OME-Files image reading and writing. More...

Namespaces
	detail
	Implementation details.

	in
	Reader implementations.

	tiff
	TIFF file format (libtiff wrapper).

Classes
class	CoreMetadata
	Core metadata values. More...

struct	FileInfo
	Basic metadata for a file. More...

class	FormatException
	Exception thrown for file format operation errors. More...

class	FormatHandler
	Interface for all biological file format readers and writers. More...

class	FormatReader
	Interface for all biological file format readers. More...

class	FormatWriter
	Interface for all biological file format writers. More...

class	MetadataConfigurable
	Metadata configuration interface. More...

class	MetadataMap
	Metadata key-value map using a restricted set of value types. More...

class	MetadataOptions
	Metadata options. More...

class	Modulo
	A subdimension of Z, C, or T. More...

class	PixelBuffer
	Buffer for a specific pixel type. More...

class	PixelBufferBase
	Base class for all PixelBuffer types. More...

struct	PixelEndianProperties
	Map the given PixelPropertiesType and Endian enums to the corresponding endian-specific language type. More...

struct	PixelEndianProperties< P, ENDIAN_BIG >
	Properties of big endian pixels. More...

struct	PixelEndianProperties< P, ENDIAN_LITTLE >
	Properties of little endian pixels. More...

struct	PixelEndianProperties< P, ENDIAN_NATIVE >
	Properties of native endian pixels. More...

struct	PixelProperties
	Map a given PixelPropertiesType enum to the corresponding language types. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::BIT >
	Properties of BIT pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::COMPLEXDOUBLE >
	Properties of COMPLEXDOUBLE pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::COMPLEXFLOAT >
	Properties of COMPLEXFLOAT pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::DOUBLE >
	Properties of DOUBLE pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::FLOAT >
	Properties of FLOAT pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::INT16 >
	Properties of INT16 pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::INT32 >
	Properties of INT32 pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::INT8 >
	Properties of INT8 pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::UINT16 >
	Properties of UINT16 pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::UINT32 >
	Properties of UINT32 pixels. More...

struct	PixelProperties<::ome::xml::model::enums::PixelType::UINT8 >
	Properties of UINT8 pixels. More...

struct	PixelPropertiesBase
	Properties common to all pixel types. More...

struct	PlaneRegion
	A rectangular region. More...

class	TileBuffer
	Tile pixel data buffer. More...

class	TileCache
	Tile cache. More...

class	TileCoverage
	Tile coverage cache. More...

class	UnknownFormatException
	Exception thrown for unrecognized or unsupported data streams or filenames. More...

class	UnsupportedCompressionException
	Exception thrown for unsupported compression types. More...

class	VariantPixelBuffer
	Buffer for all pixel types. More...

struct	Version
	Release version. More...

Typedefs
typedef std::size_t	dimension_size_type
	Size type for image dimensions.

typedef uint32_t	pixel_size_type
	Size type for pixel bit depths.

typedef uint64_t	storage_size_type
	Size type for storage size.

Enumerations
enum	Domain { UNKNOWN_DOMAIN, HCS_DOMAIN, LM_DOMAIN, EM_DOMAIN, SPM_DOMAIN, SEM_DOMAIN, FLIM_DOMAIN, MEDICAL_DOMAIN, HISTOLOGY_DOMAIN, GEL_DOMAIN, ASTRONOMY_DOMAIN, GRAPHICS_DOMAIN }
	Imaging domain. More...

enum	DomainCollection { NON_GRAPHICS_DOMAINS, NON_HCS_DOMAINS, NON_SPECIAL_DOMAINS, ALL_DOMAINS, HCS_ONLY_DOMAINS }
	Imaging domain collections.

enum	Dimensions { DIM_SPATIAL_X = 0, DIM_SPATIAL_Y = 1, DIM_SPATIAL_Z = 2, DIM_TEMPORAL_T = 3, DIM_CHANNEL = 4, DIM_SUBCHANNEL = 5, DIM_MODULO_Z = 6, DIM_MODULO_T = 7, DIM_MODULO_C = 8 }
	Dimensions. More...

enum	EndianType { ENDIAN_BIG, ENDIAN_LITTLE, ENDIAN_NATIVE }
	Endianness. More...

Functions
template<class charT , class traits >
std::basic_ostream< charT, traits > &	operator<< (std::basic_ostream< charT, traits > &os, const CoreMetadata &core)
	Output CoreMetadata to output stream. More...

template<class charT , class traits >
std::basic_ostream< charT, traits > &	operator<< (std::basic_ostream< charT, traits > &os, const FileInfo &info)
	Output FileInfo to output stream. More...

const std::string &	getDomain (Domain domain)
	Get the string corresponding to a particular Domain. More...

const std::vector< std::string > &	getDomainCollection (DomainCollection domains)
	Get the strings corresponding to a particular Domain collection. More...

dimension_size_type	getIndex (const std::string &order, dimension_size_type zSize, dimension_size_type cSize, dimension_size_type tSize, dimension_size_type num, dimension_size_type z, dimension_size_type c, dimension_size_type t)
	Get the rasterized index corresponding to the given `Z`, `C` and `T` coordinates (real sizes). More...

dimension_size_type	getIndex (const std::string &order, dimension_size_type zSize, dimension_size_type cSize, dimension_size_type tSize, dimension_size_type moduloZSize, dimension_size_type moduloCSize, dimension_size_type moduloTSize, dimension_size_type num, dimension_size_type z, dimension_size_type c, dimension_size_type t, dimension_size_type moduloZ, dimension_size_type moduloC, dimension_size_type moduloT)
	Get the rasterized index corresponding to the given `Z`, `C`, `T`, `ModuloZ`, `ModuloC` and `ModuloT` coordinates (effective sizes). More...

std::array< dimension_size_type, 3 >	getZCTCoords (const std::string &order, dimension_size_type zSize, dimension_size_type cSize, dimension_size_type tSize, dimension_size_type num, dimension_size_type index)
	Get the `Z`, `C` and `T` coordinates (real sizes) corresponding to the given rasterized index value. More...

std::array< dimension_size_type, 6 >	getZCTCoords (const std::string &order, dimension_size_type zSize, dimension_size_type cSize, dimension_size_type tSize, dimension_size_type moduloZSize, dimension_size_type moduloCSize, dimension_size_type moduloTSize, dimension_size_type num, dimension_size_type index)
	Get the `Z`, `C`, `T`, `ModuloZ`, `ModuloC` and `ModuloT` coordinates (effective sizes) corresponding to the given rasterized index value. More...

template<>
MetadataMap::value_type &	MetadataMap::get< MetadataMap::value_type > (const key_type &key)
	Get a reference to the value of a particular key from the map. More...

template<>
const MetadataMap::value_type &	MetadataMap::get< MetadataMap::value_type > (const key_type &key) const
	Get a reference to the value of a particular key from the map. More...

std::string	createID (std::string const &type, dimension_size_type idx)
	Create an object identifier for a given object type and index. More...

std::string	createID (std::string const &type, dimension_size_type idx1, dimension_size_type idx2)
	Create an object identifier for a given object type and indices. More...

std::string	createID (std::string const &type, dimension_size_type idx1, dimension_size_type idx2, dimension_size_type idx3)
	Create an object identifier for a given object type and indices. More...

