Interface for all biological file format readers (default behaviour). More...

#include <ome/bioformats/detail/FormatReader.h>

Inheritance diagram for ome::bioformats::detail::FormatReader:

Collaboration diagram for ome::bioformats::detail::FormatReader:

Public Member Functions
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 boost::filesystem::path &name, bool open=true) const
	Check if the given file is a valid instance of this file format. 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...

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

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

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

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...

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

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

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

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

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

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

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

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

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::bioformats::FormatHandler
virtual	~FormatHandler ()
	Destructor.

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

Protected Types
typedef std::vector< ome::compat::shared_ptr< ::ome::bioformats::CoreMetadata > >	coremetadata_list_type
	List type for storing CoreMetadata.

Protected Member Functions
	FormatReader (const ReaderProperties &)
	Constructor.

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

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 ome::compat::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	isFilenameThisTypeImpl (const boost::filesystem::path &name) const
	isThisType file implementation for readers. More...

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

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

virtual 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 =0
	Obtain a sub-image of an image plane. More...

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

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

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

Protected Attributes
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.

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

::ome::bioformats::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.

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

MetadataOptions	metadataOptions
	Metadata parsing options.

Private Member Functions
	FormatReader (const FormatReader &)
	Copy constructor (deleted).

FormatReader &	operator= (const FormatReader &)
	Assignment operator (deleted).

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

Static Public Member Functions inherited from ome::bioformats::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

Interface for all biological file format readers (default behaviour).

Differences from the Java implementation:

MetadataMap methods replace the use of FormatReader add*Meta/get*Meta methods; the metadata objects themselves provide these methods.
flattenHashTables isn't implemented; MetadataMaps are self-flattening when streamed, and have a flatten method and visitors to generate a flat form.
No getRotationTransform; add to AffineTransform itself.

Member Function Documentation

void ome::bioformats::detail::FormatReader::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.

Implements ome::bioformats::FormatHandler.

Reimplemented in ome::bioformats::in::OMETIFFReader, ome::bioformats::in::MinimalTIFFReader, and ome::bioformats::in::TIFFReader.

References core, coreIndex, currentId, in, plane, resolution, and series.

Referenced by ome::bioformats::in::MinimalTIFFReader::close(), ome::bioformats::in::OMETIFFReader::close(), and initFile().

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dimension_size_type ome::bioformats::detail::FormatReader::coreIndexToSeries ( dimension_size_type index ) const

virtual

Get the series corresponding to the specified core index.

Parameters

index the core index to use.

Returns: the series for the index.

Implements ome::bioformats::FormatReader.

References core, coreIndex, hasFlattenedResolutions(), and series.

Referenced by getSeriesCount(), and setCoreIndex().

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FormatReader::FileGroupOption ome::bioformats::detail::FormatReader::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.

Implements ome::bioformats::FormatReader.

Reimplemented in ome::bioformats::in::OMETIFFReader.

References ome::bioformats::FormatReader::CANNOT_GROUP.

std::vector< FileInfo > ome::bioformats::detail::FormatReader::getAdvancedSeriesUsedFiles ( bool noPixels = false ) 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 FileInfo objects representing each used file.

Implements ome::bioformats::FormatReader.

References ome::common::canonical(), ome::bioformats::FileInfo::filename, getCurrentFile(), getFormat(), getSeriesUsedFiles(), ome::bioformats::FileInfo::reader, and ome::bioformats::FileInfo::usedToInitialize.

std::vector< FileInfo > ome::bioformats::detail::FormatReader::getAdvancedUsedFiles ( bool noPixels = false ) const

virtual

Get the files used by this dataset.

Parameters

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

Returns: a list of FileInfo objects representing each used file.

Implements ome::bioformats::FormatReader.

References ome::common::canonical(), ome::bioformats::FileInfo::filename, getCurrentFile(), getFormat(), getUsedFiles(), ome::bioformats::FileInfo::reader, and ome::bioformats::FileInfo::usedToInitialize.

pixel_size_type ome::bioformats::detail::FormatReader::getBitsPerPixel ( ) const

virtual

Get the number of valid bits per pixel.

The number of valid bits per pixel is always less than or equal to the number of bits per pixel that correspond to getPixelType().

Returns: the number of valid bits per pixel.

Todo:: : Move this logic into a CoreMetadata accessor. Why are we modifying coremetadata during an explicitly nonmodifying operation??

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), ome::bioformats::bitsPerPixel(), ome::bioformats::CoreMetadata::bitsPerPixel, currentId, getCoreIndex(), getCoreMetadata(), and getPixelType().

const std::vector< boost::filesystem::path > & ome::bioformats::detail::FormatReader::getCompressionSuffixes ( ) const

virtual

Get the default compression suffixes for this file format.

Returns: a list of file suffixes.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::detail::ReaderProperties::compression_suffixes, and readerProperties.

dimension_size_type ome::bioformats::detail::FormatReader::getCoreIndex ( ) const

virtual

Get the CoreMetadata index of the current resolution/series.

Returns: the index.

Implements ome::bioformats::FormatReader.

References coreIndex.

