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

#include <ome/bioformats/FormatReader.h>

Inheritance diagram for ome::bioformats::FormatReader:

Collaboration diagram for ome::bioformats::FormatReader:

Classes
class	SaveSeries
	Sentry for saving and restoring reader series state. More...

Public Types
enum	FileGroupOption { MUST_GROUP, CAN_GROUP, CANNOT_GROUP }
	File grouping options. More...

Public Member Functions
virtual	~FormatReader ()
	Destructor.

virtual bool	isThisType (const boost::filesystem::path &name, bool open=true) const =0
	Check if the given file is a valid instance of this file format. More...

virtual bool	isThisType (const uint8_t begin, const uint8_t end) const =0
	Check if the given buffer is a valid header for this file format. More...

virtual bool	isThisType (const uint8_t *begin, std::size_t length) const =0
	Check if the given buffer is a valid header for this file format. More...

virtual bool	isThisType (std::istream &stream) const =0
	Check if the given input stream is a valid stream for this file format. More...

virtual dimension_size_type	getImageCount () const =0
	Determine the number of image planes in the current series. More...

virtual bool	isRGB (dimension_size_type channel) const =0
	Check if the image planes for a channel have more than one sub-channel per openBytes() call. More...

virtual dimension_size_type	getSizeX () const =0
	Get the size of the X dimension. More...

virtual dimension_size_type	getSizeY () const =0
	Get the size of the Y dimension. More...

virtual dimension_size_type	getSizeZ () const =0
	Get the size of the Z dimension. More...

virtual dimension_size_type	getSizeT () const =0
	Get the size of the T dimension. More...

virtual dimension_size_type	getSizeC () const =0
	Get the size of the C dimension. More...

virtual ome::xml::model::enums::PixelType	getPixelType () const =0
	Get the pixel type. More...

virtual pixel_size_type	getBitsPerPixel () const =0
	Get the number of valid bits per pixel. More...

virtual dimension_size_type	getEffectiveSizeC () const =0
	Get the effective size of the C dimension. More...

virtual dimension_size_type	getRGBChannelCount (dimension_size_type channel) const =0
	Get the number of channels returned for a call to openBytes(). More...

virtual bool	isIndexed () const =0
	Get whether the image planes are indexed color. More...

virtual bool	isFalseColor () const =0
	Get whether the image planes are false color. More...

virtual void	getLookupTable (dimension_size_type plane, VariantPixelBuffer &buf) const =0
	Get the color lookup table associated with an image plane. More...

virtual Modulo &	getModuloZ ()=0
	Get the Modulo subdivision of the Z dimension. More...

virtual const Modulo &	getModuloZ () const =0
	Get the Modulo subdivision of the Z dimension. More...

virtual Modulo &	getModuloT ()=0
	Get the Modulo subdivision of the T dimension. More...

virtual const Modulo &	getModuloT () const =0
	Get the Modulo subdivision of the T dimension. More...

virtual Modulo &	getModuloC ()=0
	Get the Modulo subdivision of the C dimension. More...

virtual const Modulo &	getModuloC () const =0
	Get the Modulo subdivision of the C dimension. More...

virtual dimension_size_type	getThumbSizeX () const =0
	Get the thumbnail size of the X dimension. More...

virtual dimension_size_type	getThumbSizeY () const =0
	Get the thumbnail size of the Y dimension. More...

virtual bool	isLittleEndian () const =0
	Get whether the data is in little-endian format. More...

virtual const std::string &	getDimensionOrder () const =0
	Get the dimension order. More...

virtual bool	isOrderCertain () const =0
	Get whether the dimension order and sizes are known, or merely guesses. More...

virtual bool	isThumbnailSeries () const =0
	Get whether the current series is a lower resolution copy of a different series. More...

virtual bool	isInterleaved () const =0
	Get whether or not the channels are interleaved. More...

virtual bool	isInterleaved (dimension_size_type channel) const =0
	Get whether or not the given channel is interleaved. More...

virtual void	openBytes (dimension_size_type plane, VariantPixelBuffer &buf) const =0
	Obtain an image plane. More...