std::string	createID (std::string const &type, dimension_size_type idx1, dimension_size_type idx2, dimension_size_type idx3, dimension_size_type idx4)
	Create an object identifier for a given object type and indices. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	createOMEXMLMetadata (ome::common::xml::dom::Document &document)
	Create OME-XML metadata from DOM Document. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	createOMEXMLMetadata (const boost::filesystem::path &file)
	Create OME-XML metadata from XML file. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	createOMEXMLMetadata (const std::string &text)
	Create OME-XML metadata from XML string. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	createOMEXMLMetadata (std::istream &stream)
	Create OME-XML metadata from XML input stream. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	createOMEXMLMetadata (const FormatReader &reader, bool doPlane=false, bool doImageName=true)
	Create OME-XML metadata from reader core metadata. More...

std::shared_ptr<::ome::xml::meta::MetadataRoot >	createOMEXMLRoot (const std::string &document)
	Create OME-XML metadata root from XML document. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	getOMEXMLMetadata (std::shared_ptr<::ome::xml::meta::MetadataRetrieve > &retrieve)
	Get OME-XML metadata from metadata. More...

std::string	getOMEXML (::ome::xml::meta::OMEXMLMetadata &omexml, bool validate=true)
	Get OME-XML document from OME-XML metadata. More...

bool	validateOMEXML (const std::string &document)
	Validate an OME-XML document. More...

bool	validateModel (::ome::xml::meta::Metadata &meta, bool correct)
	Validate a metadata store. More...

void	fillMetadata (::ome::xml::meta::MetadataStore &store, const FormatReader &reader, bool doPlane=false, bool doImageName=true)
	Fill OME-XML metadata store from reader core metadata. More...

void	fillMetadata (::ome::xml::meta::MetadataStore &store, const std::vector< std::shared_ptr< CoreMetadata >> seriesList, bool doPlane=false)
	Fill OME-XML metadata store from core metadata. More...

void	fillAllPixels (::ome::xml::meta::MetadataStore &store, const FormatReader &reader)
	Fill all OME-XML metadata store Pixels elements from reader core metadata. More...

void	fillPixels (::ome::xml::meta::MetadataStore &store, const FormatReader &reader)
	Fill an OME-XML metadata store Pixels element from reader core metadata. More...

void	fillPixels (::ome::xml::meta::MetadataStore &store, const CoreMetadata &seriesMetadata, dimension_size_type series)
	Fill an OME-XML metadata store Pixels element from core metadata. More...

void	addMetadataOnly (::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type series, bool resolve=true)
	Add a MetadataOnly element to Pixels for the specified series. More...

Modulo	getModuloAlongZ (const ::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image)
	Get ModuloAlongZ annotation from OME-XML metadata. More...

Modulo	getModuloAlongT (const ::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image)
	Get ModuloAlongT annotation from OME-XML metadata. More...

Modulo	getModuloAlongC (const ::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image)
	Get ModuloAlongC annotation from OME-XML metadata. More...

Modulo	getModulo (const ::ome::xml::meta::OMEXMLMetadata &omexml, const std::string &tag, dimension_size_type image)
	Get Modulo annotation from OME-XML metadata. More...

void	verifyMinimum (::ome::xml::meta::MetadataRetrieve &retrieve, dimension_size_type series=0U)
	Verify correctness of minimal amount of metadata in a series. More...

void	removeBinData (::ome::xml::meta::OMEXMLMetadata &omexml)
	Remove all BinData elements from OME-XML metadata. More...

void	removeTiffData (::ome::xml::meta::OMEXMLMetadata &omexml)
	Remove all TiffData elements from OME-XML metadata. More...

void	removeChannels (::ome::xml::meta::OMEXMLMetadata &omexml, dimension_size_type image, dimension_size_type sizeC)
	Remove all but the specified number of valid Channel elements from OME-XML metadata. More...

MetadataMap	getOriginalMetadata (::ome::xml::meta::OMEXMLMetadata &omexml)
	Get original metadata from OME-XML metadata StructuredAnnotations. More...

void	fillOriginalMetadata (::ome::xml::meta::OMEXMLMetadata &omexml, const MetadataMap &metadata)
	Create OriginalMetadataAnnotations from MetadataMap. More...

std::string	getModelVersion ()
	Get the currently-supported OME Data Model version. More...

std::string	getModelVersion (ome::common::xml::dom::Document &document)
	Get the model version used by an OME-XML document. More...

std::string	getModelVersion (const std::string &document)
	Get the model version used by an OME-XML document. More...

std::string	transformToLatestModelVersion (const std::string &document)
	Transform an OME-XML document to the latest model version. More...

bool	defaultCreationDateEnabled ()
	Check if default creation date is enabled. More...

void	defaultCreationDateEnabled (bool enabled)
	Enable or disable default creation date. More...

void	setDefaultCreationDate (::ome::xml::meta::MetadataStore &store, dimension_size_type series, const boost::filesystem::path &id)
	Set the creation data for a series. More...

ome::xml::model::enums::DimensionOrder	createDimensionOrder (const std::string &order)
	Create a valid DimensionOrder from string. More...

storage_size_type	pixelSize (const ::ome::xml::meta::MetadataRetrieve &meta, dimension_size_type series)
	Get the total size of pixel data in a series. More...

storage_size_type	pixelSize (const ::ome::xml::meta::MetadataRetrieve &meta)
	Get the total size of pixel data for all series. More...

storage_size_type	significantPixelSize (const ::ome::xml::meta::MetadataRetrieve &meta, dimension_size_type series)
	Get the total significant size of pixel data in a series. More...

storage_size_type	significantPixelSize (const ::ome::xml::meta::MetadataRetrieve &meta)
	Get the total significant size of pixel data for all series. More...

void	register_module_paths ()
	Register the OME-Files module paths with OME-Common. More...

template<class charT , class traits >
std::basic_ostream< charT, traits > &	operator<< (std::basic_ostream< charT, traits > &os, const Modulo &modulo)
	Output Modulo to output stream. More...

pixel_size_type	bytesPerPixel (::ome::xml::model::enums::PixelType pixeltype)
	Get the size of a PixelType, in bytes. More...

pixel_size_type	bitsPerPixel (::ome::xml::model::enums::PixelType pixeltype)
	Get the size of a PixelType, in bits. More...

pixel_size_type	significantBitsPerPixel (::ome::xml::model::enums::PixelType pixeltype)
	Get the significant (maximum bits used) size of a PixelType, in bits. More...

bool	isSigned (::ome::xml::model::enums::PixelType pixeltype)
	Check whether a PixelType is signed. More...

bool	isInteger (::ome::xml::model::enums::PixelType pixeltype)
	Check whether a PixelType is integer. More...

bool	isFloatingPoint (::ome::xml::model::enums::PixelType pixeltype)
	Check whether a PixelType is floating point. More...

bool	isComplex (::ome::xml::model::enums::PixelType pixeltype)
	Check whether a PixelType is complex. More...

::ome::xml::model::enums::PixelType	pixelTypeFromBytes (pixel_size_type bytes, bool is_signed=false, bool is_integer=true, bool is_complex=false)
	Determine a likely pixel type from its the storage size in bytes. More...

::ome::xml::model::enums::PixelType	pixelTypeFromBits (pixel_size_type bytes, bool is_signed=false, bool is_integer=true, bool is_complex=false)
	Determine a likely pixel type from its the storage size in bits. More...

template<typename T >
void	byteswap (T &value)
	Byteswap value to switch endianness. More...

template<>
void	byteswap (std::complex< float > &value)
	Byteswap value to switch endianness. More...

template<>
void	byteswap (std::complex< double > &value)
	Byteswap value to switch endianness. More...

