itkMINC2ImageIO.h

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/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef __itkMINC2ImageIO_h
#define __itkMINC2ImageIO_h


#include "itkImageIOBase.h"

#include "itkMatrix.h"

extern "C" {
#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);

  /*-------- 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);

  // 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