Referenced by getBitsPerPixel(), getDimensionOrder(), getEffectiveSizeC(), getImageCount(), getModuloC(), getModuloT(), getModuloZ(), ome::bioformats::in::OMETIFFReader::getOptimalTileHeight(), ome::bioformats::in::OMETIFFReader::getOptimalTileWidth(), getPixelType(), getRGBChannelCount(), getSeriesMetadata(), ome::bioformats::in::OMETIFFReader::getSeriesUsedFiles(), getSizeC(), getSizeT(), getSizeX(), getSizeY(), getSizeZ(), getThumbSize(), ome::bioformats::in::OMETIFFReader::ifdAtIndex(), isFalseColor(), isIndexed(), isInterleaved(), isLittleEndian(), isMetadataComplete(), isOrderCertain(), and isThumbnailSeries().

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const CoreMetadata& ome::bioformats::detail::FormatReader::getCoreMetadata ( dimension_size_type index ) const

inlineprotected

Get CoreMetadata by core index.

Parameters

index the core index.

Returns: the CoreMetadata.

Exceptions

std::range_error	if the core index is invalid.
std::logic_error	if the metadata is null.

Referenced by getBitsPerPixel(), getDimensionOrder(), getEffectiveSizeC(), getImageCount(), getModuloC(), getModuloT(), getModuloZ(), ome::bioformats::in::OMETIFFReader::getOptimalTileHeight(), ome::bioformats::in::OMETIFFReader::getOptimalTileWidth(), getPixelType(), getRGBChannelCount(), getSeriesMetadata(), ome::bioformats::in::OMETIFFReader::getSeriesUsedFiles(), getSizeC(), getSizeT(), getSizeX(), getSizeY(), getSizeZ(), getThumbSize(), ome::bioformats::in::OMETIFFReader::ifdAtIndex(), isFalseColor(), isIndexed(), isInterleaved(), isLittleEndian(), isMetadataComplete(), isOrderCertain(), and isThumbnailSeries().

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CoreMetadata& ome::bioformats::detail::FormatReader::getCoreMetadata ( dimension_size_type index )

inlineprotected

Get CoreMetadata by core index.

Parameters

index the core index.

Returns: the CoreMetadata.

Exceptions

std::range_error	if the core index is invalid.
std::logic_error	if the metadata is null.

const std::vector< ome::compat::shared_ptr<::ome::bioformats::CoreMetadata > > & ome::bioformats::detail::FormatReader::getCoreMetadataList ( ) const

virtual

Get the core metadata.

A CoreMetadata object exists to describe the each series in the dataset.

Returns: a const reference to the core metadata.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), core, and currentId.

const boost::optional< boost::filesystem::path > & ome::bioformats::detail::FormatReader::getCurrentFile ( ) const

virtual

Get the currently open file.

Returns: the filename.

Implements ome::bioformats::FormatReader.

References currentId.

Referenced by getAdvancedSeriesUsedFiles(), and getAdvancedUsedFiles().

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const std::string & ome::bioformats::detail::FormatReader::getDatasetStructureDescription ( ) const

virtual

Get a short description of the dataset structure.

Returns: a short description.

Implements ome::bioformats::FormatReader.

References datasetDescription.

const std::string & ome::bioformats::detail::FormatReader::getDimensionOrder ( ) const

virtual

Get the dimension order.

The dimension order is a five-character string representing the order in which planes will be returned. Valid orders are:

XYCTZ
XYCZT
XYTCZ
XYTZC
XYZCT
XYZTC

In cases where the channels are interleaved (e.g. CXYTZ), C will be the first dimension after X and Y (e.g. XYCTZ) and the isInterleaved() method will return true.

Returns: the dimension order.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, ome::bioformats::CoreMetadata::dimensionOrder, getCoreIndex(), and getCoreMetadata().

Referenced by getIndex(), getZCTCoords(), getZCTModuloCoords(), and readPlane().

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const std::vector< std::string > & ome::bioformats::detail::FormatReader::getDomains ( ) const

virtual

Get the domains represented by the current file.

Returns: a list of domains.

Implements ome::bioformats::FormatReader.

Reimplemented in ome::bioformats::in::OMETIFFReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and domains.

dimension_size_type ome::bioformats::detail::FormatReader::getEffectiveSizeC ( ) const

virtual

Get the effective size of the C dimension.

This guarantees that

getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount()

regardless of the result of isRGB().

Returns: the effective C dimension size.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::sizeC.

Referenced by getIndex(), getOptimalTileHeight(), getOptimalTileWidth(), getZCTCoords(), and getZCTModuloCoords().

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const std::string & ome::bioformats::detail::FormatReader::getFormat ( ) const

virtual

Get the name of this file format.

Returns: the file format name.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::detail::ReaderProperties::name, and readerProperties.

Referenced by getAdvancedSeriesUsedFiles(), and getAdvancedUsedFiles().

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const std::string & ome::bioformats::detail::FormatReader::getFormatDescription ( ) const

virtual

Get the description of this file format.

Returns: the file format description.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::detail::ReaderProperties::description, and readerProperties.

const MetadataMap & ome::bioformats::detail::FormatReader::getGlobalMetadata ( ) const

virtual

Get global metadata map.

