itkMGHImageIO.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 itkMGHImageIO_h
#define itkMGHImageIO_h

#include "itkMatrix.h"
#include "itkImageIOBase.h"
#include <fstream>
#include "itk_zlib.h"

#include "MGHIOExport.h"

namespace itk
{
class MGHIO_EXPORT MGHImageIO:public ImageIOBase
{
public:
  typedef MGHImageIO         Self;
  typedef ImageIOBase        Superclass;
  typedef SmartPointer<Self> Pointer;

  itkNewMacro(Self);

  itkTypeMacro(MGHImageIO, Superclass);

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

  virtual bool CanReadFile(const char *FileNameToRead) ITK_OVERRIDE;

  virtual void ReadImageInformation() ITK_OVERRIDE;

  virtual void Read(void *buffer) ITK_OVERRIDE;

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

  virtual bool CanWriteFile(const char *FileNameToWrite) ITK_OVERRIDE;

  virtual void WriteImageInformation() ITK_OVERRIDE;

  virtual void Write(const void *buffer) ITK_OVERRIDE;

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

  void ReadVolumeHeader();

private:
  static const int MRI_UCHAR = 0;
  static const int MRI_INT   = 1;
  static const int MRI_FLOAT = 3;
  static const int MRI_SHORT = 4;
  static const int MRI_TENSOR = 6;
  static const unsigned int FS_DIMENSION_HEADER_SIZE = sizeof(int) * 7;
  static const unsigned int FS_RAS_HEADER_SIZE = (sizeof(float) * 15) + sizeof(short);
  static const unsigned int FS_UNUSED_HEADER_SIZE = 256 - FS_RAS_HEADER_SIZE;
  static const unsigned int FS_WHOLE_HEADER_SIZE =
    FS_RAS_HEADER_SIZE + FS_DIMENSION_HEADER_SIZE + FS_UNUSED_HEADER_SIZE;

  bool IsCompressedFilename(const std::string fname);
  void SwapBytesIfNecessary(void * const buffer, const unsigned long numberOfPixels);

  // void MriDirCos();

  void WriteHeader();

  void WriteData(const void* buffer);

  void PermuteFrameValues(const void* buffer, char* tempmemory);

  unsigned int GetComponentSize() const ITK_OVERRIDE;

  std::string GetOrientation( itk::Matrix<double> directions );

  bool          m_IsCompressed;
  gzFile        m_GZFile;
  std::ofstream m_Output;

  // Utility function to assist with writing to disk in the 
  // proper format.  TInType is static_cast<TDiskType> type.
  template <typename TInType, typename TDiskType> int TWrite(const TInType inValue);
  template <typename TDiskType, typename TOutType> int TRead(TOutType &outValue);

  int TWrite(const char *buf,const unsigned long count);
  void OpenFile();
  void CloseFile();
};
} // end namespace itk

#endif // itkMGHImageIO_h