Wraps ITK image IO objects as mitk::IFileReader and mitk::IFileWriter objects. More...

#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)
	Construct an ItkImageIO from an ITK ImageIO instance. More...

	ItkImageIO (const CustomMimeType &mimeType, itk::ImageIOBase::Pointer imageIO, int rank)
	Construct an ItkImageIO with a custom MIME type and rank. More...

ConfidenceLevel	GetReaderConfidenceLevel () const override
	Get the confidence level for reading the current file. More...

void	Write () override
	Write the input data to file. More...

ConfidenceLevel	GetWriterConfidenceLevel () const override
	Get the confidence level for writing the current data. More...

std::vector< itk::SmartPointer< BaseData > >	Read () override
	Read data and create a list of BaseData objects. More...

DataStorage::SetOfObjects::Pointer	Read (mitk::DataStorage &ds) override
	Read data and add it to the given DataStorage. More...

Public Member Functions inherited from mitk::AbstractFileIO
Options	GetReaderOptions () const
	Get the reader-specific options. More...

us::Any	GetReaderOption (const std::string &name) const
	Get the value of a specific reader option. More...

void	SetReaderOptions (const Options &options)
	Set multiple reader options at once. More...

void	SetReaderOption (const std::string &name, const us::Any &value)
	Set a single reader option. More...

Options	GetWriterOptions () const
	Get the writer-specific options. More...

us::Any	GetWriterOption (const std::string &name) const
	Get the value of a specific writer option. More...

void	SetWriterOptions (const Options &options)
	Set multiple writer options at once. More...

void	SetWriterOption (const std::string &name, const us::Any &value)
	Set a single writer option. More...

std::pair< us::ServiceRegistration< IFileReader >, us::ServiceRegistration< IFileWriter > >	RegisterService (us::ModuleContext *context=us::GetModuleContext())
	Register both reader and writer as CppMicroServices services. More...

Public Member Functions inherited from mitk::AbstractFileIOReader
ConfidenceLevel	GetConfidenceLevel () const override
	Get the confidence level of this reader or writer for the current input. More...

Public Member Functions inherited from mitk::AbstractFileReader
void	SetInput (const std::string &location) override
	Set the input file path, clearing any previously set input stream. More...

void	SetInput (const std::string &location, std::istream *is) override
	Set an input stream and associated location label. More...

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

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

MimeType	GetRegisteredMimeType () const
	Get the mime-type that was registered for this reader. More...

DataStorage::SetOfObjects::Pointer	Read (mitk::DataStorage &ds) override
	Read data and add it to the given DataStorage. More...

ConfidenceLevel	GetConfidenceLevel () const override
	Determine confidence for reading the current input. More...

Options	GetOptions () const override
	Get the current option values. More...

us::Any	GetOption (const std::string &name) const override
	Get the value of a specific option. More...

void	SetOptions (const Options &options) override
	Set multiple options at once. More...

void	SetOption (const std::string &name, const us::Any &value) override
	Set a single option value. More...

void	AddProgressCallback (const ProgressCallback &callback) override
	Register a progress callback. More...

void	RemoveProgressCallback (const ProgressCallback &callback) override
	Remove a previously registered progress callback. More...

us::ServiceRegistration< IFileReader >	RegisterService (us::ModuleContext *context=us::GetModuleContext())
	Register this reader as a CppMicroServices service. More...

void	UnregisterService ()
	Unregister this reader from the CppMicroServices registry. More...

std::vector< std::string >	GetReadFiles () override
	Get the list of files consumed during the last Read() call. More...

void	SetProperties (const PropertyList *properties) override
	Set base data properties as a source of meta data for reading. 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
	Get the confidence level of this reader or writer for the current input. 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. More...

void	SetOutputLocation (const std::string &location) override
	Set the output file-system path, clearing any output stream. 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 and associated location label. More...

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

ConfidenceLevel	GetConfidenceLevel () const override
	Determine confidence for writing the current input data. More...

MimeType	GetRegisteredMimeType () const
	Get the MIME type that was registered for this writer. More...

Options	GetOptions () const override
	Get the current option values. More...

us::Any	GetOption (const std::string &name) const override
	Get the value of a specific option. More...

void	SetOptions (const Options &options) override
	Set multiple options at once. More...

void	SetOption (const std::string &name, const us::Any &value) override
	Set a single option value. More...

void	AddProgressCallback (const ProgressCallback &callback) override
	Register a progress callback. More...

void	RemoveProgressCallback (const ProgressCallback &callback) override
	Remove a previously registered progress callback. More...

us::ServiceRegistration< IFileWriter >	RegisterService (us::ModuleContext *context=us::GetModuleContext())
	Register this writer as a CppMicroServices service. More...

void	UnregisterService ()
	Unregister this writer from the CppMicroServices registry. More...

