ome-files 0.1.0

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Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
ome::files::detail::FormatWriter Class Reference

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

`#include <ome/files/detail/FormatWriter.h>`

Inheritance diagram for ome::files::detail::FormatWriter:
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## Public Member Functions
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...
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...
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...
void | setId (const boost::filesystem::path &id)
| Set the current file name. More...
void | close (bool fileOnly=false)
| Close the currently open file. 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::FormatWriter
virtual void | saveBytes (dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h)=0
| Save an image plane. More...
Public Member Functions inherited from ome::files::FormatHandler
virtual | ~FormatHandler ()
| Destructor.

## Protected Member Functions
| FormatWriter (const WriterProperties &)
| Constructor.
Protected Member Functions inherited from ome::files::FormatWriter
| FormatWriter ()
| Constructor.
Protected Member Functions inherited from ome::files::FormatHandler
| FormatHandler ()
| Constructor.

## Protected Attributes
const WriterProperties & | writerProperties
| 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::MetadataRetrieve > | metadataRetrieve
| Current metadata store. More...

## Private Member Functions
| FormatWriter (const FormatWriter &)
| Copy constructor (deleted).
FormatWriter & | operator= (const FormatWriter &)
| Assignment operator (deleted).

## Additional Inherited Members
Public Types inherited from ome::files::FormatWriter
typedef uint16_t | frame_rate_type
| Frame rate type.
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 writers (default behaviour).

Note
  The `ColorModel` isn't stored here; this is Java-specific and not implemented in C++.
  The current output stream isn't stored here; this is the responsibility of the individual writer. Having a reference to the base ostream here and keeping this in sync with the derived writer is an unnecessary complication.

## Member Function Documentation

bool ome::files::detail::FormatWriter::canDoStacks | ( |  | ) | const
| virtual

Get whether or not the writer can save multiple images in a single file.

Returns
  `true` if the writer supports multiple images, `false` otherwise.

Implements ome::files::FormatWriter.

References ome::files::detail::WriterProperties::stacks, and writerProperties.

void ome::files::detail::FormatWriter::changeOutputFile | ( | const boost::filesystem::path & | id | ) |
| virtual

Switch the output file for the current dataset.

Parameters

  id | the new file name.

Implements ome::files::FormatWriter.

References ome::files::FormatHandler::assertId(), currentId, and setId().

void ome::files::detail::FormatWriter::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::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References compression, currentId, framesPerSecond, metadataRetrieve, out, plane, sequential, and series.

Referenced by ome::files::out::MinimalTIFFWriter::close(), ome::files::out::OMETIFFWriter::close(), and ~FormatWriter().

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pixel_size_type ome::files::detail::FormatWriter::getBitsPerPixel | ( |  | ) | const
| virtual

Get the number of valid bits per pixel.

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

Returns
  the number of valid bits per pixel.

References getSeries(), metadataRetrieve, and series.

const boost::optional< std::string > & ome::files::detail::FormatWriter::getCompression | ( |  | ) | const
| virtual

Get the compression type to use when writing.

Returns
  the compression type.

Implements ome::files::FormatWriter.

References compression.

const std::vector< boost::filesystem::path > & ome::files::detail::FormatWriter::getCompressionSuffixes | ( |  | ) | const
| virtual

Get the default compression suffixes for this file format.

Returns
  a list of file suffixes.

Implements ome::files::FormatHandler.

References ome::files::detail::WriterProperties::compression_suffixes, and writerProperties.

const std::set< std::string > & ome::files::detail::FormatWriter::getCompressionTypes | ( |  | ) | const
| virtual

Get supported compression types.

Returns
  the supported compression types.

Implements ome::files::FormatWriter.

References ome::files::detail::WriterProperties::compression_types, and writerProperties.

const std::string & ome::files::detail::FormatWriter::getDimensionOrder | ( |  | ) | const
| virtual

Get the dimension order.

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

- `XYCTZ`
- `XYCZT`
- `XYTCZ`
- `XYTZC`
- `XYZCT`
- `XYZTC`

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

Returns
  the dimension order.

References getSeries(), metadataRetrieve, and series.

Referenced by getIndex(), and getZCTCoords().

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dimension_size_type ome::files::detail::FormatWriter::getEffectiveSizeC | ( |  | ) | const
| virtual

Get the effective size of the C dimension.

This guarantees that

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

regardless of the result of isRGB().

Returns
  the effective C dimension size.

References getSeries(), metadataRetrieve, and series.

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

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const std::string & ome::files::detail::FormatWriter::getFormat | ( |  | ) | const
| virtual

Get the name of this file format.

Returns
  the file format name.

Implements ome::files::FormatHandler.

References ome::files::detail::WriterProperties::name, and writerProperties.

const std::string & ome::files::detail::FormatWriter::getFormatDescription | ( |  | ) | const
| virtual

Get the description of this file format.

Returns
  the file format description.

Implements ome::files::FormatHandler.

