#include <mitkItkImageIO.h>

Inheritance diagram for mitk::ItkImageIO:

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Collaboration diagram for mitk::ItkImageIO:

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Public Member Functions
	ItkImageIO (itk::ImageIOBase::Pointer imageIO)

	ItkImageIO (const CustomMimeType &mimeType, itk::ImageIOBase::Pointer imageIO, int rank)

ConfidenceLevel	GetReaderConfidenceLevel () const override

void	Write () override
	Write the base data to the specified location or output stream. More...

ConfidenceLevel	GetWriterConfidenceLevel () const override

std::vector< itk::SmartPointer< BaseData > >	Read () override
	Reads a path or stream and creates a list of BaseData objects. More...

DataStorage::SetOfObjects::Pointer	Read (mitk::DataStorage &ds) override

Public Member Functions inherited from mitk::AbstractFileIO
Options	GetReaderOptions () const

us::Any	GetReaderOption (const std::string &name) const

void	SetReaderOptions (const Options &options)

void	SetReaderOption (const std::string &name, const us::Any &value)

Options	GetWriterOptions () const

us::Any	GetWriterOption (const std::string &name) const

void	SetWriterOptions (const Options &options)

void	SetWriterOption (const std::string &name, const us::Any &value)

std::pair< us::ServiceRegistration< IFileReader >, us::ServiceRegistration< IFileWriter > >	RegisterService (us::ModuleContext *context=us::GetModuleContext())

Public Member Functions inherited from mitk::AbstractFileIOReader
ConfidenceLevel	GetConfidenceLevel () const override
	The confidence level of the reader or writer implementation. More...

Public Member Functions inherited from mitk::AbstractFileReader
void	SetInput (const std::string &location) override
	Set the input location. More...

void	SetInput (const std::string &location, std::istream *is) override
	Set an input stream to read from. More...

std::string	GetInputLocation () const override
	Get the current input location. More...

std::istream *	GetInputStream () const override
	Get the input stream. More...

MimeType	GetRegisteredMimeType () const

std::vector< itk::SmartPointer< BaseData > >	Read () override
	Reads a path or stream and creates a list of BaseData objects. More...

DataStorage::SetOfObjects::Pointer	Read (mitk::DataStorage &ds) override
	Reads the specified file or input stream, loading its contents into the provided DataStorage. More...

ConfidenceLevel	GetConfidenceLevel () const override
	The confidence level of the reader or writer implementation. More...

Options	GetOptions () const override
	returns a list of the supported options More...

us::Any	GetOption (const std::string &name) const override

void	SetOptions (const Options &options) override

void	SetOption (const std::string &name, const us::Any &value) override

void	AddProgressCallback (const ProgressCallback &callback) override

void	RemoveProgressCallback (const ProgressCallback &callback) override

us::ServiceRegistration< IFileReader >	RegisterService (us::ModuleContext *context=us::GetModuleContext())

void	UnregisterService ()

std::vector< std::string >	GetReadFiles () override

void	SetProperties (const PropertyList *properties) override
	Optionally provide base data properties as a source of meta data. More...

Public Member Functions inherited from mitk::IFileReader
	~IFileReader () override

virtual	~IFileReader ()

Public Member Functions inherited from mitk::IFileIO
virtual	~IFileIO ()

Public Member Functions inherited from mitk::AbstractFileIOWriter
ConfidenceLevel	GetConfidenceLevel () const override
	The confidence level of the reader or writer implementation. More...

Public Member Functions inherited from mitk::AbstractFileWriter
void	SetInput (const BaseData *data) override
	Set the input data for writing. More...

const BaseData *	GetInput () const override
	Get the input data set via SetInput(). More...

void	SetOutputLocation (const std::string &location) override
	Set the output location. More...

std::string	GetOutputLocation () const override
	Get the current output location. More...

void	SetOutputStream (const std::string &location, std::ostream *os) override
	Set an output stream for writing. More...

std::ostream *	GetOutputStream () const override
	Get the output stream. More...

ConfidenceLevel	GetConfidenceLevel () const override
	The confidence level of the reader or writer implementation. More...

