itkMultiLabelSTAPLEImageFilter.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 itkMultiLabelSTAPLEImageFilter_h
#define itkMultiLabelSTAPLEImageFilter_h

#include "itkImage.h"
#include "itkImageToImageFilter.h"

#include "itkImageRegionIterator.h"
#include "itkImageRegionConstIterator.h"

#include "vector"
#include "itkArray.h"
#include "itkArray2D.h"
#include "itkNumericTraits.h"

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

  itkNewMacro(Self);

  itkTypeMacro(MultiLabelSTAPLEImageFilter, ImageToImageFilter);

  typedef typename TOutputImage::PixelType OutputPixelType;
  typedef typename TInputImage::PixelType  InputPixelType;

  itkStaticConstMacro(ImageDimension, unsigned int,
                      TOutputImage::ImageDimension);

  typedef TInputImage                       InputImageType;
  typedef TOutputImage                      OutputImageType;
  typedef typename InputImageType::Pointer  InputImagePointer;
  typedef typename OutputImageType::Pointer OutputImagePointer;

  typedef typename Superclass::OutputImageRegionType OutputImageRegionType;

  typedef ImageRegionConstIterator< TInputImage > InputConstIteratorType;
  typedef ImageRegionIterator< TOutputImage >     OutputIteratorType;

  typedef TWeights             WeightsType;
  typedef Array2D<WeightsType> ConfusionMatrixType;
  typedef Array<WeightsType>   PriorProbabilitiesType;

  itkGetConstMacro(ElapsedNumberOfIterations, unsigned int);

  void SetMaximumNumberOfIterations( const unsigned int mit )
  {
    this->m_MaximumNumberOfIterations = mit;
    this->m_HasMaximumNumberOfIterations = true;
    this->Modified();
  }
  itkGetConstMacro(MaximumNumberOfIterations, unsigned int);

  itkGetConstMacro(HasMaximumNumberOfIterations, bool);

  void UnsetMaximumNumberOfIterations()
  {
    if ( this->m_HasMaximumNumberOfIterations )
      {
      this->m_HasMaximumNumberOfIterations = false;
      this->Modified();
      }
  }

  itkSetMacro(TerminationUpdateThreshold, TWeights);
  itkGetConstMacro(TerminationUpdateThreshold, TWeights);

  void SetLabelForUndecidedPixels( const OutputPixelType l )
  {
    this->m_LabelForUndecidedPixels = l;
    this->m_HasLabelForUndecidedPixels = true;
    this->Modified();
  }

  itkGetMacro(LabelForUndecidedPixels, OutputPixelType);

  itkGetMacro(HasLabelForUndecidedPixels, bool);

  void UnsetLabelForUndecidedPixels()
  {
    if ( this->m_HasLabelForUndecidedPixels )
      {
      this->m_HasLabelForUndecidedPixels = false;
      this->Modified();
      }
  }

  void SetPriorProbabilities( const PriorProbabilitiesType& ppa )
  {
    this->m_PriorProbabilities = ppa;
    this->m_HasPriorProbabilities = true;
    this->Modified();
  }

  itkGetConstReferenceMacro(PriorProbabilities, PriorProbabilitiesType);

  itkGetMacro(HasPriorProbabilities, bool);

  void UnsetPriorProbabilities()
  {
    if ( this->m_HasPriorProbabilities )
      {
      this->m_HasPriorProbabilities = false;
      this->Modified();
      }
  }

  const ConfusionMatrixType & GetConfusionMatrix( const unsigned int i ) const
  {
    return this->m_ConfusionMatrixArray[i];
  }

protected:
  MultiLabelSTAPLEImageFilter() :
    m_TotalLabelCount(0),
    m_LabelForUndecidedPixels(NumericTraits<OutputPixelType>::ZeroValue()),
    m_HasLabelForUndecidedPixels(false),
    m_HasPriorProbabilities(false),
    m_HasMaximumNumberOfIterations(false),
    m_MaximumNumberOfIterations(0),
    m_ElapsedNumberOfIterations(0u),
    m_TerminationUpdateThreshold(1e-5)
  {
  }
  virtual ~MultiLabelSTAPLEImageFilter() {}

  void GenerateData() ITK_OVERRIDE;

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

  typename TInputImage::PixelType ComputeMaximumInputValue();

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

  // Override since the filter produces all of its output
  void EnlargeOutputRequestedRegion( DataObject * ) ITK_OVERRIDE;

private:
  ITK_DISALLOW_COPY_AND_ASSIGN(MultiLabelSTAPLEImageFilter);

  size_t m_TotalLabelCount;

  OutputPixelType    m_LabelForUndecidedPixels;
  bool               m_HasLabelForUndecidedPixels;

  bool                   m_HasPriorProbabilities;
  PriorProbabilitiesType m_PriorProbabilities;

  void InitializePriorProbabilities();

  std::vector<ConfusionMatrixType> m_ConfusionMatrixArray;
  std::vector<ConfusionMatrixType> m_UpdatedConfusionMatrixArray;

  void AllocateConfusionMatrixArray();
  void InitializeConfusionMatrixArrayFromVoting();

  bool         m_HasMaximumNumberOfIterations;
  unsigned int m_MaximumNumberOfIterations;
  unsigned int m_ElapsedNumberOfIterations;

  TWeights m_TerminationUpdateThreshold;
};

} // end namespace itk

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

#endif