ome::bioformats::tiff Namespace Reference

TIFF file format (libtiff wrapper). More...

Classes
struct	Codec
	A TIFF codec. More...
class	Exception
	Exception thrown for TIFF (libtiff) errors. More...
class	Field
	Field representing a tag value. More...
class	FieldBase
	Common functionality for fields of all types. More...
class	IFD
	Image File Directory (IFD). More...
class	IFDIterator
	Iterator for IFDs contained within a TIFF. More...
struct	IFDRange
	Range of IFDs for an image series. More...
struct	ImageJMetadata
	ImageJ metadata from IFD tags. More...
class	Sentry
	Sentry for saving and restoring libtiff state. More...
class	TIFF
	Tagged Image File Format (TIFF). More...
class	TileInfo
	Tile information for an IFD. More...
class	Value
	Field value. More...
class	ValueProxy
	Proxy for getting and setting a Field value. More...

Typedefs
typedef uint16_t	directory_index_type
	IFD index.
typedef uint64_t	offset_type
	IFD offset.
typedef unsigned int	tag_type
	Tag number.
typedef std::vector< IFDRange >	SeriesIFDRange
	Mapping between series index and IFD range.

Enumerations
enum	StringTag1 {   ARTIST, COPYRIGHT, DATETIME, DOCUMENTNAME,   HOSTCOMPUTER, IMAGEDESCRIPTION, MAKE, MODEL,   PAGENAME, SOFTWARE, TARGETPRINTER }
	String fields. More...
enum	StringTagArray1 { INKNAMES }
	String array fields. More...
enum	UInt16Tag1 {   BITSPERSAMPLE, CELLWIDTH, CELLLENGTH, CLEANFAXDATA,   DATATYPE, GRAYRESPONSEUNIT, INDEXED, INKSET,   MATTEING, MAXSAMPLEVALUE, MINSAMPLEVALUE, NUMBEROFINKS,   RESOLUTIONUNIT, SAMPLESPERPIXEL }
	Unsigned 16-bit integer fields. More...
enum	UInt16TagArray1 { GRAYRESPONSECURVE }
	Unsigned 16-bit integer array fields. More...
enum	UInt16Compression1 { COMPRESSION }
	Compression enum fields. More...
enum	UInt16FillOrder1 { FILLORDER }
	Fill order enum fields. More...
enum	UInt16Orientation1 { ORIENTATION }
	Orientation enum fields. More...
enum	UInt16PhotometricInterpretation1 { PHOTOMETRIC }
	Photometric interpretation enum fields. More...
enum	UInt16PlanarConfiguration1 { PLANARCONFIG }
	PlanarConfiguration enum fields. More...
enum	UInt16Predictor1 { PREDICTOR }
	Predictor enum fields. More...
enum	UInt16SampleFormat1 { SAMPLEFORMAT }
	Sample format enum fields. More...
enum	UInt16Threshholding1 { THRESHHOLDING }
	Threshholding enum fields. More...
enum	UInt16YCbCrPosition1 { YCBCRPOSITIONING }
	YCbCrPosition enum fields. More...
enum	UInt16Tag2 { DOTRANGE, HALFTONEHINTS, PAGENUMBER, YCBCRSUBSAMPLING }
	Unsigned 16-bit integer (×2) fields. More...
enum	UInt16Tag6 { TRANSFERRANGE }
	Unsigned 16-bit integer (×6) fields. More...
enum	UInt16ExtraSamplesArray1 { EXTRASAMPLES }
	Unsigned 16-bit integer array fields. More...
enum	UInt16TagArray3 { COLORMAP, TRANSFERFUNCTION }
	Unsigned 16-bit integer array (×3) fields. More...
enum	UInt32Tag1 {   BADFAXLINES, CONSECUTIVEBADFAXLINES, GROUP3OPTIONS, GROUP4OPTIONS,   IMAGEDEPTH, IMAGELENGTH, IMAGEWIDTH, ROWSPERSTRIP,   SUBFILETYPE, T4OPTIONS, T6OPTIONS, TILEDEPTH,   TILELENGTH, TILEWIDTH }
	Unsigned 32-bit integer fields. More...
enum	UInt32TagArray1 { IMAGEJ_META_DATA_BYTE_COUNTS, RICHTIFFIPTC }
