itkGradientWeightedIntensityImageFilter.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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 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 __itkGradientWeightedIntensityImageFilter_h
#define __itkGradientWeightedIntensityImageFilter_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 "itkMultiScaleLoGImageFilter.h"
#include "itkRescaleIntensityImageFilter.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 GradientWeightedIntensityImageFilter:
  public ImageToImageFilter< TFeatureImage, TInputImage >
{
public:
  typedef GradientWeightedIntensityImageFilter             Self;
  typedef ImageToImageFilter< TFeatureImage, TInputImage > Superclass;
  typedef SmartPointer< Self >                             Pointer;
  typedef SmartPointer< const Self >                       ConstPointer;

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

  itkNewMacro (Self);

  itkTypeMacro (GradientWeightedIntensityImageFilter, 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 MultiScaleLoGImageFilter< FeatureImageType, ImageType >
  MultiScaleLoGFilterType;
  typedef typename MultiScaleLoGFilterType::Pointer MultiScaleLoGFilterPointer;
  typedef RescaleIntensityImageFilter< ImageType, ImageType >
  RescaleFilterType;
  typedef typename RescaleFilterType::Pointer RescaleFilterPointer;

  typedef GradientMagnitudeRecursiveGaussianImageFilter< FeatureImageType, ImageType >
  GradientFilterType;
  typedef typename GradientFilterType::Pointer       GradientFilterPointer;
  typedef SigmoidImageFilter< ImageType, ImageType > SigmoidFilterType;
  typedef typename SigmoidFilterType::Pointer        SigmoidFilterPointer;

  typedef ImageRegionConstIterator< FeatureImageType > ConstIteratorType;
  typedef ImageRegionIterator< FeatureImageType >      FIteratorType;
  typedef ImageRegionIterator< ImageType >             IteratorType;
  typedef ImageRegionIteratorWithIndex< ImageType >    IndexIteratorType;

  void SetBlob(FeatureImagePointer blob)
  {
    m_Blob = blob;
  }

  void SetForm(ImagePointer form)
  {
    m_Form = form;
  }

  itkGetConstMacro (LargestCellRadius, double);
  itkSetMacro (LargestCellRadius, double);
  itkGetConstMacro (NucleiSigma, double);
  itkSetMacro (NucleiSigma, double);
  itkGetConstMacro (Alpha, double);
  itkSetMacro (Alpha, double);
  itkGetConstMacro (Beta, double);
  itkSetMacro (Beta, double);
  itkGetConstMacro (Gamma, double);
  itkSetMacro (Gamma, double);
protected:
  GradientWeightedIntensityImageFilter();
  ~GradientWeightedIntensityImageFilter() {}
  void Normalize();

  void GenerateData();

  double m_LargestCellRadius;
  double m_NucleiSigma;
  double m_Alpha;
  double m_Beta;
  double m_Gamma;

  FeatureImagePointer m_Blob;
  ImagePointer m_Form;
private:

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

#include "itkGradientWeightedIntensityImageFilter.txx"
#endif