itkMABMISImageRegistrationFilter.h

#ifndef __itkMABMISImageRegistrationFilter_h
#define __itkMABMISImageRegistrationFilter_h

#include <itkImage.h>
#include <itkImageToImageFilter.h>

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIterator.h"

#include "itkHistogramMatchingImageFilter.h"

#include "itkImage.h"

#include "itkMABMISDeformationFieldFilter.h"
#include "itkMABMISImageOperationFilter.h"

#define ImageDimension 3

namespace itk
{
namespace Statistics
{
template <class TInputImage, class TOutputImage>
class MABMISImageRegistrationFilter : public ImageToImageFilter<TInputImage, TOutputImage>
{
public:

  typedef MABMISImageRegistrationFilter                 Self;
  typedef ImageToImageFilter<TInputImage, TOutputImage> Superclass;
  typedef SmartPointer<Self>                            Pointer;
  typedef SmartPointer<const Self>                      ConstPointer;

  typedef TInputImage                 ImageType;
  typedef typename ImageType::Pointer ImagePointerType;

  typedef itk::ImageFileReader<ImageType>     ImageReaderType;
  typedef itk::ImageRegionIterator<ImageType> ImageIteratorType;

// basic data type
  typedef unsigned char                                  CharPixelType;  // for image IO usage
  typedef float                                          FloatPixelType; // for
  typedef int                                            IntPixelType;
  typedef short                                          ShortPixelType;
  typedef float                                          InternalPixelType; // for internal processing usage
  typedef itk::Vector<InternalPixelType, ImageDimension> VectorPixelType;

// basic image type
  typedef itk::Image<CharPixelType, ImageDimension>     CharImageType;
  typedef itk::Image<IntPixelType, ImageDimension>      IntImageType;
  typedef itk::Image<ShortPixelType, ImageDimension>    ShortImageType;
  typedef itk::Image<FloatPixelType, ImageDimension>    FloatImageType;
  typedef itk::Image<InternalPixelType, ImageDimension> InternalImageType;
  typedef itk::Image<VectorPixelType, ImageDimension>   DeformationFieldType;

// basic iterator type
  typedef itk::ImageRegionIterator<DeformationFieldType> DeformationFieldIteratorType;
  typedef itk::ImageRegionIterator<InternalImageType>    InternalImageIteratorType;
  typedef itk::ImageRegionIterator<CharImageType>        CharImageIteratorType;

// basic image reader/writer related type
  typedef itk::ImageFileReader<CharImageType>                     CharImageReaderType;
  typedef itk::ImageFileReader<InternalImageType>                 InternalImageReaderType;
  typedef itk::ImageFileWriter<InternalImageType>                 InternalImageWriterType;
  typedef itk::CastImageFilter<InternalImageType, CharImageType>  Internal2CharCastFilterType;
  typedef itk::CastImageFilter<InternalImageType, FloatImageType> Internal2FloatCastFilterType;
  typedef itk::CastImageFilter<InternalImageType, IntImageType>   Internal2IntCastFilterType;
  typedef itk::CastImageFilter<InternalImageType, ShortImageType> Internal2ShortCastFilterType;

  typedef itk::WarpImageFilter<InternalImageType, InternalImageType, DeformationFieldType> InternalWarpFilterType;
  typedef itk::ImageFileWriter<CharImageType>                                              CharImageWriterType;
  typedef itk::ImageFileWriter<IntImageType>                                               IntImageWriterType;
  typedef itk::ImageFileWriter<FloatImageType>                                             FloatImageWriterType;
  typedef itk::ImageFileWriter<ShortImageType>                                             ShortImageWriterType;

  typedef itk::ImageFileReader<DeformationFieldType> DeformationFieldReaderType;
  typedef itk::ImageFileWriter<DeformationFieldType> DeformationFieldWriterType;

  typedef itk::HistogramMatchingImageFilter<InternalImageType, InternalImageType> InternalHistMatchFilterType;

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

  /** Run-time type information (and related methods). */
  itkTypeMacro(MABMISImageRegistrationFilter, ImageToImageFilter);

  typedef itk::Statistics::MABMISDeformationFieldFilter<ImageType, ImageType> DeformationFieldOperationType;
  typedef itk::Statistics::MABMISImageOperationFilter<ImageType, ImageType>   ImageOperationType;

  typename DeformationFieldOperationType::Pointer dfoperator;
  typename ImageOperationType::Pointer imgoperator;

  void DoIt();

  int DiffeoDemonsRegistrationWithParameters(std::string fixedImageFileName, std::string  movingImageFileName,
                                             std::string deformedImageFileName, std::string deformationFieldFileName,
                                             double sigmaDef, bool doHistMatch, std::vector<int> iterInResolutions);

  int DiffeoDemonsRegistrationWithInitialWithParameters(std::string  fixedImageFileName, std::string movingImageFileName,
                                                        std::string initDeformationFieldFileName,
                                                        std::string deformedImageFileName, std::string deformationFieldFileName,
                                                        double sigmaDef, bool doHistMatch,
                                                        std::vector<int> iterInResolutions);

  itkSetMacro(Root, int);
private:
  MABMISImageRegistrationFilter(const Self &); // purposely not implemented
  void operator=(const Self &);                // purposely not implemented

  int m_Root;
protected:
  MABMISImageRegistrationFilter();
  ~MABMISImageRegistrationFilter();
  void PrintSelf(std::ostream& os, Indent indent) const;
};
} // namespace itk
} // namespace Statistics

#include "itkMABMISImageRegistrationFilter.hxx"

#endif