	Unsigned 32-bit integer array fields. More...
enum	UInt64TagArray1 {   FREEOFFSETS, FREEBYTECOUNTS, SUBIFD, STRIPBYTECOUNTS,   STRIPOFFSETS, TILEBYTECOUNTS, TILEOFFSETS }
	Unsigned 64-bit integer fields. More...
enum	RawDataTag1 {   ICCPROFILE, JPEGTABLES, PHOTOSHOP, XMLPACKET,   IMAGEJ_META_DATA }
	Byte (Unsigned 8-bit integer) fields. More...
enum	FloatTag1 { XRESOLUTION, YRESOLUTION, XPOSITION, YPOSITION }
	Floating point fields. More...
enum	FloatTag2 { WHITEPOINT }
	Floating point (×2) fields. More...
enum	FloatTag3 { YCBCRCOEFFICIENTS }
	Floating point (×3) fields. More...
enum	FloatTag6 { PRIMARYCHROMATICITIES, REFERENCEBLACKWHITE }
	Floating point (×6) fields. More...
enum	Type {   TYPE_NONE = 0, TYPE_BYTE = 1, TYPE_ASCII = 2, TYPE_SHORT = 3,   TYPE_LONG = 4, TYPE_RATIONAL = 5, TYPE_SBYTE = 6, TYPE_UNDEFINED = 7,   TYPE_SSHORT = 8, TYPE_SLONG = 9, TYPE_SRATIONAL = 10, TYPE_FLOAT = 11,   TYPE_DOUBLE = 12, TYPE_IFD = 13, TYPE_LONG8 = 16, TYPE_SLONG8 = 17,   TYPE_IFD8 = 18 }
	Tag types. More...
enum	Compression {   COMPRESSION_NONE = 1, COMPRESSION_CCITTRLE = 2, COMPRESSION_CCITTFAX3 = 3, COMPRESSION_CCITT_T4 = 3,   COMPRESSION_CCITTFAX4 = 4, COMPRESSION_CCITT_T6 = 4, COMPRESSION_LZW = 5, COMPRESSION_OJPEG = 6,   COMPRESSION_JPEG = 7, COMPRESSION_ADOBE_DEFLATE = 8, COMPRESSION_T85 = 9, COMPRESSION_T43 = 10,   COMPRESSION_NEXT = 32766, COMPRESSION_CCITTRLEW = 32771, COMPRESSION_PACKBITS = 32773, COMPRESSION_THUNDERSCAN = 32809,   COMPRESSION_IT8CTPAD = 32895, COMPRESSION_IT8LW = 32896, COMPRESSION_IT8MP = 32897, COMPRESSION_IT8BL = 32898,   COMPRESSION_PIXARFILM = 32908, COMPRESSION_PIXARLOG = 32909, COMPRESSION_DEFLATE = 32946, COMPRESSION_DCS = 32947,   COMPRESSION_JBIG = 34661, COMPRESSION_SGILOG = 34676, COMPRESSION_SGILOG24 = 34677, COMPRESSION_JP2000 = 34712,   COMPRESSION_LZMA = 34925 }
	Compression technique. More...
enum	ExtraSamples { UNSPECIFIED = 0, ASSOCIATED_ALPHA = 1, UNASSOCIATED_ALPHA = 2 }
	Extra components description. More...
enum	FillOrder { MSB_TO_LSB = 1, LSB_TO_MSB = 2 }
	Fill order. More...
enum	Orientation {   TOP_LEFT = 1, TOP_RIGHT = 2, BOTTOM_RIGHT = 3, BOTTOM_LEFT = 4,   LEFT_TOP = 5, RIGHT_TOP = 6, RIGHT_BOTTOM = 7, LEFT_BOTTOM = 8 }
	Image orientation. More...
enum	PhotometricInterpretation {   MIN_IS_WHITE = 0, MIN_IS_BLACK = 1, RGB = 2, PALETTE = 3,   MASK = 4, SEPARATED = 5, YCBCR = 6, CIELAB = 8,   ICCLAB = 9, ITULAB = 10, CFA_ARRAY = 32803, LOGL = 32844,   LOGLUV = 32845 }
	Photometric interpretation of pixel data. More...
enum	PlanarConfiguration { CONTIG = 1, SEPARATE = 2 }
	Planar configuration of samples. More...
enum	Predictor { NONE = 1, HORIZONTAL = 2, FLOATING_POINT = 3 }
	Prediction scheme. More...
enum	SampleFormat {   UNSIGNED_INT = 1, SIGNED_INT = 2, FLOAT = 3, VOID = 4,   COMPLEX_INT = 5, COMPLEX_FLOAT = 6 }
	Sample format. More...
enum	Threshholding { BILEVEL = 1, HALFTONE = 2, ERRORDIFFUSE = 3 }
	Thresholding scheme. More...
enum	YCbCrPosition { CENTERED = 1, COSITED = 2 }
	YCbCr positioning. More...
enum	TileType { STRIP, TILE }
	Type of tile. More...

