bioformats  5.1.6
Classes | Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
ome::bioformats::out::OMETIFFWriter Class Reference

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

#include <ome/bioformats/out/OMETIFFWriter.h>

+ Inheritance diagram for ome::bioformats::out::OMETIFFWriter:
+ Collaboration diagram for ome::bioformats::out::OMETIFFWriter:

Classes

struct  SeriesState
 Current state of an image series. More...
 
struct  TIFFState
 State of TIFF file. More...
 

Public Member Functions

 OMETIFFWriter ()
 Constructor.
 
virtual ~OMETIFFWriter ()
 Destructor.
 
void setId (const boost::filesystem::path &id)
 Set the current file name. More...
 
void close (bool fileOnly=false)
 Close the currently open file. More...
 
void setSeries (dimension_size_type series) const
 Set the active series. More...
 
void setPlane (dimension_size_type plane) const
 Set the active plane. More...
 
void saveBytes (dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h)
 Save an image plane. More...
 
void setBigTIFF (boost::optional< bool > big=true)
 Set use of BigTIFF support. More...
 
boost::optional< bool > getBigTIFF () const
 Query use of BigTIFF support. More...
 
- Public Member Functions inherited from ome::bioformats::detail::FormatWriter
virtual ~FormatWriter ()
 Destructor.
 
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...
 
virtual dimension_size_type getSeriesCount () const
 Get the number of image series in this file. More...
 
void setLookupTable (dimension_size_type plane, const VariantPixelBuffer &buf)
 Set the color lookup table associated with the current series. More...
 
void saveBytes (dimension_size_type plane, VariantPixelBuffer &buf)
 Save an image plane. More...
 
dimension_size_type getSeries () const
 Get the active series. More...
 
dimension_size_type getPlane () const
 Get the active plane. More...
 
bool canDoStacks () const
 Get whether or not the writer can save multiple images in a single file. More...
 
void setMetadataRetrieve (ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > &retrieve)
 Set the default metadata store for this writer. More...
 
const ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > & getMetadataRetrieve () const
 Get the current metadata store for this writer. More...
 
ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > & getMetadataRetrieve ()
 Get the current metadata store for this writer. More...
 
virtual dimension_size_type getImageCount () const
 Determine the number of image planes in the current series. More...
 
virtual bool isRGB (dimension_size_type channel) const
 Does a channel contain subchannels? More...
 
virtual dimension_size_type getSizeX () const
 Get the size of the X dimension. More...
 
virtual dimension_size_type getSizeY () const
 Get the size of the Y dimension. More...
 
virtual dimension_size_type getSizeZ () const
 Get the size of the Z dimension. More...
 
virtual dimension_size_type getSizeT () const
 Get the size of the T dimension. More...
 
virtual dimension_size_type getSizeC () const
 Get the size of the C dimension. More...
 
virtual ome::xml::model::enums::PixelType getPixelType () const
 Get the pixel type. More...
 
virtual pixel_size_type getBitsPerPixel () const
 Get the number of valid bits per pixel. More...
 
virtual dimension_size_type getEffectiveSizeC () const
 Get the effective size of the C dimension. More...
 
virtual dimension_size_type getRGBChannelCount (dimension_size_type channel) const
 Get the number of channels required for a call to saveBytes(). More...
 
virtual const std::string & getDimensionOrder () const
 Get the dimension order. More...
 
virtual 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...
 
virtual ome::compat::array< dimension_size_type, 3 > getZCTCoords (dimension_size_type index) const
 Get the Z, C and T coordinate of a linear index. More...
 
void setFramesPerSecond (frame_rate_type rate)
 Set the frame rate to use when writing. More...
 
frame_rate_type getFramesPerSecond () const
 Get the frame rate to use when writing. More...
 
const std::set< ome::xml::model::enums::PixelType > & getPixelTypes () const
 Get supported pixel types. More...
 
const std::set< ome::xml::model::enums::PixelType > & getPixelTypes (const std::string &codec) const
 Get supported pixel types for the given codec. More...
 
bool isSupportedType (ome::xml::model::enums::PixelType type) const
 Check if the pixel type is supported. More...
 
bool isSupportedType (ome::xml::model::enums::PixelType type, const std::string &codec) const
 Check if the pixel type is supported by the given codex. More...
 
const std::set< std::string > & getCompressionTypes () const
 Get supported compression types. More...
 
void setCompression (const std::string &compression)
 Set the compression type to use when writing. More...
 
const boost::optional< std::string > & getCompression () const
 Get the compression type to use when writing. More...
 
void setInterleaved (bool interleaved)
 Set subchannel interleaving. More...
 