Obtain the map containing the global metadata field/value pairs the current dataset.

Returns: the global metadata map.

Implements ome::bioformats::FormatReader.

References metadata.

dimension_size_type ome::bioformats::detail::FormatReader::getImageCount ( ) const

virtual

Determine the number of image planes in the current series.

Returns: the number of image planes.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::imageCount.

Referenced by getIndex(), getZCTCoords(), getZCTModuloCoords(), ome::bioformats::in::OMETIFFReader::initFile(), and setPlane().

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dimension_size_type ome::bioformats::detail::FormatReader::getIndex	(	dimension_size_type	z,
		dimension_size_type	c,
		dimension_size_type	t
	)		const

virtual

Get the linear index of a Z, C and T coordinate.

The index is computed using the DimensionOrder.

Parameters

z	the `Z` coordinate (real size).
c	the `C` coordinate (real size).
t	the `T` coordinate (real size).

Returns: the linear index.

Todo:

unify with the pixel buffer dimension indexes.

Don't use separate values to match the return of getZCTCoords.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getDimensionOrder(), getEffectiveSizeC(), getImageCount(), ome::bioformats::getIndex(), getSizeT(), and getSizeZ().

dimension_size_type ome::bioformats::detail::FormatReader::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

virtual

Get the linear index of a Z, C, T, ModuloZ, ModuloC and ModuloT coordinate.

The index is computed using the DimensionOrder.

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

z	the `Z` coordinate (effective size).
c	the `C` coordinate (effective size).
t	the `T` coordinate (effective size).
moduloZ	the `ModuloZ` coordinate (effective size).
moduloC	the `ModuloC` coordinate (effective size).
moduloT	the `ModuloT` coordinate (effective size).

Returns: the linear index.

Todo:

unify with the pixel buffer dimension indexes.

Don't use separate values to match the return of getZCTModuloCoords.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getDimensionOrder(), getEffectiveSizeC(), getImageCount(), ome::bioformats::getIndex(), getModuloC(), getModuloT(), getModuloZ(), getSizeT(), and getSizeZ().

void ome::bioformats::detail::FormatReader::getLookupTable	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf
	)		const

virtual

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.

Implements ome::bioformats::FormatReader.

Reimplemented in ome::bioformats::in::OMETIFFReader, and ome::bioformats::in::MinimalTIFFReader.

References ome::bioformats::FormatHandler::assertId(), and currentId.

const MetadataOptions & ome::bioformats::detail::FormatReader::getMetadataOptions ( ) const

virtual

Get metadata options.

Returns: the current options.

Implements ome::bioformats::MetadataConfigurable.

References metadataOptions.

MetadataOptions & ome::bioformats::detail::FormatReader::getMetadataOptions ( )

virtual

Get metadata options.

Returns: the current options.

Implements ome::bioformats::MetadataConfigurable.

References metadataOptions.

const ome::compat::shared_ptr<::ome::xml::meta::MetadataStore > & ome::bioformats::detail::FormatReader::getMetadataStore ( ) const

virtual

Get the current metadata store for this reader.

Returns: the metadata store, which will never be null.

Implements ome::bioformats::FormatReader.

References metadataStore.

Referenced by ome::bioformats::in::OMETIFFReader::getMetadataStoreForConversion(), ome::bioformats::in::OMETIFFReader::getMetadataStoreForDisplay(), ome::bioformats::in::MinimalTIFFReader::initFile(), initFile(), makeFilterMetadata(), and setId().

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ome::compat::shared_ptr<::ome::xml::meta::MetadataStore > & ome::bioformats::detail::FormatReader::getMetadataStore ( )

virtual

Get the current metadata store for this reader.

Returns: the metadata store, which will never be null.

Implements ome::bioformats::FormatReader.

References metadataStore.

const MetadataMap::value_type & ome::bioformats::detail::FormatReader::getMetadataValue ( const std::string & field ) const

virtual

Get a global metadata value.

Obtain the specified metadata field's value for the current dataset.

Parameters

field the name associated with the metadata field.

Returns: the value.

Exceptions

boost::bad_get on failure if the key was not found.

Implements ome::bioformats::FormatReader.

References ome::bioformats::MetadataMap::get(), and metadata.

Modulo & ome::bioformats::detail::FormatReader::getModuloC ( )

virtual

Get the Modulo subdivision of the C dimension.

Returns: the Modulo defining the C dimension subdivision.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::moduloC.

Referenced by getIndex(), getZCTModuloCoords(), and setId().

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const Modulo & ome::bioformats::detail::FormatReader::getModuloC ( ) const

virtual

Get the Modulo subdivision of the C dimension.

Returns: the Modulo defining the C dimension subdivision.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::moduloC.

Modulo & ome::bioformats::detail::FormatReader::getModuloT ( )

virtual

Get the Modulo subdivision of the T dimension.

Returns: the Modulo defining the T dimension subdivision.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::moduloT.

Referenced by getIndex(), getZCTModuloCoords(), and setId().

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const Modulo & ome::bioformats::detail::FormatReader::getModuloT ( ) const

virtual

Get the Modulo subdivision of the T dimension.

Returns: the Modulo defining the T dimension subdivision.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::moduloT.