Functions
std::vector< Codec >	getConfiguredCodecs ()
	Get codecs registered with the TIFF library. More...
tag_type	getWrappedTag (StringTag1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (StringTagArray1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16Tag1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16TagArray1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16Compression1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16FillOrder1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16Orientation1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16PhotometricInterpretation1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16PlanarConfiguration1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16Predictor1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16SampleFormat1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16Threshholding1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16YCbCrPosition1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16Tag2 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16Tag6 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16ExtraSamplesArray1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt16TagArray3 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt32Tag1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt32TagArray1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (UInt64TagArray1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (RawDataTag1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (FloatTag1 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (FloatTag2 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (FloatTag3 tag)
	Get the TIFF tag number for the specified tag. More...
tag_type	getWrappedTag (FloatTag6 tag)
	Get the TIFF tag number for the specified tag. More...
ome::compat::shared_ptr< CoreMetadata >	makeCoreMetadata (const IFD &ifd)
	Create CoreMetadata from an IFD. More...
void	getCoreMetadata (const IFD &ifd, CoreMetadata &core)
	Get CoreMetadata from an IFD. More...
dimension_size_type	ifdIndex (const SeriesIFDRange &seriesIFDRange, dimension_size_type series, dimension_size_type plane)
	Compute IFD index from IFD map and plane index. More...
bool	enableBigTIFF (const boost::optional< bool > &wantBig, storage_size_type pixelSize, const boost::filesystem::path &filename, ome::common::Logger &logger)
	Check if BigTIFF should be enabled. More...

Detailed Description

TIFF file format (libtiff wrapper).

Enumeration Type Documentation

enum ome::bioformats::tiff::Compression

Compression technique.

Enumerator
COMPRESSION_NONE	No compression.
COMPRESSION_CCITTRLE	CCITT modified Huffman RLE.
COMPRESSION_CCITTFAX3	CCITT Group 3 fax encoding (deprecated).
COMPRESSION_CCITT_T4	CCITT T.4 (TIFF 6 name).
COMPRESSION_CCITTFAX4	CCITT Group 4 fax encoding (deprecated).
COMPRESSION_CCITT_T6	CCITT T.6 (TIFF 6 name).
COMPRESSION_LZW	Lempel-Ziv & Welch.
COMPRESSION_OJPEG	JPEG (deprecated).
COMPRESSION_JPEG	JPEG DCT compression.
COMPRESSION_ADOBE_DEFLATE	Deflate compression (Adobe).
COMPRESSION_T85	TIFF/FX T.85 JBIG compression.
COMPRESSION_T43	TIFF/FX T.43 colour by layered JBIG compression.
COMPRESSION_NEXT	NeXT 2-bit RLE.
COMPRESSION_CCITTRLEW	1 w/ word alignment.
COMPRESSION_PACKBITS	Macintosh RLE.
COMPRESSION_THUNDERSCAN	ThunderScan RLE.
COMPRESSION_IT8CTPAD	codes 32895-32898 are reserved for ANSI IT8 TIFF/IT <dkell.nosp@m.y@ap.nosp@m.ago.c.nosp@m.om). IT8 CT w/padding.
COMPRESSION_IT8LW	IT8 Linework RLE.
COMPRESSION_IT8MP	IT8 Monochrome picture.
COMPRESSION_IT8BL	IT8 Binary line art.
COMPRESSION_PIXARFILM	compression codes 32908-32911 are reserved for Pixar. Pixar companded 10bit LZW.
COMPRESSION_PIXARLOG	Pixar companded 11bit ZIP.
COMPRESSION_DEFLATE	Deflate compression.
COMPRESSION_DCS	compression code 32947 is reserved for Oceana Matrix dev@o.nosp@m.cean.nosp@m.a.com. Kodak DCS encoding.
COMPRESSION_JBIG	ISO JBIG.
COMPRESSION_SGILOG	SGI Log Luminance RLE.
COMPRESSION_SGILOG24	SGI Log 24-bit packed.
COMPRESSION_JP2000	Leadtools JPEG2000.
COMPRESSION_LZMA	LZMA2.

enum ome::bioformats::tiff::ExtraSamples

Extra components description.