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)
	Convert a MetaDataDictionary into a PropertyList for a certain MIME type. More...

static Image::Pointer	LoadRawMitkImageFromImageIO (itk::ImageIOBase *imageIO, const std::string &path)
	Extract a raw MITK image from the given file path using the specified ImageIOBase. More...

static void	PreparImageIOToWriteImage (itk::ImageIOBase imageIO, const Image image)
	Prepare an ITK ImageIOBase instance for writing the given MITK image. More...

static void	SavePropertyListAsMetaData (itk::MetaDataDictionary &dictionary, const PropertyList *properties, const std::string &mimeTypeName)
	Save a PropertyList as meta data in an ITK MetaDataDictionary. More...

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

static std::string	PROP_MIMETYPE ()
	Service property name for the mime-type associated with this reader or 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)
	Fix up file extensions reported by the ITK ImageIO. More...

virtual void	FixUpCustomMimeTypeName (const std::string &imageIOName, CustomMimeType &customMimeType)
	Fix up the custom MIME type name based on the ITK ImageIO name. More...

virtual void	InitializeDefaultMetaDataKeys ()
	Fills the m_DefaultMetaDataKeys vector with default values. More...

std::vector< itk::SmartPointer< BaseData > >	DoRead () override
	Perform the actual reading operation. More...

Protected Member Functions inherited from mitk::AbstractFileIO
	AbstractFileIO (const AbstractFileIO &other)
	Copy constructor. More...

	AbstractFileIO (const std::string &baseDataType)
	Construct with a BaseData type name only. More...

	AbstractFileIO (const std::string &baseDataType, const CustomMimeType &mimeType, const std::string &description)
	Construct with a BaseData type, MIME type, and description. More...

void	SetMimeType (const CustomMimeType &mimeType)
	Set the shared MIME type for both reader and writer. More...

const CustomMimeType *	GetMimeType () const
	Get the shared MIME type. More...

void	SetReaderDescription (const std::string &description)
	Set the description for the reader part. More...

std::string	GetReaderDescription () const
	Get the description of the reader part. More...

void	SetWriterDescription (const std::string &description)
	Set the description for the writer part. More...

std::string	GetWriterDescription () const
	Get the description of the writer part. More...

void	SetDefaultReaderOptions (const Options &defaultOptions)
	Set default options for the reader part. More...

Options	GetDefaultReaderOptions () const
	Get the default options for the reader part. More...

void	SetDefaultWriterOptions (const Options &defaultOptions)
	Set default options for the writer part. More...

Options	GetDefaultWriterOptions () const
	Get the default options for the writer part. More...

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

int	GetReaderRanking () const
	Get the service ranking for the reader part. More...

void	SetWriterRanking (int ranking)
	Set the service ranking for the writer part. More...

int	GetWriterRanking () const
	Get the service ranking for the writer part. More...

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

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

Protected Member Functions inherited from mitk::AbstractFileReader
	AbstractFileReader ()
	Default constructor. More...

	~AbstractFileReader () override

	AbstractFileReader (const AbstractFileReader &other)
	Copy constructor. More...

	AbstractFileReader (const CustomMimeType &mimeType, const std::string &description)
	Associate this reader instance with the given MIME type. More...

virtual us::ServiceProperties	GetServiceProperties () const
	Get the service properties for registration. More...

virtual us::ServiceRegistration< CustomMimeType >	RegisterMimeType (us::ModuleContext *context)
	Register a new CustomMimeType service object. More...

void	SetMimeType (const CustomMimeType &mimeType)
	Set the MIME type this reader can handle. More...

const CustomMimeType *	GetMimeType () const
	Get the MIME type this reader can handle. More...

void	SetMimeTypePrefix (const std::string &prefix)
	Set the prefix used for auto-generated MIME type names. More...

std::string	GetMimeTypePrefix () const
	Get the current MIME type name prefix. More...

void	SetDescription (const std::string &description)
	Set the human-readable description of this reader. More...

std::string	GetDescription () const
	Get the human-readable description of this reader. More...

void	SetDefaultOptions (const Options &defaultOptions)
	Set the default options for this reader. More...

Options	GetDefaultOptions () const
	Get the default options for this reader. More...

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

int	GetRanking () const
	Get the service ranking for this file reader. More...

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

virtual void	SetDefaultDataNodeProperties (DataNode *node, const std::string &filePath)
	Set default properties on a DataNode after reading. More...

const PropertyList *	GetProperties () const override
	Get the properties set via SetProperties(). More...

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)
	Copy constructor. More...

	AbstractFileWriter (const std::string &baseDataType)
	Construct a writer for the given BaseData type name. More...

	AbstractFileWriter (const std::string &baseDataType, const CustomMimeType &mimeType, const std::string &description)
	Construct a writer for the given BaseData type, MIME type, and description. More...

virtual us::ServiceProperties	GetServiceProperties () const
	Get the service properties for registration. More...

virtual us::ServiceRegistration< CustomMimeType >	RegisterMimeType (us::ModuleContext *context)
	Register a new CustomMimeType service object. More...

void	SetMimeType (const CustomMimeType &mimeType)
	Set the MIME type this writer can handle. More...

const CustomMimeType *	GetMimeType () const
	Get the MIME type this writer can handle. More...

void	SetMimeTypePrefix (const std::string &prefix)
	Set the prefix used for auto-generated MIME type names. More...

std::string	GetMimeTypePrefix () const
	Get the current MIME type name prefix. More...