Modulo & ome::bioformats::detail::FormatReader::getModuloZ ( )

virtual

Get the Modulo subdivision of the Z dimension.

Returns: the Modulo defining the Z dimension subdivision.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::moduloZ.

Referenced by getIndex(), getZCTModuloCoords(), and setId().

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const Modulo & ome::bioformats::detail::FormatReader::getModuloZ ( ) const

virtual

Get the Modulo subdivision of the Z dimension.

Returns: the Modulo defining the Z dimension subdivision.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::moduloZ.

dimension_size_type ome::bioformats::detail::FormatReader::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.

Implements ome::bioformats::FormatReader.

Reimplemented in ome::bioformats::in::OMETIFFReader.

References ome::bioformats::FormatHandler::assertId(), ome::bioformats::bytesPerPixel(), currentId, getPixelType(), getRGBChannelCount(), getSizeX(), and getSizeY().

dimension_size_type ome::bioformats::detail::FormatReader::getOptimalTileHeight ( ) const

virtual

Get the optimal sub-image height.

This is intended for use with openBytes(). Note that this overload does not have a channel argument, and so the value returned is the smallest height for all channels for convienience and compatibility with the Java implementation. If the optimal height varies widely between channels, this may result in suboptimal performance; specify the channel to get the optimal height for each channel.

Returns: the optimal height.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and getEffectiveSizeC().

dimension_size_type ome::bioformats::detail::FormatReader::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.

Implements ome::bioformats::FormatReader.

Reimplemented in ome::bioformats::in::OMETIFFReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and getSizeX().

dimension_size_type ome::bioformats::detail::FormatReader::getOptimalTileWidth ( ) const

virtual

Get the optimal sub-image width.

This is intended for use with openBytes(). Note that this overload does not have a channel argument, and so the value returned is the smallest width for all channels for convienience and compatibility with the Java implementation. If the optimal width varies widely between channels, this may result in suboptimal performance; specify the channel to get the optimal width for each channel.

Returns: the optimal width.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and getEffectiveSizeC().

ome::xml::model::enums::PixelType ome::bioformats::detail::FormatReader::getPixelType ( ) const

virtual

Get the pixel type.

Returns: the pixel type.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::pixelType.

Referenced by getBitsPerPixel(), getOptimalTileHeight(), and readPlane().

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dimension_size_type ome::bioformats::detail::FormatReader::getPlane ( ) const

virtual

Get the active plane.

Returns: the active plane.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and plane.

const std::vector< std::string > & ome::bioformats::detail::FormatReader::getPossibleDomains ( const std::string & id ) const

virtual

Get the possible domains represented in which this format is used.

Parameters

id	filename to check.

Returns: a list of domains.

Exceptions

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

Todo:: can this be a reference to static data?

Implements ome::bioformats::FormatReader.

References domains.

uint32_t ome::bioformats::detail::FormatReader::getRequiredDirectories ( const std::vector< std::string > & files ) const

virtual

Get required parent directories.

Get the number of parent directories that are important when processing the given list of files. The number of directories is relative to the common parent. For example, given a list with these two files:

/path/to/file/foo
/path/to/file/that/is/related

A return value of 0 indicates that /path/to/file/ is irrelevant. A return value of 1 indicates that /path/to/ is irrelevant. Return values less than 0 are invalid.

All listed files are assumed to belong to datasets of the same format.

Parameters

files the file list being processed.

Returns: the number of important parent directories for the file list.

Exceptions

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

Todo:: This could use a much better explanation, it's not at all clear what the return value means. Is it an index into files? Is it an index into the path components? Of which of the files? In which order? From the root or common parent? Is the order of files important?

Implements ome::bioformats::FormatReader.

dimension_size_type ome::bioformats::detail::FormatReader::getResolution ( ) const

virtual

Get the active resolution level.

Returns: the resolution level.

See also: getResolutionCount()

Implements ome::bioformats::FormatReader.

References resolution.

dimension_size_type ome::bioformats::detail::FormatReader::getResolutionCount ( ) const

virtual

Get the number of resolutions for the current series.

Resolutions are stored in descending order of size, so the largest resolution is first and the smallest resolution is last.

Returns: the number of resolutions.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), core, currentId, getSeries(), hasFlattenedResolutions(), and seriesToCoreIndex().

Referenced by setResolution().

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dimension_size_type ome::bioformats::detail::FormatReader::getRGBChannelCount ( dimension_size_type channel ) const

virtual

Get the number of channels returned for a call to openBytes().

The most common case where this value is greater than 1 is for interleaved RGB data, such as a 24-bit color image plane. However, it is possible for this value to be greater than 1 for non-interleaved data, such as an RGB TIFF with Planar rather than Chunky configuration.

Parameters

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

Returns: the number of channels.

Implements ome::bioformats::FormatReader.

References getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::sizeC.

Referenced by getOptimalTileHeight(), and isRGB().

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dimension_size_type ome::bioformats::detail::FormatReader::getSeries ( ) const

virtual

Get the active series.

Returns: the active series.

Implements ome::bioformats::FormatReader.

References series.