Enumerator
UNSPECIFIED	Unspecified data.
ASSOCIATED_ALPHA	Associated alpha data with pre-multiplied color.
UNASSOCIATED_ALPHA	Unassociated alpha data.

enum ome::bioformats::tiff::FillOrder

Fill order.

Enumerator
MSB_TO_LSB	Most significant bit to least significant bit.
LSB_TO_MSB	Least significant bit to most significant bit.

enum ome::bioformats::tiff::FloatTag1

Floating point fields.

Enumerator
XRESOLUTION	Number of pixels per resolution unit along the image width.
YRESOLUTION	Number of pixels per resolution unit along the image height.
XPOSITION	The x position of the image in RESOLUTIONUNITs.
YPOSITION	THe y position of the image in RESOLUTIONUNITs.

enum ome::bioformats::tiff::FloatTag2

Floating point (×2) fields.

Enumerator
WHITEPOINT	Chromaticity of the white point of the image as 1931 CIE (xy).

enum ome::bioformats::tiff::FloatTag3

Floating point (×3) fields.

Enumerator
YCBCRCOEFFICIENTS	Coefficients describing the RGB to YCbCr transform.

enum ome::bioformats::tiff::FloatTag6

Floating point (×6) fields.

Enumerator
PRIMARYCHROMATICITIES	Chromaticities of primary colours as 1931 CIE R(xy) G(xy) B(xy).
REFERENCEBLACKWHITE	Reference black and white pairs for RGB or YCbCr images.

enum ome::bioformats::tiff::Orientation

Image orientation.

Enumerator
TOP_LEFT	Row 0 top, column 0 lhs.
TOP_RIGHT	Row 0 top, column 0 rhs.
BOTTOM_RIGHT	Row 0 bottom, column 0 rhs.
BOTTOM_LEFT	Row 0 bottom, column 0 lhs.
LEFT_TOP	Row 0 lhs, column 0 top.
RIGHT_TOP	Row 0 rhs, column 0 top.
RIGHT_BOTTOM	Row 0 rhs, column 0 bottom.
LEFT_BOTTOM	Row 0 lhs, column 0 bottom.

enum ome::bioformats::tiff::PhotometricInterpretation

Photometric interpretation of pixel data.

Enumerator
MIN_IS_WHITE	Minimum value is white.
MIN_IS_BLACK	Minimum value is black.
RGB	RGB subchannels.
PALETTE	Indexed colour with colormap.
MASK	Mask.
SEPARATED	Color separations.
YCBCR	CCIR 601.
CIELAB	1976 CIE L*a*b*.
ICCLAB	ICC L*a*b*.
ITULAB	ITU L*a*b*.
CFA_ARRAY	Color Filter Array.
LOGL	CIE log2(L).
LOGLUV	CIE log2(L) (u',v').

enum ome::bioformats::tiff::PlanarConfiguration

Planar configuration of samples.

Enumerator
CONTIG	Samples are contiguous (chunky).
SEPARATE	Samples are separate (planar).

enum ome::bioformats::tiff::Predictor

Prediction scheme.

Enumerator
NONE	No prediction scheme used.
HORIZONTAL	Horizontal differencing.
FLOATING_POINT	Floating point.

enum ome::bioformats::tiff::RawDataTag1

Byte (Unsigned 8-bit integer) fields.

Enumerator
ICCPROFILE	ICC profile data.
JPEGTABLES	JPEG quantization and/or Huffman tables (JPEG "abbreviated table specification" datastream).
PHOTOSHOP	Photoshop "Image Resource Blocks".
XMLPACKET	XMP metadata.
IMAGEJ_META_DATA	Private tag for ImageJ metadata.

enum ome::bioformats::tiff::SampleFormat

Sample format.

Enumerator
UNSIGNED_INT	Unsigned integer.
SIGNED_INT	Signed integer.
FLOAT	IEEE floating point.
VOID	Void.
COMPLEX_INT	Complex integer.
COMPLEX_FLOAT	Complex IEEE floating point.

enum ome::bioformats::tiff::StringTag1

String fields.

