TIFF reader with support for OME-XML metadata. More...

#include <ome/files/in/OMETIFFReader.h>

Inheritance diagram for ome::files::in::OMETIFFReader:

Collaboration diagram for ome::files::in::OMETIFFReader:

Public Member Functions
	OMETIFFReader ()
	Constructor.

virtual	~OMETIFFReader ()
	Destructor.

bool	isSingleFile (const boost::filesystem::path &id) const
	Is this a single-file format? More...

bool	isThisType (const boost::filesystem::path &name, bool open) const
	Check if the given file is a valid instance of this file format. More...

void	close (bool fileOnly=false)
	Close the currently open file. More...

const std::vector< std::string > &	getDomains () const
	Get the domains represented by the current file. More...

const std::vector< boost::filesystem::path >	getSeriesUsedFiles (bool noPixels) const
	Get the files used by the active series. More...

FormatReader::FileGroupOption	fileGroupOption (const std::string &id)
	Returns an enum indicating that we cannot, must, or might group the files in this dataset. More...

dimension_size_type	getOptimalTileWidth (dimension_size_type channel) const
	Get the optimal sub-image width. More...

dimension_size_type	getOptimalTileHeight (dimension_size_type channel) const
	Get the optimal sub-image height. More...

void	initFile (const boost::filesystem::path &id)
	Initialize the given file. More...

std::shared_ptr< ome::xml::meta::MetadataStore >	getMetadataStoreForConversion ()
	Get a MetadataStore suitable for writing. More...

std::shared_ptr< ome::xml::meta::MetadataStore >	getMetadataStoreForDisplay ()
	Get a MetadataStore suitable for display. More...

Public Member Functions inherited from ome::files::detail::FormatReader
virtual	~FormatReader ()
	Destructor.

const std::set< MetadataOptions::MetadataLevel > &	getSupportedMetadataLevels ()
	Get the supported metadata levels. More...

void	setMetadataOptions (const MetadataOptions &options)
	Set metadata options. More...

const MetadataOptions &	getMetadataOptions () const
	Get metadata options. More...

MetadataOptions &	getMetadataOptions ()
	Get metadata options. More...

const MetadataMap &	getGlobalMetadata () const
	Get global metadata map. More...

const MetadataMap::value_type &	getMetadataValue (const std::string &field) const
	Get a global metadata value. More...

const MetadataMap &	getSeriesMetadata () const
	Get series metadata map. More...

const MetadataMap::value_type &	getSeriesMetadataValue (const MetadataMap::key_type &field) const
	Get a series metadata value. More...

bool	isThisType (const uint8_t *begin, std::size_t length) const
	Check if the given buffer is a valid header for this file format. More...

bool	isThisType (const uint8_t begin, const uint8_t end) const
	Check if the given buffer is a valid header for this file format. More...

bool	isThisType (std::istream &stream) const
	Check if the given input stream is a valid stream for this file format. More...

dimension_size_type	getImageCount () const
	Determine the number of image planes in the current series. More...

bool	isRGB (dimension_size_type channel) const
	Check if the image planes for a channel have more than one sub-channel per openBytes() call. More...

dimension_size_type	getSizeX () const
	Get the size of the X dimension. More...

dimension_size_type	getSizeY () const
	Get the size of the Y dimension. More...

dimension_size_type	getSizeZ () const
	Get the size of the Z dimension. More...

dimension_size_type	getSizeT () const
	Get the size of the T dimension. More...

dimension_size_type	getSizeC () const
	Get the size of the C dimension. More...

ome::xml::model::enums::PixelType	getPixelType () const
	Get the pixel type. More...

pixel_size_type	getBitsPerPixel () const
	Get the number of valid bits per pixel. More...

dimension_size_type	getEffectiveSizeC () const
	Get the effective size of the C dimension. More...

dimension_size_type	getRGBChannelCount (dimension_size_type channel) const
	Get the number of channels returned for a call to openBytes(). More...

bool	isIndexed () const
	Get whether the image planes are indexed color. More...

bool	isFalseColor () const
	Get whether the image planes are false color. More...

Modulo &	getModuloZ ()
	Get the Modulo subdivision of the Z dimension. More...

const Modulo &	getModuloZ () const
	Get the Modulo subdivision of the Z dimension. More...

Modulo &	getModuloT ()
	Get the Modulo subdivision of the T dimension. More...

const Modulo &	getModuloT () const
	Get the Modulo subdivision of the T dimension. More...