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

virtual void	openThumbBytes (dimension_size_type plane, VariantPixelBuffer &buf) const =0
	Obtain a thumbnail of an image plane. More...

virtual dimension_size_type	getSeriesCount () const =0
	Get the number of image series in this file. More...

virtual void	setSeries (dimension_size_type series) const =0
	Set the active series. More...

virtual dimension_size_type	getSeries () const =0
	Get the active series. More...

virtual void	setPlane (dimension_size_type plane) const =0
	Set the active plane. More...

virtual dimension_size_type	getPlane () const =0
	Get the active plane. More...

virtual void	setNormalized (bool normalize)=0
	Set float normalization. More...

virtual bool	isNormalized () const =0
	Get float normalization. More...

virtual void	setOriginalMetadataPopulated (bool populate)=0
	Specifies whether or not to save proprietary metadata in the MetadataStore.

virtual bool	isOriginalMetadataPopulated () const =0
	Get proprietary metadata storage. More...

virtual void	setGroupFiles (bool group)=0
	Set file grouping. More...

virtual bool	isGroupFiles () const =0
	Get file grouping. More...

virtual bool	isMetadataComplete () const =0
	Get status of metadata parsing. More...

virtual FileGroupOption	fileGroupOption (const std::string &id)=0
	Returns an enum indicating that we cannot, must, or might group the files in this dataset. More...

virtual const std::vector< boost::filesystem::path >	getUsedFiles (bool noPixels=false) const =0
	Get the files used by this dataset. More...

virtual const std::vector< boost::filesystem::path >	getSeriesUsedFiles (bool noPixels=false) const =0
	Get the files used by the active series. More...

virtual std::vector< FileInfo >	getAdvancedUsedFiles (bool noPixels=false) const =0
	Get the files used by this dataset. More...

virtual std::vector< FileInfo >	getAdvancedSeriesUsedFiles (bool noPixels=false) const =0
	Get the files used by the active series. More...

virtual const boost::optional< boost::filesystem::path > &	getCurrentFile () const =0
	Get the currently open file. More...

virtual const std::vector< std::string > &	getDomains () const =0
	Get the domains represented by the current file. More...

virtual dimension_size_type	getIndex (dimension_size_type z, dimension_size_type c, dimension_size_type t) const =0
	Get the linear index of a `Z`, `C` and `T` coordinate. More...

virtual 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 =0
	Get the linear index of a `Z`, `C`, `T`, `ModuloZ`, `ModuloC` and `ModuloT` coordinate. More...

virtual ome::compat::array< dimension_size_type, 3 >	getZCTCoords (dimension_size_type index) const =0
	Get the `Z`, `C` and `T` coordinate of a linear index. More...

virtual ome::compat::array< dimension_size_type, 6 >	getZCTModuloCoords (dimension_size_type index) const =0
	Get the `Z`, `C`, `T`, `ModuloZ`, `ModuloC` and `ModuloT` coordinate of a linear index. More...

virtual const MetadataMap::value_type &	getMetadataValue (const std::string &field) const =0
	Get a global metadata value. More...

virtual const MetadataMap::value_type &	getSeriesMetadataValue (const MetadataMap::key_type &field) const =0
	Get a series metadata value. More...

virtual const MetadataMap &	getGlobalMetadata () const =0
	Get global metadata map. More...

virtual const MetadataMap &	getSeriesMetadata () const =0
	Get series metadata map. More...

virtual const std::vector< ome::compat::shared_ptr< CoreMetadata > > &	getCoreMetadataList () const =0
	Get the core metadata. More...

virtual void	setMetadataFiltered (bool filter)=0
	Set metadata filtering. More...

virtual bool	isMetadataFiltered () const =0
	Get metadata filtering. More...

virtual void	setMetadataStore (ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > &store)=0
	Set the default metadata store for this reader. More...

virtual const ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > &	getMetadataStore () const =0
	Get the current metadata store for this reader. More...

virtual ome::compat::shared_ptr< ::ome::xml::meta::MetadataStore > &	getMetadataStore ()=0
	Get the current metadata store for this reader. More...

virtual std::vector< ome::compat::shared_ptr< FormatReader > >	getUnderlyingReaders () const =0
	Get all underlying readers. More...

virtual bool	isSingleFile (const boost::filesystem::path &id) const =0
	Is this a single-file format? More...

virtual uint32_t	getRequiredDirectories (const std::vector< std::string > &files) const =0
	Get required parent directories. More...

virtual const std::string &	getDatasetStructureDescription () const =0
	Get a short description of the dataset structure. More...

