itkRGBGibbsPriorFilter.h

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/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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 itkRGBGibbsPriorFilter_h
#define itkRGBGibbsPriorFilter_h
 
#include "vnl/vnl_vector.h"
#include "vnl/vnl_matrix.h"
 
#include "itkMRFImageFilter.h"
 
#include <memory> // For unique_ptr.
 
namespace itk
{
template <typename TInputImage, typename TClassifiedImage>
class ITK_TEMPLATE_EXPORT RGBGibbsPriorFilter : public MRFImageFilter<TInputImage, TClassifiedImage>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(RGBGibbsPriorFilter);

  using Self = RGBGibbsPriorFilter;
  using Superclass = MRFImageFilter<TInputImage, TClassifiedImage>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(RGBGibbsPriorFilter);

  using typename Superclass::InputImagePixelType;
  using typename Superclass::InputImageRegionConstIterator;
  using typename Superclass::InputImageRegionIterator;
  using typename Superclass::LabelledImageRegionIterator;
  using typename Superclass::LabelledImagePixelType;
  using typename Superclass::IndexValueType;

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

  using InputPixelType = typename TInputImage::PixelType;

  using ClassifiedImageType = TClassifiedImage;
  using TrainingImageType = typename TClassifiedImage::Pointer;

  using LabelledImageType = typename TClassifiedImage::Pointer;

  using LabelledImageIndexType = typename TClassifiedImage::IndexType;

  using LabelType = unsigned int;

  using ClassifierType = ImageClassifierBase<TInputImage, TClassifiedImage>;

  using InputImageVecType = typename TInputImage::PixelType;
  using IndexType = typename TInputImage::IndexType;

  itkSetMacro(TrainingImage, TrainingImageType);
  itkGetConstMacro(TrainingImage, TrainingImageType);

  void
  SetLabelledImage(LabelledImageType image);

  LabelledImageType
  GetLabelledImage()
  {
    return m_LabelledImage;
  }

  void
  SetClassifier(typename ClassifierType::Pointer ptrToClassifier);

  void
  SetNumberOfClasses(const unsigned int numberOfClasses) override
  {
    itkDebugMacro("setting NumberOfClasses to " << numberOfClasses);
    if (this->m_NumberOfClasses != numberOfClasses)
    {
      this->m_NumberOfClasses = numberOfClasses;
      this->Modified();
    }
  }


  unsigned int
  GetNumberOfClasses() const override
  {
    return this->m_NumberOfClasses;
  }

  void
  SetMaximumNumberOfIterations(const unsigned int numberOfIterations) override
  {
    itkDebugMacro("setting MaximumNumberOfIterations to " << numberOfIterations);
    if (this->m_MaximumNumberOfIterations != numberOfIterations)
    {
      this->m_MaximumNumberOfIterations = numberOfIterations;
      this->Modified();
    }
  }


  unsigned int
  GetMaximumNumberOfIterations() const override
  {
    return this->m_MaximumNumberOfIterations;
  }

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

  itkSetMacro(ObjectLabel, LabelType);
  itkGetConstMacro(ObjectLabel, LabelType);

  static constexpr unsigned int ImageDimension = TInputImage::ImageDimension;
 
  itkSetMacro(StartPoint, IndexType);
  itkGetConstMacro(StartPoint, IndexType);
 
  itkSetMacro(BoundaryGradient, unsigned int);
  itkGetConstMacro(BoundaryGradient, unsigned int);
 
  itkSetMacro(ObjectThreshold, double);
  itkGetConstMacro(ObjectThreshold, double);

  itkSetMacro(CliqueWeight_1, double);
  itkGetConstMacro(CliqueWeight_1, double);
  itkSetMacro(CliqueWeight_2, double);
  itkGetConstMacro(CliqueWeight_2, double);
  itkSetMacro(CliqueWeight_3, double);
  itkGetConstMacro(CliqueWeight_3, double);
  itkSetMacro(CliqueWeight_4, double);
  itkGetConstMacro(CliqueWeight_4, double);
  itkSetMacro(CliqueWeight_5, double);
  itkGetConstMacro(CliqueWeight_5, double);
  itkSetMacro(CliqueWeight_6, double);
  itkGetConstMacro(CliqueWeight_6, double);

  using MatrixType = vnl_matrix<double>;
 
protected:
  RGBGibbsPriorFilter();
  ~RGBGibbsPriorFilter() override = default;
  void
  PrintSelf(std::ostream & os, Indent indent) const override;

  void
  Allocate();
 
  void
  MinimizeFunctional() override;
 
  void
  GenerateData() override;
 
  virtual void
  ApplyGibbsLabeller();
 
  virtual void
  ApplyGPImageFilter();
 
  itkConceptMacro(
    SameDimension,
    (Concept::SameDimension<Self::InputImageType::ImageDimension, Self::ClassifiedImageType::ImageDimension>));
  itkConceptMacro(DimensionShouldBe3, (Concept::SameDimension<Self::InputImageType::ImageDimension, 3>));
 
private:
  using InputImageSizeType = typename TInputImage::SizeType;

  InputImageConstPointer m_InputImage{};

  TrainingImageType m_TrainingImage{};

  LabelledImageType m_LabelledImage{};

  unsigned int m_NumberOfClasses{ 0 };

  unsigned int m_MaximumNumberOfIterations{ 10 };
 
  typename ClassifierType::Pointer m_ClassifierPtr{};

  unsigned int m_BoundaryGradient{ 7 };

  double m_BoundaryWeight{ 1 };

  double m_GibbsPriorWeight{ 1 };

  int m_StartRadius{ 10 };

  int m_RecursiveNumber{ 0 };

  std::unique_ptr<LabelType[]> m_LabelStatus{ nullptr };

  InputImagePointer m_MediumImage{};

  unsigned int m_Temp{ 0 };

  IndexType m_StartPoint{};

  unsigned int m_ImageWidth{ 0 };

  unsigned int m_ImageHeight{ 0 };

  unsigned int m_ImageDepth{ 0 };

  unsigned int m_ClusterSize{ 10 };

  LabelType m_ObjectLabel{ 1 };

  unsigned int m_VecDim{ 0 };

  InputPixelType m_LowPoint{};

  std::unique_ptr<unsigned short[]> m_Region{ nullptr };

  std::unique_ptr<unsigned short[]> m_RegionCount{ nullptr };
 
  // Weights for different clique configurations.

  double m_CliqueWeight_1{ 0.0 };

  double m_CliqueWeight_2{ 0.0 };

  double m_CliqueWeight_3{ 0.0 };

  double m_CliqueWeight_4{ 0.0 };

  double m_CliqueWeight_5{ 0.0 };

  double m_CliqueWeight_6{ 0.0 };

  void
  GibbsTotalEnergy(int i);

  double
  GibbsEnergy(unsigned int i, unsigned int k, unsigned int k1);

  int
  Sim(int a, int b);

  unsigned int
  LabelRegion(int i, int l, int change);

  void
  RegionEraser();

  void
  GenerateMediumImage();

  void
  GreyScalarBoundary(LabelledImageIndexType Index3D);
 
  double m_ObjectThreshold{ 5.0 };
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkRGBGibbsPriorFilter.hxx"
#endif
#endif