Modulo &	getModuloC ()
	Get the Modulo subdivision of the C dimension. More...

const Modulo &	getModuloC () const
	Get the Modulo subdivision of the C dimension. More...

dimension_size_type	getThumbSizeX () const
	Get the thumbnail size of the X dimension. More...

dimension_size_type	getThumbSizeY () const
	Get the thumbnail size of the Y dimension. More...

bool	isLittleEndian () const
	Get whether the data is in little-endian format. More...

const std::string &	getDimensionOrder () const
	Get the dimension order. More...

bool	isOrderCertain () const
	Get whether the dimension order and sizes are known, or merely guesses. More...

bool	isThumbnailSeries () const
	Get whether the current series is a lower resolution copy of a different series. More...

bool	isInterleaved () const
	Get whether or not the channels are interleaved. More...

bool	isInterleaved (dimension_size_type subC) const
	Get whether or not the given channel is interleaved. More...

void	openBytes (dimension_size_type plane, VariantPixelBuffer &buf) const
	Obtain an image plane. More...

void	openBytes (dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h) const
	Obtain a sub-image of an image plane. More...

void	openThumbBytes (dimension_size_type plane, VariantPixelBuffer &buf) const
	Obtain a thumbnail of an image plane. More...

dimension_size_type	getSeriesCount () const
	Get the number of image series in this file. More...

void	setSeries (dimension_size_type series) const
	Set the active series. More...

dimension_size_type	getSeries () const
	Get the active series. More...

void	setPlane (dimension_size_type plane) const
	Set the active plane. More...

dimension_size_type	getPlane () const
	Get the active plane. More...

void	setGroupFiles (bool group)
	Set file grouping. More...

bool	isGroupFiles () const
	Get file grouping. More...

bool	isMetadataComplete () const
	Get status of metadata parsing. More...

void	setNormalized (bool normalize)
	Set float normalization. More...

bool	isNormalized () const
	Get float normalization. More...

void	setOriginalMetadataPopulated (bool populate)
	Specifies whether or not to save proprietary metadata in the MetadataStore. More...

bool	isOriginalMetadataPopulated () const
	Get proprietary metadata storage. More...

const std::vector< boost::filesystem::path >	getUsedFiles (bool noPixels=false) const
	Get the files used by this dataset. More...

std::vector< FileInfo >	getAdvancedUsedFiles (bool noPixels=false) const
	Get the files used by this dataset. More...

std::vector< FileInfo >	getAdvancedSeriesUsedFiles (bool noPixels=false) const
	Get the files used by the active series. More...

const boost::optional< boost::filesystem::path > &	getCurrentFile () const
	Get the currently open file. More...

dimension_size_type	getIndex (dimension_size_type z, dimension_size_type c, dimension_size_type t) const
	Get the linear index of a `Z`, `C` and `T` coordinate. More...

dimension_size_type	getIndex (dimension_size_type z, dimension_size_type c, dimension_size_type t, dimension_size_type moduloZ, dimension_size_type moduloC, dimension_size_type moduloT) const
	Get the linear index of a `Z`, `C`, `T`, `ModuloZ`, `ModuloC` and `ModuloT` coordinate. More...

std::array< dimension_size_type, 3 >	getZCTCoords (dimension_size_type index) const
	Get the `Z`, `C` and `T` coordinate of a linear index. More...

std::array< dimension_size_type, 6 >	getZCTModuloCoords (dimension_size_type index) const
	Get the `Z`, `C`, `T`, `ModuloZ`, `ModuloC` and `ModuloT` coordinate of a linear index. More...

const std::vector< std::shared_ptr<::ome::files::CoreMetadata > > &	getCoreMetadataList () const
	Get the core metadata. More...

void	setMetadataFiltered (bool filter)
	Set metadata filtering. More...

bool	isMetadataFiltered () const
	Get metadata filtering. More...

void	setMetadataStore (std::shared_ptr<::ome::xml::meta::MetadataStore > &store)
	Set the default metadata store for this reader. More...

const std::shared_ptr<::ome::xml::meta::MetadataStore > &	getMetadataStore () const
	Get the current metadata store for this reader. More...

std::shared_ptr<::ome::xml::meta::MetadataStore > &	getMetadataStore ()
	Get the current metadata store for this reader. More...

std::vector< std::shared_ptr<::ome::files::FormatReader > >	getUnderlyingReaders () const
	Get all underlying readers. More...

uint32_t	getRequiredDirectories (const std::vector< std::string > &files) const
	Get required parent directories. More...

const std::string &	getDatasetStructureDescription () const
	Get a short description of the dataset structure. More...

const std::vector< std::string > &	getPossibleDomains (const std::string &id) const
	Get the possible domains represented in which this format is used. More...

bool	hasCompanionFiles () const
	Does this format support multi-file datasets? More...

dimension_size_type	getOptimalTileWidth () const
	Get the optimal sub-image width. More...

dimension_size_type	getOptimalTileHeight () const
	Get the optimal sub-image height. More...

dimension_size_type	seriesToCoreIndex (dimension_size_type series) const
	Get the first core index corresponding to the specified series. More...

dimension_size_type	coreIndexToSeries (dimension_size_type index) const
	Get the series corresponding to the specified core index. More...

dimension_size_type	getCoreIndex () const
	Get the CoreMetadata index of the current resolution/series. More...

void	setCoreIndex (dimension_size_type index) const
	Set the current resolution/series (ignoring sub-resolutions). More...

dimension_size_type	getResolutionCount () const
	Get the number of resolutions for the current series. More...

void	setResolution (dimension_size_type resolution) const
	Set the active resolution level. More...

dimension_size_type	getResolution () const
	Get the active resolution level. More...

bool	hasFlattenedResolutions () const
	Get resolution flattening. More...

void	setFlattenedResolutions (bool flatten)
	Set resolution flattening. More...

void	setId (const boost::filesystem::path &id)
	Set the current file name. More...

const std::string &	getFormat () const
	Get the name of this file format. More...

const std::string &	getFormatDescription () const
	Get the description of this file format. More...

const std::vector< boost::filesystem::path > &	getSuffixes () const
	Get the default file suffixes for this file format. More...

const std::vector< boost::filesystem::path > &	getCompressionSuffixes () const
	Get the default compression suffixes for this file format. More...

