libinsighttoolkit3-dev 3.20.1+git20120521-6build1 / usr / include / InsightToolkit / Review / itkMINC2ImageIO.h

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

  Program:   Insight Segmentation & Registration Toolkit
  Module:    itkMINC2ImageIO.h
  Language:  C++
  Date:      $Date$
  Version:   $Revision$

  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.

=========================================================================*/
/**
 *         The specification for this file format is taken from the
 *         web site http://www.bic.mni.mcgill.ca/software/minc
 * \author Leila Baghdadi
 *         Mouse Imaging Centre, Toronto, Canada 2005.
 */


#ifndef __itkMINC2ImageIO_h
#define __itkMINC2ImageIO_h

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

#include "itkImageIOBase.h"

#include "itkMatrix.h"

extern "C" {
#include <minc2.h>
}

namespace itk
{

/** \class MINC2ImageIO
 *
 * \author Leila Baghdadi
 * \brief Class that defines how to read MINC2 file format. Note,like
 * ITK, MINC2 is N dimensional and dimensions can be submitted in any 
 * arbitrary order. Here we make sure the dimensions are ordered as
 * xspace, yspace, zspace, time and vector_dimension and so on or
 * xfrequencey, yfrequency, zfrequency, tfrequency and
 * vector_dimension and so on
 * NOTE** This class only reads the regularly sampled dimensions as I
 * am not sure how to deal with "iregularly sampled" dimensions yet!
 * \ingroup IOFilters
 *
 */
class ITK_EXPORT MINC2ImageIO : public ImageIOBase
{
public:
  /** Standard class typedefs. */
  typedef MINC2ImageIO            Self;
  typedef ImageIOBase             Superclass;
  typedef SmartPointer<Self>      Pointer;
  typedef Matrix<float,3,3>       MatrixType;
  /** Method for creation through the object factory. */
  itkNewMacro(Self);

  /** Run-time type information (and related methods). */
  itkTypeMacro(MINC2ImageIO, ImageIOBase);

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

  /** Determine the file type. Returns true if this ImageIO can read the
   * file specified. */
  virtual bool CanReadFile(const char*);
  
  /** Set the spacing and dimension information for the set filename. */
  virtual void ReadImageInformation();
  
  /** Reads the data from disk into the memory buffer provided. */
  virtual void Read(void* buffer);

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

  /** Determine the file type. Returns true if this ImageIO can read the
   * file specified. */
  virtual bool CanWriteFile(const char*);

  /** Writes the spacing and dimentions of the image.
   * Assumes SetFileName has been called with a valid file name. */
  virtual void WriteImageInformation();

  /** Writes the data to disk from the memory buffer provided. Make sure
   * that the IORegion has been set properly. */
  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);

  // Num. dimensions in base class (c.f. GetNumberOfDimensions); why keep a second copy here?
  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