itkMRFImageFilter.h

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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
 *
 *         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 itkMRFImageFilter_h
#define itkMRFImageFilter_h

#include "vnl/vnl_vector.h"
#include "vnl/vnl_matrix.h"

#include "itkImageClassifierBase.h"

#include "itkImageToImageFilter.h"

#include "itkConstNeighborhoodIterator.h"
#include "itkNeighborhoodAlgorithm.h"
#include "itkSize.h"

namespace itk
{
template< typename TInputImage, typename TClassifiedImage >
class ITK_TEMPLATE_EXPORT MRFImageFilter:
  public ImageToImageFilter< TInputImage, TClassifiedImage >
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(MRFImageFilter);

  using Self = MRFImageFilter;
  using Superclass = ImageToImageFilter< TInputImage, TClassifiedImage >;
  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;
  using OutputImagePointer = typename Superclass::OutputImagePointer;

  itkNewMacro(Self);

  itkTypeMacro(MRFImageFilter, Object);

  using InputImageType = TInputImage;
  using InputImagePointer = typename TInputImage::Pointer;
  using InputImageConstPointer = typename TInputImage::ConstPointer;

  using InputImagePixelType = typename TInputImage::PixelType;

  using InputImageRegionType = typename TInputImage::RegionType;

  using InputImageRegionIterator = ImageRegionIterator< TInputImage >;
  using InputImageRegionConstIterator = ImageRegionConstIterator< TInputImage >;

  static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension;

  using TrainingImagePointer = typename TClassifiedImage::Pointer;

  using TrainingImagePixelType = typename TClassifiedImage::PixelType;

  using LabelledImagePointer = typename TClassifiedImage::Pointer;

  using LabelledImagePixelType = typename TClassifiedImage::PixelType;

  using LabelledImageRegionType = typename TClassifiedImage::RegionType;

  using LabelledImageIndexType = typename TClassifiedImage::IndexType;
  using IndexValueType = typename LabelledImageIndexType::IndexValueType;

  using LabelledImageOffsetType = typename TClassifiedImage::OffsetType;

  using LabelledImageRegionIterator = ImageRegionIterator< TClassifiedImage >;

  static constexpr unsigned int ClassifiedImageDimension = TClassifiedImage::ImageDimension;

  using ClassifierType = ImageClassifierBase< TInputImage, TClassifiedImage >;

  using SizeType = typename TInputImage::SizeType;

  using NeighborhoodRadiusType = typename TInputImage::SizeType;

  using InputImageNeighborhoodIterator = ConstNeighborhoodIterator<TInputImage>;

  using InputImageNeighborhoodRadiusType = typename InputImageNeighborhoodIterator::RadiusType;

  using InputImageFacesCalculator = NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<TInputImage>;

  using InputImageFaceListType = typename InputImageFacesCalculator::FaceListType;

  using InputImageFaceListIterator = typename InputImageFaceListType::iterator;

  using LabelledImageNeighborhoodIterator = NeighborhoodIterator< TClassifiedImage >;

  using LabelledImageNeighborhoodRadiusType = typename LabelledImageNeighborhoodIterator::RadiusType;

  using LabelledImageFacesCalculator = NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< TClassifiedImage >;

  using LabelledImageFaceListType = typename LabelledImageFacesCalculator::FaceListType;

  using LabelledImageFaceListIterator = typename LabelledImageFaceListType::iterator;

  void SetClassifier(typename ClassifierType::Pointer ptrToClassifier);

  itkSetMacro(NumberOfClasses, unsigned int);
  itkGetConstMacro(NumberOfClasses, unsigned int);

  itkSetMacro(MaximumNumberOfIterations, unsigned int);
  itkGetConstMacro(MaximumNumberOfIterations, unsigned int);

  itkSetMacro(ErrorTolerance, double);
  itkGetConstMacro(ErrorTolerance, double);

  itkSetMacro(SmoothingFactor, double);
  itkGetConstMacro(SmoothingFactor, double);

  void SetNeighborhoodRadius(const NeighborhoodRadiusType &);

  void SetNeighborhoodRadius(const SizeValueType);

  void SetNeighborhoodRadius(const SizeValueType *radiusArray);

  const NeighborhoodRadiusType GetNeighborhoodRadius() const
  {
    NeighborhoodRadiusType radius;

    for ( int i = 0; i < InputImageDimension; ++i )
      {
      radius[i] = m_InputImageNeighborhoodRadius[i];
      }
    return radius;
  }

  virtual void SetMRFNeighborhoodWeight(std::vector< double > BetaMatrix);

  virtual std::vector< double > GetMRFNeighborhoodWeight()
  {
    return m_MRFNeighborhoodWeight;
  }

