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 *  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
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 *         http://www.apache.org/licenses/LICENSE-2.0.txt
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 *  distributed under the License is distributed on an "AS IS" BASIS,
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#ifndef itkMattesMutualInformationImageToImageMetricv4_h
#define itkMattesMutualInformationImageToImageMetricv4_h

#include "itkImageToImageMetricv4.h"
#include "itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.h"
#include "itkPoint.h"
#include "itkIndex.h"
#include "itkBSplineDerivativeKernelFunction.h"
#include "itkArray2D.h"
#include "itkThreadedIndexedContainerPartitioner.h"
#include "itkMutexLockHolder.h"

namespace itk
{

/** \class MattesMutualInformationImageToImageMetricv4
 *
 * \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 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.
 *
 * 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.
 *
 * \warning Local-support transforms are not yet supported. If used,
 * an exception is thrown during Initialize().
 *
 * \note The per-iteration post-processing code is not multi-threaded, but could be
 * readily be made so for a small performance gain.
 * See GetValueCommonAfterThreadedExecution(), GetValueAndDerivative()
 * and threader::AfterThreadedExecution().
 *
 * The algorithm and much of the code was copied from the previous
 * Mattes MI metric, i.e. itkMattesMutualInformationImageToImageMetric.
 *
 * See
 *  MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::ProcessPoint
 *  for poritons of the algorithm implementation.
 *
 * See ImageToImageMetricv4 for details of common metric operation and options.
 *
 * 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.
 *
 * \sa itkImageToImageMetricv4
 * \ingroup ITKMetricsv4
 */
template <typename TFixedImage, typename TMovingImage, typename TVirtualImage = TFixedImage,
          typename TInternalComputationValueType = double,
          typename TMetricTraits = DefaultImageToImageMetricTraitsv4<TFixedImage,TMovingImage,TVirtualImage,TInternalComputationValueType>
          >
class MattesMutualInformationImageToImageMetricv4 :
  public ImageToImageMetricv4<TFixedImage, TMovingImage, TVirtualImage, TInternalComputationValueType, TMetricTraits>
{
public:
  /** Standard class typedefs. */
  typedef MattesMutualInformationImageToImageMetricv4                      Self;
  typedef ImageToImageMetricv4<TFixedImage, TMovingImage, TVirtualImage,
                             TInternalComputationValueType,TMetricTraits>  Superclass;
  typedef SmartPointer<Self>                                               Pointer;
  typedef SmartPointer<const Self>                                         ConstPointer;

  /** Method for creation through the object factory. */
  itkNewMacro(Self);

  /** Run-time type information (and related methods). */
  itkTypeMacro(MattesMutualInformationImageToImageMetricv4, ImageToImageMetricv4);

  /** Superclass types */
  typedef typename Superclass::MeasureType             MeasureType;
  typedef typename Superclass::DerivativeType          DerivativeType;
  typedef typename DerivativeType::ValueType           DerivativeValueType;

  typedef typename Superclass::FixedImageType          FixedImageType;
  typedef typename Superclass::FixedImagePointType     FixedImagePointType;
  typedef typename Superclass::FixedImageIndexType     FixedImageIndexType;
  typedef typename Superclass::FixedImagePixelType     FixedImagePixelType;
  typedef typename Superclass::FixedImageGradientType  FixedImageGradientType;

  typedef typename Superclass::MovingImagePointType    MovingImagePointType;
  typedef typename Superclass::MovingImagePixelType    MovingImagePixelType;
  typedef typename Superclass::MovingImageGradientType MovingImageGradientType;

  typedef typename Superclass::MovingTransformType     MovingTransformType;
  typedef typename Superclass::JacobianType            JacobianType;
  typedef typename Superclass::VirtualImageType        VirtualImageType;
  typedef typename Superclass::VirtualIndexType        VirtualIndexType;
  typedef typename Superclass::VirtualPointType        VirtualPointType;
  typedef typename Superclass::VirtualPointSetType     VirtualPointSetType;

  /** Types inherited from Superclass. */
  typedef typename Superclass::FixedSampledPointSetPointer    FixedSampledPointSetPointer;