Public Member Functions inherited from ome::files::FormatHandler
virtual	~FormatHandler ()
	Destructor.

Public Member Functions inherited from ome::files::MetadataConfigurable
virtual	~MetadataConfigurable ()
	Destructor.

Protected Types
typedef std::map< std::string, boost::filesystem::path >	uuid_file_map
	Map UUID to filename.

typedef std::map< boost::filesystem::path, boost::filesystem::path >	invalid_file_map
	Map filename to another file.

typedef std::map< boost::filesystem::path, std::shared_ptr< ome::files::tiff::TIFF > >	tiff_map
	Map filename to open TIFF handle.

Protected Types inherited from ome::files::detail::FormatReader
typedef std::vector< std::shared_ptr<::ome::files::CoreMetadata > >	coremetadata_list_type
	List type for storing CoreMetadata.

Protected Member Functions
bool	isFilenameThisTypeImpl (const boost::filesystem::path &name) const
	isThisType file implementation for readers. More...

void	getLookupTable (dimension_size_type plane, VariantPixelBuffer &buf) const
	Get the color lookup table associated with an image plane. More...

void	openBytesImpl (dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h) const
	Obtain a sub-image of an image plane. More...

const std::shared_ptr< const tiff::IFD >	ifdAtIndex (dimension_size_type plane) const
	Get the IFD index for a plane in the current series. More...

void	addTIFF (const boost::filesystem::path &tiff)
	Add a TIFF file to the internal TIFF map. More...

const std::shared_ptr< const ome::files::tiff::TIFF >	getTIFF (const boost::filesystem::path &tiff) const
	Get a an open TIFF file from the internal TIFF map. More...

bool	validTIFF (const boost::filesystem::path &tiff) const
	Check if a cached TIFF is valid (can be opened). More...

void	closeTIFF (const boost::filesystem::path &tiff)
	Close an open TIFF file from the internal TIFF map. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	readMetadata (const ome::files::tiff::TIFF &tiff)
	Read metadata into metadata store from an open TIFF. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	readMetadata (const boost::filesystem::path &id)
	Read metadata into metadata store from a TIFF or companion XML file. More...

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	cacheMetadata (const boost::filesystem::path &id) const
	Read and cache metadata. More...

Protected Member Functions inherited from ome::files::detail::FormatReader
	FormatReader (const ReaderProperties &)
	Constructor.

virtual bool	isUsedFile (const boost::filesystem::path &file)
	Check if a file is in the used files list. More...

virtual void	readPlane (std::istream &source, VariantPixelBuffer &dest, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h, dimension_size_type samples)
	Read a raw plane. More...

virtual void	readPlane (std::istream &source, VariantPixelBuffer &dest, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h, dimension_size_type scanlinePad, dimension_size_type samples)
	Read a raw plane with scanline padding. More...

virtual std::shared_ptr<::ome::xml::meta::MetadataStore >	makeFilterMetadata ()
	Create a configured FilterMetadata instance. More...

const CoreMetadata &	getCoreMetadata (dimension_size_type index) const
	Get CoreMetadata by core index. More...

CoreMetadata &	getCoreMetadata (dimension_size_type index)
	Get CoreMetadata by core index. More...

virtual bool	isStreamThisTypeImpl (std::istream &stream) const
	isThisType stream implementation for readers. More...

std::array< dimension_size_type, 2 >	getThumbSize () const
	Get the thumbnail size of the X and Y dimensions. More...

Protected Member Functions inherited from ome::files::FormatReader
	FormatReader ()
	Constructor.

Protected Member Functions inherited from ome::files::FormatHandler
	FormatHandler ()
	Constructor.

Protected Member Functions inherited from ome::files::MetadataConfigurable
	MetadataConfigurable ()
	Constructor.

Protected Attributes
ome::common::Logger	logger
	Message logger.

uuid_file_map	files
	UUID to filename mapping.

invalid_file_map	invalidFiles
	Invalid filename to valid filename mapping.

tiff_map	tiffs
	Open TIFF files.

boost::filesystem::path	metadataFile
	Metadata file.

std::vector< boost::filesystem::path >	usedFiles
	Used files.

bool	hasSPW
	Has screen-plate-well metadata.

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata >	cachedMetadata
	Cached metadata (for re-using parsed metadata).

boost::filesystem::path	cachedMetadataFile
	Cached metadata file location (for re-using parsed metadata).