PlaneRegion	operator & (const PlaneRegion &a, const PlaneRegion &b)
	Intersect two regions. More...

PlaneRegion	operator\| (const PlaneRegion &a, const PlaneRegion &b)
	Combine (union) two regions. More...

template<class charT , class traits >
std::basic_ostream< charT, traits > &	operator<< (std::basic_ostream< charT, traits > &os, const PlaneRegion &region)
	Output PlaneRegion to output stream. More...

std::string	escapeXML (const std::string &s)
	Replace special characters with XML entities in an XML string. More...

std::string	sanitizeXML (const std::string &s)
	Filter control codes and invalid sequences in an XML string. More...

bool	validateXML (const std::string &s, const std::string &loc="XML")
	Validate XML in an XML string. More...

template<class charT , class traits >
std::basic_ostream< charT, traits > &	operator<< (std::basic_ostream< charT, traits > &os, const Version &version)
	Output Version to output stream. More...

Variables
const Version	release_version (OME_FILES_VERSION_MAJOR, OME_FILES_VERSION_MINOR, OME_FILES_VERSION_PATCH, OME_FILES_VERSION_EXTRA_S)
	The release version number of the library currently being linked against.

Detailed Description

OME-Files image reading and writing.

Enumeration Type Documentation

◆ Dimensions

enum ome::files::Dimensions

Dimensions.

The OME data model currently supports five dimensions (XYZTC), plus an implicit dimension (subchannel) and three modulo dimensions which subdivide Z, T and C. This enumeration is used to refer to specific dimensions, and the value is the logical dimension order used for the PixelBuffer interface.

The current interface requires all dimensions to be present even if unused. Future model changes may remove this requirement.

Enumerator
DIM_SPATIAL_X	Spatial x dimension (X).
DIM_SPATIAL_Y	Spatial y dimension (Y).
DIM_SPATIAL_Z	Spatial z dimension (Z).
DIM_TEMPORAL_T	Temporal t dimension (T).
DIM_CHANNEL	Logical channel (typically detectors of specific wavelengths) (C).
DIM_SUBCHANNEL	Logical sub-channel (typically used for RGB channel sub-components) (S).
DIM_MODULO_Z	Logical subdivision of the spatial z dimension (z).
DIM_MODULO_T	Logical subdivision of the temporal t dimension (t).
DIM_MODULO_C	Logical subdivision of the logical channel dimension (c).

◆ Domain

enum ome::files::Domain

Imaging domain.

Enumerator
UNKNOWN_DOMAIN	Unknown.
HCS_DOMAIN	High-Content Screening (HCS)
LM_DOMAIN	Light Microscopy (LM)
EM_DOMAIN	Electron Microscopy (EM)
SPM_DOMAIN	Scanning Probe Microscopy (SPM)
SEM_DOMAIN	Scanning Electron Microscopy (SEM)
FLIM_DOMAIN	Fluorescence-Lifetime Imaging (FLIM)
MEDICAL_DOMAIN	Medical Imaging.
HISTOLOGY_DOMAIN	Histology.
GEL_DOMAIN	Gel/Blot Imaging.
ASTRONOMY_DOMAIN	Astronomy.
GRAPHICS_DOMAIN	Graphics.

◆ EndianType

enum ome::files::EndianType

Endianness.

Enumerator
ENDIAN_BIG	Big endian.
ENDIAN_LITTLE	Little endian.
ENDIAN_NATIVE	Native endian.

Function Documentation

◆ addMetadataOnly()

void ome::files::addMetadataOnly	(	::ome::xml::meta::OMEXMLMetadata &	omexml,
		dimension_size_type	series,
		bool	resolve = `true`
	)

Add a MetadataOnly element to Pixels for the specified series.

Parameters

omexml	the OME-XML metadata store.
series	the series containing the Pixels element to add MetadataOnly to.
resolve	`true` to resolve references, `false` to skip resolving references

References addMetadataOnly(), ome::xml::meta::OMEXMLMetadata::getRoot(), and ome::xml::meta::OMEXMLMetadata::resolveReferences().

Referenced by addMetadataOnly(), and fillMetadata().

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◆ bitsPerPixel()

pixel_size_type ome::files::bitsPerPixel ( ::ome::xml::model::enums::PixelType pixeltype )

Get the size of a PixelType, in bits.

Parameters

pixeltype the PixelType to query.

Returns: the size, in bits

Referenced by ome::files::detail::FormatReader::getBitsPerPixel(), ome::files::tiff::getCoreMetadata(), ome::files::in::OMETIFFReader::initFile(), ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ bytesPerPixel()

pixel_size_type ome::files::bytesPerPixel ( ::ome::xml::model::enums::PixelType pixeltype )

Get the size of a PixelType, in bytes.

Parameters

pixeltype the PixelType to query.

Returns: the size, in bytes

Referenced by ome::files::detail::FormatReader::getOptimalTileHeight(), pixelSize(), pixelTypeFromBytes(), and ome::files::detail::FormatReader::readPlane().

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◆ byteswap() [1/3]

template<typename T >

void ome::files::byteswap ( T & value )

inline

Byteswap value to switch endianness.

Parameters

value the value to swap.

Referenced by ome::files::detail::FormatReader::readPlane().

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◆ byteswap() [2/3]

template<>

void ome::files::byteswap ( std::complex< float > & value )

inline

Byteswap value to switch endianness.

Parameters

value the value to swap.

◆ byteswap() [3/3]

template<>

void ome::files::byteswap ( std::complex< double > & value )

inline

Byteswap value to switch endianness.

Parameters

value the value to swap.

◆ createDimensionOrder()

ome::xml::model::enums::DimensionOrder ome::files::createDimensionOrder ( const std::string & order )

Create a valid DimensionOrder from string.

Any duplicate dimension will have all duplicates following the initial instance removed. Any missing dimension will be suffixed to the resulting dimension order; the order of these dimensions is unspecified (since they weren't provided, the expectation is that the caller did not care).

Parameters

order the string dimension order.

Returns: the dimension order.

Exceptions

std::logic_error if the provided order is invalid.

References createDimensionOrder().

Referenced by createDimensionOrder().

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◆ createID() [1/4]

std::string ome::files::createID	(	std::string const &	type,
		dimension_size_type	idx
	)

Create an object identifier for a given object type and index.

Parameters

type	the object type.
idx	the object index.

Returns: the identifier.

References createID().

Referenced by createID(), fillMetadata(), fillOriginalMetadata(), and fillPixels().

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◆ createID() [2/4]

std::string ome::files::createID	(	std::string const &	type,
		dimension_size_type	idx1,
		dimension_size_type	idx2
	)

Create an object identifier for a given object type and indices.

Parameters

type	the object type.
idx1	the first object index.
idx2	the second object index.

Returns: the identifier.

References createID().

◆ createID() [3/4]

std::string ome::files::createID	(	std::string const &	type,
		dimension_size_type	idx1,
		dimension_size_type	idx2,
		dimension_size_type	idx3
	)

Create an object identifier for a given object type and indices.

Parameters

type	the object type.
idx1	the first object index.
idx2	the second object index.
idx3	the third object index.

Returns: the identifier.

References createID().

◆ createID() [4/4]

std::string ome::files::createID	(	std::string const &	type,
		dimension_size_type	idx1,
		dimension_size_type	idx2,
		dimension_size_type	idx3,
		dimension_size_type	idx4
	)

Create an object identifier for a given object type and indices.

