libgofigure-dev 0.9.0-3 / usr / include / gofigure2 / itkCellForegroundExtraction.h

/*=========================================================================
 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 __itkCellForegroundExtraction_h
#define __itkCellForegroundExtraction_h

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

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkAffineTransform.h"
#include "itkImageToImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkMedianImageFilter.h"
#include "itkAffineTransform.h"
#include "itkGrayscaleFillholeImageFilter.h"
#include "itkRecursiveGaussianImageFilter.h"
#include "itkRegionOfInterestImageFilter.h"
#include "itkDiscreteGaussianImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkResampleImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkGaussianProfileMatchingImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkImageRegion.h"
#include "itkRegion.h"
#include "itkIndex.h"
#include "itkSize.h"

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

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

  /** Method for creation through object factory */
  itkNewMacro (Self);

  /** Run-time type information */
  itkTypeMacro (CellForegroundExtraction, ImageToImageFilter);

  /** Display */
  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 RegionOfInterestImageFilter< FeatureImageType, FeatureImageType >
  ROIFilterType;
  typedef typename ROIFilterType::Pointer ROIFilterPointer;

  typedef CastImageFilter< FeatureImageType, FeatureImageType > CastFilterType;
  typedef typename CastFilterType::Pointer                      CastFilterPointer;

  typedef ResampleImageFilter< FeatureImageType, FeatureImageType > ResampleFeatureFilterType;
  typedef typename ResampleFeatureFilterType::Pointer               ResampleFeatureFilterPointer;

  typedef LinearInterpolateImageFunction< FeatureImageType > InterpolatorFeatureType;
  typedef typename InterpolatorFeatureType::Pointer          InterpolatorFeaturePointer;

  typedef ResampleImageFilter< ImageType, ImageType > ResampleFilterType;
  typedef typename ResampleFilterType::Pointer        ResampleFilterPointer;

  typedef LinearInterpolateImageFunction< ImageType > InterpolatorType;
  typedef typename InterpolatorType::Pointer          InterpolatorPointer;

  typedef AffineTransform< double, ImageDimension > TransformType;
  typedef typename TransformType::Pointer           TransformPointer;
  typedef RescaleIntensityImageFilter< ImageType, ImageType >
  RescaleFilterType;
  typedef typename RescaleFilterType::Pointer RescaleFilterPointer;

  typedef GaussianProfileMatchingImageFilter< TFeatureImage,
                                              TInputImage, TSegmentImage > GaussProfileFilterType;
  typedef typename GaussProfileFilterType::Pointer GaussProfileFilterPointer;

  typedef ImageRegionConstIterator< FeatureImageType >     FeatureConstIteratorType;
  typedef ImageRegionIteratorWithIndex< FeatureImageType > FeatureIndexIteratorType;
  typedef ImageRegionIterator< ImageType >                 IteratorType;
  typedef ImageRegionIterator< SegmentImageType >          SegmentIteratorType;
  typedef ImageRegionIteratorWithIndex< ImageType >        IndexIteratorType;

  itkGetConstMacro (SigmaForm, double);
  itkSetMacro (SigmaForm, double);
  itkGetConstMacro (ThresholdCellmin, double);
  itkSetMacro (ThresholdCellmin, double);
  itkGetConstMacro (ThresholdCellmax, double);
  itkSetMacro (ThresholdCellmax, double);
  itkGetConstMacro (ThresholdMembrane, double);
  itkSetMacro (ThresholdMembrane, double);
  itkGetConstMacro (ThresholdForm, double);
  itkSetMacro (ThresholdForm, double);
  itkGetConstMacro (LargestCellRadius, double);
  itkSetMacro (LargestCellRadius, double);

  void SetSampling(float *sampling)
  {
    m_Sampling = sampling;
  }

  ImagePointer GetGaussCorrImage(void) const
  {
    return gauss;
  }

protected:
  CellForegroundExtraction();
  ~CellForegroundExtraction() {}

  FeatureImagePointer ResampleInput(FeatureImageConstPointer input, FeatureImageSpacingType spacing,
                                    FeatureImageSizeType size, FeatureImagePointType origin);

  ImagePointer Resample(ImagePointer input, FeatureImageSpacingType spacing,
                        FeatureImageSizeType size, FeatureImagePointType origin);

  void GenerateData();

  double m_SigmaForm;
  double m_ThresholdCellmin;
  double m_ThresholdCellmax;
  double m_ThresholdMembrane;   // Change to size threshold
  double m_ThresholdForm;
  double m_LargestCellRadius;
  float *m_Sampling;
  ImagePointer gauss;
private:
  CellForegroundExtraction (Self &);  // intentionally not implemented
  void operator=(const Self &);       // intentionally not implemented
};
} /* namespace itk */

#include "itkCellForegroundExtraction.txx"
#endif