Base class for creating mitk::BaseData objects from files or streams. More...

#include <mitkAbstractFileReader.h>

Inheritance diagram for mitk::AbstractFileReader:

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Collaboration diagram for mitk::AbstractFileReader:

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Classes
class	InputStream
	An input stream wrapper. More...

Public Member Functions
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=0
	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

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

virtual	~IFileReader ()

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

Protected Member Functions
	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)

Protected Attributes
std::vector< std::string >	m_ReadFiles

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

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...

Detailed Description

Base class for creating mitk::BaseData objects from files or streams.

Definition at line 42 of file mitkAbstractFileReader.h.

Constructor & Destructor Documentation

◆ AbstractFileReader() [1/3]

mitk::AbstractFileReader::AbstractFileReader ( )

protected

Definition at line 60 of file mitkAbstractFileReader.cpp.

◆ ~AbstractFileReader()

mitk::AbstractFileReader::~AbstractFileReader ( )

overrideprotected

Definition at line 61 of file mitkAbstractFileReader.cpp.

References UnregisterService().

◆ AbstractFileReader() [2/3]

mitk::AbstractFileReader::AbstractFileReader ( const AbstractFileReader & other )

protected

Definition at line 73 of file mitkAbstractFileReader.cpp.

◆ AbstractFileReader() [3/3]

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

explicitprotected

Associate this reader instance with the given MIME type.

If mimeType does not provide an extension list, an already registered mime-type object is used. Otherwise, the first entry in the extensions list is used to construct a mime-type name and register it as a new CustomMimeType service object in the default implementation of RegisterMimeType().

Parameters

mimeType	The mime type this reader can read.
description	A human readable description of this reader.

Exceptions

std::invalid_argument if mimeType is empty.

See also: RegisterService

Definition at line 77 of file mitkAbstractFileReader.cpp.

Member Function Documentation

◆ AddProgressCallback()

void mitk::AbstractFileReader::AddProgressCallback ( const ProgressCallback & callback )

overridevirtual

Implements mitk::IFileIO.

Definition at line 271 of file mitkAbstractFileReader.cpp.

◆ GetConfidenceLevel()

IFileReader::ConfidenceLevel mitk::AbstractFileReader::GetConfidenceLevel ( ) const

overridevirtual

The confidence level of the reader or writer implementation.

Returns: Confidence level.

The level is used to rank multiple competing implementations.

Implements mitk::IFileIO.

Reimplemented in mitk::BaseDICOMReaderService.

Definition at line 116 of file mitkAbstractFileReader.cpp.

References GetInputLocation(), mitk::IFileIO::Supported, and mitk::IFileIO::Unsupported.

Referenced by mitk::BaseDICOMReaderService::GetConfidenceLevel(), and mitk::AbstractFileIOReader::GetReaderConfidenceLevel().

◆ GetDefaultOptions()

IFileReader::Options mitk::AbstractFileReader::GetDefaultOptions ( ) const

protected

Definition at line 244 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::GetDefaultReaderOptions().

◆ GetDescription()

std::string mitk::AbstractFileReader::GetDescription ( ) const

protected

Definition at line 282 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::GetReaderDescription(), and GetServiceProperties().

◆ GetInputLocation()

std::string mitk::AbstractFileReader::GetInputLocation ( ) const

overridevirtual

◆ GetInputStream()

std::istream * mitk::AbstractFileReader::GetInputStream ( ) const

overridevirtual

Get the input stream.

Returns: The currently set input stream.

Implements mitk::IFileReader.

Definition at line 263 of file mitkAbstractFileReader.cpp.

Referenced by mitk::ImageVtkXmlIO::GetReaderConfidenceLevel(), mitk::SurfaceVtkXmlIO::GetReaderConfidenceLevel(), mitk::ImageVtkXmlIO::Read(), mitk::SurfaceVtkXmlIO::Read(), and mitk::NavigationDataReaderXML::Read().

◆ GetLocalFileName()

std::string mitk::AbstractFileReader::GetLocalFileName ( ) const

protected

Get a local file name for reading.

This is a convenience method for readers which cannot work natively with input streams. If no input stream has been been set, this method just returns the result of GetLocation(). However, if SetLocation(std::string, std::istream*) has been called with a non-null input stream, this method writes the contents of the stream to a temporary file and returns the name of the temporary file.

The temporary file is deleted when either SetLocation(std::string, std::istream*) is called again with a different input stream or the destructor of this class is called.

This method does not validate file names set via SetInput(std::string).

Returns: A file path in the local file-system for reading.

Definition at line 210 of file mitkAbstractFileReader.cpp.