Enumerator
ARTIST	Person who created the image.
COPYRIGHT	Copyright notice.
DATETIME	Date and time of image creation.
DOCUMENTNAME	Name of the document from which the image originated.
HOSTCOMPUTER	Computer and/or operating system creating the image.
IMAGEDESCRIPTION	Description of the image.
MAKE	Scanner manufacturer.
MODEL	Scanner model name or number.
PAGENAME	Name of the page from which the image originated.
SOFTWARE	Name and version of the software creating the image.
TARGETPRINTER	Description of the printing environment.

enum ome::bioformats::tiff::StringTagArray1

String array fields.

Enumerator
INKNAMES	Names of each ink used in a separated image.

enum ome::bioformats::tiff::Threshholding

Thresholding scheme.

Enumerator
BILEVEL	Black and white.
HALFTONE	Dithered.
ERRORDIFFUSE	Error diffusion (Floyd-Steinberg).

enum ome::bioformats::tiff::TileType

Type of tile.

Enumerator
STRIP	Strips.
TILE	Tiles.

enum ome::bioformats::tiff::Type

Tag types.

Enumerator
TYPE_NONE	Placeholder.
TYPE_BYTE	8-bit unsigned integer.
TYPE_ASCII	8-bit bytes with NUL terminator.
TYPE_SHORT	16-bit unsigned integer.
TYPE_LONG	32-bit unsigned integer.
TYPE_RATIONAL	64-bit unsigned fraction.
TYPE_SBYTE	8-bit signed integer.
TYPE_UNDEFINED	8-bit untyped data.
TYPE_SSHORT	16-bit signed integer.
TYPE_SLONG	32-bit signed integer.
TYPE_SRATIONAL	64-bit signed fraction.
TYPE_FLOAT	32-bit IEEE floating point.
TYPE_DOUBLE	64-bit IEEE floating point.
TYPE_IFD	32-bit unsigned integer (offset).
TYPE_LONG8	BigTIFF 64-bit unsigned integer.
TYPE_SLONG8	BigTIFF 64-bit signed integer.
TYPE_IFD8	BigTIFF 64-bit unsigned integer (offset).

enum ome::bioformats::tiff::UInt16Compression1

Compression enum fields.

Enumerator
COMPRESSION	Compression scheme in use on the image data.

enum ome::bioformats::tiff::UInt16ExtraSamplesArray1

Unsigned 16-bit integer array fields.

Enumerator
EXTRASAMPLES	Description of extra components.

enum ome::bioformats::tiff::UInt16FillOrder1

Fill order enum fields.

Enumerator
FILLORDER	Logical order of bits within a byte.

enum ome::bioformats::tiff::UInt16Orientation1

Orientation enum fields.

Enumerator
ORIENTATION	Image orientation.

enum ome::bioformats::tiff::UInt16PhotometricInterpretation1

Photometric interpretation enum fields.

Enumerator
PHOTOMETRIC	Photometric interpretation; colour space of image data.

enum ome::bioformats::tiff::UInt16PlanarConfiguration1

PlanarConfiguration enum fields.

Enumerator
PLANARCONFIG	How components of each pixel are stored.

enum ome::bioformats::tiff::UInt16Predictor1

Predictor enum fields.

Enumerator
PREDICTOR	Mathematical operation applied before encoding.

enum ome::bioformats::tiff::UInt16SampleFormat1

Sample format enum fields.

Enumerator
SAMPLEFORMAT	How to interpret each data sample in a pixel.

enum ome::bioformats::tiff::UInt16Tag1

Unsigned 16-bit integer fields.

Enumerator
BITSPERSAMPLE	Number of bits per component.
CELLWIDTH	Width of dithering or halftoning matrix for bilevel data.
CELLLENGTH	Height of dithering or halftoning matrix for bilevel data.
CLEANFAXDATA	How bad scanlines were handled.
DATATYPE	Use SAMPLEFORMAT [obsolete].
GRAYRESPONSEUNIT	Precision of GRAYRESPONSECURVE.
INDEXED	Image uses indexed color in any color space.
INKSET	Inkset used in a separated image.
MATTEING	Use EXTRASAMPLES [obsolete].
MAXSAMPLEVALUE	Maximum component value.
MINSAMPLEVALUE	Minimum component value.
NUMBEROFINKS	Number of inks.
RESOLUTIONUNIT	Unit of measurement for XRESOLUTION and YRESOLUTION.
SAMPLESPERPIXEL	Number of components per pixel.

enum ome::bioformats::tiff::UInt16Tag2

Unsigned 16-bit integer (×2) fields.

