itkScalarImageKmeansImageFilter.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 itkScalarImageKmeansImageFilter_h
#define itkScalarImageKmeansImageFilter_h


#include "itkKdTree.h"
#include "itkKdTreeBasedKmeansEstimator.h"
#include "itkWeightedCentroidKdTreeGenerator.h"

#include "itkSampleClassifierFilter.h"
#include "itkImageToListSampleAdaptor.h"
#include "itkMinimumDecisionRule.h"

#include "itkRegionOfInterestImageFilter.h"

#include <vector>

namespace itk
{
template< typename TInputImage,
          typename TOutputImage = Image< unsigned char, TInputImage::ImageDimension > >
class ScalarImageKmeansImageFilter:
  public ImageToImageFilter< TInputImage, TOutputImage >
{
public:
  itkStaticConstMacro(ImageDimension, unsigned int,
                      TInputImage::ImageDimension);

  typedef TInputImage  InputImageType;
  typedef TOutputImage OutputImageType;

  typedef ScalarImageKmeansImageFilter                          Self;
  typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
  typedef SmartPointer< Self >                                  Pointer;
  typedef SmartPointer< const Self >                            ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(ScalarImageKmeansImageFilter, ImageToImageFilter);

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

  typedef typename NumericTraits< InputPixelType >::RealType RealPixelType;

  typedef itk::Statistics::ImageToListSampleAdaptor< InputImageType > AdaptorType;

  typedef typename AdaptorType::MeasurementVectorType MeasurementVectorType;

  typedef itk::Statistics::DistanceToCentroidMembershipFunction< MeasurementVectorType > MembershipFunctionType;
  typedef itk::Statistics::SampleClassifierFilter< AdaptorType >                         ClassifierType;
  typedef itk::Statistics::MinimumDecisionRule  DecisionRuleType;

  typedef typename ClassifierType::ClassLabelVectorType ClassLabelVectorType;

  typedef typename ClassifierType::MembershipFunctionVectorType MembershipFunctionVectorType;
  typedef typename MembershipFunctionType::CentroidType         MembershipFunctionOriginType;

  typedef typename MembershipFunctionType::Pointer MembershipFunctionPointer;

  typedef itk::Statistics::WeightedCentroidKdTreeGenerator< AdaptorType > TreeGeneratorType;
  typedef typename TreeGeneratorType::KdTreeType                          TreeType;
  typedef itk::Statistics::KdTreeBasedKmeansEstimator< TreeType >         EstimatorType;

  typedef typename EstimatorType::ParametersType ParametersType;

  typedef typename InputImageType::RegionType ImageRegionType;

  typedef RegionOfInterestImageFilter<
    InputImageType,
    InputImageType  > RegionOfInterestFilterType;

  void AddClassWithInitialMean(RealPixelType mean);

  itkGetConstReferenceMacro(FinalMeans, ParametersType);

  itkSetMacro(UseNonContiguousLabels, bool);
  itkGetConstReferenceMacro(UseNonContiguousLabels, bool);
  itkBooleanMacro(UseNonContiguousLabels);

  void SetImageRegion(const ImageRegionType & region);

  itkGetConstReferenceMacro(ImageRegion, ImageRegionType);

#ifdef ITK_USE_CONCEPT_CHECKING
  // Begin concept checking
  itkConceptMacro( InputHasNumericTraitsCheck,
                   ( Concept::HasNumericTraits< InputPixelType > ) );
  // End concept checking
#endif

protected:
  ScalarImageKmeansImageFilter();
  virtual ~ScalarImageKmeansImageFilter() {}
  void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

  void GenerateData() ITK_OVERRIDE;

  /* See superclass for doxygen. This methods additionally checks that
   * the number of means is not 0. */
  virtual void VerifyPreconditions() ITK_OVERRIDE;

private:
  ScalarImageKmeansImageFilter(const Self &); //purposely not implemented
  void operator=(const Self &);               //purposely not implemented

  typedef std::vector< RealPixelType > MeansContainer;

  MeansContainer m_InitialMeans;

  ParametersType m_FinalMeans;

  bool m_UseNonContiguousLabels;

  ImageRegionType m_ImageRegion;

  bool m_ImageRegionDefined;
};
} // end namespace itk

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

#endif