Parameters

type	the object type.
idx1	the first object index.
idx2	the second object index.
idx3	the third object index.
idx4	the fourth object index.

Returns: the identifier.

References createID().

◆ createOMEXMLMetadata() [1/5]

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::createOMEXMLMetadata ( ome::common::xml::dom::Document & document )

Create OME-XML metadata from DOM Document.

Parameters

document the XML document.

Returns: the OME-XML metadata.

References createOMEXMLMetadata(), ome::common::xml::dom::ParseParameters::doSchema, ome::common::xml::dom::Document::getDocumentElement(), ome::xml::model::detail::OMEModel::resolveReferences(), ome::common::xml::dom::ParseParameters::validationSchemaFullChecking, and ome::common::xml::dom::writeDocument().

Referenced by ome::files::in::OMETIFFReader::cacheMetadata(), createOMEXMLMetadata(), createOMEXMLRoot(), ome::files::in::OMETIFFReader::initFile(), and ome::files::in::OMETIFFReader::readMetadata().

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◆ createOMEXMLMetadata() [2/5]

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::createOMEXMLMetadata ( const boost::filesystem::path & file )

Create OME-XML metadata from XML file.

Parameters

file	the XML file.

Returns: the OME-XML metadata.

References createOMEXMLMetadata(), ome::common::xml::dom::ParseParameters::doSchema, and ome::common::xml::dom::ParseParameters::validationSchemaFullChecking.

◆ createOMEXMLMetadata() [3/5]

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::createOMEXMLMetadata ( const std::string & text )

Create OME-XML metadata from XML string.

Parameters

text	the XML string.

Returns: the OME-XML metadata.

References createOMEXMLMetadata(), ome::common::xml::dom::ParseParameters::doSchema, and ome::common::xml::dom::ParseParameters::validationSchemaFullChecking.

◆ createOMEXMLMetadata() [4/5]

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::createOMEXMLMetadata ( std::istream & stream )

Create OME-XML metadata from XML input stream.

Parameters

stream the XML input stream.

Returns: the OME-XML metadata.

References createOMEXMLMetadata(), ome::common::xml::dom::ParseParameters::doSchema, and ome::common::xml::dom::ParseParameters::validationSchemaFullChecking.

◆ createOMEXMLMetadata() [5/5]

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::createOMEXMLMetadata	(	const FormatReader &	reader,
		bool	doPlane = `false`,
		bool	doImageName = `true`
	)

Create OME-XML metadata from reader core metadata.

Parameters

reader	the reader to use.
doPlane	create Plane elements if `true`.
doImageName	set image name if `true`.

Returns: the OME-XML metadata.

References createOMEXMLMetadata(), and fillMetadata().

◆ createOMEXMLRoot()

std::shared_ptr<::ome::xml::meta::MetadataRoot > ome::files::createOMEXMLRoot ( const std::string & document )

Create OME-XML metadata root from XML document.

Parameters

document the XML document source.

Returns: the OME-XML metadata root.

Todo:: Implement model transforms.

References createOMEXMLMetadata(), and createOMEXMLRoot().

Referenced by createOMEXMLRoot().

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◆ defaultCreationDateEnabled() [1/2]

bool ome::files::defaultCreationDateEnabled ( )

Check if default creation date is enabled.

Returns: true if enabled, false otherwise.

References defaultCreationDateEnabled().

Referenced by defaultCreationDateEnabled(), and setDefaultCreationDate().

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◆ defaultCreationDateEnabled() [2/2]

void ome::files::defaultCreationDateEnabled ( bool enabled )

Enable or disable default creation date.

This setting enables or disables the replacement of missing creation dates.

See also: setDefaultCreationDate().

Parameters

enabled true to enable, false to disable.

References defaultCreationDateEnabled().

◆ escapeXML()

std::string ome::files::escapeXML ( const std::string & s )

Replace special characters with XML entities in an XML string.

Parameters

s	the string to escape.

Returns: the escaped string.

◆ fillAllPixels()

void ome::files::fillAllPixels	(	::ome::xml::meta::MetadataStore &	store,
		const FormatReader &	reader
	)

Fill all OME-XML metadata store Pixels elements from reader core metadata.

Set Pixels metadata for all series.

Parameters

store	the OME-XML metadata store.
reader	the reader to use.

References fillAllPixels(), fillPixels(), ome::files::FormatReader::getSeries(), ome::files::FormatReader::getSeriesCount(), and ome::files::FormatReader::setSeries().

Referenced by fillAllPixels().

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◆ fillMetadata() [1/2]

void ome::files::fillMetadata	(	::ome::xml::meta::MetadataStore &	store,
		const FormatReader &	reader,
		bool	doPlane = `false`,
		bool	doImageName = `true`
	)

Fill OME-XML metadata store from reader core metadata.

The metadata store is expected to be empty.

Parameters

store	the OME-XML metadata store.
reader	the reader to use.
doPlane	create Plane elements if `true`.
doImageName	set image name if `true`.

References addMetadataOnly(), createID(), fillMetadata(), fillPixels(), ome::files::FormatReader::getCurrentFile(), ome::files::FormatReader::getImageCount(), ome::xml::meta::OMEXMLMetadata::getPixelsBinDataCount(), ome::files::FormatReader::getPixelType(), ome::files::FormatReader::getSeries(), ome::files::FormatReader::getSeriesCount(), ome::xml::meta::OMEXMLMetadata::getTiffDataCount(), ome::files::FormatReader::getZCTCoords(), setDefaultCreationDate(), ome::xml::meta::MetadataStore::setImageID(), ome::xml::meta::MetadataStore::setPlaneTheC(), ome::xml::meta::MetadataStore::setPlaneTheT(), ome::xml::meta::MetadataStore::setPlaneTheZ(), and ome::files::FormatReader::setSeries().

Referenced by createOMEXMLMetadata(), fillMetadata(), ome::files::in::MinimalTIFFReader::initFile(), and ome::files::in::OMETIFFReader::initFile().

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◆ fillMetadata() [2/2]

void ome::files::fillMetadata	(	::ome::xml::meta::MetadataStore &	store,
		const std::vector< std::shared_ptr< CoreMetadata >>	seriesList,
		bool	doPlane = `false`
	)

Fill OME-XML metadata store from core metadata.

The metadata store is expected to be empty.

Parameters

store	the OME-XML metadata store.
seriesList	the core metadata to use.
doPlane	create Plane elements if `true`.

References addMetadataOnly(), createID(), fillMetadata(), fillPixels(), ome::xml::meta::OMEXMLMetadata::getPixelsBinDataCount(), ome::xml::meta::OMEXMLMetadata::getTiffDataCount(), getZCTCoords(), ome::xml::meta::MetadataStore::setImageID(), ome::xml::meta::MetadataStore::setPlaneTheC(), ome::xml::meta::MetadataStore::setPlaneTheT(), and ome::xml::meta::MetadataStore::setPlaneTheZ().

◆ fillOriginalMetadata()

void ome::files::fillOriginalMetadata	(	::ome::xml::meta::OMEXMLMetadata &	omexml,
		const MetadataMap &	metadata
	)

Create OriginalMetadataAnnotations from MetadataMap.

Parameters

omexml	the OME-XML metadata store.
metadata	the original metadata.

References createID(), ome::files::MetadataMap::empty(), fillOriginalMetadata(), ome::files::MetadataMap::flatten(), ome::xml::meta::OMEXMLMetadata::getRoot(), ome::xml::meta::OMEXMLMetadata::getXMLAnnotationID(), and ome::xml::meta::OMEXMLMetadata::resolveReferences().