References mitk::IOUtil::CreateTemporaryFile(), and GetInputLocation().

Referenced by mitk::ImageVtkLegacyIO::GetReaderConfidenceLevel(), mitk::SurfaceVtkLegacyIO::GetReaderConfidenceLevel(), mitk::MAPRegistrationWrapperIO::GetReaderConfidenceLevel(), mitk::RandomForestFileIO::GetReaderConfidenceLevel(), mitk::ItkImageIO::GetReaderConfidenceLevel(), mitk::LabelSetImageIO::GetReaderConfidenceLevel(), mitk::DICOMSegmentationIO::GetReaderConfidenceLevel(), mitk::BaseDICOMReaderService::GetRelevantFiles(), mitk::SurfaceStlIO::Read(), mitk::ImageVtkLegacyIO::Read(), mitk::SurfaceVtkLegacyIO::Read(), mitk::LegacyFileReaderService::Read(), mitk::MAPRegistrationWrapperIO::Read(), mitk::BaseDICOMReaderService::Read(), mitk::RawImageFileReaderService::Read(), mitk::ItkImageIO::Read(), mitk::LabelSetImageIO::Read(), mitk::DICOMSegmentationIO::Read(), and mitk::MAPRegistrationWrapperIO::Write().

◆ GetMimeType()

const CustomMimeType * mitk::AbstractFileReader::GetMimeType ( ) const

protected

Returns: The mime-type this reader can handle.

Definition at line 279 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::GetMimeType(), GetServiceProperties(), and RegisterService().

◆ GetMimeTypePrefix()

std::string mitk::AbstractFileReader::GetMimeTypePrefix ( ) const

protected

Definition at line 281 of file mitkAbstractFileReader.cpp.

Referenced by mitk::DummyLsetFileReader::DummyLsetFileReader(), and mitk::ItkImageIO::FixUpCustomMimeTypeName().

◆ GetOption()

us::Any mitk::AbstractFileReader::GetOption ( const std::string & name ) const

overridevirtual

Implements mitk::IFileIO.

Definition at line 266 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::GetReaderOption().

◆ GetOptions()

IFileReader::Options mitk::AbstractFileReader::GetOptions ( ) const

overridevirtual

returns a list of the supported options

Options are strings that are treated as flags when passed to the write method.

Implements mitk::IFileIO.

Definition at line 265 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::GetReaderOptions(), mitk::CESTDICOMReaderService::Read(), and mitk::RawImageFileReaderService::Read().

◆ GetRanking()

int mitk::AbstractFileReader::GetRanking ( ) const

protected

Definition at line 209 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::GetReaderRanking(), and GetServiceProperties().

◆ GetReadFiles()

std::vector< std::string > mitk::AbstractFileReader::GetReadFiles ( )

overridevirtual

Returns: A list of files that were loaded during the last call of Read. Has to be filled by the actual reader class.

Implements mitk::IFileReader.

Definition at line 204 of file mitkAbstractFileReader.cpp.

References m_ReadFiles.

◆ GetRegisteredMimeType()

MimeType mitk::AbstractFileReader::GetRegisteredMimeType ( ) const

Definition at line 264 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::RegisterService(), and SetDefaultDataNodeProperties().

◆ GetServiceProperties()

us::ServiceProperties mitk::AbstractFileReader::GetServiceProperties ( ) const

protectedvirtual

Definition at line 189 of file mitkAbstractFileReader.cpp.

References GetDescription(), GetMimeType(), mitk::CustomMimeType::GetName(), GetRanking(), mitk::IFileIO::PROP_DESCRIPTION(), mitk::IFileIO::PROP_MIMETYPE(), and us::ServiceConstants::SERVICE_RANKING().

Referenced by RegisterService().

◆ Read() [1/2]

std::vector< BaseData::Pointer > mitk::AbstractFileReader::Read ( )

overridepure virtual

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

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::IFileReader.

Definition at line 85 of file mitkAbstractFileReader.cpp.

References mitk::StandaloneDataStorage::New().

Referenced by Read().

◆ Read() [2/2]

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

overridevirtual

Reads the specified file or input stream, loading its contents into the provided DataStorage.

Parameters

ds	The DataStorage to which the data is added.

Returns: The set of added DataNodes to ds.

This method may be overridden by implementations to create or reconstructed a hierarchy of mitk::DataNode instances in the provided mitk::DataStorage.

Exceptions

mitk::Exception

Implements mitk::IFileReader.

Definition at line 101 of file mitkAbstractFileReader.cpp.

References mitk::DataStorage::Add(), GetInputLocation(), mitk::DataNode::New(), Read(), and SetDefaultDataNodeProperties().

