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

  typedef SmartPointer< Self >       Pointer;
  typedef SmartPointer< const Self > ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(BayesianClassifierImageFilter, ImageToImageFilter);

  typedef typename Superclass::InputImageType InputImageType;

  itkStaticConstMacro(Dimension, unsigned int,
                       InputImageType ::ImageDimension);

  typedef Image< TLabelsType,
                 itkGetStaticConstMacro(Dimension) >        OutputImageType;
  typedef typename InputImageType::ConstPointer InputImagePointer;
  typedef typename OutputImageType::Pointer     OutputImagePointer;
  typedef typename InputImageType::RegionType   ImageRegionType;

  typedef ImageRegionConstIterator< InputImageType > InputImageIteratorType;
  typedef ImageRegionIterator< OutputImageType >     OutputImageIteratorType;

  typedef typename InputImageType::PixelType  InputPixelType;
  typedef typename OutputImageType::PixelType OutputPixelType;

  typedef VectorImage< TPriorsPrecisionType,
                       itkGetStaticConstMacro(Dimension) >                  PriorsImageType;
  typedef typename PriorsImageType::PixelType         PriorsPixelType;
  typedef typename PriorsImageType::Pointer           PriorsImagePointer;
  typedef ImageRegionConstIterator< PriorsImageType > PriorsImageIteratorType;

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

  typedef VectorImage< TPosteriorsPrecisionType,
                       itkGetStaticConstMacro(Dimension) >                  PosteriorsImageType;
  typedef typename PosteriorsImageType::PixelType    PosteriorsPixelType;
  typedef typename PosteriorsImageType::Pointer      PosteriorsImagePointer;
  typedef ImageRegionIterator< PosteriorsImageType > PosteriorsImageIteratorType;

  typedef Statistics::MaximumDecisionRule DecisionRuleType;
  typedef DecisionRuleType::Pointer       DecisionRulePointer;

  typedef typename Superclass::DataObjectPointer DataObjectPointer;

  typedef itk::Image< TPosteriorsPrecisionType,
                      itkGetStaticConstMacro(Dimension) >                ExtractedComponentImageType;

  typedef ImageToImageFilter<
    ExtractedComponentImageType,
    ExtractedComponentImageType  >         SmoothingFilterType;

  typedef typename SmoothingFilterType::Pointer SmoothingFilterPointer;

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

  virtual void SetPriors(const PriorsImageType *);

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

  typedef ProcessObject::DataObjectPointerArraySizeType DataObjectPointerArraySizeType;
  using Superclass::MakeOutput;
  virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx) ITK_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();
  virtual ~BayesianClassifierImageFilter() ITK_OVERRIDE {}
  void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

  virtual void GenerateData() ITK_OVERRIDE;

  virtual void GenerateOutputInformation(void) ITK_OVERRIDE;

  virtual void ComputeBayesRule();

  virtual void NormalizeAndSmoothPosteriors();

  virtual void ClassifyBasedOnPosteriors();

  PosteriorsImageType * GetPosteriorImage();

private:

  ITK_DISALLOW_COPY_AND_ASSIGN(BayesianClassifierImageFilter);


  bool m_UserProvidedPriors;

  bool m_UserProvidedSmoothingFilter;

  SmoothingFilterPointer m_SmoothingFilter;

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

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

#endif