iDeformationElastic.hh

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#ifndef IDEFORMATIONELASTIC_HH
#define IDEFORMATIONELASTIC_HH 1

// (Optional) may be required if one want access to the image matrices
#include "oImageSpace.hh"
// Required to automatically add the class in the CASToR code
#include "sAddonManager.hh"
// Mother class of deformation model
#include "vDeformation.hh"

#ifdef CASTOR_ELASTIX
  #include "itkImage.h"
  #include "itkPoint.h"
//  #include "itkRawImageIO.h"
  #include "itkImageFileReader.h"
  #include "itkImageFileWriter.h"
  
  #include "elastixlib.h"
  #include "transformixlib.h"
  #include "elxParameterObject.h"
  #include "itkParameterFileParser.h"
#endif


#ifdef CASTOR_ELASTIX
  using namespace transformix;
  typedef TRANSFORMIX::ParameterMapType RegistrationParametersType;
  typedef itk::ParameterFileParser ParserType;
  typedef itk::ParameterFileParser::ParameterMapType                ParameterMapType;

  enum { Dimension =  3 };
  typedef  float                                      PixelType;
  typedef  itk::Image< PixelType, Dimension >         ImageType;
  typedef  ImageType::IndexType      PixelIndex;
  typedef  ImageType::RegionType     RegionType;
  typedef  ImageType::SizeType       RegionSize;
  typedef  ImageType::IndexType      RegionStart;
  typedef  ImageType::SpacingType    SpacingType;
  typedef  itk::ImageFileReader< ImageType >  ReaderType;
  typedef  itk::ImageFileWriter< ImageType >  WriterType;
#endif


class iDeformationElastic : public vDeformation
{
  // -----------------------------------------------------------------------------------------
  // Constructor & Destructor
  public:
    iDeformationElastic();
    ~iDeformationElastic();


  // -----------------------------------------------------------------------------------------
  // Public member functions
  public:
    // Function for automatic insertion (put the class name as the parameters and do not add semi-colon at the end of the line)
    FUNCTION_DEFORMATION(iDeformationElastic)
    int ReadAndCheckConfigurationFile(const string& a_fileOptions);
    int ReadAndCheckOptionsList(const string& a_listOptions);
    int CheckSpecificParameters();
    int Initialize();
    void ShowHelp();
    int ApplyDeformations(FLTNB* ap_inputImage, FLTNB* ap_outputImage, int a_direction, int a_defIdx);


  // -----------------------------------------------------------------------------------------
  // Private member functions
  private:


  // -----------------------------------------------------------------------------------------
  // Data members
  private:
    vector<string> m_pathToFwdDeformationFiles; 
    vector<string> m_pathToBwdDeformationFiles; 
    //ParserType::Pointer file_parser;
    #ifdef CASTOR_ELASTIX
    ImageType::Pointer          ITK_inputImage;
    ImageType::Pointer          ITK_outputImage;
    PixelIndex                  m_PixelIndex;
    RegionType                  m_RegionInputImage;
    RegionSize                  m_RegionSizeInputImage;
    RegionStart                 m_RegionStartInputImage;
    SpacingType                 m_RegionSpacingInputImage;
    #endif
};

// Class for automatic insertion (set here the visible image deformation's name, put the class name as the parameters and do not add semi-colon at the end of the line)
CLASS_DEFORMATION(deformationElastic,iDeformationElastic)

#endif