itkMINC2ImageIO.h

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkMINC2ImageIO.h,v $
  Language:  C++
  Date:      $Date: 2008/01/27 12:53:07 $
  Version:   $Revision: 1.4 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#ifndef __itkMINC2ImageIO_h
#define __itkMINC2ImageIO_h

#ifdef _MSC_VER
#pragma warning ( disable : 4786 )
#endif

#include "itkImageIOBase.h"

#include "itkMatrix.h"

extern "C" {
#include <netcdf.h>
#include <hdf5.h>
#include <minc2.h>

}
namespace itk
{

class ITK_EXPORT MINC2ImageIO : public ImageIOBase
{
public:
  typedef MINC2ImageIO            Self;
  typedef ImageIOBase             Superclass;
  typedef SmartPointer<Self>      Pointer;
  typedef Matrix<float,3,3>       MatrixType;

  itkNewMacro(Self);

  itkTypeMacro(MINC2ImageIO, ImageIOBase);

  /*-------- This part of the interface deals with reading data. ------ */

  virtual bool CanReadFile(const char*);

  virtual void ReadImageInformation();

  virtual void Read(void* buffer);

  virtual void ReadVolume(void* buffer);

  /*-------- This part of the interfaces deals with writing data. ----- */

  virtual bool CanWriteFile(const char*);

  virtual void WriteImageInformation();

  virtual void Write(const void* buffer);

  char *GetDimensionOrder() { return m_DimensionOrder; }
  void SetDimensionOrder(char *dimorder) { m_DimensionOrder = dimorder; }

  void XYZFromDirectionCosines(midimhandle_t *hdims, int *dim_indices, unsigned int *number_of_components);

protected:
  MINC2ImageIO();
  ~MINC2ImageIO();
  void PrintSelf(std::ostream& os, Indent indent) const;

  void WriteSlice(std::string& fileName, const void* buffer);

  unsigned int m_NDims;

  char **m_DimensionName;
  virtual void SetDimensionName(unsigned int i, char *name);
  virtual char * GetDimensionName(unsigned int i){ return m_DimensionName[i]; }

  char *m_DimensionOrder;
  
  // shift and scale parameter (god help me with slice scaling!!)
  double m_Shift;
  double m_Scale;

  // dimension size and start and step
  unsigned int * m_DimensionSize;
  double       * m_DimensionStart;
  double       * m_DimensionStep;
  MatrixType     m_DirectionCosines;

  int * m_DimensionIndices;

  // Description:
  // Check the DimensionOrder and adjust according to what
  // dimensions the user has actually specified via
  // SetDimensionOrder()
  int CheckDimensionOrder(char *userdimorder);

  double m_OriginalStart[3];
  // complex type images, composed of complex numbers  
  int m_Complex;
private:
  MINC2ImageIO(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented
  // Description
  // Get slice scaling from local slice scaling
  void SetSliceScalingFromLocalScaling(mihandle_t volume);
    
  // Description
  // Get slice scaling from global slice scaling
  void SetSliceScalingFromGlobalScaling(mihandle_t volume);

};

} // end namespace itk

#endif // __itkMINC2ImageIO_h

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