  /* Image dimension accessors */
  itkStaticConstMacro(VirtualImageDimension, typename TVirtualImage::ImageDimensionType, TVirtualImage::ImageDimension);
  itkStaticConstMacro(FixedImageDimension,   typename TFixedImage::ImageDimensionType,   TFixedImage::ImageDimension);
  itkStaticConstMacro(MovingImageDimension,  typename TMovingImage::ImageDimensionType,  TMovingImage::ImageDimension);

  /** Number of bins to used in the histogram. Typical 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<SizeValueType>::max() );
  itkGetConstReferenceMacro(NumberOfHistogramBins, SizeValueType);

  virtual void Initialize(void) throw ( itk::ExceptionObject ) ITK_OVERRIDE;

  /** The marginal PDFs are stored as std::vector. */
  //NOTE:  floating point precision is not as stable.
  // Double precision proves faster and more robust in real-world testing.
  typedef TInternalComputationValueType PDFValueType;

  /** Typedef for the joint PDF and PDF derivatives are stored as ITK Images. */
  typedef Image<PDFValueType, 2> JointPDFType;
  typedef Image<PDFValueType, 3> JointPDFDerivativesType;

  /**
   * Get the internal JointPDF image that was used in
   * creating the metric value.
   */
  const typename JointPDFType::Pointer GetJointPDF () const
    {
    if( this->m_ThreaderJointPDF.size() == 0 )
      {
      return typename JointPDFType::Pointer(ITK_NULLPTR);
      }
    return this->m_ThreaderJointPDF[0];
    }

  /**
   * Get the internal JointPDFDeriviative image that was used in
   * creating the metric derivative value.
   * This is only created when a global support transform is used, and
   * derivatives are requested.
   */
  const typename JointPDFDerivativesType::Pointer GetJointPDFDerivatives () const
    {
    return this->m_JointPDFDerivatives;
    }

  virtual void FinalizeThread( const ThreadIdType threadId ) ITK_OVERRIDE;

protected:
  MattesMutualInformationImageToImageMetricv4();
  virtual ~MattesMutualInformationImageToImageMetricv4();

  friend class MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedImageRegionPartitioner< Superclass::VirtualImageDimension >, Superclass, Self >;
  friend class MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedIndexedContainerPartitioner, Superclass, Self >;
  typedef MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedImageRegionPartitioner< Superclass::VirtualImageDimension >, Superclass, Self >
    MattesMutualInformationDenseGetValueAndDerivativeThreaderType;
  typedef MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedIndexedContainerPartitioner, Superclass, Self >
    MattesMutualInformationSparseGetValueAndDerivativeThreaderType;

  void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;

  typedef typename JointPDFType::IndexType             JointPDFIndexType;
  typedef typename JointPDFType::PixelType             JointPDFValueType;
  typedef typename JointPDFType::RegionType            JointPDFRegionType;
  typedef typename JointPDFType::SizeType              JointPDFSizeType;
  typedef typename JointPDFDerivativesType::IndexType  JointPDFDerivativesIndexType;
  typedef typename JointPDFDerivativesType::PixelType  JointPDFDerivativesValueType;
  typedef typename JointPDFDerivativesType::RegionType JointPDFDerivativesRegionType;
  typedef typename JointPDFDerivativesType::SizeType   JointPDFDerivativesSizeType;

  /** Typedefs for BSpline kernel and derivative functions. */
  typedef BSplineKernelFunction<3,PDFValueType>           CubicBSplineFunctionType;
  typedef BSplineDerivativeKernelFunction<3,PDFValueType> CubicBSplineDerivativeFunctionType;

  /** Post-processing code common to both GetValue
   * and GetValueAndDerivative. */
  virtual void GetValueCommonAfterThreadedExecution();

  OffsetValueType ComputeSingleFixedImageParzenWindowIndex( const FixedImagePixelType & value ) const;

  /** 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 std::vector<PRatioType>   PRatioArrayType;

  mutable PRatioArrayType           m_PRatioArray;

  /** Helper array for storing per-parameter linearized index to
   * retrieve the pRatio during evaluation with local-support transform. */
  mutable std::vector<OffsetValueType>   m_JointPdfIndex1DArray;

