itkWatershedBasedCellSegmentation.h

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/*=========================================================================
 Authors: The GoFigure Dev. Team.
 at Megason Lab, Systems biology, Harvard Medical school, 2009-11

 Copyright (c) 2009-11, President and Fellows of Harvard College.
 All rights reserved.

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 this list of conditions and the following disclaimer.
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#ifndef __itkWatershedBasedCellSegmentation_h
#define __itkWatershedBasedCellSegmentation_h

#if defined( _MSC_VER )
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkImageToImageFilter.h"
#include "itkPreprocessImageFilter.h"
#include "itkCellForegroundExtraction.h"
#include "itkGradientWeightedDistanceImageFilter.h"
#include "itkInvertIntensityImageFilter.h"
#include "itkMorphologicalWatershedImageFilter2.h"
#include "itkImageRegionIterator.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkMinimumMaximumImageCalculator.h"
#include "itkAntiAliasBinaryImageFilter.h"

namespace itk
{
template< class TFeatureImage, class TInputImage, class TSegmentImage >
class WatershedBasedCellSegmentation:public ImageToImageFilter<
    TFeatureImage, TSegmentImage >
{
public:
  typedef WatershedBasedCellSegmentation                     Self;
  typedef ImageToImageFilter< TFeatureImage, TSegmentImage > Superclass;
  typedef SmartPointer< Self >                               Pointer;
  typedef SmartPointer< const Self >                         ConstPointer;

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

  itkNewMacro (Self);

  itkTypeMacro (WatershedBasedCellSegmentation, ImageToImageFilter);

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

  typedef TFeatureImage                                FeatureImageType;
  typedef typename FeatureImageType::Pointer           FeatureImagePointer;
  typedef typename FeatureImageType::ConstPointer      FeatureImageConstPointer;
  typedef typename FeatureImageType::PixelType         FeatureImagePixelType;
  typedef typename FeatureImageType::RegionType        FeatureImageRegionType;
  typedef typename FeatureImageType::SizeType          FeatureImageSizeType;
  typedef typename FeatureImageSizeType::SizeValueType FeatureImageSizeValueType;
  typedef typename FeatureImageType::SpacingType       FeatureImageSpacingType;
  typedef typename FeatureImageType::IndexType         FeatureImageIndexType;
  typedef typename FeatureImageType::PointType         FeatureImagePointType;

  typedef TInputImage                                InputImageType;
  typedef typename InputImageType::Pointer           InputImagePointer;
  typedef typename InputImageType::ConstPointer      InputImageConstPointer;
  typedef typename InputImageType::PixelType         InputImagePixelType;
  typedef typename InputImageType::RegionType        InputImageRegionType;
  typedef typename InputImageType::SizeType          InputImageSizeType;
  typedef typename InputImageSizeType::SizeValueType InputImageSizeValueType;
  typedef typename InputImageType::SpacingType       InputImageSpacingType;
  typedef typename InputImageType::IndexType         InputImageIndexType;
  typedef typename InputImageType::PointType         InputImagePointType;

  typedef TSegmentImage                           SegmentImageType;
  typedef typename SegmentImageType::Pointer      SegmentImagePointer;
  typedef typename SegmentImageType::ConstPointer SegmentImageConstPointer;
  typedef typename SegmentImageType::IndexType    SegmentImageIndexType;
  typedef typename SegmentImageType::PixelType    SegmentImagePixelType;
  typedef typename SegmentImageType::SizeType    SegmentImageSizeType;
  typedef typename SegmentImageIndexType::IndexValueType SegmentImageIndexValueType;
  typedef typename SegmentImageType::RegionType        SegmentImageRegionType;

  typedef PreprocessImageFilter< FeatureImageType, FeatureImageType >
    PreprocessFilterType;
  typedef typename PreprocessFilterType::Pointer PreprocessFilterPointer;

  typedef CellForegroundExtraction< FeatureImageType, InputImageType, SegmentImageType >
  ForegroundFilterType;
  typedef typename ForegroundFilterType::Pointer ForegroundFilterPointer;

  typedef GradientWeightedDistanceImageFilter< FeatureImageType, InputImageType, SegmentImageType >
  DistanceFilterType;
  typedef typename DistanceFilterType::Pointer DistanceFilterPointer;

  typedef InvertIntensityImageFilter< InputImageType, InputImageType >
  RInvertType;
  typedef typename RInvertType::Pointer RInvertPointer;

  typedef MorphologicalWatershedImageFilter2< InputImageType, SegmentImageType >
  WatershedFilterType;
  typedef typename WatershedFilterType::Pointer WatershedFilterPointer;

  typedef MinimumMaximumImageCalculator< InputImageType > MinMaxCalculatorType;

  typedef ImageRegionIterator< FeatureImageType > FeatureIteratorType;
  typedef ImageRegionIterator< InputImageType > InputIteratorType;
  typedef ImageRegionIteratorWithIndex< SegmentImageType > SegmentIteratorType;

  typedef AntiAliasBinaryImageFilter< SegmentImageType, InputImageType > AntiAliasFilterType;
  typedef typename AntiAliasFilterType::Pointer AntiAliasFilterPointer;

  itkGetConstMacro (NucleusRadius, double);
  itkSetMacro (NucleusRadius, double);
  itkGetConstMacro (CorrelationKernelSigma, double);
  itkSetMacro (CorrelationKernelSigma, double);
  itkGetConstMacro (NucleusThresholdMin, double);
  itkSetMacro (NucleusThresholdMin, double);
  itkGetConstMacro (NucleusThresholdMax, double);
  itkSetMacro (NucleusThresholdMax, double);
  itkGetConstMacro (CorrelationThreshold1, double);
  itkSetMacro (CorrelationThreshold1, double);
  itkGetConstMacro (MembraneThreshold, double);
  itkSetMacro (MembraneThreshold, double);
  itkGetConstMacro (Alpha, float);
  itkSetMacro (Alpha, float);
  itkGetConstMacro (Beta, float);
  itkSetMacro (Beta, float);
protected:
  WatershedBasedCellSegmentation();
  ~WatershedBasedCellSegmentation() {}
  void GenerateData();

  double m_NucleusRadius;
  double m_CorrelationKernelSigma;
  int m_NucleusThresholdMin;
  int m_NucleusThresholdMax;
  double m_CorrelationThreshold1;
  int m_MembraneThreshold;
  float m_Alpha;
  float m_Beta;
private:
  WatershedBasedCellSegmentation (Self &); // intentionally not implemented
  void operator=(const Self &);            // intentionally not implemented
};
} /* namespace itk */

#include "itkWatershedBasedCellSegmentation.txx"
#endif