainer; typedef typename Superclass::ImageDerivativesType ImageDerivativesType; typedef typename Superclass::WeightsValueType WeightsValueType; typedef typename Superclass::IndexValueType IndexValueType; typedef typename FixedImageType::OffsetValueType OffsetValueType; /** 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) ITK_OVERRIDE; /** Get the value. */ MeasureType GetValue(const ParametersType & parameters) const ITK_OVERRIDE; /** Get the derivatives of the match measure. */ void GetDerivative(const ParametersType & parameters, DerivativeType & Derivative) const ITK_OVERRIDE; /** Get the value and derivatives for single valued optimizers. */ void GetValueAndDerivative(const ParametersType & parameters, MeasureType & Value, DerivativeType & Derivative) const ITK_OVERRIDE; /** Number of bins to used in the histogram. * According to Mattes et al the optimum value is 50. * The minimum value is 5 due to the padding required by the Parzen * windowing with a cubic-BSpline kernel. Note that even if the metric * is used on binary images, the number of bins should at least be * equal to five. */ itkSetClampMacro( NumberOfHistogramBins, SizeValueType, 5, NumericTraits::max() ); itkGetConstReferenceMacro(NumberOfHistogramBins, SizeValueType); /** 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 floating point values 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 floating point values with size equals to (number of * histogram bins)^2. This method is well suited for Transforms with a large * number of parameters, such as, BSplineTransforms. */ itkSetMacro(UseExplicitPDFDerivatives, bool); itkGetConstReferenceMacro(UseExplicitPDFDerivatives, bool); itkBooleanMacro(UseExplicitPDFDerivatives); /** The marginal PDFs are stored as std::vector. */ typedef double PDFValueType; //NOTE: floating point precision is not as stable. Double precision proves faster and more robust in real-world testing. /** Typedef for the joint PDF and PDF derivatives are stored as ITK Images. */ typedef Image JointPDFType; typedef Image JointPDFDerivativesType; /** * Get the internal JointPDF image that was used in * creating the metric value. */ const typename JointPDFType::Pointer GetJointPDF () const { if( this->m_MMIMetricPerThreadVariables == ITK_NULLPTR ) { return JointPDFType::Pointer(ITK_NULLPTR); } return this->m_MMIMetricPerThreadVariables[0].JointPDF; } /** * Get the internal JointPDFDeriviative image that was used in * creating the metric derivative value. * This is only created when UseExplicitPDFDerivatives is ON, and * derivatives are requested. */ const typename JointPDFDerivativesType::Pointer GetJointPDFDerivatives () const { if( this->m_MMIMetricPerThreadVariables == ITK_NULLPTR ) { return JointPDFDerivativesType::Pointer(ITK_NULLPTR); } return this->m_MMIMetricPerThreadVariables[0].JointPDFDerivatives; } protected: MattesMutualInformationImageToImageMetric(); virtual ~MattesMutualInformationImageToImageMetric() ITK_OVERRIDE; void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE; private: ITK_DISALLOW_COPY_AND_ASSIGN(MattesMutualInformationImageToImageMetric); typedef JointPDFType::IndexType JointPDFIndexType; typedef JointPDFType::PixelType JointPDFValueType; typedef JointPDFType::RegionType JointPDFRegionType; typedef JointPDFType::SizeType JointPDFSizeType; typedef JointPDFDerivativesType::IndexType JointPDFDerivativesIndexType; typedef JointPDFDerivativesType::PixelType JointPDFDerivativesValueType; typedef JointPDFDerivativesType::RegionType JointPDFDerivativesRegionType; typedef JointPDFDerivativesType::SizeType JointPDFDerivativesSizeType; /** Typedefs for BSpline kernel and derivative functions. */ typedef BSplineKernelFunction<3,PDFValueType> CubicBSplineFunctionType; typedef