Referenced by fillOriginalMetadata(), and ome::files::detail::FormatReader::setId().

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◆ fillPixels() [1/2]

void ome::files::fillPixels	(	::ome::xml::meta::MetadataStore &	store,
		const FormatReader &	reader
	)

Fill an OME-XML metadata store Pixels element from reader core metadata.

Set Pixels metadata for the reader's current series.

Parameters

store	the OME-XML metadata store.
reader	the reader to use.

Referenced by fillAllPixels(), fillMetadata(), and fillPixels().

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◆ fillPixels() [2/2]

void ome::files::fillPixels	(	::ome::xml::meta::MetadataStore &	store,
		const CoreMetadata &	seriesMetadata,
		dimension_size_type	series
	)

Fill an OME-XML metadata store Pixels element from core metadata.

Set Pixels metadata for the the specified series.

Parameters

store	the OME-XML metadata store.
seriesMetadata	the seriesMetadata the metadata to use.
series	the series to set.

◆ getDomain()

const std::string & ome::files::getDomain ( Domain domain )

Get the string corresponding to a particular Domain.

Parameters

domain the Domain to use.

Returns: the string description of the Domain.

References ASTRONOMY_DOMAIN, EM_DOMAIN, FLIM_DOMAIN, GEL_DOMAIN, GRAPHICS_DOMAIN, HCS_DOMAIN, HISTOLOGY_DOMAIN, LM_DOMAIN, MEDICAL_DOMAIN, SEM_DOMAIN, SPM_DOMAIN, and UNKNOWN_DOMAIN.

Referenced by ome::files::in::MinimalTIFFReader::MinimalTIFFReader().

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◆ getDomainCollection()

const std::vector< std::string > & ome::files::getDomainCollection ( DomainCollection domains )

Get the strings corresponding to a particular Domain collection.

Parameters

domains the Domain collection to use.

Returns: the string descriptions of the Domain collection.

References ASTRONOMY_DOMAIN, EM_DOMAIN, FLIM_DOMAIN, GEL_DOMAIN, GRAPHICS_DOMAIN, HCS_DOMAIN, HISTOLOGY_DOMAIN, LM_DOMAIN, MEDICAL_DOMAIN, SEM_DOMAIN, SPM_DOMAIN, and UNKNOWN_DOMAIN.

Referenced by ome::files::in::OMETIFFReader::getDomains(), and ome::files::in::OMETIFFReader::OMETIFFReader().

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◆ getIndex() [1/2]

dimension_size_type ome::files::getIndex	(	const std::string &	order,
		dimension_size_type	zSize,
		dimension_size_type	cSize,
		dimension_size_type	tSize,
		dimension_size_type	num,
		dimension_size_type	z,
		dimension_size_type	c,
		dimension_size_type	t
	)

Get the rasterized index corresponding to the given Z, C and T coordinates (real sizes).

Parameters

order	dimension order.
zSize	total number of focal planes (real size).
cSize	total number of channels (real size).
tSize	total number of time points (real size).
num	total number of image planes (zSize * cSize * tSize), specified as a consistency check.
z	the `Z` coordinate of ZCT coordinate triple to convert to 1D index (real size).
c	the `C` coordinate of ZCT coordinate triple to convert to 1D index (real size).
t	the `T` coordinate of ZCT coordinate triple to convert to 1D index (real size).

Returns: the 1D index.

Referenced by ome::files::detail::FormatReader::getCoreMetadata(), ome::files::detail::FormatWriter::getIndex(), getIndex(), ome::files::detail::FormatReader::getIndex(), and ome::files::in::OMETIFFReader::initFile().

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◆ getIndex() [2/2]

dimension_size_type ome::files::getIndex	(	const std::string &	order,
		dimension_size_type	zSize,
		dimension_size_type	cSize,
		dimension_size_type	tSize,
		dimension_size_type	moduloZSize,
		dimension_size_type	moduloCSize,
		dimension_size_type	moduloTSize,
		dimension_size_type	num,
		dimension_size_type	z,
		dimension_size_type	c,
		dimension_size_type	t,
		dimension_size_type	moduloZ,
		dimension_size_type	moduloC,
		dimension_size_type	moduloT
	)

Get the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes).

Note: The Z, C and T coordinates take the modulo dimension sizes into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.

Parameters

order	dimension order.
zSize	total number of focal planes (real size).
cSize	total number of channels (real size).
tSize	total number of time points (real size).
moduloZSize	total number of ModuloZ planes (real size).
moduloCSize	total number of ModuloC channels (real size).
moduloTSize	total number of ModuloT time points (real size).
num	total number of image planes (zSize * cSize * tSize), specified as a consistency check.
z	the `Z` coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
c	the `C` coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
t	the `T` coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
moduloZ	the `ModuloZ` coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
moduloC	the `ModuloC` coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
moduloT	the `ModuloT` coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).

Returns: the 1D index.

References getIndex().

◆ getModelVersion() [1/3]

std::string ome::files::getModelVersion ( )

Get the currently-supported OME Data Model version.

Returns: the model version.

◆ getModelVersion() [2/3]

std::string ome::files::getModelVersion ( ome::common::xml::dom::Document & document )

Get the model version used by an OME-XML document.

Parameters

document the OME-XML document.

Returns: the model version.

References ome::common::xml::dom::Document::getDocumentElement().

◆ getModelVersion() [3/3]

std::string ome::files::getModelVersion ( const std::string & document )

Get the model version used by an OME-XML document.

Parameters

document the OME-XML document.

Returns: the model version.

◆ getModulo()

Modulo ome::files::getModulo	(	const ::ome::xml::meta::OMEXMLMetadata &	omexml,
		const std::string &	tag,
		dimension_size_type	image
	)

Get Modulo annotation from OME-XML metadata.

Parameters

omexml	the OME-XML metadata store.
tag	the Modulo annotation XML tag name.
image	the image index.

Returns: the Modulo annotation.

References ome::common::xml::dom::NodeList::empty(), ome::common::xml::dom::Document::getElementsByTagName(), getModulo(), ome::xml::meta::OMEXMLMetadata::getRoot(), and ome::common::xml::dom::Node::getTextContent().

Referenced by getModulo(), getModuloAlongC(), getModuloAlongT(), and getModuloAlongZ().

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◆ getModuloAlongC()

Modulo ome::files::getModuloAlongC	(	const ::ome::xml::meta::OMEXMLMetadata &	omexml,
		dimension_size_type	image
	)

Get ModuloAlongC annotation from OME-XML metadata.

Parameters

omexml	the OME-XML metadata store.
image	the image index.

Returns: the Modulo annotation.

References getModulo(), and getModuloAlongC().

Referenced by getModuloAlongC(), and ome::files::in::OMETIFFReader::initFile().

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◆ getModuloAlongT()

Modulo ome::files::getModuloAlongT	(	const ::ome::xml::meta::OMEXMLMetadata &	omexml,
		dimension_size_type	image
	)

Get ModuloAlongT annotation from OME-XML metadata.

Parameters

omexml	the OME-XML metadata store.
image	the image index.

Returns: the Modulo annotation.

References getModulo(), and getModuloAlongT().

Referenced by getModuloAlongT(), and ome::files::in::OMETIFFReader::initFile().

