itkMIDASHelper.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 itkMIDASHelper_h
#define itkMIDASHelper_h

#include <niftkITKWin32ExportHeader.h>

#include <itkImageRegionIteratorWithIndex.h>
#include <itkImage.h>
#include <itkImageRegionConstIterator.h>
#include <itkConversionUtils.h>
#include <itkSpatialOrientationAdapter.h>
#include <itkSpatialOrientation.h>
#include <itkMatrix.h>

namespace itk
{
  enum Orientation {
    ORIENTATION_AXIAL = 0,
    ORIENTATION_SAGITTAL = 1,
    ORIENTATION_CORONAL = 2,
    ORIENTATION_UNKNOWN = -1
  };

  template <class TImage>
  NIFTKITK_WINEXPORT ITK_EXPORT void LimitMaskByRegion(TImage* mask,
                         typename TImage::RegionType &region,
                         typename TImage::PixelType outValue
                         );

  template<typename TPixel, unsigned int VImageDimension>
  NIFTKITK_WINEXPORT ITK_EXPORT
  void
  GetVolumeFromITKImage(
    const itk::Image<TPixel, VImageDimension>* itkImage,
    double &imageVolume
    );


  template<unsigned int VImageDimension>
  NIFTKITK_WINEXPORT ITK_EXPORT
  void
  GetOrientationString(
    const itk::Matrix<double, VImageDimension, VImageDimension>& directionMatrix,
    std::string &orientationString
    );


  NIFTKITK_WINEXPORT ITK_EXPORT int GetAxisFromOrientationString(const std::string& orientationString, const itk::Orientation& orientation);


  NIFTKITK_WINEXPORT ITK_EXPORT int GetUpDirection(const std::string& orientationString, const int& axisOfInterest);

  NIFTKITK_WINEXPORT ITK_EXPORT std::string GetMajorAxisFromPatientRelativeDirectionCosine(double x,double y,double z);

  template<typename TPixel, unsigned int VImageDimension>
  NIFTKITK_WINEXPORT ITK_EXPORT
  void
  GetOrientationStringFromITKImage(
    const itk::Image<TPixel, VImageDimension>* itkImage,
    std::string &orientationString
    );


  template<typename TPixel, unsigned int VImageDimension>
  NIFTKITK_WINEXPORT ITK_EXPORT
  void
  GetAxisFromITKImage(
    const itk::Image<TPixel, VImageDimension>* itkImage,
    const itk::Orientation orientation,
    int &outputAxis
    );


  template<typename TPixel, unsigned int VImageDimension>
  NIFTKITK_WINEXPORT ITK_EXPORT
  void
  GetUpDirectionFromITKImage(
      const itk::Image<TPixel, VImageDimension>* itkImage,
      const itk::Orientation orientation,
      int &upDirection
      );

  template<typename TPixel, unsigned int VImageDimension>
  NIFTKITK_WINEXPORT ITK_EXPORT
  void GetOrientationLabelFromITKImage(
      const itk::Image<TPixel, VImageDimension>* itkImage, std::string &label);

}


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

#endif