itkConnectedAdaptiveThresholdImageFilter.h

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/*============================================================================
 
The Medical Imaging Interaction Toolkit (MITK)
 
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
 
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
 
============================================================================*/
#ifndef __itkConnectedAdaptiveThresholdImageFilter_h
#define __itkConnectedAdaptiveThresholdImageFilter_h
 
#include "itkConnectedThresholdImageFilter.h"
#include "itkImage.h"
 
namespace itk
{
  template <class TInputImage, class TOutputImage>
  class ITK_EXPORT ConnectedAdaptiveThresholdImageFilter
    : public ConnectedThresholdImageFilter<TInputImage, TOutputImage>
  {
  public:
    typedef ConnectedAdaptiveThresholdImageFilter Self;
    typedef ConnectedThresholdImageFilter<TInputImage, TOutputImage> Superclass;
    typedef SmartPointer<Self> Pointer;
    typedef SmartPointer<const Self> ConstPointer;
 
    itkFactorylessNewMacro(Self);
    itkCloneMacro(Self);
 
      itkTypeMacro(ConnectedAdaptiveThresholdImageFilter, ConnectedThresholdImageFilter);
 
    typedef TInputImage InputImageType;
    typedef TOutputImage OutputImageType;
    typedef typename OutputImageType::Pointer OutputImagePointer;
    typedef typename InputImageType::IndexType IndexType;
    typedef typename InputImageType::PixelType PixelType;
 
    void SetGrowingDirectionIsUpwards(bool upwards) { m_GrowingDirectionIsUpwards = upwards; }
    /* Switch between fine and raw leakage detection. */
    void SetFineDetectionMode(bool fine)
    {
      m_FineDetectionMode = fine;
      m_DiscardLastPreview = false;
    }
 
    int GetSeedpointValue(void) { return m_SeedpointValue; }
    int GetLeakagePoint(void) { return m_DetectedLeakagePoint; }
 
    /*
    * Correct the position of the seed point, only performed if seed point value is outside threshold range
    * @param sizeOfVolume edge length of the square volume in which the search for a "better" seed is performed
    */
    IndexType CorrectSeedPointPosition(unsigned int sizeOfVolume, int lowerTh, int upperTh);
 
    /* Sets all voxels in a square volume with the size of @param croppingSize
    * and the center point equal to @param seedPoint to the value zero.
    */
    void CropMask(unsigned int croppingSize);
 
    /* Modifies the iterator mask to keep all previous segmentation results in the same mask.
    * @returnParam largest value in the segmentation mask
    */
    unsigned int AdjustIteratorMask();
 
    /* Sets parameters needed for adjusting the iterator mask
    * @param iteratorMaskForFineSegmentation pointer to the image containing the complete segmentation result of one
    * leaf (inclusively leakage-segmentation)
    * @param adjLowerTh lower threshold value of the segmentation without leakage-segmentation
    * @param adjLowerTh upper threshold value of the segmentation without leakage-segmentation
    * @param discardLeafSegmentation flag if the last segmentation preview ended with a leakage already in the first
    * step
    */
    void SetParameterForFineSegmentation(TOutputImage *iteratorMaskForFineSegmentation,
                                         unsigned int adjLowerTh,
                                         unsigned int adjUpperTh,
                                         itk::Index<3> seedPoint,
                                         bool discardLeafSegmentation);
 
    TOutputImage *GetResultImage();
 
  protected:
    ConnectedAdaptiveThresholdImageFilter();
    ~ConnectedAdaptiveThresholdImageFilter() override{};
 
    void GenerateData() override;
 
  private:
    OutputImagePointer m_OutoutImageMaskFineSegmentation;
    bool m_GrowingDirectionIsUpwards;
    PixelType m_SeedpointValue;
    PixelType m_DetectedLeakagePoint;
    PixelType m_InitValue;
    unsigned int m_AdjLowerTh;
    unsigned int m_AdjUpperTh;
    itk::Index<3> m_SeedPointIndex;
 
    /* Flag for switching between raw segmentation and fine segmentation (Bronchial tree segmentation) */
    bool m_FineDetectionMode;
 
    bool m_DiscardLastPreview;
    bool m_SegmentationCancelled;
  };
 
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkConnectedAdaptiveThresholdImageFilter.txx"
#endif
 
#endif