itkCellFeatureGenerator.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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 and/or other materials provided with the distribution.
 Neither the name of the  President and Fellows of Harvard College
 nor the names of its contributors may be used to endorse or promote
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=========================================================================*/

#ifndef __itkCellFeatureGenerator_h
#define __itkCellFeatureGenerator_h

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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkImageToImageFilter.h"
#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
#include "itkSigmoidImageFilter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkSignedMaurerDistanceMapImageFilter.h"
#include "itkAbsImageFilter.h"
#include "itkThresholdImageFilter.h"
#include "itkMinimumMaximumImageCalculator.h"
#include "itkImageRegionIterator.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegion.h"
#include "itkRegion.h"
#include "itkIndex.h"
#include "itkSize.h"

#include "itkImageFileWriter.h"

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

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

  itkNewMacro (Self);

  itkTypeMacro (CellFeatureGenerator, 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                           ImageType;
  typedef typename ImageType::Pointer           ImagePointer;
  typedef typename ImageType::ConstPointer      ImageConstPointer;
  typedef typename ImageType::PixelType         ImagePixelType;
  typedef typename ImageType::RegionType        ImageRegionType;
  typedef typename ImageType::SizeType          ImageSizeType;
  typedef typename ImageSizeType::SizeValueType ImageSizeValueType;
  typedef typename ImageType::SpacingType       ImageSpacingType;
  typedef typename ImageType::IndexType         ImageIndexType;
  typedef typename ImageType::PointType         ImagePointType;

  typedef TSegmentImage                           SegmentImageType;
  typedef typename SegmentImageType::Pointer      SegmentImagePointer;
  typedef typename SegmentImageType::ConstPointer SegmentImageConstPointer;
  typedef typename SegmentImageType::IndexType    SegmentImageIndexType;
  typedef typename SegmentImageType::PixelType    SegmentImagePixelType;

  typedef GradientMagnitudeRecursiveGaussianImageFilter< FeatureImageType, ImageType >
  GradientFilterType;
  typedef typename GradientFilterType::Pointer         GradientFilterPointer;
  typedef SigmoidImageFilter< ImageType, ImageType >   SigmoidFilterType;
  typedef typename SigmoidFilterType::Pointer          SigmoidFilterPointer;
  typedef AbsImageFilter< ImageType, ImageType >       AbsFilterType;
  typedef typename AbsFilterType::Pointer              AbsFilterPointer;
  typedef ThresholdImageFilter< ImageType >            ThreshFilterType;
  typedef typename ThreshFilterType::Pointer           ThreshFilterPointer;
  typedef ImageRegionConstIterator< FeatureImageType > ConstIteratorType;
  typedef ImageRegionIterator< ImageType >             IteratorType;
  typedef ImageRegionIteratorWithIndex< ImageType >    IndexIteratorType;
  typedef SignedMaurerDistanceMapImageFilter< SegmentImageType, ImageType >
  MaurerType;
  typedef typename MaurerType::Pointer                      MaurerPointer;
  typedef MinimumMaximumImageCalculator< ImageType >        MinMaxCalculatorType;
  typedef typename MinMaxCalculatorType::Pointer            MinMaxCalculatorPointer;
  typedef MinimumMaximumImageCalculator< FeatureImageType > FeatureMinMaxCalculatorType;
  typedef typename FeatureMinMaxCalculatorType::Pointer     FeatureMinMaxCalculatorPointer;

  itkGetConstMacro (NucleiSigma, double);
  itkSetMacro (NucleiSigma, double);
  itkGetConstMacro (MembraneSigma, double);
  itkSetMacro (MembraneSigma, double);
  itkGetConstMacro (LargestCellRadius, double);
  itkSetMacro (LargestCellRadius, double);
  itkGetConstMacro (DistanceMapWeight, double);
  itkSetMacro (DistanceMapWeight, double);
  itkGetConstMacro (NucleiGradientWeight, double);
  itkSetMacro (NucleiGradientWeight, double);
  itkGetConstMacro (MembraneWeight, double);
  itkSetMacro (MembraneWeight, double);

  void SetForeground(SegmentImagePointer fg)
  {
    m_ForegroundMap = fg;
  }

  ImagePointer GetDistanceMap()
  {
    return m_DistanceMap;
  }

  ImagePointer GetGradient()
  {
    return m_Gradient;
  }

protected:
  CellFeatureGenerator();
  ~CellFeatureGenerator() {}
  void DistanceMap();

  void Gradient();

  void Normalize();

  void GenerateData();

  double m_NucleiSigma;
  double m_MembraneSigma;
  double m_LargestCellRadius;
  double m_DistanceMapWeight;
  double m_NucleiGradientWeight;
  double m_MembraneWeight;

  SegmentImagePointer m_ForegroundMap;
  ImagePointer m_DistanceMap;
  ImagePointer m_Gradient;
private:

  CellFeatureGenerator (Self &);        // intentionally not implemented
  void operator=(const Self &);         // intentionally not implemented
};
}   /* namespace itk */

#include "itkCellFeatureGenerator.txx"
#endif