  /** The moving image marginal PDF. */
  mutable std::vector<PDFValueType>               m_MovingImageMarginalPDF;
  mutable std::vector<std::vector<PDFValueType> > m_ThreaderFixedImageMarginalPDF;

  /** The joint PDF and PDF derivatives. */
  typename std::vector<typename JointPDFType::Pointer>            m_ThreaderJointPDF;

  /* \class DerivativeBufferManager
   * A helper class to manage complexities of minimizing memory
   * needs for mattes mutual information derivative computations
   * per thread.
   *
   * Thread safety note:
   * A seperate object is used locally per each thread. Only the members
   * m_ParentJointPDFDerivativesLockPtr and m_ParentJointPDFDerivatives
   * are shared between threads and access to m_ParentJointPDFDerivatives
   * is controlled with the m_ParentJointPDFDerivativesLockPtr mutex lock.
   * \ingroup ITKMetricsv4
   */
  class DerivativeBufferManager
  {
    typedef DerivativeBufferManager Self;
public:
    /* All these methods are thread safe except ReduceBuffer */

    void Initialize( size_t maxBufferLength, const size_t cachedNumberOfLocalParameters,
                     SimpleFastMutexLock * parentDerivativeLockPtr,
                     typename JointPDFDerivativesType::Pointer parentJointPDFDerivatives);

    void DoubleBufferSize();

    DerivativeBufferManager() :
      m_CurrentFillSize(0),
      m_MemoryBlock(0)
    {
    }

    ~DerivativeBufferManager()
    {
    }

    size_t GetCachedNumberOfLocalParameters() const
    {
      return this->m_CachedNumberOfLocalParameters;
    }

    /**
     * Attempt to dump the buffer if it is full.
     * If the attempt to acquire the lock fails, double the buffer size and try again.
     */
    void CheckAndReduceIfNecessary();

    /**
     * Force the buffer to dump by blocking.
     */
    void BlockAndReduce();

    // If offset is same as previous offset, then accumulate with previous
    PDFValueType * GetNextElementAndAddOffset(const OffsetValueType & offset)
    {
      m_BufferOffsetContainer[m_CurrentFillSize] = offset;
      PDFValueType * PDFBufferForWriting = m_BufferPDFValuesContainer[m_CurrentFillSize];
      ++m_CurrentFillSize;
      return PDFBufferForWriting;
    }

    /**
     * Apply the operations stored in the buffer.
     * This method is not thread safe and requires a lock while threading.
     */
    void ReduceBuffer();

private:
    // How many AccumlatorElements used
    size_t                       m_CurrentFillSize;
    // Continguous chunk of memory for efficiency
    std::vector<PDFValueType>    m_MemoryBlock;
    // The (number of lines in the buffer) * (cells per line)
    size_t                       m_MemoryBlockSize;
    std::vector<PDFValueType *>  m_BufferPDFValuesContainer;
    std::vector<OffsetValueType> m_BufferOffsetContainer;
    size_t                       m_CachedNumberOfLocalParameters;
    size_t                       m_MaxBufferSize;
    // Pointer handle to parent version
    SimpleFastMutexLock *   m_ParentJointPDFDerivativesLockPtr;
    // Smart pointer handle to parent version
    typename JointPDFDerivativesType::Pointer m_ParentJointPDFDerivatives;
  };

  std::vector<DerivativeBufferManager>      m_ThreaderDerivativeManager;
  SimpleFastMutexLock                       m_JointPDFDerivativesLock;
  typename JointPDFDerivativesType::Pointer m_JointPDFDerivatives;

  PDFValueType m_JointPDFSum;

  /** Store the per-point local derivative result by parzen window bin.
   * For local-support transforms only. */
  mutable std::vector<DerivativeType>              m_LocalDerivativeByParzenBin;

private:
  MattesMutualInformationImageToImageMetricv4(const Self &) ITK_DELETE_FUNCTION;
  void operator = (const Self &) ITK_DELETE_FUNCTION;

  /** Perform the final step in computing results */
  virtual void ComputeResults() const;

};

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkMattesMutualInformationImageToImageMetricv4.hxx"
#endif

#endif