virtual const std::vector< std::string > &	getPossibleDomains (const std::string &id) const =0
	Get the possible domains represented in which this format is used. More...

virtual bool	hasCompanionFiles () const =0
	Does this format support multi-file datasets? More...

virtual dimension_size_type	getOptimalTileWidth (dimension_size_type channel) const =0
	Get the optimal sub-image width. More...

virtual dimension_size_type	getOptimalTileHeight (dimension_size_type channel) const =0
	Get the optimal sub-image height. More...

virtual dimension_size_type	getOptimalTileWidth () const =0
	Get the optimal sub-image width. More...

virtual dimension_size_type	getOptimalTileHeight () const =0
	Get the optimal sub-image height. More...

virtual dimension_size_type	seriesToCoreIndex (dimension_size_type series) const =0
	Get the first core index corresponding to the specified series. More...

virtual dimension_size_type	coreIndexToSeries (dimension_size_type index) const =0
	Get the series corresponding to the specified core index. More...

virtual dimension_size_type	getCoreIndex () const =0
	Get the CoreMetadata index of the current resolution/series. More...

virtual void	setCoreIndex (dimension_size_type index) const =0
	Set the current resolution/series (ignoring sub-resolutions). More...

virtual dimension_size_type	getResolutionCount () const =0
	Get the number of resolutions for the current series. More...

virtual void	setResolution (dimension_size_type resolution) const =0
	Set the active resolution level. More...

virtual dimension_size_type	getResolution () const =0
	Get the active resolution level. More...

virtual bool	hasFlattenedResolutions () const =0
	Get resolution flattening. More...

virtual void	setFlattenedResolutions (bool flatten)=0
	Set resolution flattening. More...

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

virtual const std::string &	getFormat () const =0
	Get the name of this file format. More...

virtual const std::string &	getFormatDescription () const =0
	Get the description of this file format. More...

virtual const std::vector< boost::filesystem::path > &	getSuffixes () const =0
	Get the default file suffixes for this file format. More...

virtual const std::vector< boost::filesystem::path > &	getCompressionSuffixes () const =0
	Get the default compression suffixes for this file format. More...

virtual void	setId (const boost::filesystem::path &id)=0
	Set the current file name. More...

virtual void	close (bool fileOnly=false)=0
	Close the currently open file. More...

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

virtual const std::set< MetadataOptions::MetadataLevel > &	getSupportedMetadataLevels ()=0
	Get the supported metadata levels. More...

virtual void	setMetadataOptions (const MetadataOptions &options)=0
	Set metadata options. More...

virtual const MetadataOptions &	getMetadataOptions () const =0
	Get metadata options. More...

virtual MetadataOptions &	getMetadataOptions ()=0
	Get metadata options. More...

Protected Member Functions
	FormatReader ()
	Constructor.

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

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

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

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

Additional Inherited Members
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.

Note: No IOException in C++.

Member Enumeration Documentation

enum ome::bioformats::FormatReader::FileGroupOption

File grouping options.

Enumerator
MUST_GROUP	Files must be grouped.
CAN_GROUP	Files may be grouped.
CANNOT_GROUP	Files can not be grouped.

Member Function Documentation

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

pure virtual

Get the series corresponding to the specified core index.

Parameters

index the core index to use.

Returns: the series for the index.

Implemented in ome::bioformats::detail::FormatReader.

virtual FileGroupOption ome::bioformats::FormatReader::fileGroupOption ( const std::string & id )

pure 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.

Implemented in ome::bioformats::detail::FormatReader, and ome::bioformats::in::OMETIFFReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::qtwidgets::gl::Image2D::create(), and ome::bioformats::fillPixels().

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

pure virtual

Get the CoreMetadata index of the current resolution/series.

Returns: the index.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::FormatReader::SaveSeries::~SaveSeries().

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the currently open file.

Returns: the filename.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillMetadata().

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

pure virtual

Get a short description of the dataset structure.

Returns: a short description.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure virtual

Get the domains represented by the current file.

Returns: a list of domains.

Implemented in ome::bioformats::detail::FormatReader, and ome::bioformats::in::OMETIFFReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure virtual

Get global metadata map.

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

Returns: the global metadata map.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Determine the number of image planes in the current series.

Returns: the number of image planes.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillMetadata().

