itkNiftiImageIO.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 itkNiftiImageIO_h
#define itkNiftiImageIO_h
#include "ITKIONIFTIExport.h"


#include <fstream>
#include <memory>
#include "itkImageIOBase.h"

namespace itk
{
class ITKIONIFTI_EXPORT NiftiImageIO:public ImageIOBase
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(NiftiImageIO);

  using Self = NiftiImageIO;
  using Superclass = ImageIOBase;
  using Pointer = SmartPointer< Self >;

  itkNewMacro(Self);

  itkTypeMacro(NiftiImageIO, Superclass);

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

  enum FileType {

    TwoFileNifti = 2,

    OneFileNifti = 1,

    Analyze75 = 0,

    OtherOrError = -1,
  };

  FileType DetermineFileType(const char *FileNameToRead);

  bool CanReadFile(const char *FileNameToRead) override;

  void ReadImageInformation() override;

  void Read(void *buffer) override;

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

  bool CanWriteFile(const char *FileNameToWrite) override;

  void WriteImageInformation() override;

  void Write(const void *buffer) override;

  ImageIORegion
  GenerateStreamableReadRegionFromRequestedRegion(const ImageIORegion & requestedRegion) const override;

  itkSetMacro(RescaleSlope, double);
  itkSetMacro(RescaleIntercept, double);

  itkSetMacro(LegacyAnalyze75Mode, bool);
  itkGetConstMacro(LegacyAnalyze75Mode, bool);

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

  virtual bool GetUseLegacyModeForTwoFileWriting() const { return false; }

private:
  //Try to use the Q and S form codes from MetaDataDictionary if they are specified
  //there, otherwise default to the backwards compatible values from earlier
  //versions of ITK. The qform guess would probably been better to have
  //been guessed as NIFTI_XFORM_SCANNER_ANAT
  unsigned int getSFormCodeFromDictionary() const;
  unsigned int getQFormCodeFromDictionary() const;

  bool  MustRescale();

  void  DefineHeaderObjectDataType();

  void  SetNIfTIOrientationFromImageIO(unsigned short int origdims, unsigned short int dims);

  void  SetImageIOOrientationFromNIfTI(unsigned short int dims);

  void  SetImageIOMetadataFromNIfTI();

  //This proxy class provides a nifti_image pointer interface to the internal implementation
  //of itk::NiftiImageIO, while hiding the niftilib interface from the external ITK interface.
  class NiftiImageProxy;

  //Note that it is essential that m_NiftiImageHolder is defined before m_NiftiImage, to ensure that
  //m_NiftiImage can directly get a proxy from m_NiftiImageHolder during NiftiImageIO construction.
  const std::unique_ptr<NiftiImageProxy> m_NiftiImageHolder;

  NiftiImageProxy& m_NiftiImage;

  double m_RescaleSlope{1.0};
  double m_RescaleIntercept{0.0};

  IOComponentType m_OnDiskComponentType{UNKNOWNCOMPONENTTYPE};

  bool m_LegacyAnalyze75Mode{true};

};
} // end namespace itk

#endif // itkNiftiImageIO_h