Protected Attributes inherited from ome::files::detail::FormatReader
const ReaderProperties &	readerProperties
	Reader properties specific to the derived file format.

boost::optional< boost::filesystem::path >	currentId
	The identifier (path) of the currently open file.

std::shared_ptr< std::istream >	in
	Current input.

::ome::files::MetadataMap	metadata
	Mapping of metadata key/value pairs.

dimension_size_type	coreIndex
	The number of the current series (flattened). More...

dimension_size_type	series
	The number of the current series (non-flattened). More...

dimension_size_type	plane
	The number of the current plane in the current series. More...

coremetadata_list_type	core
	Core metadata values.

dimension_size_type	resolution
	The number of the current resolution. More...

bool	flattenedResolutions
	Whether or not resolutions are flattened.

bool	suffixNecessary
	Whether the file extension matching one of the reader's suffixes is necessary to identify the file as an instance of this format.

bool	suffixSufficient
	Whether the file extension matching one of the reader's suffixes is sufficient to identify the file as an instance of this format.

bool	companionFiles
	Whether this format supports multi-file datasets.

std::string	datasetDescription
	Short description of the structure of the dataset.

bool	normalizeData
	Whether or not to normalize float data.

bool	filterMetadata
	Whether or not to filter out invalid metadata.

bool	saveOriginalMetadata
	Whether or not to save proprietary metadata in the MetadataStore.

bool	indexedAsRGB
	Whether or not MetadataStore sets C = 3 for indexed color images.

bool	group
	Whether or not to group multi-file formats.

std::vector< std::string >	domains
	List of domains in which this format is used.

std::shared_ptr<::ome::xml::meta::MetadataStore >	metadataStore
	Current metadata store. More...

MetadataOptions	metadataOptions
	Metadata parsing options.

Private Member Functions
void	findUsedFiles (const ome::xml::meta::OMEXMLMetadata &meta, const boost::filesystem::path &currentId, const boost::filesystem::path &currentDir, const boost::optional< std::string > &currentUUID)
	Get UUID to file associations and used files. More...

void	getAcquisitionDates (const ome::xml::meta::OMEXMLMetadata &meta, std::vector< boost::optional< ome::xml::model::primitives::Timestamp >> &timestamps)
	Get acquisition dates for each image. More...

void	cleanMetadata (ome::xml::meta::OMEXMLMetadata &meta)
	Clean up OME-XML metadata. More...

dimension_size_type	seriesFileSamplesPerPixel (const ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series)
	Get the samples per pixel from the first IFD for a series. More...

void	seriesIndexStart (const ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &zIndexStart, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &tIndexStart, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &cIndexStart)
	Get starting index for each dimension. More...

bool	getTiffDataValues (const ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series, ome::xml::meta::BaseMetadata::index_type tiffData, boost::optional< ome::xml::model::primitives::NonNegativeInteger > &tdIFD, ome::xml::model::primitives::NonNegativeInteger &numPlanes, ome::xml::model::primitives::NonNegativeInteger &firstZ, ome::xml::model::primitives::NonNegativeInteger &firstT, ome::xml::model::primitives::NonNegativeInteger &firstC)
	Get values from a TiffData element. More...

void	fixOMEROMetadata (ome::xml::meta::OMEXMLMetadata &meta, ome::xml::meta::BaseMetadata::index_type series)
	Fix invalid OMERO OME-TIFF metadata. More...

void	fixDimensions (ome::xml::meta::BaseMetadata::index_type series)
	Attempt to correct logically inconsistent dimensions. More...

Additional Inherited Members
Public Types inherited from ome::files::FormatReader
enum	FileGroupOption { MUST_GROUP, CAN_GROUP, CANNOT_GROUP }
	File grouping options. More...

Static Public Member Functions inherited from ome::files::FormatHandler
static bool	checkSuffix (const boost::filesystem::path &name, const boost::filesystem::path &suffix)
	Perform suffix matching for the given filename. More...

static bool	checkSuffix (const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes)
	Perform suffix matching for the given filename. More...

static bool	checkSuffix (const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes, const std::vector< boost::filesystem::path > &compression_suffixes)
	Perform suffix matching for the given filename. More...

static void	assertId (const boost::optional< boost::filesystem::path > &id, bool notNull=true)
	Assert that the current file is valid. More...

Detailed Description

TIFF reader with support for OME-XML metadata.

Member Function Documentation

◆ addTIFF()

void ome::files::in::OMETIFFReader::addTIFF ( const boost::filesystem::path & tiff )

protected

Add a TIFF file to the internal TIFF map.

Parameters

tiff	the TIFF file to add.

References tiffs.

Referenced by initFile(), and readMetadata().

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◆ cacheMetadata()

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::in::OMETIFFReader::cacheMetadata ( const boost::filesystem::path & id ) const

protected

Read and cache metadata.

Optimisation to allow sharing of previously parsed metadata. The metadata will be cached in the meta member, but will not be cached if the reader has been fully initialised. If the metadata was previously read and cached, the cached copy will be returned.