MimeType	GetRegisteredMimeType () const

Options	GetOptions () const override
	returns a list of the supported options More...

us::Any	GetOption (const std::string &name) const override

void	SetOptions (const Options &options) override

void	SetOption (const std::string &name, const us::Any &value) override

void	AddProgressCallback (const ProgressCallback &callback) override

void	RemoveProgressCallback (const ProgressCallback &callback) override

us::ServiceRegistration< IFileWriter >	RegisterService (us::ModuleContext *context=us::GetModuleContext())

void	UnregisterService ()

Public Member Functions inherited from mitk::IFileWriter
	~IFileWriter () override

Static Public Member Functions
static PropertyList::Pointer	ExtractMetaDataAsPropertyList (const itk::MetaDataDictionary &dictionary, const std::string &mimeTypeName, const std::vector< std::string > &defaultMetaDataKeys)

static Image::Pointer	LoadRawMitkImageFromImageIO (itk::ImageIOBase *imageIO, const std::string &path)

static void	PreparImageIOToWriteImage (itk::ImageIOBase imageIO, const Image image)

static void	SavePropertyListAsMetaData (itk::MetaDataDictionary &dictionary, const PropertyList *properties, const std::string &mimeTypeName)

Static Public Member Functions inherited from mitk::IFileIO
static std::string	PROP_DESCRIPTION ()
	Service property name for a description. More...

static std::string	PROP_MIMETYPE ()
	Service property name for the mime-type associated with this file writer. More...

Static Public Member Functions inherited from mitk::IFileWriter
static std::string	PROP_BASEDATA_TYPE ()
	Service property name for the supported mitk::BaseData sub-class. More...

Protected Member Functions
virtual std::vector< std::string >	FixUpImageIOExtensions (const std::string &imageIOName)

virtual void	FixUpCustomMimeTypeName (const std::string &imageIOName, CustomMimeType &customMimeType)

virtual void	InitializeDefaultMetaDataKeys ()

std::vector< itk::SmartPointer< BaseData > >	DoRead () override

Protected Member Functions inherited from mitk::AbstractFileIO
	AbstractFileIO (const AbstractFileIO &other)

	AbstractFileIO (const std::string &baseDataType)

	AbstractFileIO (const std::string &baseDataType, const CustomMimeType &mimeType, const std::string &description)

void	SetMimeType (const CustomMimeType &mimeType)

const CustomMimeType *	GetMimeType () const

void	SetReaderDescription (const std::string &description)

std::string	GetReaderDescription () const

void	SetWriterDescription (const std::string &description)

std::string	GetWriterDescription () const

void	SetDefaultReaderOptions (const Options &defaultOptions)

Options	GetDefaultReaderOptions () const

void	SetDefaultWriterOptions (const Options &defaultOptions)

Options	GetDefaultWriterOptions () const

void	SetReaderRanking (int ranking)
	Set the service ranking for this file reader. More...

int	GetReaderRanking () const

void	SetWriterRanking (int ranking)

int	GetWriterRanking () const

Protected Member Functions inherited from mitk::AbstractFileIOReader
	AbstractFileIOReader ()

	AbstractFileIOReader (const CustomMimeType &mimeType, const std::string &description)

Protected Member Functions inherited from mitk::AbstractFileReader
	AbstractFileReader ()

	~AbstractFileReader () override

	AbstractFileReader (const AbstractFileReader &other)

	AbstractFileReader (const CustomMimeType &mimeType, const std::string &description)

virtual us::ServiceProperties	GetServiceProperties () const

virtual us::ServiceRegistration< CustomMimeType >	RegisterMimeType (us::ModuleContext *context)

void	SetMimeType (const CustomMimeType &mimeType)

const CustomMimeType *	GetMimeType () const

void	SetMimeTypePrefix (const std::string &prefix)

std::string	GetMimeTypePrefix () const

void	SetDescription (const std::string &description)

std::string	GetDescription () const

void	SetDefaultOptions (const Options &defaultOptions)

Options	GetDefaultOptions () const

void	SetRanking (int ranking)
	Set the service ranking for this file reader. More...

int	GetRanking () const

std::string	GetLocalFileName () const
	Get a local file name for reading. More...