Referenced by getResolutionCount(), ome::bioformats::in::MinimalTIFFReader::ifdAtIndex(), and setResolution().

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dimension_size_type ome::bioformats::detail::FormatReader::getSeriesCount ( ) const

virtual

Get the number of image series in this file.

Returns: the number of image series.

Exceptions

std::logic_error if the sub-resolution metadata (if any) is invalid; this will only occur if the reader sets invalid metadata.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), core, coreIndexToSeries(), currentId, and hasFlattenedResolutions().

Referenced by ome::bioformats::in::OMETIFFReader::getMetadataStoreForConversion(), ome::bioformats::in::OMETIFFReader::getMetadataStoreForDisplay(), getUsedFiles(), and setId().

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const MetadataMap & ome::bioformats::detail::FormatReader::getSeriesMetadata ( ) const

virtual

Get series metadata map.

Obtain the map containing the series metadata field/value pairs the active series in the current dataset.

Returns: the series metadata map.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::seriesMetadata.

Referenced by getSeriesMetadataValue(), and setId().

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const MetadataMap::value_type & ome::bioformats::detail::FormatReader::getSeriesMetadataValue ( const MetadataMap::key_type & field ) const

virtual

Get a series metadata value.

Obtain the specified metadata field's value for the active series in the current dataset.

Parameters

field the name associated with the metadata field.

Returns: the value.

Exceptions

boost::bad_get on failure if the key was not found.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, ome::bioformats::MetadataMap::get(), and getSeriesMetadata().

const std::vector< boost::filesystem::path > ome::bioformats::detail::FormatReader::getSeriesUsedFiles ( bool noPixels = false ) 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.

Implements ome::bioformats::FormatReader.

Reimplemented in ome::bioformats::in::OMETIFFReader.

References currentId.

Referenced by getAdvancedSeriesUsedFiles(), and getUsedFiles().

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dimension_size_type ome::bioformats::detail::FormatReader::getSizeC ( ) const

virtual

Get the size of the C dimension.

Returns: the C dimension size.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), and getCoreMetadata().

dimension_size_type ome::bioformats::detail::FormatReader::getSizeT ( ) const

virtual

Get the size of the T dimension.

Returns: the T dimension size.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::sizeT.

Referenced by getIndex(), getZCTCoords(), and getZCTModuloCoords().

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dimension_size_type ome::bioformats::detail::FormatReader::getSizeX ( ) const

virtual

Get the size of the X dimension.

Returns: the X dimension size.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::sizeX.

Referenced by getOptimalTileHeight(), getOptimalTileWidth(), getThumbSize(), and openBytes().

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dimension_size_type ome::bioformats::detail::FormatReader::getSizeY ( ) const

virtual

Get the size of the Y dimension.

Returns: the Y dimension size.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::sizeY.

Referenced by getOptimalTileHeight(), getThumbSize(), and openBytes().

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dimension_size_type ome::bioformats::detail::FormatReader::getSizeZ ( ) const

virtual

Get the size of the Z dimension.

Returns: the Z dimension size.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::sizeZ.

Referenced by getIndex(), getZCTCoords(), and getZCTModuloCoords().

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const std::vector< boost::filesystem::path > & ome::bioformats::detail::FormatReader::getSuffixes ( ) const

virtual

Get the default file suffixes for this file format.

Returns: a list of file suffixes.

Implements ome::bioformats::FormatHandler.

References readerProperties, and ome::bioformats::detail::ReaderProperties::suffixes.

const std::set< MetadataOptions::MetadataLevel > & ome::bioformats::detail::FormatReader::getSupportedMetadataLevels ( )

virtual

Get the supported metadata levels.

Returns: a set of supported metadata levels.

Implements ome::bioformats::MetadataConfigurable.

References ome::bioformats::detail::ReaderProperties::metadata_levels, and readerProperties.

ome::compat::array< dimension_size_type, 2 > ome::bioformats::detail::FormatReader::getThumbSize ( ) const

protected

Get the thumbnail size of the X and Y dimensions.

Returns: an array containing the X and Y dimension thumbnail size (in that order).

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), getSizeX(), getSizeY(), ome::bioformats::CoreMetadata::thumbSizeX, and ome::bioformats::CoreMetadata::thumbSizeY.

Referenced by getThumbSizeX(), and getThumbSizeY().

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dimension_size_type ome::bioformats::detail::FormatReader::getThumbSizeX ( ) const

virtual

Get the thumbnail size of the X dimension.

Returns: the X dimension thumbnail size.

Implements ome::bioformats::FormatReader.

References getThumbSize().

dimension_size_type ome::bioformats::detail::FormatReader::getThumbSizeY ( ) const

virtual

Get the thumbnail size of the Y dimension.

Returns: the Y dimension thumbnail size.

Implements ome::bioformats::FormatReader.

References getThumbSize().

std::vector< ome::compat::shared_ptr<::ome::bioformats::FormatReader > > ome::bioformats::detail::FormatReader::getUnderlyingReaders ( ) const

virtual

Get all underlying readers.

Note: If there are no underlying readers, the list will be empty.

Returns: a list of readers.