Enumerator
DOTRANGE	Component values corresponding to a 0% dot and 100% dot.
HALFTONEHINTS	Range of detail (low-high) for which tonal detail should be retained.
PAGENUMBER	Number of the page from which the image originated.
YCBCRSUBSAMPLING	Subsampling factors used for YCbCr chrominance components.

enum ome::bioformats::tiff::UInt16Tag6

Unsigned 16-bit integer (×6) fields.

Enumerator
TRANSFERRANGE	Expand range of TransferFunction.

enum ome::bioformats::tiff::UInt16TagArray1

Unsigned 16-bit integer array fields.

Enumerator
GRAYRESPONSECURVE	Optical density of greyscale pixel values.

enum ome::bioformats::tiff::UInt16TagArray3

Unsigned 16-bit integer array (×3) fields.

Enumerator
COLORMAP	Colour map for palette colour images.
TRANSFERFUNCTION	Transfer function for the image.

enum ome::bioformats::tiff::UInt16Threshholding1

Threshholding enum fields.

Enumerator
THRESHHOLDING	Method used to convert to black and white pixels.

enum ome::bioformats::tiff::UInt16YCbCrPosition1

YCbCrPosition enum fields.

Enumerator
YCBCRPOSITIONING	Positioning of subsampled chrominance components relative to luminance samples.

enum ome::bioformats::tiff::UInt32Tag1

Unsigned 32-bit integer fields.

Enumerator
BADFAXLINES	Number of bad scan lines encountered.
CONSECUTIVEBADFAXLINES	Maximum number of consecutive bad scan lines encountered.
GROUP3OPTIONS	Options for Group 3 Fax compression (T4Options).
GROUP4OPTIONS	Options for Group 4 Fax compression (T6Options).
IMAGEDEPTH	Number of z planes in the image.
IMAGELENGTH	Number of rows in the image (pixels per column).
IMAGEWIDTH	Number of columns in the image (pixels per row).
ROWSPERSTRIP	Number of rows per strip.
SUBFILETYPE	Type of data in this subfile [new tag].
T4OPTIONS	Options for Group3 fax compression.
T6OPTIONS	Options for Group4 fax compression.
TILEDEPTH	Tile depth in pixels (z planes).
TILELENGTH	Tile height in pixels (rows).
TILEWIDTH	Tile width in pixels (columns).

enum ome::bioformats::tiff::UInt32TagArray1

Unsigned 32-bit integer array fields.

Enumerator
IMAGEJ_META_DATA_BYTE_COUNTS	Private tag for ImageJ metadata byte counts.
RICHTIFFIPTC	IPTC (International Press Telecommunications Council) metadata.

enum ome::bioformats::tiff::UInt64TagArray1

Unsigned 64-bit integer fields.

Enumerator
FREEOFFSETS	Offsets of free bytes [unused].
FREEBYTECOUNTS	Sizes of free bytes [unused].
SUBIFD	Offsets of child IFDs.
STRIPBYTECOUNTS	Number of bytes in each strip (after compression).
STRIPOFFSETS	Byte offset of each strip.
TILEBYTECOUNTS	Number of bytes in each tile (after compression).
TILEOFFSETS	Byte offset of each tile.

enum ome::bioformats::tiff::YCbCrPosition

YCbCr positioning.

Enumerator
CENTERED	Centered.
COSITED	Co-sited.

Function Documentation

bool ome::bioformats::tiff::enableBigTIFF	(	const boost::optional< bool > &	wantBig,
		storage_size_type	pixelSize,
		const boost::filesystem::path &	filename,
		ome::common::Logger &	logger
	)

Check if BigTIFF should be enabled.

A number of factors determine if BigTIFF support should be enabled:

• Does the system libtiff support BigTIFF
• Did the user request it
• Is the pixel data over the size limit for non-BigTIFF and the user did not explicitly disable BigTIFF
• Was a BigTIFF file extension used?

If BigTIFF could not be enabled when requested or needed then an appropriate warning will be logged.

