itkVectorConfidenceConnectedImageFilter.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 itkVectorConfidenceConnectedImageFilter_h
#define itkVectorConfidenceConnectedImageFilter_h

#include "itkImageToImageFilter.h"
#include "itkMahalanobisDistanceThresholdImageFunction.h"

namespace itk
{
template< typename TInputImage, typename TOutputImage >
class ITK_TEMPLATE_EXPORT VectorConfidenceConnectedImageFilter:
  public ImageToImageFilter< TInputImage, TOutputImage >
{
public:
  typedef VectorConfidenceConnectedImageFilter            Self;
  typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
  typedef SmartPointer< Self >                            Pointer;
  typedef SmartPointer< const Self >                      ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(VectorConfidenceConnectedImageFilter,
               ImageToImageFilter);

  typedef TInputImage                         InputImageType;
  typedef typename InputImageType::Pointer    InputImagePointer;
  typedef typename InputImageType::RegionType InputImageRegionType;
  typedef typename InputImageType::PixelType  InputImagePixelType;
  typedef typename InputImageType::IndexType  IndexType;
  typedef typename InputImageType::SizeType   SizeType;

  typedef TOutputImage                         OutputImageType;
  typedef typename OutputImageType::Pointer    OutputImagePointer;
  typedef typename OutputImageType::RegionType OutputImageRegionType;
  typedef typename OutputImageType::PixelType  OutputImagePixelType;

  typedef std::vector< IndexType > SeedsContainerType;

  typedef MahalanobisDistanceThresholdImageFunction<
    InputImageType >
  DistanceThresholdFunctionType;

  typedef typename DistanceThresholdFunctionType::CovarianceMatrixType CovarianceMatrixType;
  typedef typename DistanceThresholdFunctionType::MeanVectorType       MeanVectorType;

  typedef  typename DistanceThresholdFunctionType::Pointer DistanceThresholdFunctionPointer;

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

  void SetSeed(const IndexType & seed);

  void AddSeed(const IndexType & seed);

  void ClearSeeds();

  itkSetMacro(Multiplier, double);
  itkGetConstMacro(Multiplier, double);

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

  itkSetMacro(ReplaceValue, OutputImagePixelType);
  itkGetConstMacro(ReplaceValue, OutputImagePixelType);

  itkSetMacro(InitialNeighborhoodRadius, unsigned int);
  itkGetConstReferenceMacro(InitialNeighborhoodRadius, unsigned int);

  const MeanVectorType & GetMean() const;

  const CovarianceMatrixType & GetCovariance() const;

  virtual const SeedsContainerType &GetSeeds() const;


#ifdef ITK_USE_CONCEPT_CHECKING
  // Begin concept checking
  itkConceptMacro( OutputEqualityComparableCheck,
                   ( Concept::EqualityComparable< OutputImagePixelType > ) );
  itkConceptMacro( InputHasNumericTraitsCheck,
                   ( Concept::HasNumericTraits< typename InputImagePixelType::ValueType > ) );
  itkConceptMacro( OutputOStreamWritableCheck,
                   ( Concept::OStreamWritable< OutputImagePixelType > ) );
  // End concept checking
#endif

protected:
  VectorConfidenceConnectedImageFilter();

  // Override since the filter needs all the data for the algorithm
  void GenerateInputRequestedRegion() ITK_OVERRIDE;

  // Override since the filter produces the entire dataset
  void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;

  void GenerateData() ITK_OVERRIDE;

private:
  ITK_DISALLOW_COPY_AND_ASSIGN(VectorConfidenceConnectedImageFilter);

  SeedsContainerType   m_Seeds;
  double               m_Multiplier;
  unsigned int         m_NumberOfIterations;
  OutputImagePixelType m_ReplaceValue;
  unsigned int         m_InitialNeighborhoodRadius;

  DistanceThresholdFunctionPointer m_ThresholdFunction;
};
} // end namespace itk

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

#endif