virtual void	SetDefaultDataNodeProperties (DataNode *node, const std::string &filePath)

const PropertyList *	GetProperties () const override

Protected Member Functions inherited from mitk::AbstractFileIOWriter
	AbstractFileIOWriter (const std::string &baseDataType)

	AbstractFileIOWriter (const std::string &baseDataType, const CustomMimeType &mimeType, const std::string &description)

Protected Member Functions inherited from mitk::AbstractFileWriter
	~AbstractFileWriter () override

	AbstractFileWriter (const AbstractFileWriter &other)

	AbstractFileWriter (const std::string &baseDataType)

	AbstractFileWriter (const std::string &baseDataType, const CustomMimeType &mimeType, const std::string &description)

virtual us::ServiceProperties	GetServiceProperties () const

virtual us::ServiceRegistration< CustomMimeType >	RegisterMimeType (us::ModuleContext *context)

void	SetMimeType (const CustomMimeType &mimeType)

const CustomMimeType *	GetMimeType () const

void	SetMimeTypePrefix (const std::string &prefix)

std::string	GetMimeTypePrefix () const

void	SetDescription (const std::string &description)
	Sets a human readable description of this writer. More...

std::string	GetDescription () const

void	SetDefaultOptions (const Options &defaultOptions)

Options	GetDefaultOptions () const

void	SetRanking (int ranking)
	Set the service ranking for this file writer. More...

int	GetRanking () const

void	SetBaseDataType (const std::string &baseDataType)
	Sets the name of the mitk::Basedata that this writer is able to handle. More...

virtual std::string	GetBaseDataType () const

void	ValidateOutputLocation () const

Additional Inherited Members
Public Types inherited from mitk::IFileIO
enum	ConfidenceLevel { Unsupported, PartiallySupported, Supported }
	A confidence level describing the confidence of the reader or writer in handling the given data. More...

typedef std::map< std::string, us::Any >	Options
	Options for reading or writing data. More...

typedef mitk::MessageAbstractDelegate1< float >	ProgressCallback

Protected Attributes inherited from mitk::AbstractFileReader
std::vector< std::string >	m_ReadFiles

Detailed Description

This class wraps ITK image IO objects as mitk::IFileReader and mitk::IFileWriter objects.

Instantiating this class with a given itk::ImageIOBase instance will register corresponding MITK reader/writer services for that ITK ImageIO object. For all ITK ImageIOs that support the serialization of MetaData (e.g. nrrd or mhd) the ItkImageIO ensures the serialization of Identification UID.

Definition at line 33 of file mitkItkImageIO.h.

Constructor & Destructor Documentation

◆ ItkImageIO() [1/2]

mitk::ItkImageIO::ItkImageIO ( itk::ImageIOBase::Pointer imageIO )

◆ ItkImageIO() [2/2]

mitk::ItkImageIO::ItkImageIO	(	const CustomMimeType &	mimeType,
		itk::ImageIOBase::Pointer	imageIO,
		int	rank
	)

Member Function Documentation

◆ DoRead()

std::vector<itk::SmartPointer<BaseData> > mitk::ItkImageIO::DoRead ( )

overrideprotectedvirtual

Method that should be implemented by derived classes and does the real loading. This method is called by Read(). This method must be implemented for each specific reader. Call GetInputStream() first and check for a non-null stream to read from. If the input stream is nullptr, use GetInputLocation() to read from a local file-system path.

If the reader cannot use streams directly, use GetLocalFileName() instead.

Returns: The created BaseData objects.

Exceptions

mitk::Exception

See also: GetLocalFileName(); IFileReader::Read()

Implements mitk::AbstractFileReader.

◆ ExtractMetaDataAsPropertyList()

static PropertyList::Pointer mitk::ItkImageIO::ExtractMetaDataAsPropertyList	(	const itk::MetaDataDictionary &	dictionary,
		const std::string &	mimeTypeName,
		const std::vector< std::string > &	defaultMetaDataKeys
	)

static

Helper function that can be used to convert a MetaDataDictionary into a PropertyList for a certain mimeType. The function uses the Property serialization service for that.