Parameters

id	the file from which to read the metadata.

Returns: the parsed metadata as a metadata store.

References cachedMetadata, cachedMetadataFile, canonical(), and ome::files::createOMEXMLMetadata().

Referenced by initFile(), isFilenameThisTypeImpl(), and isSingleFile().

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◆ cleanMetadata()

void ome::files::in::OMETIFFReader::cleanMetadata ( ome::xml::meta::OMEXMLMetadata & meta )

private

Clean up OME-XML metadata.

Remove invalid channels.

Parameters

meta	the metadata store to clean up.

References ome::xml::meta::OMEXMLMetadata::getImageCount(), ome::xml::meta::OMEXMLMetadata::getPixelsSizeC(), and ome::files::removeChannels().

Referenced by initFile().

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◆ close()

void ome::files::in::OMETIFFReader::close ( bool fileOnly = false )

virtual

Close the currently open file.

An exception may be thrown when closing the file, for example if there are problems flushing any pending writes, or if there are any inconsistencies in the metadata which prevent completing any final writes. The causes are reader- or writer-dependent, and the exception type is dependent upon the implementation details of the reader or writer in use. It is advised to always explicitly close writers, since if this is automatically called at destruction time, any errors will be lost. If an exception is thrown, the object may be left in an inconsistent state and should not be reused.

Parameters

fileOnly close the open file only if true, or else free all internal state if false; only meaningful for readers, since writers will always free all internal state.

Exceptions

On	error; exception type may vary.

Reimplemented from ome::files::detail::FormatReader.

References cachedMetadata, cachedMetadataFile, ome::files::detail::FormatReader::close(), files, hasSPW, invalidFiles, metadataFile, tiffs, and usedFiles.

Referenced by initFile(), and ~OMETIFFReader().

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◆ closeTIFF()

void ome::files::in::OMETIFFReader::closeTIFF ( const boost::filesystem::path & tiff )

protected

Close an open TIFF file from the internal TIFF map.

If the file is currently open, it will be closed.

Parameters

tiff	the TIFF file to add.

References tiffs.

◆ fileGroupOption()

FormatReader::FileGroupOption ome::files::in::OMETIFFReader::fileGroupOption ( const std::string & id )

virtual

Returns an enum indicating that we cannot, must, or might group the files in this dataset.

Parameters

id	filename to check.

Returns: the grouping option for the specified file.

Reimplemented from ome::files::detail::FormatReader.

References ome::files::FormatReader::CAN_GROUP, ome::files::detail::FormatReader::group, isSingleFile(), and ome::files::FormatReader::MUST_GROUP.

◆ findUsedFiles()

void ome::files::in::OMETIFFReader::findUsedFiles	(	const ome::xml::meta::OMEXMLMetadata &	meta,
		const boost::filesystem::path &	currentId,
		const boost::filesystem::path &	currentDir,
		const boost::optional< std::string > &	currentUUID
	)

private

Get UUID to file associations and used files.

Updates both the files map and the used files list.

Parameters

meta	the metadata store to use.
currentId	the current file.
currentDir	the current directory.
currentUUID	the current UUID (if any).

References canonical(), ome::files::detail::FormatReader::currentId, files, ome::xml::meta::OMEXMLMetadata::getImageCount(), ome::xml::meta::OMEXMLMetadata::getTiffDataCount(), ome::xml::meta::OMEXMLMetadata::getUUIDFileName(), ome::xml::meta::OMEXMLMetadata::getUUIDValue(), logger, ome::files::detail::FormatReader::series, and usedFiles.

Referenced by initFile().

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◆ fixDimensions()

void ome::files::in::OMETIFFReader::fixDimensions ( ome::xml::meta::BaseMetadata::index_type series )

private

Attempt to correct logically inconsistent dimensions.

If the product of SizeZ, SizeT and SizeC is not equal to the total image count, attempt to correct it by finding the dimension equal to the image count, and setting all other dimension sizes to 1. If a match isn't found, fall back to setting SizeT to the image count.

Parameters

series the series to correct.

References ome::files::detail::FormatReader::core.

Referenced by initFile().

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◆ fixOMEROMetadata()

void ome::files::in::OMETIFFReader::fixOMEROMetadata	(	ome::xml::meta::OMEXMLMetadata &	meta,
		ome::xml::meta::BaseMetadata::index_type	series
	)

private

Fix invalid OMERO OME-TIFF metadata.

OMERO has in the past written OME-TIFF with incorrect DimensionOrder. Attempt to identify such data and reset the dimension order to XYZCT.

Parameters

meta	the metadata store to query.
series	the series to correct.

References ome::files::detail::FormatReader::core, files, ome::xml::meta::OMEXMLMetadata::getChannelCount(), ome::xml::meta::OMEXMLMetadata::getChannelName(), ome::xml::meta::OMEXMLMetadata::getTiffDataCount(), and ome::xml::meta::OMEXMLMetadata::getUUIDFileName().

Referenced by initFile().

