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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.
*
*=========================================================================*/
/**
* The specification for this file format is taken from the
* web site https://analyzedirect.com/support/10.0Documents/Analyze_Resource_01.pdf
* \author Hans J. Johnson
* The University of Iowa 2002
*/
#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 HDF5ImageIO
*
* \author Kent Williams
* \brief Class that defines how to read HDF5 file format.
* HDF5 IMAGE FILE FORMAT - As much information as I can determine from sourceforge.net/projects/HDF5lib
*
* \ingroup ITKIOHDF5
*
* HDF5 paths for elements in file
* \li N is dimension of image
* \li \/ITKVersion ITK Library Version string
* \li \/HDFVersion HDF Version String
* \li \/ITKImage Root Image Group
* \li \/ITKImage\/\<name\> name is arbitrary, but to parallel Transform I/O
* keep an image in a subgroup. The idea is to
* parallel transform file structure.
* \li \/ITKImage\/\<name\>\/Origin N-D point double
* \li \/ITKImage\/\<name\>\/Directions N N-vectors double
* \li \/ITKImage\/\<name\>\/Spacing N-vector double
* \li \/ITKImage\/\<name\>\/Dimensions N-vector itk::SizeValueType
* \li \/ITKImage\/\<name\>\/VoxelType String representing voxel type.
* This can be inferred from the VoxelData
* type info, but it makes the file more
* user friendly with respect to HDF5 viewers.
* \li \/ITKImage\/\<name\>\/VoxelData multi-dim array of voxel data
* in the case of non-scalar voxel type,
* keep voxel components together, to make
* loading possible without
* \li \/ITKImage\/\<name\>\/MetaData Group for storing metadata from
* MetaDataDictionary
* \li \/ITKImage\/\<name\>\/MetaData\/\<item-name\>
* Dataset containing data for item-name
* in the MetaDataDictionary
* re-arrangement.
*
*
*/
class ITKIOHDF5_EXPORT HDF5ImageIO : public StreamingImageIOBase
{
public:
ITK_DISALLOW_COPY_AND_MOVE(HDF5ImageIO);
/** Standard class type aliases. */
using Self = HDF5ImageIO;
using Superclass = StreamingImageIOBase;
using Pointer = SmartPointer<Self>;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** \see LightObject::GetNameOfClass() */
itkOverrideGetNameOfClassMacro(HDF5ImageIO);
/*-------- This part of the interfaces deals with reading data. ----- */
/** Determine if the file can be read with this ImageIO implementation.
* \author Hans J Johnson
* \param FileNameToRead The name of the file to test for reading.
* \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
* \return Returns true if this ImageIO can read the file specified.
*/
bool
CanReadFile(const char * FileNameToRead) override;
/** Set the spacing and dimension information for the set filename. */
void
ReadImageInformation() override;
/** Reads the data from disk into the memory buffer provided. */
void
Read(void * buffer) override;
/*-------- This part of the interfaces deals with writing data. ----- */
/** Determine if the file can be written with this ImageIO implementation.
* \param name The name of the file to test for writing.
* \author Hans J. Johnson
* \post Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
* \return Returns true if this ImageIO can write the file specified.
*/
bool
CanWriteFile(const char * name) override;
/** Set the spacing and dimension information for the set filename. */
void
WriteImageInformation() override;
/** Writes the data to disk from the memory buffer provided. Make sure
* that the IORegions has been set properly. */
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
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