Parameters

wantBig	user requirement (true to enable, false to disable, unset if unspecified).
pixelSize	the total size of pixel data to be written
filename	the name of the TIFF file to write (if a known BigTIFF extension is used, BigTIFF will be enabled).
logger	the logger to use to log errors.

Returns

true to enable BigTIFF or false to disable.

std::vector< Codec > ome::bioformats::tiff::getConfiguredCodecs

(

)

Get codecs registered with the TIFF library.

Returns

a list of available codecs.

References ome::bioformats::tiff::Codec::name, and ome::bioformats::tiff::Codec::scheme.

void ome::bioformats::tiff::getCoreMetadata	(	const IFD &	ifd,
		CoreMetadata &	core
	)

Get CoreMetadata from an IFD.

Parameters

ifd	the IFD to use.
core	the CoreMetadata to set.

Todo:

EXIF IFDs

Todo:

Text stream output for Tag enums.

Todo:

Metadata type for PhotometricInterpretation.

Todo:

Image orientation (storage order and direction) from ORIENTATION; fix up width and length from orientation.

Todo:

Only set if debugging/verbose.

Todo:

Only set if debugging/verbose.

Todo:

sminsamplevalue

Todo:

smaxsamplevalue

Todo:

Only set if debugging/verbose.

Todo:

JPEG tags

References ARTIST, ome::bioformats::bitsPerPixel(), ome::bioformats::CoreMetadata::bitsPerPixel, BITSPERSAMPLE, CELLLENGTH, CELLWIDTH, CFA_ARRAY, COLORMAP, COMPRESSION, COMPRESSION_CCITT_T4, COMPRESSION_CCITT_T6, COMPRESSION_LZW, CONTIG, COPYRIGHT, DATETIME, ome::bioformats::CoreMetadata::dimensionOrder, DOCUMENTNAME, DOTRANGE, EXTRASAMPLES, FILLORDER, ome::bioformats::tiff::IFD::getBitsPerSample(), ome::bioformats::tiff::IFD::getField(), ome::bioformats::tiff::IFD::getImageHeight(), ome::bioformats::tiff::IFD::getImageWidth(), ome::bioformats::tiff::IFD::getPhotometricInterpretation(), ome::bioformats::tiff::IFD::getPixelType(), ome::bioformats::tiff::IFD::getPlanarConfiguration(), ome::bioformats::tiff::IFD::getSamplesPerPixel(), GRAYRESPONSECURVE, GRAYRESPONSEUNIT, HALFTONE, HALFTONEHINTS, HOSTCOMPUTER, ome::bioformats::CoreMetadata::imageCount, IMAGELENGTH, IMAGEWIDTH, INDEXED, ome::bioformats::CoreMetadata::indexed, INKNAMES, INKSET, ome::bioformats::CoreMetadata::interleaved, ome::bioformats::CoreMetadata::littleEndian, MAKE, MAXSAMPLEVALUE, MINSAMPLEVALUE, MODEL, NUMBEROFINKS, ORIENTATION, PAGENAME, PAGENUMBER, PALETTE, PHOTOMETRIC, ome::bioformats::CoreMetadata::pixelType, PLANARCONFIG, PREDICTOR, PRIMARYCHROMATICITIES, REFERENCEBLACKWHITE, RESOLUTIONUNIT, RGB, SAMPLEFORMAT, SAMPLESPERPIXEL, ome::bioformats::CoreMetadata::seriesMetadata, ome::bioformats::MetadataMap::set(), ome::bioformats::significantBitsPerPixel(), ome::bioformats::CoreMetadata::sizeC, ome::bioformats::CoreMetadata::sizeT, ome::bioformats::CoreMetadata::sizeX, ome::bioformats::CoreMetadata::sizeY, ome::bioformats::CoreMetadata::sizeZ, SOFTWARE, SUBFILETYPE, T4OPTIONS, T6OPTIONS, TARGETPRINTER, THRESHHOLDING, TILELENGTH, TILEWIDTH, TRANSFERFUNCTION, TRANSFERRANGE, WHITEPOINT, XPOSITION, XRESOLUTION, ome::xml::model::enums::DimensionOrder::XYCZT, YCBCRCOEFFICIENTS, YCBCRPOSITIONING, YCBCRSUBSAMPLING, YPOSITION, and YRESOLUTION.

Referenced by makeCoreMetadata().