◆ RegisterMimeType()

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

protectedvirtual

Registers a new CustomMimeType service object.

This method is called from RegisterService and the default implementation registers a new mime-type service object if all of the following conditions are true:

TODO

Parameters

context

Returns

Exceptions

std::invalid_argument if context is nullptr.

Definition at line 199 of file mitkAbstractFileReader.cpp.

◆ RegisterService()

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

Associate this reader with the MIME type returned by the current IMimeTypeProvider service for the provided extension if the MIME type exists, otherwise registers a new MIME type when RegisterService() is called.

If no MIME type for extension is already registered, a call to RegisterService() will register a new MIME type and associate this reader instance with it. The MIME type id can be set via SetMimeType() or it will be auto-generated using extension, having the form "application/vnd.mitk.<extension>".

Parameters

extension	The file extension (without a leading period) for which a registered mime-type object is looked up and associated with this reader instance.
description	A human readable description of this reader.

Definition at line 135 of file mitkAbstractFileReader.cpp.

References GetMimeType(), us::GetModuleContext(), GetName(), GetServiceProperties(), and MITK_WARN.

Referenced by mitk::AutoSelectingDICOMReaderService::AutoSelectingDICOMReaderService(), mitk::CESTDICOMReaderService::CESTDICOMReaderService(), mitk::ClassicDICOMSeriesReaderService::ClassicDICOMSeriesReaderService(), mitk::ContourModelReader::ContourModelReader(), mitk::ContourModelSetReader::ContourModelSetReader(), mitk::DummyLsetFileReader::DummyLsetFileReader(), mitk::ExampleDataStructureReaderService::ExampleDataStructureReaderService(), mitk::GeometryDataReaderService::GeometryDataReaderService(), mitk::LegacyFileReaderService::LegacyFileReaderService(), mitk::NavigationDataReaderCSV::NavigationDataReaderCSV(), mitk::NavigationDataReaderXML::NavigationDataReaderXML(), mitk::PointSetReaderService::PointSetReaderService(), mitk::RawImageFileReaderService::RawImageFileReaderService(), mitk::AbstractFileIO::RegisterService(), mitk::RTDoseReaderService::RTDoseReaderService(), mitk::RTPlanReaderService::RTPlanReaderService(), mitk::RTStructureSetReaderService::RTStructureSetReaderService(), mitk::SimpleVolumeDICOMSeriesReaderService::SimpleVolumeDICOMSeriesReaderService(), and mitk::USDeviceReaderXML::USDeviceReaderXML().

◆ RemoveProgressCallback()

void mitk::AbstractFileReader::RemoveProgressCallback ( const ProgressCallback & callback )

overridevirtual

Implements mitk::IFileIO.

Definition at line 272 of file mitkAbstractFileReader.cpp.

◆ SetDefaultDataNodeProperties()

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

protectedvirtual

Definition at line 283 of file mitkAbstractFileReader.cpp.

References mitk::DataNode::GetData(), mitk::DataNode::GetProperty(), mitk::BaseData::GetProperty(), GetRegisteredMimeType(), mitk::StringProperty::New(), mitk::DataNode::NO_NAME_VALUE(), mitk::StringProperty::PATH, mitk::DataNode::SetProperty(), and mitk::DataNode::SetVisibility().

Referenced by Read().

◆ SetDefaultOptions()

void mitk::AbstractFileReader::SetDefaultOptions ( const Options & defaultOptions )

protected

Definition at line 239 of file mitkAbstractFileReader.cpp.

Referenced by mitk::CESTDICOMReaderService::CESTDICOMReaderService(), mitk::RawImageFileReaderService::RawImageFileReaderService(), and mitk::AbstractFileIO::SetDefaultReaderOptions().

◆ SetDescription()

void mitk::AbstractFileReader::SetDescription ( const std::string & description )

protected

Definition at line 207 of file mitkAbstractFileReader.cpp.

Referenced by mitk::ContourModelReader::ContourModelReader(), mitk::ContourModelSetReader::ContourModelSetReader(), mitk::DummyLsetFileReader::DummyLsetFileReader(), mitk::LegacyFileReaderService::LegacyFileReaderService(), mitk::MAPRegistrationWrapperIO::MAPRegistrationWrapperIO(), and mitk::AbstractFileIO::SetReaderDescription().

◆ SetInput() [1/2]

void mitk::AbstractFileReader::SetInput ( const std::string & location )

overridevirtual

Set the input location.

Parameters

location The file name to read from.

Implements mitk::IFileReader.

Definition at line 245 of file mitkAbstractFileReader.cpp.