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◆ getModuloAlongZ()

Modulo ome::files::getModuloAlongZ	(	const ::ome::xml::meta::OMEXMLMetadata &	omexml,
		dimension_size_type	image
	)

Get ModuloAlongZ annotation from OME-XML metadata.

Parameters

omexml	the OME-XML metadata store.
image	the image index.

Returns: the Modulo annotation.

References getModulo(), and getModuloAlongZ().

Referenced by getModuloAlongZ(), and ome::files::in::OMETIFFReader::initFile().

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◆ getOMEXML()

std::string ome::files::getOMEXML	(	::ome::xml::meta::OMEXMLMetadata &	omexml,
		bool	validate = `true`
	)

Get OME-XML document from OME-XML metadata.

This will convert the OME-XML metadata to an XML document string.

Parameters

omexml	the OME-XML metadata store.
validate	`true` to validate the OME-XML, `false` to skip validation.

Returns: the OME-XML metadata as an XML document string.

References ome::xml::meta::OMEXMLMetadata::dumpXML(), getOMEXML(), and validateOMEXML().

Referenced by ome::files::out::OMETIFFWriter::getOMEXML(), and getOMEXML().

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◆ getOMEXMLMetadata()

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::getOMEXMLMetadata ( std::shared_ptr<::ome::xml::meta::MetadataRetrieve > & retrieve )

Get OME-XML metadata from metadata.

This will convert the metadata to OME-XML metadata if required.

Parameters

retrieve the metadata to use.

Returns: the OME-XML metadata.

References getOMEXMLMetadata().

Referenced by getOMEXMLMetadata().

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◆ getOriginalMetadata()

MetadataMap ome::files::getOriginalMetadata ( ::ome::xml::meta::OMEXMLMetadata & omexml )

Get original metadata from OME-XML metadata StructuredAnnotations.

Parameters

omexml the OME-XML metadata store.

Returns: a map of the original metadata annotations.

Todo:: log error

References ome::xml::model::detail::OMEModelObject::getChildrenByTagName(), ome::common::xml::dom::Document::getDocumentElement(), getOriginalMetadata(), ome::xml::meta::OMEXMLMetadata::getRoot(), ome::files::MetadataMap::set(), and ome::common::xml::dom::ParseParameters::validationScheme.

Referenced by getOriginalMetadata(), and ome::files::in::OMETIFFReader::initFile().

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◆ getZCTCoords() [1/2]

std::array< dimension_size_type, 3 > ome::files::getZCTCoords	(	const std::string &	order,
		dimension_size_type	zSize,
		dimension_size_type	cSize,
		dimension_size_type	tSize,
		dimension_size_type	num,
		dimension_size_type	index
	)

Get the Z, C and T coordinates (real sizes) corresponding to the given rasterized index value.

Parameters

order	dimension order.
zSize	total number of focal planes (real size).
cSize	total number of channels (real size).
tSize	total number of time points (real size).
num	total number of image planes (zSize * cSize * tSize), specified as a consistency check.
index	1D (rasterized) index to convert to ZCT coordinates.

Returns: an array containing the ZCT coordinates (real sizes, in that order).

Referenced by ome::files::out::OMETIFFWriter::fillMetadata(), fillMetadata(), ome::files::detail::FormatReader::getCoreMetadata(), ome::files::detail::FormatWriter::getZCTCoords(), getZCTCoords(), ome::files::detail::FormatReader::getZCTCoords(), and ome::files::detail::FormatReader::getZCTModuloCoords().

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◆ getZCTCoords() [2/2]

std::array< dimension_size_type, 6 > ome::files::getZCTCoords	(	const std::string &	order,
		dimension_size_type	zSize,
		dimension_size_type	cSize,
		dimension_size_type	tSize,
		dimension_size_type	moduloZSize,
		dimension_size_type	moduloCSize,
		dimension_size_type	moduloTSize,
		dimension_size_type	num,
		dimension_size_type	index
	)

Get the Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes) corresponding to the given rasterized index value.

Note: The Z, C and T coordinates are not the same as those returned by ome::files::getZCTCoords(const std::string&, dimension_size_type, dimension_size_type, dimension_size_type, dimension_size_type, dimension_size_type) because the size of the modulo dimensions is taken into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.

Parameters

order	dimension order.
zSize	total number of focal planes (effective size).
cSize	total number of channels (effective size).
tSize	total number of time points (effective size).
moduloZSize	total number of ModuloZ planes (effective size).
moduloCSize	total number of ModuloC channels (effective size).
moduloTSize	total number of ModuloT time points (effective size).
num	total number of image planes (zSize * cSize * tSize), specified as a consistency check.
index	1D (rasterized) index to convert to ZCTmZmCmT coordinates.

Returns: an array containing the ZCTmZmCmT coordinates (effective sizes, in that order).

References getZCTCoords().

◆ isComplex()

bool ome::files::isComplex ( ::ome::xml::model::enums::PixelType pixeltype )

Check whether a PixelType is complex.

Parameters

pixeltype the PixelType to query.

Returns: true if complex, false otherwise.

◆ isFloatingPoint()

bool ome::files::isFloatingPoint ( ::ome::xml::model::enums::PixelType pixeltype )

Check whether a PixelType is floating point.

Parameters

pixeltype the PixelType to query.

Note: Equivalent to !isInteger().

Returns: true if floating point, false otherwise.

References isInteger().

◆ isInteger()

bool ome::files::isInteger ( ::ome::xml::model::enums::PixelType pixeltype )

Check whether a PixelType is integer.

Parameters

pixeltype the PixelType to query.

Returns: true if integer, false otherwise.

Referenced by isFloatingPoint().

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◆ isSigned()

bool ome::files::isSigned ( ::ome::xml::model::enums::PixelType pixeltype )

Check whether a PixelType is signed.

Parameters

pixeltype the PixelType to query.

Returns: true if signed, false otherwise.

◆ MetadataMap::get< MetadataMap::value_type >() [1/2]

template<>

MetadataMap::value_type& ome::files::MetadataMap::get< MetadataMap::value_type > ( const key_type & key )

inline

Get a reference to the value of a particular key from the map.

If the key was not found, or the type of value does not match the stored value type, value will remain unmodified.

Parameters

key	the key to find.

Returns: a reference to the stored value.

Exceptions

boost::bad_get on failure if the key was not found or if the type did not match the stored value type.

References ome::files::MetadataMap::discriminating_map.

◆ MetadataMap::get< MetadataMap::value_type >() [2/2]

template<>

const MetadataMap::value_type& ome::files::MetadataMap::get< MetadataMap::value_type > ( const key_type & key ) const

inline

Get a reference to the value of a particular key from the map.

If the key was not found, or the type of value does not match the stored value type, value will remain unmodified.

Parameters

key	the key to find.

Returns: a reference to the stored value.

Exceptions

boost::bad_get on failure if the key was not found or if the type did not match the stored value type.

References ome::files::MetadataMap::discriminating_map.

◆ operator &()

PlaneRegion ome::files::operator&	(	const PlaneRegion &	a,
		const PlaneRegion &	b
	)

inline

Intersect two regions.

If the regions do not intersect, a default-constructed region of zero size will be returned.

Parameters

a	the first region.
b	the second region.

Returns: the intersection of the two regions.

References ome::files::PlaneRegion::h, ome::files::PlaneRegion::PlaneRegion(), ome::files::PlaneRegion::w, ome::files::PlaneRegion::x, and ome::files::PlaneRegion::y.