Parameters

mimeTypeName	Mime type that should be assumed for the meta data deserialization.
defaultMetaDataKeys	Vector of keys that should be assumed as defaults. For defaults no PropertyInfo will be registered at the PropertyPersistence service, as they are assumed to be handled anyways. For all other keys an info will be registered to ensure that they will be serialized again, even if unknown.
dictionary	Reference to the meta data dictionary that contains the information that should be extracted.

◆ FixUpCustomMimeTypeName()

virtual void mitk::ItkImageIO::FixUpCustomMimeTypeName	(	const std::string &	imageIOName,
		CustomMimeType &	customMimeType
	)

protectedvirtual

◆ FixUpImageIOExtensions()

virtual std::vector<std::string> mitk::ItkImageIO::FixUpImageIOExtensions ( const std::string & imageIOName )

protectedvirtual

◆ GetReaderConfidenceLevel()

ConfidenceLevel mitk::ItkImageIO::GetReaderConfidenceLevel ( ) const

overridevirtual

Reimplemented from mitk::AbstractFileIO.

◆ GetWriterConfidenceLevel()

ConfidenceLevel mitk::ItkImageIO::GetWriterConfidenceLevel ( ) const

overridevirtual

Reimplemented from mitk::AbstractFileIO.

◆ InitializeDefaultMetaDataKeys()

virtual void mitk::ItkImageIO::InitializeDefaultMetaDataKeys ( )

protectedvirtual

◆ LoadRawMitkImageFromImageIO()

static Image::Pointer mitk::ItkImageIO::LoadRawMitkImageFromImageIO	(	itk::ImageIOBase *	imageIO,
		const std::string &	path
	)

static

Helper function that van be used to extract a raw mitk image for the passed path using the also passed ImageIOBase instance. Raw means, that only the pixel data and geometry information is loaded. But e.g. no properties etc...

◆ PreparImageIOToWriteImage()

static void mitk::ItkImageIO::PreparImageIOToWriteImage	(	itk::ImageIOBase *	imageIO,
		const Image *	image
	)

static

Helper function that van be used to extract a raw mitk image for the passed path using the also passed ImageIOBase instance. Raw means, that only the pixel data and geometry information is loaded. But e.g. no properties etc...

◆ Read() [1/2]

std::vector<itk::SmartPointer<BaseData> > mitk::AbstractFileReader::Read

override

Reads a path or stream and creates a list of BaseData objects.

The default implementation of this method (1) calls DoRead() (Implement the specific reader operation there) and (2) it adds general meta information about the loading process.

◆ Read() [2/2]

DataStorage::SetOfObjects::Pointer mitk::AbstractFileReader::Read

override

◆ SavePropertyListAsMetaData()

static void mitk::ItkImageIO::SavePropertyListAsMetaData	(	itk::MetaDataDictionary &	dictionary,
		const PropertyList *	properties,
		const std::string &	mimeTypeName
	)

static

◆ Write()

void mitk::ItkImageIO::Write ( )

overridevirtual

Write the base data to the specified location or output stream.

This method must be implemented for each specific writer. Call GetOutputStream() first and check for a non-null stream to write to. If the output stream is nullptr, use GetOutputLocation() to write to a local file-system path.

If the reader cannot use streams directly, use GetLocalFile() to retrieve a temporary local file name instead.

Exceptions

mitk::Exception

See also: GetLocalFile(); IFileWriter::Write()

Implements mitk::AbstractFileWriter.

The documentation for this class was generated from the following file:

mitkItkImageIO.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ItkImageIO() [1/2]

◆ ItkImageIO() [2/2]

Member Function Documentation

◆ DoRead()

◆ ExtractMetaDataAsPropertyList()

◆ FixUpCustomMimeTypeName()

◆ FixUpImageIOExtensions()

◆ GetReaderConfidenceLevel()

◆ GetWriterConfidenceLevel()

◆ InitializeDefaultMetaDataKeys()

◆ LoadRawMitkImageFromImageIO()

◆ PreparImageIOToWriteImage()

◆ Read() [1/2]

◆ Read() [2/2]

◆ SavePropertyListAsMetaData()

◆ Write()