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 MRFImageFilter:
  public ImageToImageFilter< TInputImage, TClassifiedImage >
{
public:
  typedef MRFImageFilter                                      Self;
  typedef ImageToImageFilter< TInputImage, TClassifiedImage > Superclass;
  typedef SmartPointer< Self >                                Pointer;
  typedef SmartPointer< const Self >                          ConstPointer;
  typedef typename Superclass::OutputImagePointer             OutputImagePointer;

  itkNewMacro(Self);

  itkTypeMacro(MRFImageFilter, Object);

  typedef TInputImage                        InputImageType;
  typedef typename TInputImage::Pointer      InputImagePointer;
  typedef typename TInputImage::ConstPointer InputImageConstPointer;

  typedef typename TInputImage::PixelType InputImagePixelType;

  typedef typename TInputImage::RegionType InputImageRegionType;

  typedef ImageRegionIterator< TInputImage >      InputImageRegionIterator;
  typedef ImageRegionConstIterator< TInputImage > InputImageRegionConstIterator;

  itkStaticConstMacro(InputImageDimension, unsigned int,
                      TInputImage::ImageDimension);

  typedef typename TClassifiedImage::Pointer TrainingImagePointer;

  typedef typename TClassifiedImage::PixelType TrainingImagePixelType;

  typedef typename TClassifiedImage::Pointer LabelledImagePointer;

  typedef typename TClassifiedImage::PixelType LabelledImagePixelType;

  typedef typename TClassifiedImage::RegionType LabelledImageRegionType;

  typedef typename TClassifiedImage::IndexType            LabelledImageIndexType;
  typedef typename LabelledImageIndexType::IndexValueType IndexValueType;

  typedef typename TClassifiedImage::OffsetType LabelledImageOffsetType;

  typedef ImageRegionIterator< TClassifiedImage >
  LabelledImageRegionIterator;

  itkStaticConstMacro(ClassifiedImageDimension, unsigned int,
                      TClassifiedImage::ImageDimension);

  typedef ImageClassifierBase< TInputImage, TClassifiedImage > ClassifierType;

  typedef typename TInputImage::SizeType SizeType;

  typedef typename TInputImage::SizeType NeighborhoodRadiusType;

  typedef ConstNeighborhoodIterator< TInputImage >
  InputImageNeighborhoodIterator;

  typedef typename InputImageNeighborhoodIterator::RadiusType
  InputImageNeighborhoodRadiusType;

  typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< TInputImage >
  InputImageFacesCalculator;

  typedef typename InputImageFacesCalculator::FaceListType
  InputImageFaceListType;

  typedef typename InputImageFaceListType::iterator
  InputImageFaceListIterator;

  typedef NeighborhoodIterator< TClassifiedImage >
  LabelledImageNeighborhoodIterator;

  typedef typename LabelledImageNeighborhoodIterator::RadiusType
  LabelledImageNeighborhoodRadiusType;

  typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< TClassifiedImage >
  LabelledImageFacesCalculator;

  typedef typename LabelledImageFacesCalculator::FaceListType
  LabelledImageFaceListType;

  typedef typename LabelledImageFaceListType::iterator
  LabelledImageFaceListIterator;

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

  void Allocate();

  virtual void ApplyMRFImageFilter();

  virtual void MinimizeFunctional();

  typedef Image< int, itkGetStaticConstMacro(InputImageDimension) > LabelStatusImageType;
  typedef typename LabelStatusImageType::IndexType                  LabelStatusIndexType;
  typedef typename LabelStatusImageType::RegionType                 LabelStatusRegionType;
  typedef typename LabelStatusImageType::Pointer                    LabelStatusImagePointer;
  typedef ImageRegionIterator< LabelStatusImageType >               LabelStatusImageIterator;

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

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

  virtual void GenerateData() ITK_OVERRIDE;

  virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;

  virtual void EnlargeOutputRequestedRegion(DataObject *) ITK_OVERRIDE;

  virtual void GenerateOutputInformation() ITK_OVERRIDE;

private:
  MRFImageFilter(const Self &); //purposely not implemented
  void operator=(const Self &); //purposely not implemented

  typedef typename TInputImage::SizeType InputImageSizeType;

  typedef typename LabelStatusImageNeighborhoodIterator::RadiusType
  LabelStatusImageNeighborhoodRadiusType;

  typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< LabelStatusImageType >
  LabelStatusImageFacesCalculator;

  typedef typename LabelStatusImageFacesCalculator::FaceListType
  LabelStatusImageFaceListType;

  typedef typename LabelStatusImageFaceListType::iterator
  LabelStatusImageFaceListIterator;

  InputImageNeighborhoodRadiusType       m_InputImageNeighborhoodRadius;
  LabelledImageNeighborhoodRadiusType    m_LabelledImageNeighborhoodRadius;
  LabelStatusImageNeighborhoodRadiusType m_LabelStatusImageNeighborhoodRadius;

  unsigned int m_NumberOfClasses;
  unsigned int m_MaximumNumberOfIterations;
  unsigned int m_KernelSize;

  int               m_ErrorCounter;
  int               m_NeighborhoodSize;
  int               m_TotalNumberOfValidPixelsInOutputImage;
  int               m_TotalNumberOfPixelsInInputImage;
  double            m_ErrorTolerance;
  double            m_SmoothingFactor;
  double *          m_ClassProbability;         //Class liklihood
  unsigned int      m_NumberOfIterations;
  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