MorphologicalSegmentorPipeline.h

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/*=============================================================================

  NifTK: A software platform for medical image computing.

  Copyright (c) University College London (UCL). All rights reserved.

  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.

  See LICENSE.txt in the top level directory for details.

=============================================================================*/

#ifndef MorphologicalSegmentorPipeline_h
#define MorphologicalSegmentorPipeline_h

#include "MorphologicalSegmentorPipelineParams.h"
#include "MorphologicalSegmentorPipelineInterface.h"

#include <itkImage.h>
#include <itkBinaryThresholdImageFilter.h>
#include "itkMIDASMaskByRegionImageFilter.h"
#include "itkMIDASConditionalErosionFilter.h"
#include "itkMIDASConditionalDilationFilter.h"
#include "itkMIDASRethresholdingFilter.h"
#include "itkMIDASMorphologicalSegmentorLargestConnectedComponentImageFilter.h"

template<typename TPixel, unsigned int VImageDimension>
class MorphologicalSegmentorPipeline : public MorphologicalSegmentorPipelineInterface
{
public:

  typedef itk::Image<TPixel, VImageDimension> GreyScaleImageType;
  typedef itk::Image<unsigned char, VImageDimension> SegmentationImageType;
  typedef itk::BinaryThresholdImageFilter<GreyScaleImageType, SegmentationImageType> ThresholdingFilterType;
  typedef itk::MIDASMaskByRegionImageFilter<SegmentationImageType, SegmentationImageType> MaskByRegionFilterType;
  typedef itk::MIDASMorphologicalSegmentorLargestConnectedComponentImageFilter<SegmentationImageType, SegmentationImageType> LargestConnectedComponentFilterType;
  typedef itk::MIDASConditionalErosionFilter<SegmentationImageType, GreyScaleImageType, SegmentationImageType> ErosionFilterType;
  typedef itk::MIDASConditionalDilationFilter<SegmentationImageType, GreyScaleImageType, SegmentationImageType> DilationFilterType;
  typedef itk::MIDASRethresholdingFilter<GreyScaleImageType, SegmentationImageType, SegmentationImageType> RethresholdingFilterType;

  MorphologicalSegmentorPipeline();

  virtual ~MorphologicalSegmentorPipeline();

  void SetInputs(const GreyScaleImageType* referenceImage,
                 const SegmentationImageType* erosionsAdditionsImage,
                 const SegmentationImageType* erosionsSubtractionsImage,
                 const SegmentationImageType* dilationsAdditionsImage,
                 const SegmentationImageType* dilationsSubtractionsImage);

  void SetErosionSubtractionsInput(const SegmentationImageType* erosionsSubtractionsImage);

  void SetDilationSubtractionsInput(const SegmentationImageType* dilationsSubtractionsImage);

  void SetParams(const MorphologicalSegmentorPipelineParams& params);

  void SetForegroundValue(unsigned char foregroundValue);

  void SetBackgroundValue(unsigned char backgroundValue);

  void Update(const std::vector<bool>& editingFlags, const std::vector<int>& editingRegion);

  typename SegmentationImageType::Pointer GetOutput();

  typename SegmentationImageType::Pointer GetOutput(int stage);


  typename ThresholdingFilterType::Pointer                     m_ThresholdingFilter;
  typename MaskByRegionFilterType::Pointer                     m_ThresholdingMaskFilter;
  typename LargestConnectedComponentFilterType::Pointer        m_ThresholdingConnectedComponentFilter;
  typename ErosionFilterType::Pointer                          m_ErosionFilter;
  typename MaskByRegionFilterType::Pointer                     m_ErosionMaskFilter;
  typename LargestConnectedComponentFilterType::Pointer        m_ErosionConnectedComponentFilter;
  typename DilationFilterType::Pointer                         m_DilationFilter;
  typename MaskByRegionFilterType::Pointer                     m_DilationMaskFilter;
  typename LargestConnectedComponentFilterType::Pointer        m_DilationConnectedComponentFilter;
  typename RethresholdingFilterType::Pointer                   m_RethresholdingFilter;

private:

  void UpdateForegroundValues();

  void UpdateBackgroundValues();

  unsigned char m_ForegroundValue;

  unsigned char m_BackgroundValue;

  int m_Stage;

};

#ifndef ITK_MANUAL_INSTANTIATION
#include "MorphologicalSegmentorPipeline.txx"
#endif

#endif