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

std::string	GetDescription () const
	Get the human-readable description of this writer. More...

void	SetDefaultOptions (const Options &defaultOptions)
	Set the default options for this writer. More...

Options	GetDefaultOptions () const
	Get the default options for this writer. More...

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

int	GetRanking () const
	Get the service ranking for this file writer. More...

void	SetBaseDataType (const std::string &baseDataType)
	Set the name of the mitk::BaseData sub-class this writer supports. More...

virtual std::string	GetBaseDataType () const
	Get the name of the mitk::BaseData sub-class this writer supports. More...

void	ValidateOutputLocation () const
	Validate the output location or stream. More...

Additional Inherited Members
Public Types inherited from mitk::IFileIO
enum	ConfidenceLevel { Unsupported , PartiallySupported , Supported }
	A confidence level describing the reader's or writer's ability to handle the given data or file format. More...

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

typedef mitk::MessageAbstractDelegate1< float >	ProgressCallback
	Callback delegate type for progress reporting. More...

Protected Attributes inherited from mitk::AbstractFileReader
std::vector< std::string >	m_ReadFiles
	List of files consumed during the last Read() call. Must be filled by DoRead(). More...

Detailed Description

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.

See also: AbstractFileIO

Definition at line 34 of file mitkItkImageIO.h.

Constructor & Destructor Documentation

◆ ItkImageIO() [1/2]

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

Construct an ItkImageIO from an ITK ImageIO instance.

Parameters

imageIO The ITK ImageIO base instance to wrap.

◆ ItkImageIO() [2/2]

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

Construct an ItkImageIO with a custom MIME type and rank.

Parameters

mimeType	The custom MIME type for this IO.
imageIO	The ITK ImageIO base instance to wrap.
rank	The service ranking.

Member Function Documentation

◆ DoRead()

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

overrideprotectedvirtual

Perform the actual reading operation.

Subclasses must implement this method. The implementation should 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: A vector of created BaseData objects.

Exceptions

mitk::Exception if reading fails.

See also: GetLocalFileName(); 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

Convert a MetaDataDictionary into a PropertyList for a certain MIME type.

The function uses the Property serialization service for the conversion.

Parameters

dictionary	Reference to the meta data dictionary that contains the information to extract.
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.

Returns: A PropertyList containing the extracted meta data.

◆ FixUpCustomMimeTypeName()

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

protectedvirtual

Fix up the custom MIME type name based on the ITK ImageIO name.

Parameters

imageIOName	The name of the ITK ImageIO.
customMimeType	The custom MIME type to fix up.

◆ FixUpImageIOExtensions()

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

protectedvirtual

Fix up file extensions reported by the ITK ImageIO.

Parameters

imageIOName The name of the ITK ImageIO.

Returns: A corrected list of file extensions.

◆ GetReaderConfidenceLevel()

ConfidenceLevel mitk::ItkImageIO::GetReaderConfidenceLevel ( ) const

overridevirtual

Get the confidence level for reading the current file.

Reimplemented from mitk::AbstractFileIO.

◆ GetWriterConfidenceLevel()

ConfidenceLevel mitk::ItkImageIO::GetWriterConfidenceLevel ( ) const

overridevirtual

Get the confidence level for writing the current data.

Reimplemented from mitk::AbstractFileIO.

◆ InitializeDefaultMetaDataKeys()

virtual void mitk::ItkImageIO::InitializeDefaultMetaDataKeys ( )

protectedvirtual

Fills the m_DefaultMetaDataKeys vector with default values.

◆ LoadRawMitkImageFromImageIO()

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

static

Extract a raw MITK image from the given file path using the specified ImageIOBase.

Raw means that only the pixel data and geometry information is loaded (no properties, etc.).

Parameters

imageIO	The ITK ImageIOBase instance to use for loading.
path	The file path to read from.

Returns: The loaded MITK image.

◆ PreparImageIOToWriteImage()

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

static

Prepare an ITK ImageIOBase instance for writing the given MITK image.

Parameters

imageIO	The ITK ImageIOBase instance to configure.
image	The MITK image to be written.

◆ Read() [1/2]

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

overridevirtual

Read data and create a list of BaseData objects.

The default implementation calls DoRead() and then annotates each resulting BaseData with meta-information about the reader, MIME type, input location, and reader options.

Returns: A vector of created BaseData objects.

Exceptions

mitk::Exception if reading fails.

Reimplemented from mitk::AbstractFileReader.

◆ Read() [2/2]

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

overridevirtual

Read data and add it to the given DataStorage.

Parameters

[in,out] ds The DataStorage to add nodes to.

Returns: The set of DataNode objects added to ds.

Exceptions

mitk::Exception if reading fails.

Reimplemented from mitk::AbstractFileReader.

◆ SavePropertyListAsMetaData()

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

static

Save a PropertyList as meta data in an ITK MetaDataDictionary.

Parameters

dictionary	The target meta data dictionary.
properties	The PropertyList to save.
mimeTypeName	The MIME type to assume for serialization.

◆ Write()

void mitk::ItkImageIO::Write ( )

overridevirtual

Write the input data to file.

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()