itkBayesianClassifierImageFilter.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 itkBayesianClassifierImageFilter_h
#define itkBayesianClassifierImageFilter_h

#include "itkVectorImage.h"
#include "itkImageToImageFilter.h"
#include "itkMaximumDecisionRule.h"
#include "itkImageRegionIterator.h"

namespace itk
{
template< typename TInputVectorImage, typename TLabelsType = unsigned char,
          typename TPosteriorsPrecisionType = double, typename TPriorsPrecisionType = double >
class ITK_TEMPLATE_EXPORT BayesianClassifierImageFilter:
  public ImageToImageFilter<
    TInputVectorImage, Image< TLabelsType,
                               TInputVectorImage ::ImageDimension > >
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(BayesianClassifierImageFilter);

  using Self = BayesianClassifierImageFilter;
  using Superclass = ImageToImageFilter<
    TInputVectorImage,
    Image< TLabelsType, TInputVectorImage::ImageDimension > >;

  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;

  itkNewMacro(Self);

  itkTypeMacro(BayesianClassifierImageFilter, ImageToImageFilter);

  using InputImageType = typename Superclass::InputImageType;

  static constexpr unsigned int Dimension = InputImageType ::ImageDimension;

  using OutputImageType = Image< TLabelsType,
                 Self::Dimension >;
  using InputImagePointer = typename InputImageType::ConstPointer;
  using OutputImagePointer = typename OutputImageType::Pointer;
  using ImageRegionType = typename InputImageType::RegionType;

  using InputImageIteratorType = ImageRegionConstIterator< InputImageType >;
  using OutputImageIteratorType = ImageRegionIterator< OutputImageType >;

  using InputPixelType = typename InputImageType::PixelType;
  using OutputPixelType = typename OutputImageType::PixelType;

  using PriorsImageType = VectorImage< TPriorsPrecisionType,
                       Self::Dimension >;
  using PriorsPixelType = typename PriorsImageType::PixelType;
  using PriorsImagePointer = typename PriorsImageType::Pointer;
  using PriorsImageIteratorType = ImageRegionConstIterator< PriorsImageType >;

  using MembershipImageType = TInputVectorImage;
  using MembershipPixelType = typename MembershipImageType::PixelType;
  using MembershipImagePointer = typename MembershipImageType::Pointer;
  using MembershipImageIteratorType = ImageRegionConstIterator< MembershipImageType >;

  using PosteriorsImageType = VectorImage< TPosteriorsPrecisionType,
                       Self::Dimension >;
  using PosteriorsPixelType = typename PosteriorsImageType::PixelType;
  using PosteriorsImagePointer = typename PosteriorsImageType::Pointer;
  using PosteriorsImageIteratorType = ImageRegionIterator< PosteriorsImageType >;

  using DecisionRuleType = Statistics::MaximumDecisionRule;
  using DecisionRulePointer = DecisionRuleType::Pointer;

  using DataObjectPointer = typename Superclass::DataObjectPointer;

  using ExtractedComponentImageType = itk::Image< TPosteriorsPrecisionType,
                      Self::Dimension >;

  using SmoothingFilterType = ImageToImageFilter<
    ExtractedComponentImageType,
    ExtractedComponentImageType  >;

  using SmoothingFilterPointer = typename SmoothingFilterType::Pointer;

  void SetSmoothingFilter(SmoothingFilterType *);
  itkGetConstMacro(SmoothingFilter, SmoothingFilterPointer);

  virtual void SetPriors(const PriorsImageType *);

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

  using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType;
  using Superclass::MakeOutput;
  DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx) override;

#ifdef ITK_USE_CONCEPT_CHECKING
  // Begin concept checking
  itkConceptMacro( UnsignedIntConvertibleToLabelsCheck,
                   ( Concept::Convertible< unsigned int, TLabelsType > ) );
  itkConceptMacro( PosteriorsAdditiveOperatorsCheck,
                   ( Concept::AdditiveOperators< TPosteriorsPrecisionType > ) );
  itkConceptMacro( IntConvertibleToPosteriorsCheck,
                   ( Concept::Convertible< int, TPosteriorsPrecisionType > ) );
  itkConceptMacro( InputHasNumericTraitsCheck,
                   ( Concept::HasNumericTraits< typename InputPixelType::ValueType > ) );
  itkConceptMacro( PosteriorsHasNumericTraitsCheck,
                   ( Concept::HasNumericTraits< TPosteriorsPrecisionType > ) );
  itkConceptMacro( PriorsHasNumericTraitsCheck,
                   ( Concept::HasNumericTraits< TPriorsPrecisionType > ) );
  itkConceptMacro( InputPriorsPosteriorsMultiplyOperatorCheck,
                   ( Concept::MultiplyOperator< typename InputPixelType::ValueType,
                                                PriorsPixelType, PosteriorsPixelType > ) );
  // End concept checking
#endif

protected:

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

  void GenerateData() override;

  void GenerateOutputInformation() override;

  virtual void ComputeBayesRule();

  virtual void NormalizeAndSmoothPosteriors();

  virtual void ClassifyBasedOnPosteriors();

  PosteriorsImageType * GetPosteriorImage();

private:


  bool m_UserProvidedPriors{ false };

  bool m_UserProvidedSmoothingFilter{ false };

  SmoothingFilterPointer m_SmoothingFilter;

  unsigned int m_NumberOfSmoothingIterations{ 0 };
};
} // end namespace itk

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

#endif