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

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

Inheritance diagram for ome::files::detail::FormatReader:

Collaboration diagram for ome::files::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. More...

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

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

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...

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

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

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

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

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

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

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

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

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

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

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

Protected Types
typedef std::vector< std::shared_ptr<::ome::files::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 std::shared_ptr<::ome::xml::meta::MetadataStore >	makeFilterMetadata ()
	Create a configured FilterMetadata instance. More...

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

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

virtual bool	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...

std::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::files::FormatReader
	FormatReader ()
	Constructor.

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

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

Protected Attributes
const ReaderProperties &	readerProperties
	Reader properties specific to the derived file format.

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

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

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

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

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

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

coremetadata_list_type	core
	Core metadata values.

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

bool	flattenedResolutions
	Whether or not resolutions are flattened.

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

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

bool	companionFiles
	Whether this format supports multi-file datasets.

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

bool	normalizeData
	Whether or not to normalize float data.

bool	filterMetadata
	Whether or not to filter out invalid metadata.

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

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

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

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

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

MetadataOptions	metadataOptions
	Metadata parsing options.

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

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

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

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

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

Detailed Description

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

◆ close()

void ome::files::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::files::FormatHandler.

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

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

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

Here is the caller graph for this function:

◆ coreIndexToSeries()

dimension_size_type ome::files::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.

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

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

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).

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

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.

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

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.

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ close()

◆ coreIndexToSeries()

◆ fileGroupOption()

◆ getAdvancedSeriesUsedFiles()

◆ getAdvancedUsedFiles()

◆ getBitsPerPixel()

◆ getCompressionSuffixes()

◆ getCoreIndex()

◆ getCoreMetadata() [1/2]

◆ getCoreMetadata() [2/2]

◆ getCoreMetadataList()

◆ getCurrentFile()

◆ getDatasetStructureDescription()

◆ getDimensionOrder()

◆ getDomains()

◆ getEffectiveSizeC()

◆ getFormat()

◆ getFormatDescription()

◆ getGlobalMetadata()

◆ getImageCount()

◆ getIndex() [1/2]

◆ getIndex() [2/2]

◆ getLookupTable()

◆ getMetadataOptions() [1/2]

◆ getMetadataOptions() [2/2]

◆ getMetadataStore() [1/2]

◆ getMetadataStore() [2/2]

◆ getMetadataValue()

◆ getModuloC() [1/2]

◆ getModuloC() [2/2]

◆ getModuloT() [1/2]

◆ getModuloT() [2/2]

◆ getModuloZ() [1/2]

◆ getModuloZ() [2/2]

◆ getOptimalTileHeight() [1/2]

◆ getOptimalTileHeight() [2/2]

◆ getOptimalTileWidth() [1/2]

◆ getOptimalTileWidth() [2/2]

◆ getPixelType()

◆ getPlane()

◆ getPossibleDomains()

◆ getRequiredDirectories()

◆ getResolution()

◆ getResolutionCount()

◆ getRGBChannelCount()

◆ getSeries()

◆ getSeriesCount()

◆ getSeriesMetadata()

◆ getSeriesMetadataValue()

◆ getSeriesUsedFiles()

◆ getSizeC()

◆ getSizeT()

◆ getSizeX()

◆ getSizeY()

◆ getSizeZ()

◆ getSuffixes()

◆ getSupportedMetadataLevels()

◆ getThumbSize()

◆ getThumbSizeX()

◆ getThumbSizeY()

◆ getUnderlyingReaders()

◆ getUsedFiles()

◆ getZCTCoords()

◆ getZCTModuloCoords()

◆ hasCompanionFiles()

◆ hasFlattenedResolutions()

◆ initFile()

◆ isFalseColor()

◆ isFilenameThisTypeImpl()

◆ isGroupFiles()

◆ isIndexed()

◆ isInterleaved() [1/2]

◆ isInterleaved() [2/2]