const boost::optional< bool > & getInterleaved () const
 Set subchannel interleaving. More...
 
void changeOutputFile (const boost::filesystem::path &id)
 Switch the output file for the current dataset. More...
 
void setWriteSequentially (bool sequential=true)
 Write planes sequentially. More...
 
bool getWriteSequentially () const
 Check if planes are written sequentially. More...
 
const std::string & getFormat () const
 Get the name of this file format. More...
 
const std::string & getFormatDescription () const
 Get the description of this file format. More...
 
const std::vector< boost::filesystem::path > & getSuffixes () const
 Get the default file suffixes for this file format. More...
 
const std::vector< boost::filesystem::path > & getCompressionSuffixes () const
 Get the default compression suffixes for this file format. More...
 
- Public Member Functions inherited from ome::bioformats::FormatHandler
virtual ~FormatHandler ()
 Destructor.
 

Protected Types

typedef std::map< boost::filesystem::path, std::string > file_uuid_map
 Map filename to UUID.
 
typedef std::map< boost::filesystem::path, TIFFStatetiff_map
 Map filename to TIFF state.
 
typedef std::vector< SeriesStateseries_list
 Vector of SeriesState objects.
 

Protected Member Functions

void nextIFD () const
 Flush current IFD and create new IFD.
 
void setupIFD () const
 Set IFD parameters for the current series.
 
- Protected Member Functions inherited from ome::bioformats::detail::FormatWriter
 FormatWriter (const WriterProperties &)
 Constructor.
 
- Protected Member Functions inherited from ome::bioformats::FormatWriter
 FormatWriter ()
 Constructor.
 
- Protected Member Functions inherited from ome::bioformats::FormatHandler
 FormatHandler ()
 Constructor.
 

Protected Attributes

ome::common::Logger logger
 Message logger.
 
boost::filesystem::path baseDir
 Base path for computing relative paths in the OME-XML.
 
file_uuid_map files
 UUID to filename mapping.
 
tiff_map tiffs
 Open TIFF files.
 
tiff_map::iterator currentTIFF
 Current TIFF file.
 
std::string flags
 TIFF flags.
 
series_list seriesState
 State of each series.
 
ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieveoriginalMetadataRetrieve
 Original MetadataRetrieve. More...
 
ome::compat::shared_ptr< ome::xml::meta::OMEXMLMetadataomeMeta
 OME-XML metadata for embedding in the TIFF.
 
- Protected Attributes inherited from ome::bioformats::detail::FormatWriter
const WriterPropertieswriterProperties
 Writer properties specific to the derived file format.
 
boost::optional< boost::filesystem::path > currentId
 The identifier (path) of the currently open file.
 
ome::compat::shared_ptr< std::ostream > out
 Current output.
 
dimension_size_type series
 Current series.
 
dimension_size_type plane
 Current plane.
 
boost::optional< std::string > compression
 The compression type to use.
 
boost::optional< bool > interleaved
 Subchannel interleaving enabled.
 
bool sequential
 Planes are written sequentially.
 
frame_rate_type framesPerSecond
 The frames per second to use when writing.
 
ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrievemetadataRetrieve
 Current metadata store. More...
 

Private Member Functions

void fillMetadata ()
 Fill MetadataStore with cached metadata. More...
 
std::string getOMEXML (const boost::filesystem::path &id)
 Get OME-XML for embedding into the specified TIFF file. More...
 
void saveComment (const boost::filesystem::path &id, const std::string &xml)
 Save OME-XML text in the first IFD of the specified TIFF file. More...
 

Private Attributes

boost::optional< bool > bigTIFF
 Write a Big TIFF.
 

Additional Inherited Members

- Public Types inherited from ome::bioformats::FormatWriter
typedef uint16_t frame_rate_type
 Frame rate type.
 
- 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

TIFF writer with support for OME-XML metadata.

Member Function Documentation

void ome::bioformats::out::OMETIFFWriter::close ( bool  fileOnly = false)
virtual

Close the currently open file.

Parameters
fileOnlyclose the open file only if true, or else free all internal state if false.

Reimplemented from ome::bioformats::detail::FormatWriter.

References bigTIFF, ome::bioformats::detail::FormatWriter::close(), ome::bioformats::detail::FormatWriter::currentId, currentTIFF, files, fillMetadata(), flags, getOMEXML(), nextIFD(), omeMeta, originalMetadataRetrieve, ome::bioformats::removeBinData(), saveComment(), seriesState, and tiffs.

Referenced by ~OMETIFFWriter().

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void ome::bioformats::out::OMETIFFWriter::fillMetadata ( )
private

Fill MetadataStore with cached metadata.

Set Image, Channel and TiffData elements.