◆ operator<<() [1/5]

template<class charT , class traits >

std::basic_ostream<charT,traits>& ome::files::operator<<	(	std::basic_ostream< charT, traits > &	os,
		const Version &	version
	)

inline

Output Version to output stream.

Parameters

os	the output stream.
version	the Version to output.

Returns: the output stream.

References ome::files::Version::major.

◆ operator<<() [2/5]

template<class charT , class traits >

std::basic_ostream<charT,traits>& ome::files::operator<<	(	std::basic_ostream< charT, traits > &	os,
		const Modulo &	modulo
	)

inline

Output Modulo to output stream.

Parameters

os	the output stream.
modulo	the Modulo to output.

Returns: the output stream.

References ome::files::Modulo::parentDimension.

◆ operator<<() [3/5]

template<class charT , class traits >

std::basic_ostream<charT,traits>& ome::files::operator<<	(	std::basic_ostream< charT, traits > &	os,
		const FileInfo &	info
	)

inline

Output FileInfo to output stream.

Parameters

os	the output stream.
info	the FileInfo to output.

Returns: the output stream.

References ome::files::FileInfo::filename.

◆ operator<<() [4/5]

template<class charT , class traits >

std::basic_ostream<charT,traits>& ome::files::operator<<	(	std::basic_ostream< charT, traits > &	os,
		const CoreMetadata &	core
	)

inline

Output CoreMetadata to output stream.

Parameters

os	the output stream.
core	the CoreMetadata to output.

Returns: the output stream.

References ome::files::CoreMetadata::sizeX.

◆ operator<<() [5/5]

template<class charT , class traits >

std::basic_ostream<charT,traits>& ome::files::operator<<	(	std::basic_ostream< charT, traits > &	os,
		const PlaneRegion &	region
	)

inline

Output PlaneRegion to output stream.

Parameters

os	the output stream.
region	the PlaneRegion to output.

Returns: the output stream.

References ome::files::PlaneRegion::x.

◆ operator|()

PlaneRegion ome::files::operator\|	(	const PlaneRegion &	a,
		const PlaneRegion &	b
	)

inline

Combine (union) two regions.

If the regions do not abut about a common edge, a default-constructed region of zero size will be returned.

Parameters

a	the first region.
b	the second region.

Returns: the union of the two regions.

References ome::files::PlaneRegion::h, ome::files::PlaneRegion::PlaneRegion(), ome::files::PlaneRegion::w, ome::files::PlaneRegion::x, and ome::files::PlaneRegion::y.

◆ pixelSize() [1/2]

storage_size_type ome::files::pixelSize	(	const ::ome::xml::meta::MetadataRetrieve &	meta,
		dimension_size_type	series
	)

Get the total size of pixel data in a series.

The size for the pixel type is rounded up to the nearest byte before multiplying by the dimension sizes.

Parameters

meta	the metadata to use.
series	the image series to use.

Returns: the size (in bytes).

References bytesPerPixel(), and pixelSize().

Referenced by pixelSize(), ome::files::out::MinimalTIFFWriter::setId(), ome::files::out::OMETIFFWriter::setId(), and significantPixelSize().

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◆ pixelSize() [2/2]

storage_size_type ome::files::pixelSize ( const ::ome::xml::meta::MetadataRetrieve & meta )

Get the total size of pixel data for all series.

The size for the pixel type is rounded up to the nearest byte before multiplying by the dimension sizes.

Parameters

meta	the metadata to use.

Returns: the size (in bytes).

References pixelSize().

◆ pixelTypeFromBits()

ome::xml::model::enums::PixelType ome::files::pixelTypeFromBits	(	pixel_size_type	bytes,
		bool	is_signed = `false`,
		bool	is_integer = `true`,
		bool	is_complex = `false`
	)

Determine a likely pixel type from its the storage size in bits.

Note that the BIT type will never be returned due to having the same storage size as other types.

Parameters

bytes	the storage size in bits.
is_signed	`true` if signed, `false` if unsigned.
is_integer	`true` if integer, `false` otherwise.
is_complex	:c true if complex, `false` otherwise.

Returns: the corresponding pixel type.

Exceptions

if	no pixel type was identified or the parameters are invalid.

References pixelTypeFromBytes().

◆ pixelTypeFromBytes()

ome::xml::model::enums::PixelType ome::files::pixelTypeFromBytes	(	pixel_size_type	bytes,
		bool	is_signed = `false`,
		bool	is_integer = `true`,
		bool	is_complex = `false`
	)

Determine a likely pixel type from its the storage size in bytes.

Note that the BIT type will never be returned due to having the same storage size as other types.

Parameters

bytes	the storage size in bytes.
is_signed	`true` if signed, `false` if unsigned.
is_integer	`true` if integer, `false` otherwise.
is_complex	:c true if complex, `false` otherwise.

Returns: the corresponding pixel type.

Exceptions

if	no pixel type was identified or the parameters are invalid.

References bytesPerPixel(), ome::xml::model::enums::PixelType::COMPLEXDOUBLE, ome::xml::model::enums::PixelType::COMPLEXFLOAT, ome::xml::model::enums::PixelType::DOUBLE, ome::xml::model::enums::PixelType::FLOAT, ome::xml::model::enums::PixelType::INT16, ome::xml::model::enums::PixelType::INT32, ome::xml::model::enums::PixelType::INT8, ome::xml::model::enums::PixelType::UINT16, ome::xml::model::enums::PixelType::UINT32, and ome::xml::model::enums::PixelType::UINT8.

Referenced by pixelTypeFromBits().

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◆ register_module_paths()

void ome::files::register_module_paths ( )

Register the OME-Files module paths with OME-Common.

This function forces path registration.

Note: This is a hack to allow static linking to work on Windows; without this, the module object is omitted and the paths aren't automatically registered. This will no longer be required once it is built as a DLL. Its only purpose is to force object inclusion when static linking, and ensure that the registration happens independently of object static construction order to allow use prior to main() entry. You should not use this.

References register_module_paths(), and ome::common::register_module_paths().

◆ removeBinData()

void ome::files::removeBinData ( ::ome::xml::meta::OMEXMLMetadata & omexml )

Remove all BinData elements from OME-XML metadata.

Parameters

omexml the OME-XML metadata store.

References ome::xml::meta::OMEXMLMetadata::getRoot(), removeBinData(), and ome::xml::meta::OMEXMLMetadata::resolveReferences().

Referenced by ome::files::out::OMETIFFWriter::close(), and removeBinData().

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◆ removeChannels()

void ome::files::removeChannels	(	::ome::xml::meta::OMEXMLMetadata &	omexml,
		dimension_size_type	image,
		dimension_size_type	sizeC
	)

Remove all but the specified number of valid Channel elements from OME-XML metadata.

Parameters

omexml	the OME-XML metadata store.
image	the image index.
sizeC	the number of channels to retain.

References ome::xml::meta::OMEXMLMetadata::getRoot(), removeChannels(), and ome::xml::meta::OMEXMLMetadata::resolveReferences().

Referenced by ome::files::in::OMETIFFReader::cleanMetadata(), and removeChannels().

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◆ removeTiffData()

void ome::files::removeTiffData ( ::ome::xml::meta::OMEXMLMetadata & omexml )

Remove all TiffData elements from OME-XML metadata.

Parameters

omexml the OME-XML metadata store.

References ome::xml::meta::OMEXMLMetadata::getRoot(), removeTiffData(), and ome::xml::meta::OMEXMLMetadata::resolveReferences().

Referenced by ome::files::out::OMETIFFWriter::close(), and removeTiffData().