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◆ getAcquisitionDates()

void ome::files::in::OMETIFFReader::getAcquisitionDates	(	const ome::xml::meta::OMEXMLMetadata &	meta,
		std::vector< boost::optional< ome::xml::model::primitives::Timestamp >> &	timestamps
	)

private

Get acquisition dates for each image.

If no date was specified for the image, the timestamp will be unset.

Parameters

meta	the metadata store to use.
timestamps	the acquisition dates, indexed by image.

References ome::xml::meta::OMEXMLMetadata::getImageAcquisitionDate(), and ome::xml::meta::OMEXMLMetadata::getImageCount().

Referenced by initFile().

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◆ getDomains()

const std::vector< std::string > & ome::files::in::OMETIFFReader::getDomains ( ) const

virtual

Get the domains represented by the current file.

Returns: a list of domains.

Reimplemented from ome::files::detail::FormatReader.

References ome::files::FormatHandler::assertId(), ome::files::detail::FormatReader::currentId, ome::files::getDomainCollection(), and hasSPW.

◆ getLookupTable()

void ome::files::in::OMETIFFReader::getLookupTable	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf
	)		const

protectedvirtual

Get the color lookup table associated with an image plane.

If no image planes have been opened, or if isIndexed() returns false, then this may throw an exception.

The VariantPixelBuffer will use the X dimension for the value index and the sub-channel dimension for the color samples (order is RGB). Depending upon the image type, the size of the X dimension may vary. It will typically be 2^8 or 2^16, but other sizes are possible.

Parameters

buf	the destination pixel buffer.
plane	the plane index within the series.

Exceptions

FormatException if a lookup table could not be obtained.

Reimplemented from ome::files::detail::FormatReader.

References ome::files::FormatHandler::assertId(), ome::files::detail::FormatReader::currentId, ifdAtIndex(), and ome::files::detail::FormatReader::setPlane().

◆ getMetadataStoreForConversion()

std::shared_ptr< ome::xml::meta::MetadataStore > ome::files::in::OMETIFFReader::getMetadataStoreForConversion ( )

Get a MetadataStore suitable for writing.

Note: Historically, this method created metadata suitable for use with FormatWriter, but would possibly not generate valid OME-XML if both BinData and TiffData elements were present. This is no longer the case; the general FormatReader::getMetadataStore() method will always create valid metadata which is suitable for use with FormatWriter, and so should be used instead.

Returns: the metadata store.

Deprecated:: Use the general FormatReader::getMetadataStore() method.

Todo:: Remove in 0.3

References ome::files::detail::FormatReader::getMetadataStore().

◆ getMetadataStoreForDisplay()

std::shared_ptr< ome::xml::meta::MetadataStore > ome::files::in::OMETIFFReader::getMetadataStoreForDisplay ( )

Get a MetadataStore suitable for display.

Note: Historically, this method removed certain elements for display purposes and was not be suitable for use with FormatWriter due to not containing required BinData BigEndian attributes pthis requirement has long been unnecessary]. This is no longer the case, and has never been the case for the C++ implementation; the general FormatReader::getMetadataStore() method will always create valid metadata which is suitable for both display and use with FormatWriter, and so should be used instead.

Returns: the metadata store.

Deprecated:: Use the general FormatReader::getMetadataStore() method.

Todo:: Remove in 0.3

References ome::files::detail::FormatReader::getMetadataStore().

◆ getOptimalTileHeight()

dimension_size_type ome::files::in::OMETIFFReader::getOptimalTileHeight ( dimension_size_type channel ) const

virtual

Get the optimal sub-image height.

This is intended for use with openBytes().

Parameters

channel the channel to use, range [0, EffectiveSizeC).

Returns: the optimal height.

Reimplemented from ome::files::detail::FormatReader.

References ome::files::FormatHandler::assertId(), ome::files::detail::FormatReader::currentId, ome::files::detail::FormatReader::getCoreIndex(), and ome::files::detail::FormatReader::getCoreMetadata().

◆ getOptimalTileWidth()

dimension_size_type ome::files::in::OMETIFFReader::getOptimalTileWidth ( dimension_size_type channel ) const

virtual

Get the optimal sub-image width.

This is intended for use with openBytes().

Parameters

channel the channel to use, range [0, EffectiveSizeC).

Returns: the optimal width.

Reimplemented from ome::files::detail::FormatReader.

References ome::files::FormatHandler::assertId(), ome::files::detail::FormatReader::currentId, ome::files::detail::FormatReader::getCoreIndex(), and ome::files::detail::FormatReader::getCoreMetadata().

◆ getSeriesUsedFiles()

const std::vector< boost::filesystem::path > ome::files::in::OMETIFFReader::getSeriesUsedFiles ( bool noPixels ) const

virtual

Get the files used by the active series.

Parameters

noPixels exclude pixel data files if true, or include them if false.

Returns: a list of filenames.

Reimplemented from ome::files::detail::FormatReader.

References ome::files::FormatHandler::assertId(), ome::files::detail::FormatReader::currentId, ome::files::detail::FormatReader::getCoreIndex(), ome::files::detail::FormatReader::getCoreMetadata(), metadataFile, and ome::files::detail::FormatReader::plane.