BSplineDerivativeKernelFunction<3,PDFValueType> CubicBSplineDerivativeFunctionType; /** Precompute fixed image parzen window indices. */ void ComputeFixedImageParzenWindowIndices( FixedImageSampleContainer & samples); /** Compute PDF derivative contribution for each parameter. */ void ComputePDFDerivatives(ThreadIdType threadId, unsigned int sampleNumber, int movingImageParzenWindowIndex, const ImageDerivativesType & movingImageGradientValue, PDFValueType cubicBSplineDerivativeValue) const; virtual void GetValueThreadPreProcess(ThreadIdType threadId, bool withinSampleThread) const ITK_OVERRIDE; virtual void GetValueThreadPostProcess(ThreadIdType threadId, bool withinSampleThread) const ITK_OVERRIDE; //NOTE: The signature in base class requires that movingImageValue is of type double virtual bool GetValueThreadProcessSample(ThreadIdType threadId, SizeValueType fixedImageSample, const MovingImagePointType & mappedPoint, double movingImageValue) const ITK_OVERRIDE; virtual void GetValueAndDerivativeThreadPreProcess( ThreadIdType threadId, bool withinSampleThread) const ITK_OVERRIDE; virtual void GetValueAndDerivativeThreadPostProcess( ThreadIdType threadId, bool withinSampleThread) const ITK_OVERRIDE; //NOTE: The signature in base class requires that movingImageValue is of type double virtual bool GetValueAndDerivativeThreadProcessSample(ThreadIdType threadId, SizeValueType fixedImageSample, const MovingImagePointType & mappedPoint, double movingImageValue, const ImageDerivativesType & movingImageGradientValue) const ITK_OVERRIDE; /** Variables to define the marginal and joint histograms. */ SizeValueType m_NumberOfHistogramBins; PDFValueType m_MovingImageNormalizedMin; PDFValueType m_FixedImageNormalizedMin; PDFValueType m_FixedImageTrueMin; PDFValueType m_FixedImageTrueMax; PDFValueType m_MovingImageTrueMin; PDFValueType m_MovingImageTrueMax; PDFValueType m_FixedImageBinSize; PDFValueType m_MovingImageBinSize; /** Cubic BSpline kernel for computing Parzen histograms. */ typename CubicBSplineFunctionType::Pointer m_CubicBSplineKernel; typename CubicBSplineDerivativeFunctionType::Pointer m_CubicBSplineDerivativeKernel; /** Helper array for storing the values of the JointPDF ratios. */ typedef PDFValueType PRatioType; typedef Array2D PRatioArrayType; mutable PRatioArrayType m_PRatioArray; /** The moving image marginal PDF. */ typedef std::vector< PDFValueType > MarginalPDFType; mutable MarginalPDFType m_MovingImageMarginalPDF; struct MMIMetricPerThreadStruct { int JointPDFStartBin; int JointPDFEndBin; PDFValueType JointPDFSum; /** Helper variable for accumulating the derivative of the metric. */ DerivativeType MetricDerivative; /** The joint PDF and PDF derivatives. */ typename JointPDFType::Pointer JointPDF; typename JointPDFDerivativesType::Pointer JointPDFDerivatives; typename TransformType::JacobianType Jacobian; MarginalPDFType FixedImageMarginalPDF; }; #if !defined(ITK_WRAPPING_PARSER) itkPadStruct( ITK_CACHE_LINE_ALIGNMENT, MMIMetricPerThreadStruct, PaddedMMIMetricPerThreadStruct); itkAlignedTypedef( ITK_CACHE_LINE_ALIGNMENT, PaddedMMIMetricPerThreadStruct, AlignedMMIMetricPerThreadStruct ); // Due to a bug in older version of Visual Studio where std::vector resize // uses a value instead of a const reference, this must be a pointer. // See // http://thetweaker.wordpress.com/2010/05/05/stdvector-of-aligned-elements/ // http://connect.microsoft.com/VisualStudio/feedback/details/692988 mutable AlignedMMIMetricPerThreadStruct * m_MMIMetricPerThreadVariables; #endif bool m_UseExplicitPDFDerivatives; mutable bool m_ImplicitDerivativesSecondPass; }; } // end namespace itk #ifndef ITK_MANUAL_INSTANTIATION #include "itkMattesMutualInformationImageToImageMetric.hxx" #endif #endif