Referenced by mitk::ContourModelSetReader::Read().

◆ SetInput() [2/2]

void mitk::AbstractFileReader::SetInput	(	const std::string &	location,
		std::istream *	is
	)

overridevirtual

Set an input stream to read from.

Parameters

location	A custom label for the input stream.
is	The input stream.

If is is nullptr, this clears the current input stream and location is interpreted as a file-system path. Otherwise, location is a custom label describing the input stream is.

Implements mitk::IFileReader.

Definition at line 251 of file mitkAbstractFileReader.cpp.

◆ SetMimeType()

void mitk::AbstractFileReader::SetMimeType ( const CustomMimeType & mimeType )

protected

Definition at line 206 of file mitkAbstractFileReader.cpp.

Referenced by mitk::ContourModelReader::ContourModelReader(), mitk::ContourModelSetReader::ContourModelSetReader(), mitk::DummyLsetFileReader::DummyLsetFileReader(), mitk::ItkImageIO::ItkImageIO(), mitk::LegacyFileReaderService::LegacyFileReaderService(), mitk::MAPRegistrationWrapperIO::MAPRegistrationWrapperIO(), mitk::RandomForestFileIO::RandomForestFileIO(), and mitk::AbstractFileIO::SetMimeType().

◆ SetMimeTypePrefix()

void mitk::AbstractFileReader::SetMimeTypePrefix ( const std::string & prefix )

protected

Definition at line 280 of file mitkAbstractFileReader.cpp.

Referenced by mitk::ItkImageIO::ItkImageIO(), mitk::LegacyFileReaderService::LegacyFileReaderService(), and mitk::RandomForestFileIO::RandomForestFileIO().

◆ SetOption()

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

overridevirtual

Implements mitk::IFileIO.

Definition at line 268 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::SetReaderOption().

◆ SetOptions()

void mitk::AbstractFileReader::SetOptions ( const Options & options )

overridevirtual

Implements mitk::IFileIO.

Definition at line 267 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AbstractFileIO::SetReaderOptions().

◆ SetRanking()

void mitk::AbstractFileReader::SetRanking ( int ranking )

protected

Set the service ranking for this file reader.

Default is zero and should only be chosen differently for a reason. The ranking is used to determine which reader to use if several equivalent readers have been found. It may be used to replace a default reader from MITK in your own project. E.g. if you want to use your own reader for nrrd files instead of the default, implement it and give it a higher ranking than zero.

Definition at line 208 of file mitkAbstractFileReader.cpp.

Referenced by mitk::AutoSelectingDICOMReaderService::AutoSelectingDICOMReaderService(), mitk::DICOMPMIO::DICOMPMIO(), mitk::DICOMSegmentationIO::DICOMSegmentationIO(), mitk::ItkImageIO::ItkImageIO(), mitk::LabelSetImageIO::LabelSetImageIO(), and mitk::AbstractFileIO::SetReaderRanking().

◆ UnregisterService()

void mitk::AbstractFileReader::UnregisterService ( )

Definition at line 178 of file mitkAbstractFileReader.cpp.

Referenced by ~AbstractFileReader().

Member Data Documentation

◆ m_ReadFiles

std::vector< std::string > mitk::AbstractFileReader::m_ReadFiles

protected

Definition at line 219 of file mitkAbstractFileReader.h.

Referenced by GetReadFiles(), and mitk::BaseDICOMReaderService::Read().

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AbstractFileReader() [1/3]

◆ ~AbstractFileReader()

◆ AbstractFileReader() [2/3]

◆ AbstractFileReader() [3/3]

Member Function Documentation

◆ AddProgressCallback()

◆ GetConfidenceLevel()

◆ GetDefaultOptions()

◆ GetDescription()

◆ GetInputLocation()

◆ GetInputStream()

◆ GetLocalFileName()

◆ GetMimeType()

◆ GetMimeTypePrefix()

◆ GetOption()

◆ GetOptions()

◆ GetRanking()

◆ GetReadFiles()

◆ GetRegisteredMimeType()

◆ GetServiceProperties()

◆ Read() [1/2]

◆ Read() [2/2]

◆ RegisterMimeType()

◆ RegisterService()

◆ RemoveProgressCallback()

◆ SetDefaultDataNodeProperties()

◆ SetDefaultOptions()

◆ SetDescription()

◆ SetInput() [1/2]

◆ SetInput() [2/2]

◆ SetMimeType()

◆ SetMimeTypePrefix()

◆ SetOption()

◆ SetOptions()

◆ SetRanking()

◆ UnregisterService()

Member Data Documentation

◆ m_ReadFiles