◆ getTIFF()

const std::shared_ptr< const ome::files::tiff::TIFF > ome::files::in::OMETIFFReader::getTIFF ( const boost::filesystem::path & tiff ) const

protected

Get a an open TIFF file from the internal TIFF map.

If the file does not exist in the map, the file will be added to the internal map first. If the file is not currently open it will be opened.

Parameters

tiff	the TIFF file to get.

Returns: the open TIFF.

Exceptions

FormatException if invalid.

References logger, ome::files::tiff::TIFF::open(), and tiffs.

Referenced by ifdAtIndex(), initFile(), readMetadata(), and validTIFF().

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◆ getTiffDataValues()

bool ome::files::in::OMETIFFReader::getTiffDataValues	(	const ome::xml::meta::OMEXMLMetadata &	meta,
		ome::xml::meta::BaseMetadata::index_type	series,
		ome::xml::meta::BaseMetadata::index_type	tiffData,
		boost::optional< ome::xml::model::primitives::NonNegativeInteger > &	tdIFD,
		ome::xml::model::primitives::NonNegativeInteger &	numPlanes,
		ome::xml::model::primitives::NonNegativeInteger &	firstZ,
		ome::xml::model::primitives::NonNegativeInteger &	firstT,
		ome::xml::model::primitives::NonNegativeInteger &	firstC
	)

private

Get values from a TiffData element.

Parameters

meta	the metadata store to query.
series	the series to check.
tiffData	the TiffData index to check.
tdIFD	the starting IFD.
numPlanes	the number of planes.
firstZ	the first Z plane.
firstT	the first T plane.
firstC	the first C plane.

Returns: true if read successfully, false otherwise.

References ome::files::detail::FormatReader::core, ome::xml::meta::OMEXMLMetadata::getTiffDataFirstC(), ome::xml::meta::OMEXMLMetadata::getTiffDataFirstT(), ome::xml::meta::OMEXMLMetadata::getTiffDataFirstZ(), ome::xml::meta::OMEXMLMetadata::getTiffDataIFD(), and ome::xml::meta::OMEXMLMetadata::getTiffDataPlaneCount().

Referenced by initFile().

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◆ ifdAtIndex()

const std::shared_ptr< const tiff::IFD > ome::files::in::OMETIFFReader::ifdAtIndex ( dimension_size_type plane ) const

protected

Get the IFD index for a plane in the current series.

Parameters

plane the plane index within the series.

Returns: the IFD index.

Exceptions

FormatException if out of range.

References ome::files::detail::FormatReader::getCoreIndex(), ome::files::detail::FormatReader::getCoreMetadata(), getTIFF(), and ome::files::detail::FormatReader::plane.

Referenced by getLookupTable(), and openBytesImpl().

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◆ initFile()

void ome::files::in::OMETIFFReader::initFile ( const boost::filesystem::path & id )

virtual

Initialize the given file.

This will parse header information, etc. and is called by setId. Most subclasses should override this method to perform initialization operations such as parsing metadata.

Parameters

id	the filename to open.

Exceptions

FormatException if a parsing error occurs processing the file.

See also: ome::files::FormatHandler::setId.

Todo:: Log.

Reimplemented from ome::files::detail::FormatReader.

◆ isFilenameThisTypeImpl()

bool ome::files::in::OMETIFFReader::isFilenameThisTypeImpl ( const boost::filesystem::path & name ) const

protectedvirtual

isThisType file implementation for readers.

Readers which require opening a file in order to determine its type should override this method with their own implementation. Reader implementations should open the specified file using their preferred method and check its validity.

Parameters

name	the file to open for checking.

Returns: true if the file is valid, false otherwise.

Reimplemented from ome::files::detail::FormatReader.

References cacheMetadata(), ome::files::FormatHandler::checkSuffix(), ome::files::detail::FormatReader::getSuffixes(), ome::files::detail::FormatReader::isGroupFiles(), isSingleFile(), metadataFile, and ome::files::verifyMinimum().

◆ isSingleFile()

bool ome::files::in::OMETIFFReader::isSingleFile ( const boost::filesystem::path & id ) const

virtual

Is this a single-file format?

Parameters

id	filename to check.

Returns: true if this is a single-file format, false otherwise.

Exceptions

FormatException if there was a problem parsing the metadata of the file.

Reimplemented from ome::files::detail::FormatReader.

References cacheMetadata(), ome::files::FormatHandler::checkSuffix(), and ome::files::FormatReader::isSingleFile().

Referenced by fileGroupOption(), and isFilenameThisTypeImpl().

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◆ isThisType()

bool ome::files::in::OMETIFFReader::isThisType	(	const boost::filesystem::path &	name,
		bool	open
	)		const

virtual

Check if the given file is a valid instance of this file format.

Parameters

name	the file to open for checking.
open	If `true`, and the file extension is insufficient to determine the file type, the file may be opened for further analysis, or other relatively expensive file system operations (such as file existence tests and directory listings) may be performed. If `false`, file system access is not allowed.