Implements ome::bioformats::FormatReader.

const std::vector< boost::filesystem::path > ome::bioformats::detail::FormatReader::getUsedFiles ( bool noPixels = false ) const

virtual

Get the files used by this dataset.

Parameters

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

Returns: a list of filenames.

Implements ome::bioformats::FormatReader.

References getSeriesCount(), getSeriesUsedFiles(), and setSeries().

Referenced by getAdvancedUsedFiles(), initFile(), and isUsedFile().

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ome::compat::array< dimension_size_type, 3 > ome::bioformats::detail::FormatReader::getZCTCoords ( dimension_size_type index ) const

virtual

Get the Z, C and T coordinate of a linear index.

Parameters

index the linear index.

Returns: an array containing Z, C and T values (real sizes).

Todo:: unify with the pixel buffer dimension indexes.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getDimensionOrder(), getEffectiveSizeC(), getImageCount(), getSizeT(), getSizeZ(), and ome::bioformats::getZCTCoords().

ome::compat::array< dimension_size_type, 6 > ome::bioformats::detail::FormatReader::getZCTModuloCoords ( dimension_size_type index ) const

virtual

Get the Z, C, T, ModuloZ, ModuloC and ModuloT coordinate of a linear index.

Note: The Z, C and T coordinates are not the same as those returned by getZCTCoords(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

index the linear index.

Returns: an array containing Z, C, T, ModuloZ, ModuloC and ModuloT values (effective sizes).

Todo:: unify with the pixel buffer dimension indexes.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getDimensionOrder(), getEffectiveSizeC(), getImageCount(), getModuloC(), getModuloT(), getModuloZ(), getSizeT(), getSizeZ(), and ome::bioformats::getZCTCoords().

bool ome::bioformats::detail::FormatReader::hasCompanionFiles ( ) const

virtual

Does this format support multi-file datasets?

Returns: true if multiple files are supported, false otherwise.

Implements ome::bioformats::FormatReader.

References companionFiles.

bool ome::bioformats::detail::FormatReader::hasFlattenedResolutions ( ) const

virtual

Get resolution flattening.

Returns: true if flattening is enabled, false otherwise.

Implements ome::bioformats::FormatReader.

References flattenedResolutions.

Referenced by coreIndexToSeries(), getResolutionCount(), getSeriesCount(), and seriesToCoreIndex().

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void ome::bioformats::detail::FormatReader::initFile ( const boost::filesystem::path & id )

protectedvirtual

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::bioformats::FormatHandler::setId.

Reimplemented in ome::bioformats::in::OMETIFFReader, and ome::bioformats::in::MinimalTIFFReader.

References ome::bioformats::MetadataMap::clear(), close(), core, coreIndex, currentId, getMetadataStore(), getUsedFiles(), metadata, and series.

Referenced by ome::bioformats::in::MinimalTIFFReader::initFile(), ome::bioformats::in::OMETIFFReader::initFile(), and setId().

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bool ome::bioformats::detail::FormatReader::isFalseColor ( ) const

virtual

Get whether the image planes are false color.

This will be false if isIndexed() is false, or if isIndexed() is true and the lookup table represents "real" color data. This will be true if isIndexed() is true and the lookup table is only present to aid in visualization.

Returns: true if false color, false otherwise.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, ome::bioformats::CoreMetadata::falseColor, getCoreIndex(), and getCoreMetadata().

bool ome::bioformats::detail::FormatReader::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 in ome::bioformats::in::OMETIFFReader, and ome::bioformats::in::MinimalTIFFReader.

Referenced by isThisType().

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bool ome::bioformats::detail::FormatReader::isGroupFiles ( ) const

virtual

Get file grouping.

Returns: true if grouping is enabled, false otherwise.

Implements ome::bioformats::FormatReader.

References group.

bool ome::bioformats::detail::FormatReader::isIndexed ( ) const

virtual

Get whether the image planes are indexed color.

This value does not affect getSizeC(), getEffectiveSizeC() or getRGBChannelCount().

Returns: true if indexed, false otherwise.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::indexed.

bool ome::bioformats::detail::FormatReader::isInterleaved ( ) const

virtual

Get whether or not the channels are interleaved.

This method exists because X and Y must appear first in the dimension order. For interleaved data, getDimensionOrder() returns XYCTZ or XYCZT and this method returns true.

Note that this flag returns whether or not the data returned by openBytes() is interleaved. In most cases, this will match the interleaving in the original file, but for some formats (e.g. TIFF) channel re-ordering is done internally and the return value of this method will not match what is in the original file.

Returns: true if the channels are interleaved, false otherwise.

Implements ome::bioformats::FormatReader.

Referenced by readPlane().

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bool ome::bioformats::detail::FormatReader::isInterleaved ( dimension_size_type channel ) const

virtual

Get whether or not the given channel is interleaved.

Some data with multiple channels within C have the sub-channels of one sub-dimension interleaved, and the other not. For example, SDTReader handles spectral-lifetime data with interleaved lifetime bins and non-interleaved spectral channels.

Parameters

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

Returns: true if the sub-channel is interleaved, false otherwise.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::interleaved.

bool ome::bioformats::detail::FormatReader::isLittleEndian ( ) const

virtual

Get whether the data is in little-endian format.

