itkHDF5ImageIO.h

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/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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 itkHDF5ImageIO_h
#define itkHDF5ImageIO_h
#include "ITKIOHDF5Export.h"
#include "itkMetaDataObjectBase.h"
#include "itkMetaDataDictionary.h"
#include <memory> // For unique_ptr.
 
// itk namespace first suppresses
// kwstyle error for the H5 namespace below
namespace itk
{}
namespace H5
{
class H5File;
class DataSpace;
class DataSet;
} // namespace H5
 
#include "itkStreamingImageIOBase.h"
 
namespace itk
{
 
class ITKIOHDF5_EXPORT HDF5ImageIO : public StreamingImageIOBase
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(HDF5ImageIO);

  using Self = HDF5ImageIO;
  using Superclass = StreamingImageIOBase;
  using Pointer = SmartPointer<Self>;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(HDF5ImageIO);
 
  /*-------- This part of the interfaces deals with reading data. ----- */

  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 * name) override;

  void
  WriteImageInformation() override;

  void
  Write(const void * buffer) override;
 
protected:
  HDF5ImageIO();
  ~HDF5ImageIO() override;
 
  SizeType
  GetHeaderSize() const override;
 
  void
  PrintSelf(std::ostream & os, Indent indent) const override;
 
private:
  void
  WriteString(const std::string & path, const std::string & value);
  void
  WriteString(const std::string & path, const char * s);
  std::string
  ReadString(const std::string & path);
 
  void
  WriteScalar(const std::string & path, const bool value);
  void
  WriteScalar(const std::string & path, const long value);
  void
  WriteScalar(const std::string & path, const unsigned long value);
  void
  WriteScalar(const std::string & path, const long long value);
  void
  WriteScalar(const std::string & path, const unsigned long long value);
 
  template <typename TScalar>
  void
  WriteScalar(const std::string & path, const TScalar & value);
 
  template <typename TScalar>
  TScalar
  ReadScalar(const std::string & DataSetName);
 
  template <typename TScalar>
  void
  WriteVector(const std::string & path, const std::vector<TScalar> & vec);
 
  template <typename TScalar>
  std::vector<TScalar>
  ReadVector(const std::string & DataSetName);
 
  void
  WriteDirections(const std::string & path, const std::vector<std::vector<double>> & dir);
 
  std::vector<std::vector<double>>
  ReadDirections(const std::string & path);
 
  template <typename TType>
  bool
  WriteMeta(const std::string & name, MetaDataObjectBase * metaObjBase);
  template <typename TType>
  bool
  WriteMetaArray(const std::string & name, MetaDataObjectBase * metaObjBase);
  template <typename TType>
  void
  StoreMetaData(MetaDataDictionary * metaDict,
                const std::string &  HDFPath,
                const std::string &  name,
                unsigned long        numElements);
  void
  SetupStreaming(H5::DataSpace * imageSpace, H5::DataSpace * slabSpace);
 
  /* A convenience function to ensure that the
   * state of the HDF5ImageIO object is returned
   * to a state similar to constructing a new
   * object.  This is needed to ensure that
   * an HDF5ImageIO object can be used multiple
   * times to read/write many images.
   */
  void
  ResetToInitialState();
 
  std::unique_ptr<H5::H5File>  m_H5File;
  std::unique_ptr<H5::DataSet> m_VoxelDataSet;
  bool                         m_ImageInformationWritten{ false };
};
} // end namespace itk
 
#endif // itkHDF5ImageIO_h