Returns: true if the file is valid, false otherwise.

Todo:: Could this method be static?

Reimplemented from ome::files::detail::FormatReader.

References ome::files::FormatHandler::checkSuffix(), and ome::files::detail::FormatReader::isThisType().

◆ openBytesImpl()

void ome::files::in::OMETIFFReader::openBytesImpl	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf,
		dimension_size_type	x,
		dimension_size_type	y,
		dimension_size_type	w,
		dimension_size_type	h
	)		const

protectedvirtual

Obtain a sub-image of an image plane.

Obtain and copy the sub-image of an image plane from the current series into a VariantPixelBuffer of size

w * h * bytesPerPixel * getRGBChannelCount(channel)

Parameters

plane	the plane index within the series.
buf	the destination pixel buffer.
x	the `X` coordinate of the upper-left corner of the sub-image.
y	the `Y` coordinate of the upper-left corner of the sub-image.
w	the width of the sub-image.
h	the height of the sub-image.

Exceptions

FormatException if there was a problem parsing the metadata of the file.

Implements ome::files::detail::FormatReader.

References ome::files::FormatHandler::assertId(), ome::files::detail::FormatReader::currentId, and ifdAtIndex().

◆ readMetadata() [1/2]

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::in::OMETIFFReader::readMetadata ( const ome::files::tiff::TIFF & tiff )

protected

Read metadata into metadata store from an open TIFF.

Parameters

tiff	the TIFF from which to read the metadata.

Returns: the parsed metadata as a metadata store.

References ome::files::createOMEXMLMetadata().

Referenced by initFile().

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◆ readMetadata() [2/2]

std::shared_ptr<::ome::xml::meta::OMEXMLMetadata > ome::files::in::OMETIFFReader::readMetadata ( const boost::filesystem::path & id )

protected

Read metadata into metadata store from a TIFF or companion XML file.

Parameters

id	the file from which to read the metadata.

Returns: the parsed metadata as a metadata store.

References addTIFF(), ome::files::FormatHandler::checkSuffix(), ome::files::createOMEXMLMetadata(), and getTIFF().

◆ seriesFileSamplesPerPixel()

dimension_size_type ome::files::in::OMETIFFReader::seriesFileSamplesPerPixel	(	const ome::xml::meta::OMEXMLMetadata &	meta,
		ome::xml::meta::BaseMetadata::index_type	series
	)

private

Get the samples per pixel from the first IFD for a series.

Parameters

meta	the metadata store to query.
series	the series to check.

Returns: the samples per pixel.

◆ seriesIndexStart()

void ome::files::in::OMETIFFReader::seriesIndexStart	(	const ome::xml::meta::OMEXMLMetadata &	meta,
		ome::xml::meta::BaseMetadata::index_type	series,
		boost::optional< ome::xml::model::primitives::NonNegativeInteger > &	zIndexStart,
		boost::optional< ome::xml::model::primitives::NonNegativeInteger > &	tIndexStart,
		boost::optional< ome::xml::model::primitives::NonNegativeInteger > &	cIndexStart
	)

private

Get starting index for each dimension.

This is to cater for files which have been incorrectly written, where the starting index is not zero.

Parameters

meta	the metadata store to query.
series	the series to check.
zIndexStart	the Z starting index.
tIndexStart	the T starting index.
cIndexStart	the C starting index.

References ome::xml::meta::OMEXMLMetadata::getTiffDataCount(), ome::xml::meta::OMEXMLMetadata::getTiffDataFirstC(), and ome::xml::meta::OMEXMLMetadata::getTiffDataFirstT().

Referenced by initFile().

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◆ validTIFF()

bool ome::files::in::OMETIFFReader::validTIFF ( const boost::filesystem::path & tiff ) const

protected

Check if a cached TIFF is valid (can be opened).

Parameters

tiff	the TIFF file to get.

Returns: true if valid, false if invalid.

References getTIFF().

Referenced by initFile().

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

ome/files/in/OMETIFFReader.h
ome/files/in/OMETIFFReader.cpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ addTIFF()

◆ cacheMetadata()

◆ cleanMetadata()

◆ close()

◆ closeTIFF()

◆ fileGroupOption()

◆ findUsedFiles()

◆ fixDimensions()

◆ fixOMEROMetadata()

◆ getAcquisitionDates()

◆ getDomains()

◆ getLookupTable()

◆ getMetadataStoreForConversion()

◆ getMetadataStoreForDisplay()

◆ getOptimalTileHeight()

◆ getOptimalTileWidth()

◆ getSeriesUsedFiles()

◆ getTIFF()

◆ getTiffDataValues()

◆ ifdAtIndex()

◆ initFile()

◆ isFilenameThisTypeImpl()

◆ isSingleFile()

◆ isThisType()

◆ openBytesImpl()

◆ readMetadata() [1/2]

◆ readMetadata() [2/2]

◆ seriesFileSamplesPerPixel()

◆ seriesIndexStart()

◆ validTIFF()