Returns: false if big endian, true if little endian.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::littleEndian.

Referenced by ome::bioformats::in::OMETIFFReader::getMetadataStoreForConversion().

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bool ome::bioformats::detail::FormatReader::isMetadataComplete ( ) const

virtual

Get status of metadata parsing.

Returns: true if this format's metadata is completely parsed, false otherwise.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::metadataComplete.

bool ome::bioformats::detail::FormatReader::isMetadataFiltered ( ) const

virtual

Get metadata filtering.

Returns: true if metadata filtering is enabled, false if disabled.

Implements ome::bioformats::FormatReader.

References filterMetadata.

Referenced by makeFilterMetadata().

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bool ome::bioformats::detail::FormatReader::isNormalized ( ) const

virtual

Get float normalization.

Returns: true if float normalization is enabled, false otherwise.

Implements ome::bioformats::FormatReader.

References normalizeData.

bool ome::bioformats::detail::FormatReader::isOrderCertain ( ) const

virtual

Get whether the dimension order and sizes are known, or merely guesses.

Returns: true if the order is known, false otherwise.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::orderCertain.

bool ome::bioformats::detail::FormatReader::isOriginalMetadataPopulated ( ) const

virtual

Get proprietary metadata storage.

Returns: true if proprietary metadata is saved in the MetadataStore, false otherwise.

Todo:: The name of this method is awful.

Implements ome::bioformats::FormatReader.

References saveOriginalMetadata.

bool ome::bioformats::detail::FormatReader::isRGB ( dimension_size_type channel ) const

virtual

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

Parameters

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

Returns: true if and only if getRGBChannelCount() returns a value greater than 1, false otherwise.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and getRGBChannelCount().

bool ome::bioformats::detail::FormatReader::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.

Implements ome::bioformats::FormatReader.

Reimplemented in ome::bioformats::in::OMETIFFReader.

bool ome::bioformats::detail::FormatReader::isStreamThisTypeImpl ( std::istream & stream ) const

protectedvirtual

isThisType stream implementation for readers.

Readers which require opening a file in order to determine its type, and which can handle istream data, should override this method with their own implementation. Reader implementations should check the validity of the stream data.

Parameters

stream the input stream to check.

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

Referenced by isThisType().

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bool ome::bioformats::detail::FormatReader::isThisType	(	const boost::filesystem::path &	name,
		bool	open = `true`
	)		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?

Implements ome::bioformats::FormatHandler.

Reimplemented in ome::bioformats::in::OMETIFFReader.

References ome::bioformats::FormatHandler::checkSuffix(), ome::bioformats::detail::ReaderProperties::compression_suffixes, isFilenameThisTypeImpl(), readerProperties, ome::bioformats::detail::ReaderProperties::suffixes, suffixNecessary, and suffixSufficient.

Referenced by ome::bioformats::in::OMETIFFReader::isThisType(), and isThisType().

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bool ome::bioformats::detail::FormatReader::isThisType	(	const uint8_t *	begin,
		std::size_t	length
	)		const

virtual

Check if the given buffer is a valid header for this file format.

The buffer is defined as a half-open range using two iterators.

Parameters

begin	the start of the buffer.
length	the buffer length.

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

Todo:: Could this method be static and/or const?

Implements ome::bioformats::FormatReader.

References isThisType().

bool ome::bioformats::detail::FormatReader::isThisType	(	const uint8_t *	begin,
		const uint8_t *	end
	)		const

virtual

Check if the given buffer is a valid header for this file format.

The buffer is defined as a half-open range using two iterators.

Parameters

begin	the start of the buffer.
end	one past the end of the buffer.

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

Todo:: Could this method be static and/or const?

Implements ome::bioformats::FormatReader.

References isThisType().

bool ome::bioformats::detail::FormatReader::isThisType ( std::istream & stream ) const

virtual

Check if the given input stream is a valid stream for this file format.

Parameters

stream the input stream to check.

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

Todo:: Could this method be static and/or const?

Implements ome::bioformats::FormatReader.

References isStreamThisTypeImpl().

bool ome::bioformats::detail::FormatReader::isThumbnailSeries ( ) const

virtual

Get whether the current series is a lower resolution copy of a different series.

Returns: true if a low resolution copy, false otherwise.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, getCoreIndex(), getCoreMetadata(), and ome::bioformats::CoreMetadata::thumbnail.

bool ome::bioformats::detail::FormatReader::isUsedFile ( const boost::filesystem::path & file )

protectedvirtual

Check if a file is in the used files list.

Parameters

file	the file to check.

Returns: true if the file is used, false if not used.

Todo:: : Use a set rather than a list?

References ome::common::canonical(), and getUsedFiles().

ome::compat::shared_ptr<::ome::xml::meta::MetadataStore > ome::bioformats::detail::FormatReader::makeFilterMetadata ( )

protectedvirtual

Create a configured FilterMetadata instance.

This creates, configures and returns an instance of ome::xml::meta::FilterMetadata.

Returns: a FilterMetadata instance.

References getMetadataStore(), and isMetadataFiltered().

void ome::bioformats::detail::FormatReader::openBytes	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf
	)		const

virtual

Obtain an image plane.