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

virtual dimension_size_type ome::bioformats::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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

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

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

pure virtual

Get the current metadata store for this reader.

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the current metadata store for this reader.

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the Modulo subdivision of the C dimension.

Returns: the Modulo defining the C dimension subdivision.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the Modulo subdivision of the C dimension.

Returns: the Modulo defining the C dimension subdivision.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the Modulo subdivision of the T dimension.

Returns: the Modulo defining the T dimension subdivision.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the Modulo subdivision of the T dimension.

Returns: the Modulo defining the T dimension subdivision.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the Modulo subdivision of the Z dimension.

Returns: the Modulo defining the Z dimension subdivision.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the Modulo subdivision of the Z dimension.

Returns: the Modulo defining the Z dimension subdivision.

Implemented in ome::bioformats::detail::FormatReader.

virtual dimension_size_type ome::bioformats::FormatReader::getOptimalTileHeight ( dimension_size_type channel ) const

pure 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.

Implemented in ome::bioformats::detail::FormatReader, and ome::bioformats::in::OMETIFFReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

virtual dimension_size_type ome::bioformats::FormatReader::getOptimalTileWidth ( dimension_size_type channel ) const

pure 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.

Implemented in ome::bioformats::detail::FormatReader, and ome::bioformats::in::OMETIFFReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the pixel type.

Returns: the pixel type.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::qtwidgets::gl::Image2D::create(), ome::bioformats::fillMetadata(), and ome::bioformats::fillPixels().

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

pure virtual

Get the active plane.

Returns: the active plane.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::FormatReader::SaveSeries::~SaveSeries().

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

pure 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?

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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?

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the active resolution level.

Returns: the resolution level.

See also: getResolutionCount()

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure virtual

Get the active series.

Returns: the active series.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::qtwidgets::gl::Image2D::create(), ome::bioformats::fillAllPixels(), ome::bioformats::fillMetadata(), ome::bioformats::fillPixels(), and ome::qtwidgets::gl::Image2D::setPlane().

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillAllPixels(), and ome::bioformats::fillMetadata().

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader, and ome::bioformats::in::OMETIFFReader.

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

pure virtual

Get the size of the C dimension.

Returns: the C dimension size.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure virtual

Get the size of the T dimension.

Returns: the T dimension size.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure virtual

Get the size of the X dimension.

Returns: the X dimension size.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::qtwidgets::gl::Image2D::create(), and ome::bioformats::fillPixels().

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

pure virtual

Get the size of the Y dimension.

Returns: the Y dimension size.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::qtwidgets::gl::Image2D::create(), and ome::bioformats::fillPixels().

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

pure virtual

Get the size of the Z dimension.

Returns: the Z dimension size.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure virtual

Get the thumbnail size of the X dimension.

Returns: the X dimension thumbnail size.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get the thumbnail size of the Y dimension.

Returns: the Y dimension thumbnail size.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get all underlying readers.

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

Returns: a list of readers.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillMetadata().

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Does this format support multi-file datasets?

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get resolution flattening.

Returns: true if flattening is enabled, false otherwise.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get file grouping.

Returns: true if grouping is enabled, false otherwise.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get whether the image planes are indexed color.

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

Returns: true if indexed, false otherwise.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get whether the data is in little-endian format.

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

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::fillPixels().

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

pure virtual

Get status of metadata parsing.

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get metadata filtering.

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Get float normalization.

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

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

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

virtual bool ome::bioformats::FormatReader::isSingleFile ( const boost::filesystem::path & id ) const

pure 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.

Implemented in ome::bioformats::detail::FormatReader, and ome::bioformats::in::OMETIFFReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader, and ome::bioformats::in::OMETIFFReader.

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

pure 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?

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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?

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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?

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

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

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

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::qtwidgets::gl::Image2D::setPlane().

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virtual void ome::bioformats::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

pure 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::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

Referenced by ome::bioformats::FormatReader::SaveSeries::~SaveSeries().

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure 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.

Implemented in ome::bioformats::detail::FormatReader.

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

pure virtual

Set the default metadata store for this reader.

Parameters

store a metadata store implementation.

Implemented in ome::bioformats::detail::FormatReader.

virtual void ome::bioformats::FormatReader::setNormalized ( bool normalize )

pure virtual

Set float normalization.