References baseDir, ome::bioformats::detail::FormatWriter::getSeriesCount(), ome::bioformats::getZCTCoords(), ome::common::make_relative(), ome::bioformats::detail::FormatWriter::metadataRetrieve, omeMeta, ome::bioformats::detail::FormatWriter::plane, ome::bioformats::detail::OMETIFFPlane::PRESENT, ome::bioformats::detail::FormatWriter::series, seriesState, and tiffs.

Referenced by close().

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boost::optional< bool > ome::bioformats::out::OMETIFFWriter::getBigTIFF ( ) const

Query use of BigTIFF support.

If setBigTIFF has not been used to enable or disable BigTIFF explicitly, BigTIFF support will be disabled by default for data less than 4GiB, unless the data would be larger than 4GiB, in which case it will be enabled by default.

Returns
true if BigTIFF support are enabled, or false if disabled.

References bigTIFF.

std::string ome::bioformats::out::OMETIFFWriter::getOMEXML ( const boost::filesystem::path &  id)
private

Get OME-XML for embedding into the specified TIFF file.

Parameters
idthe TIFF in which to embed the OME-XML.
Returns
the OME-XML text for embedding.

References baseDir, ome::bioformats::getOMEXML(), ome::common::make_relative(), omeMeta, and tiffs.

Referenced by close().

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void ome::bioformats::out::OMETIFFWriter::saveBytes ( dimension_size_type  plane,
VariantPixelBuffer buf,
dimension_size_type  x,
dimension_size_type  y,
dimension_size_type  w,
dimension_size_type  h 
)
virtual

Save an image plane.

Write an image plane from a VariantPixelBuffer of size

to the current series in the current file.

Parameters
planethe plane index within the series.
bufthe source pixel buffer.
xthe X coordinate of the upper-left corner of the sub-image.
ythe Y coordinate of the upper-left corner of the sub-image.
wthe width of the sub-image.
hthe height of the sub-image.
Exceptions
FormatExceptionif any of the parameters are invalid.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::FormatHandler::assertId(), ome::bioformats::detail::FormatWriter::currentId, currentTIFF, ome::bioformats::detail::FormatWriter::getSeries(), ome::bioformats::detail::OMETIFFPlane::id, ome::bioformats::detail::OMETIFFPlane::PRESENT, seriesState, and setPlane().

void ome::bioformats::out::OMETIFFWriter::saveComment ( const boost::filesystem::path &  id,
const std::string &  xml 
)
private

Save OME-XML text in the first IFD of the specified TIFF file.

Parameters
idthe TIFF in which to embed the OME-XML.
xmlthe OME-XML text to embed.

References ome::bioformats::ENDIAN_BIG, ome::bioformats::ENDIAN_LITTLE, and ome::bioformats::ENDIAN_NATIVE.

Referenced by close().

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void ome::bioformats::out::OMETIFFWriter::setBigTIFF ( boost::optional< bool >  big = true)

Set use of BigTIFF support.

Enable or disable use of BigTIFF support for writing files larger than 4GiB.

Note
libtiff must be compiled with BigTIFF support enabled for this option to have any effect.
Parameters
bigtrue to enable or false to disable BigTIFF support.

References bigTIFF.

void ome::bioformats::out::OMETIFFWriter::setId ( const boost::filesystem::path &  id)
virtual
void ome::bioformats::out::OMETIFFWriter::setPlane ( dimension_size_type  plane) const
virtual

Set the active plane.

Parameters
planethe plane to activate.
Todo:
Remove use of stateful API which requires use of plane switching in const methods.

Reimplemented from ome::bioformats::detail::FormatWriter.

References ome::bioformats::detail::FormatWriter::getPlane(), nextIFD(), ome::bioformats::detail::FormatWriter::setPlane(), and setupIFD().

Referenced by saveBytes().

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void ome::bioformats::out::OMETIFFWriter::setSeries ( dimension_size_type  series) const
virtual

Set the active series.

Parameters
seriesthe series to activate.
Todo:
Remove use of stateful API which requires use of series switching in const methods.

Reimplemented from ome::bioformats::detail::FormatWriter.

References ome::bioformats::detail::FormatWriter::getSeries(), nextIFD(), ome::bioformats::detail::FormatWriter::setSeries(), and setupIFD().

Member Data Documentation

ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve> ome::bioformats::out::OMETIFFWriter::originalMetadataRetrieve
protected

Original MetadataRetrieve.

We replace it with the generated OME-XML metadata store.

Todo:
Overriding getMetadataRetrieve will be a cleaner solution, but need to eliminate all direct use of metadataRetrieve in all writers first.

Referenced by close(), and setId().


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