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

getSizeX * getSizeY * bytesPerPixel * getRGBChannelCount(channel)

Parameters

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

Exceptions

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

Implements ome::bioformats::FormatReader.

References getSizeX(), and getSizeY().

void ome::bioformats::detail::FormatReader::openBytes	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf,
		dimension_size_type	x,
		dimension_size_type	y,
		dimension_size_type	w,
		dimension_size_type	h
	)		const

virtual

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::bioformats::FormatReader.

References openBytesImpl(), and setPlane().

virtual void ome::bioformats::detail::FormatReader::openBytesImpl	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf,
		dimension_size_type	x,
		dimension_size_type	y,
		dimension_size_type	w,
		dimension_size_type	h
	)		const

protectedpure virtual

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.

Implemented in ome::bioformats::in::OMETIFFReader, and ome::bioformats::in::MinimalTIFFReader.

Referenced by openBytes().

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void ome::bioformats::detail::FormatReader::openThumbBytes	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf
	)		const

virtual

Obtain a thumbnail of an image plane.

Obtail and copy the thumbnail for the specified image plane from the current series into a VariantPixelBuffer.

Parameters

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

Todo:: Implement openThumbBytes. This requires implementing image rescaling/resampling.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), and currentId.

void ome::bioformats::detail::FormatReader::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
	)

protectedvirtual

Read a raw plane.

Note that the pixel buffer must be of the correct size to store the pixel data.

Parameters

source	the stream to read the plane from.
dest	the pixel buffer in which to store the plane.
x	the left edge of the plane.
y	the top edge of the plane.
w	the width of the plane.
h	the height of the plane.
samples	the number of samples per pixel.

void ome::bioformats::detail::FormatReader::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
	)

protectedvirtual

Read a raw plane with scanline padding.

Note that the pixel buffer must be of the correct size to store the pixel data.

Parameters

source	the stream to read the plane from.
dest	the pixel buffer in which to store the plane.
x	the left edge of the plane.
y	the top edge of the plane.
w	the width of the plane.
h	the height of the plane.
scanlinePad	the scanline padding.
samples	the number of samples per pixel.

dimension_size_type ome::bioformats::detail::FormatReader::seriesToCoreIndex ( dimension_size_type series ) const

virtual

Get the first core index corresponding to the specified series.

Parameters

series the series to use.

Returns: the first for index for the series.

Implements ome::bioformats::FormatReader.

References core, coreIndex, hasFlattenedResolutions(), resolution, and series.

Referenced by getResolutionCount(), setCoreIndex(), setResolution(), and setSeries().

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void ome::bioformats::detail::FormatReader::setCoreIndex ( dimension_size_type index ) const

virtual

Set the current resolution/series (ignoring sub-resolutions).

Equivalent to setSeries(), but with flattened resolutions always set to false.

Parameters

index the core index to set.

Todo:: Remove use of stateful API which requires use of series switching in const methods.

Exceptions

std::logic_error if the index is invalid.

Implements ome::bioformats::FormatReader.

References core, coreIndex, coreIndexToSeries(), plane, resolution, series, and seriesToCoreIndex().

void ome::bioformats::detail::FormatReader::setFlattenedResolutions ( bool flatten )

virtual

Set resolution flattening.

This controls whether or not resolution levels are flattened into individual series. This alters the behaviour of setSeries() and getSeries() but does not affect the behaviour of setCoreIndex() and getCoreIndex(), which are resolution-independent.

Parameters

flatten true to enable flattening, false to disable.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and flattenedResolutions.

void ome::bioformats::detail::FormatReader::setGroupFiles ( bool group )

virtual

Set file grouping.

This specifies whether or not to force grouping in multi-file formats.

Parameters

group true to enable grouping, false to disable.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and group.

void ome::bioformats::detail::FormatReader::setId ( const boost::filesystem::path & id )

virtual

Set the current file name.

Note this will throw FormatException if there are problems opening the file.

Parameters

id	the filename to open.

Todo:: Implement addModuloAlong. Requires bits of MetadataTools OMEXMLServiceImpl.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::MetadataMap::begin(), ome::common::canonical(), currentId, ome::bioformats::MetadataMap::end(), ome::bioformats::fillOriginalMetadata(), getMetadataStore(), getModuloC(), getModuloT(), getModuloZ(), getSeriesCount(), getSeriesMetadata(), initFile(), metadata, saveOriginalMetadata, series, ome::bioformats::MetadataMap::set(), setSeries(), and ome::common::trim().

void ome::bioformats::detail::FormatReader::setMetadataFiltered ( bool filter )

virtual

Set metadata filtering.

If filtering is enabled, "ugly" metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.

Parameters

filter true to enable filtering, false to disable.

Implements ome::bioformats::FormatReader.

References ome::bioformats::FormatHandler::assertId(), currentId, and filterMetadata.

void ome::bioformats::detail::FormatReader::setMetadataOptions ( const MetadataOptions & options )

virtual

Set metadata options.

Parameters

options the options to set.

Implements ome::bioformats::MetadataConfigurable.

References metadataOptions.

void ome::bioformats::detail::FormatReader::setMetadataStore ( ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > & store )