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:
  ITK_DISALLOW_COPY_AND_ASSIGN(VectorConfidenceConnectedImageFilter);

  using Self = VectorConfidenceConnectedImageFilter;
  using Superclass = ImageToImageFilter< TInputImage, TOutputImage >;
  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;

  itkNewMacro(Self);

  itkTypeMacro(VectorConfidenceConnectedImageFilter,
               ImageToImageFilter);

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

  using OutputImageType = TOutputImage;
  using OutputImagePointer = typename OutputImageType::Pointer;
  using OutputImageRegionType = typename OutputImageType::RegionType;
  using OutputImagePixelType = typename OutputImageType::PixelType;

  using SeedsContainerType = std::vector< IndexType >;

  using DistanceThresholdFunctionType = MahalanobisDistanceThresholdImageFunction<InputImageType>;

  using CovarianceMatrixType = typename DistanceThresholdFunctionType::CovarianceMatrixType;
  using MeanVectorType = typename DistanceThresholdFunctionType::MeanVectorType;

  using DistanceThresholdFunctionPointer = typename DistanceThresholdFunctionType::Pointer;

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

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

  void GenerateData() override;

private:
  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