itkCorrectGMUsingPVMapFilter.h

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/*=============================================================================

  NifTK: A software platform for medical image computing.

  Copyright (c) University College London (UCL). All rights reserved.

  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.

  See LICENSE.txt in the top level directory for details.

=============================================================================*/

#ifndef itkCorrectGMUsingPVMapFilter_h
#define itkCorrectGMUsingPVMapFilter_h

#include <itkImage.h>
#include "itkBaseCTESegmentationFilter.h"


namespace itk
{
template <class TImageType>
class ITK_EXPORT CorrectGMUsingPVMapFilter : 
    public BaseCTESegmentationFilter< TImageType >
{
public:
  typedef CorrectGMUsingPVMapFilter                  Self;
  typedef BaseCTESegmentationFilter<TImageType>      Superclass;
  typedef SmartPointer<Self>                         Pointer;
  typedef SmartPointer<const Self>                   ConstPointer;

  itkNewMacro(Self);

  itkTypeMacro(CorrectGMUsingPVMap, BaseCTESegmentationFilter);
  
  typedef typename Superclass::InputImageType          InputImageType;
  typedef typename Superclass::InputPixelType          InputPixelType;
  typedef typename Superclass::InputIndexType          InputIndexType;
  typedef typename Superclass::InputImagePointer       InputImagePointer;
  typedef typename Superclass::InputImageConstPointer  InputImageConstPointer;
  typedef typename Superclass::OutputPixelType         OutputPixelType;
  typedef typename Superclass::OutputImageType         OutputImageType;
  typedef typename Superclass::OutputImagePointer      OutputImagePointer;
  typedef typename Superclass::OutputImageConstPointer OutputImageConstPointer;

  void SetSegmentedImage(const InputImageType *image) {this->SetNthInput(0, const_cast<InputImageType *>(image)); }

  void SetGMPVMap(const InputImageType *image) {this->SetNthInput(1, const_cast<InputImageType *>(image)); }
  
  const std::vector<InputIndexType>& GetListOfGreyMatterPixelsBeforeCorrection() const;
  
  const std::vector<InputIndexType>& GetListOfGreyMatterPixelsAfterCorrection() const;
  
  itkSetMacro(GreyMatterThreshold, double);
  itkGetMacro(GreyMatterThreshold, double);

  itkSetMacro(DoGreyMatterCheck, bool);
  itkGetMacro(DoGreyMatterCheck, bool);

  itkSetMacro(DoCSFCheck, bool);
  itkGetMacro(DoCSFCheck, bool);

protected:
  
  CorrectGMUsingPVMapFilter();
  virtual ~CorrectGMUsingPVMapFilter()  {};

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

  /* The main filter method. Note, single threaded. */
  virtual void GenerateData();
  
private:

  CorrectGMUsingPVMapFilter(const Self&); // purposely not implemented
  void operator=(const Self&); // purposely not implemented

  std::vector<InputIndexType> m_ListOfGreyMatterVoxelsBeforeCorrection;
  
  std::vector<InputIndexType> m_ListOfGreyMatterVoxelsAfterCorrection;
  
  bool m_DoGreyMatterCheck;
  
  bool m_DoCSFCheck;
  
  double m_GreyMatterThreshold;
  
};
  
} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkCorrectGMUsingPVMapFilter.txx"
#endif

#endif