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tag_type ome::bioformats::tiff::getWrappedTag

(

StringTag1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References ARTIST, COPYRIGHT, DATETIME, DOCUMENTNAME, HOSTCOMPUTER, IMAGEDESCRIPTION, MAKE, MODEL, PAGENAME, SOFTWARE, and TARGETPRINTER.

tag_type ome::bioformats::tiff::getWrappedTag

(

StringTagArray1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References INKNAMES.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16Tag1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References BITSPERSAMPLE, CELLLENGTH, CELLWIDTH, CLEANFAXDATA, DATATYPE, GRAYRESPONSEUNIT, INDEXED, INKSET, MATTEING, MAXSAMPLEVALUE, MINSAMPLEVALUE, NUMBEROFINKS, RESOLUTIONUNIT, and SAMPLESPERPIXEL.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16TagArray1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References GRAYRESPONSECURVE.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16Compression1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References COMPRESSION.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16FillOrder1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References FILLORDER.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16Orientation1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References ORIENTATION.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16PhotometricInterpretation1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References PHOTOMETRIC.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16PlanarConfiguration1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References PLANARCONFIG.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16Predictor1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References PREDICTOR.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16SampleFormat1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References SAMPLEFORMAT.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16Threshholding1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References THRESHHOLDING.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16YCbCrPosition1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References YCBCRPOSITIONING.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16Tag2

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References DOTRANGE, HALFTONEHINTS, PAGENUMBER, and YCBCRSUBSAMPLING.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16Tag6

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References TRANSFERRANGE.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16ExtraSamplesArray1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References EXTRASAMPLES.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt16TagArray3

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References COLORMAP, and TRANSFERFUNCTION.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt32Tag1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References BADFAXLINES, CONSECUTIVEBADFAXLINES, GROUP3OPTIONS, GROUP4OPTIONS, IMAGEDEPTH, IMAGELENGTH, IMAGEWIDTH, ROWSPERSTRIP, SUBFILETYPE, T4OPTIONS, T6OPTIONS, TILEDEPTH, TILELENGTH, and TILEWIDTH.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt32TagArray1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References IMAGEJ_META_DATA_BYTE_COUNTS, and RICHTIFFIPTC.

tag_type ome::bioformats::tiff::getWrappedTag

(

UInt64TagArray1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References FREEBYTECOUNTS, FREEOFFSETS, STRIPBYTECOUNTS, STRIPOFFSETS, SUBIFD, TILEBYTECOUNTS, and TILEOFFSETS.

tag_type ome::bioformats::tiff::getWrappedTag

(

RawDataTag1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References ICCPROFILE, IMAGEJ_META_DATA, JPEGTABLES, PHOTOSHOP, and XMLPACKET.

tag_type ome::bioformats::tiff::getWrappedTag

(

FloatTag1

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References XPOSITION, XRESOLUTION, YPOSITION, and YRESOLUTION.

tag_type ome::bioformats::tiff::getWrappedTag

(

FloatTag2

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References WHITEPOINT.

tag_type ome::bioformats::tiff::getWrappedTag

(

FloatTag3

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References YCBCRCOEFFICIENTS.

tag_type ome::bioformats::tiff::getWrappedTag

(

FloatTag6

tag

)

Get the TIFF tag number for the specified tag.

Parameters

tag	the tag to use.

Returns

the tag number, or zero if not implemented.

References PRIMARYCHROMATICITIES, and REFERENCEBLACKWHITE.

dimension_size_type ome::bioformats::tiff::ifdIndex	(	const SeriesIFDRange &	seriesIFDRange,
		dimension_size_type	series,
		dimension_size_type	plane
	)

Compute IFD index from IFD map and plane index.

Parameters

seriesIFDRange	the series–IFD range mapping.
series	the series to use.
plane	the plane within the series to use.

Returns

the IFD index.

References ome::bioformats::tiff::IFDRange::begin.

Referenced by ome::bioformats::in::MinimalTIFFReader::ifdAtIndex(), and ome::bioformats::out::MinimalTIFFWriter::saveBytes().

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ome::compat::shared_ptr< CoreMetadata > ome::bioformats::tiff::makeCoreMetadata

(

const IFD &

ifd

)

Create CoreMetadata from an IFD.

Parameters

ifd	the IFD to use.

Returns

the CoreMetadata.

References getCoreMetadata().

Referenced by ome::bioformats::in::TIFFReader::readIFDs().

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