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◆ sanitizeXML()

std::string ome::files::sanitizeXML ( const std::string & s )

Filter control codes and invalid sequences in an XML string.

Remove all control codes except for LF, HT and CR. Also replace &# with #.

Parameters

s	the string to filter.

Returns: the filtered string.

◆ setDefaultCreationDate()

void ome::files::setDefaultCreationDate	(	::ome::xml::meta::MetadataStore &	store,
		dimension_size_type	series,
		const boost::filesystem::path &	id
	)

Set the creation data for a series.

If the specified file exists, the modification time of this file will be used as the creation date. If it does not exist, the current system time will be used as a fallback.

This function will do nothing unless defaultCreationDateEnabled(bool) is enabled.

Parameters

store	the OME-XML metadata store.
series	the series for which to set the creation date.
id	the filename for the series.

References defaultCreationDateEnabled(), setDefaultCreationDate(), and ome::xml::meta::MetadataStore::setImageAcquisitionDate().

Referenced by fillMetadata(), and setDefaultCreationDate().

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◆ significantBitsPerPixel()

pixel_size_type ome::files::significantBitsPerPixel ( ::ome::xml::model::enums::PixelType pixeltype )

Get the significant (maximum bits used) size of a PixelType, in bits.

Parameters

pixeltype the PixelType to query.

Returns: the size, in bits

Referenced by ome::files::tiff::getCoreMetadata(), ome::files::tiff::IFD::setBitsPerSample(), and significantPixelSize().

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◆ significantPixelSize() [1/2]

storage_size_type ome::files::significantPixelSize	(	const ::ome::xml::meta::MetadataRetrieve &	meta,
		dimension_size_type	series
	)

Get the total significant size of pixel data in a series.

The significant size for the pixel type (in bits) is multiplied by the dimension sizes before converting to bytes.

Parameters

meta	the metadata to use.
series	the image series to use.

Returns: the size (in bytes).

References significantBitsPerPixel(), and significantPixelSize().

Referenced by ome::files::out::MinimalTIFFWriter::setId(), ome::files::out::OMETIFFWriter::setId(), and significantPixelSize().

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◆ significantPixelSize() [2/2]

storage_size_type ome::files::significantPixelSize ( const ::ome::xml::meta::MetadataRetrieve & meta )

Get the total significant size of pixel data for all series.

The significant size for the pixel type (in bits) is multiplied by the dimension sizes before converting to bytes.

Parameters

meta	the metadata to use.

Returns: the size (in bytes).

References pixelSize(), and significantPixelSize().

◆ transformToLatestModelVersion()

std::string ome::files::transformToLatestModelVersion ( const std::string & document )

Transform an OME-XML document to the latest model version.

Parameters

document the OME-XML document.

Returns: the transformed OME-XML document.

References transformToLatestModelVersion().

Referenced by transformToLatestModelVersion().

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◆ validateModel()

bool ome::files::validateModel	(	::ome::xml::meta::Metadata &	meta,
		bool	correct
	)

Validate a metadata store.

Note that unlike validateOMEXML(const std::string&) this does not perform XML validation. It will look for missing or inconsistent metadata and (if specified) attempt to correct the metadata to make it valid.

Parameters

meta	the metadata store.
correct	`true` to attempt correction, `false` to leave unmodified.

Returns: true if valid, false if invalid.

Exceptions

FormatException if correction of invalid metadata fails.

Referenced by ome::files::out::OMETIFFWriter::setId(), and validateModel().

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◆ validateOMEXML()

bool ome::files::validateOMEXML ( const std::string & document )

Validate an OME-XML document.

Parameters

document the XML document source.

Returns: true if valid, false if invalid.

References validateOMEXML(), and validateXML().

Referenced by getOMEXML(), and validateOMEXML().

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◆ validateXML()

bool ome::files::validateXML	(	const std::string &	s,
		const std::string &	loc = `"XML"`
	)

Validate XML in an XML string.

Parameters

s	the string to validate.
loc	the file location or other descriptive text for the string; used for error reporting only.

Returns: true if valid, false if invalid.

Referenced by validateOMEXML().

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◆ verifyMinimum()

void ome::files::verifyMinimum	(	::ome::xml::meta::MetadataRetrieve &	retrieve,
		dimension_size_type	series = `0U`
	)

Verify correctness of minimal amount of metadata in a series.

Parameters

retrieve	the OME-XML metadata store.
series	the image series to verify.

Exceptions

FormatException if any metadata is missing.

References ome::xml::meta::MetadataRetrieve::getChannelCount(), ome::xml::meta::MetadataRetrieve::getChannelID(), ome::xml::meta::MetadataRetrieve::getImageID(), ome::xml::meta::MetadataRetrieve::getPixelsID(), ome::xml::meta::MetadataStore::getRoot(), and verifyMinimum().

Referenced by ome::files::in::OMETIFFReader::isFilenameThisTypeImpl(), and verifyMinimum().

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Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Enumeration Type Documentation

◆ Dimensions

◆ Domain

◆ EndianType

Function Documentation

◆ addMetadataOnly()

◆ bitsPerPixel()

◆ bytesPerPixel()

◆ byteswap() [1/3]

◆ byteswap() [2/3]

◆ byteswap() [3/3]

◆ createDimensionOrder()

◆ createID() [1/4]

◆ createID() [2/4]

◆ createID() [3/4]

◆ createID() [4/4]

◆ createOMEXMLMetadata() [1/5]

◆ createOMEXMLMetadata() [2/5]

◆ createOMEXMLMetadata() [3/5]

◆ createOMEXMLMetadata() [4/5]

◆ createOMEXMLMetadata() [5/5]

◆ createOMEXMLRoot()

◆ defaultCreationDateEnabled() [1/2]

◆ defaultCreationDateEnabled() [2/2]

◆ escapeXML()

◆ fillAllPixels()

◆ fillMetadata() [1/2]

◆ fillMetadata() [2/2]

◆ fillOriginalMetadata()

◆ fillPixels() [1/2]

◆ fillPixels() [2/2]

◆ getDomain()

◆ getDomainCollection()

◆ getIndex() [1/2]

◆ getIndex() [2/2]

◆ getModelVersion() [1/3]

◆ getModelVersion() [2/3]

◆ getModelVersion() [3/3]

◆ getModulo()

◆ getModuloAlongC()

◆ getModuloAlongT()

◆ getModuloAlongZ()

◆ getOMEXML()

◆ getOMEXMLMetadata()

◆ getOriginalMetadata()

◆ getZCTCoords() [1/2]

◆ getZCTCoords() [2/2]

◆ isComplex()

◆ isFloatingPoint()

◆ isInteger()

◆ isSigned()

◆ MetadataMap::get< MetadataMap::value_type >() [1/2]

◆ MetadataMap::get< MetadataMap::value_type >() [2/2]

◆ operator &()

◆ operator<<() [1/5]

◆ operator<<() [2/5]

◆ operator<<() [3/5]

◆ operator<<() [4/5]

◆ operator<<() [5/5]

◆ operator|()

◆ pixelSize() [1/2]

◆ pixelSize() [2/2]

◆ pixelTypeFromBits()

◆ pixelTypeFromBytes()

◆ register_module_paths()

◆ removeBinData()

◆ removeChannels()

◆ removeTiffData()

◆ sanitizeXML()

◆ setDefaultCreationDate()

◆ significantBitsPerPixel()

◆ significantPixelSize() [1/2]

◆ significantPixelSize() [2/2]