//Enum to get the stopping condition of the MRF filter
  typedef enum {
    MaximumNumberOfIterations = 1,
    ErrorTolerance
    } StopConditionType;

  itkGetConstReferenceMacro(StopCondition, StopConditionType);

  /* Get macro for number of iterations */
  itkGetConstReferenceMacro(NumberOfIterations, unsigned int);

#ifdef ITK_USE_CONCEPT_CHECKING
  // Begin concept checking
  itkConceptMacro( UnsignedIntConvertibleToClassifiedCheck,
                   ( Concept::Convertible< unsigned int, LabelledImagePixelType > ) );
  itkConceptMacro( ClassifiedConvertibleToUnsignedIntCheck,
                   ( Concept::Convertible< LabelledImagePixelType, unsigned int > ) );
  itkConceptMacro( ClassifiedConvertibleToIntCheck,
                   ( Concept::Convertible< LabelledImagePixelType, int > ) );
  itkConceptMacro( IntConvertibleToClassifiedCheck,
                   ( Concept::Convertible< int, LabelledImagePixelType > ) );
  itkConceptMacro( SameDimensionCheck,
                   ( Concept::SameDimension< InputImageDimension, ClassifiedImageDimension > ) );
  // End concept checking
#endif

protected:
  MRFImageFilter();
  ~MRFImageFilter() override = default;
  void PrintSelf(std::ostream & os, Indent indent) const override;

  void Allocate();

  virtual void ApplyMRFImageFilter();

  virtual void MinimizeFunctional();

  using LabelStatusImageType = Image< int, Self::InputImageDimension >;
  using LabelStatusIndexType = typename LabelStatusImageType::IndexType;
  using LabelStatusRegionType = typename LabelStatusImageType::RegionType;
  using LabelStatusImagePointer = typename LabelStatusImageType::Pointer;
  using LabelStatusImageIterator = ImageRegionIterator< LabelStatusImageType >;

  using LabelStatusImageNeighborhoodIterator = NeighborhoodIterator<LabelStatusImageType>;
  //Function implementing the neighborhood operation

  virtual void DoNeighborhoodOperation(const InputImageNeighborhoodIterator & imageIter,
                                       LabelledImageNeighborhoodIterator & labelledIter,
                                       LabelStatusImageNeighborhoodIterator & labelStatusIter);

  void GenerateData() override;

  void GenerateInputRequestedRegion() override;

  void EnlargeOutputRequestedRegion(DataObject *) override;

  void GenerateOutputInformation() override;

private:
  using InputImageSizeType = typename TInputImage::SizeType;

  using LabelStatusImageNeighborhoodRadiusType = typename LabelStatusImageNeighborhoodIterator::RadiusType;

  using LabelStatusImageFacesCalculator = NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<LabelStatusImageType>;

  using LabelStatusImageFaceListType = typename LabelStatusImageFacesCalculator::FaceListType;

  using LabelStatusImageFaceListIterator = typename LabelStatusImageFaceListType::iterator;

  InputImageNeighborhoodRadiusType       m_InputImageNeighborhoodRadius;
  LabelledImageNeighborhoodRadiusType    m_LabelledImageNeighborhoodRadius;
  LabelStatusImageNeighborhoodRadiusType m_LabelStatusImageNeighborhoodRadius;

  unsigned int m_NumberOfClasses{0};
  unsigned int m_MaximumNumberOfIterations{50};
  unsigned int m_KernelSize;

  int               m_ErrorCounter{0};
  int               m_NeighborhoodSize{27};
  int               m_TotalNumberOfValidPixelsInOutputImage{1};
  int               m_TotalNumberOfPixelsInInputImage{1};
  double            m_ErrorTolerance{0.2};
  double            m_SmoothingFactor{1};
  double *          m_ClassProbability{nullptr};         //Class liklihood
  unsigned int      m_NumberOfIterations{0};
  StopConditionType m_StopCondition;

  LabelStatusImagePointer m_LabelStatusImage;

  std::vector< double > m_MRFNeighborhoodWeight;
  std::vector< double > m_NeighborInfluence;
  std::vector< double > m_MahalanobisDistance;
  std::vector< double > m_DummyVector;

  typename ClassifierType::Pointer m_ClassifierPtr;

  virtual void SetDefaultMRFNeighborhoodWeight();

  //Function implementing the ICM algorithm to label the images
  void ApplyICMLabeller();
}; // class MRFImageFilter
} // namespace itk

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

#endif