itkMultiLabelSTAPLEImageFilter.h

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/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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:
  ITK_DISALLOW_COPY_AND_MOVE(MultiLabelSTAPLEImageFilter);

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

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(MultiLabelSTAPLEImageFilter);

  using OutputPixelType = typename TOutputImage::PixelType;
  using InputPixelType = typename TInputImage::PixelType;

  static constexpr unsigned int ImageDimension = TOutputImage::ImageDimension;

  using InputImageType = TInputImage;
  using OutputImageType = TOutputImage;
  using InputImagePointer = typename InputImageType::Pointer;
  using OutputImagePointer = typename OutputImageType::Pointer;

  using typename Superclass::OutputImageRegionType;

  using InputConstIteratorType = ImageRegionConstIterator<TInputImage>;
  using OutputIteratorType = ImageRegionIterator<TOutputImage>;

  using WeightsType = TWeights;
  using ConfusionMatrixType = Array2D<WeightsType>;
  using PriorProbabilitiesType = Array<WeightsType>;

  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_LabelForUndecidedPixels(OutputPixelType{})
    , m_TerminationUpdateThreshold(1e-5)
  {}
  ~MultiLabelSTAPLEImageFilter() override = default;
 
  void
  GenerateData() override;
 
  void
  PrintSelf(std::ostream &, Indent) const override;

  typename TInputImage::PixelType
  ComputeMaximumInputValue();
 
  // Override since the filter needs all the data for the algorithm
  void
  GenerateInputRequestedRegion() override;
 
  // Override since the filter produces all of its output
  void
  EnlargeOutputRequestedRegion(DataObject *) override;
 
private:
  size_t m_TotalLabelCount{ 0 };
 
  OutputPixelType m_LabelForUndecidedPixels{};
  bool            m_HasLabelForUndecidedPixels{ false };
 
  bool                   m_HasPriorProbabilities{ false };
  PriorProbabilitiesType m_PriorProbabilities{};
 
  void
  InitializePriorProbabilities();
 
  std::vector<ConfusionMatrixType> m_ConfusionMatrixArray{};
  std::vector<ConfusionMatrixType> m_UpdatedConfusionMatrixArray{};
 
  void
  AllocateConfusionMatrixArray();
  void
  InitializeConfusionMatrixArrayFromVoting();
 
  bool         m_HasMaximumNumberOfIterations{ false };
  unsigned int m_MaximumNumberOfIterations{ 0 };
  unsigned int m_ElapsedNumberOfIterations{ 0u };
 
  TWeights m_TerminationUpdateThreshold{};
};
 
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkMultiLabelSTAPLEImageFilter.hxx"
#endif
 
#endif