References ome::files::detail::WriterProperties::description, and writerProperties.

FormatWriter::frame_rate_type ome::files::detail::FormatWriter::getFramesPerSecond | ( |  | ) | const
| virtual

Get the frame rate to use when writing.

Returns
  the frame rate (number of frames per second).

Implements ome::files::FormatWriter.

References framesPerSecond.

dimension_size_type ome::files::detail::FormatWriter::getImageCount | ( |  | ) | const
| virtual

Determine the number of image planes in the current series.

Returns
  the number of image planes.

References getEffectiveSizeC(), getSizeT(), and getSizeZ().

Referenced by getIndex(), getZCTCoords(), ome::files::out::MinimalTIFFWriter::setId(), and setPlane().

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dimension_size_type ome::files::detail::FormatWriter::getIndex | ( | dimension_size_type | z,
|  | dimension_size_type | c,
|  | dimension_size_type | t
| ) |  | const
| virtual

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

The index is computed using the DimensionOrder.

Parameters

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

Returns
  the linear index.

Todo:

  unify with the pixel buffer dimension indexes.

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

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

const boost::optional< bool > & ome::files::detail::FormatWriter::getInterleaved | ( |  | ) | const
| virtual

Set subchannel interleaving.

Returns
  the current interleaving setting; `false` if unset.

Implements ome::files::FormatWriter.

References interleaved.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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const ome::compat::shared_ptr<::ome::xml::meta::MetadataRetrieve > & ome::files::detail::FormatWriter::getMetadataRetrieve | ( |  | ) | const
| virtual

Get the current metadata store for this writer.

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

Implements ome::files::FormatWriter.

References metadataRetrieve.

Referenced by ome::files::out::MinimalTIFFWriter::setId(), and ome::files::out::OMETIFFWriter::setId().

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ome::compat::shared_ptr<::ome::xml::meta::MetadataRetrieve > & ome::files::detail::FormatWriter::getMetadataRetrieve | ( |  | ) |
| virtual

Get the current metadata store for this writer.

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

Implements ome::files::FormatWriter.

References metadataRetrieve.

ome::xml::model::enums::PixelType ome::files::detail::FormatWriter::getPixelType | ( |  | ) | const
| virtual

Get the pixel type.

Returns
  the pixel type.

References getSeries(), metadataRetrieve, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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const std::set< ome::xml::model::enums::PixelType > & ome::files::detail::FormatWriter::getPixelTypes | ( |  | ) | const
| virtual

Get supported pixel types.

Returns
  the supported pixel types.

Implements ome::files::FormatWriter.

Referenced by isSupportedType().

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const std::set< ome::xml::model::enums::PixelType > & ome::files::detail::FormatWriter::getPixelTypes | ( | const std::string & | codec | ) | const
| virtual

Get supported pixel types for the given codec.

Parameters

  codec | the codec to check.

Returns
  the supported pixel types.

Implements ome::files::FormatWriter.

References ome::files::detail::WriterProperties::codec_pixel_types, and writerProperties.

dimension_size_type ome::files::detail::FormatWriter::getPlane | ( |  | ) | const
| virtual

Get the active plane.

Returns
  the active plane.

Implements ome::files::FormatWriter.

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

Referenced by ome::files::out::MinimalTIFFWriter::setPlane(), ome::files::out::OMETIFFWriter::setPlane(), setPlane(), ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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dimension_size_type ome::files::detail::FormatWriter::getRGBChannelCount | ( | dimension_size_type | channel | ) | const
| virtual

Get the number of channels required for a call to saveBytes().

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.

References getSeries(), metadataRetrieve, and series.

Referenced by isRGB(), ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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dimension_size_type ome::files::detail::FormatWriter::getSeries | ( |  | ) | const
| virtual

Get the active series.

Returns
  the active series.

Implements ome::files::FormatWriter.

References ome::files::FormatHandler::assertId(), currentId, and series.

Referenced by getBitsPerPixel(), getDimensionOrder(), getEffectiveSizeC(), getPixelType(), getRGBChannelCount(), getSizeC(), getSizeT(), getSizeX(), getSizeY(), getSizeZ(), ome::files::out::MinimalTIFFWriter::saveBytes(), ome::files::out::OMETIFFWriter::saveBytes(), saveBytes(), ome::files::out::MinimalTIFFWriter::setSeries(), ome::files::out::OMETIFFWriter::setSeries(), and setSeries().

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dimension_size_type ome::files::detail::FormatWriter::getSeriesCount | ( |  | ) | const
| virtual

Get the number of image series in this file.

Returns
  the number of image series.

Exceptions

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

References metadataRetrieve.

Referenced by ome::files::out::OMETIFFWriter::fillMetadata(), and setSeries().

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dimension_size_type ome::files::detail::FormatWriter::getSizeC | ( |  | ) | const
| virtual

Get the size of the C dimension.

Returns
  the C dimension size.

References getSeries(), metadataRetrieve, and series.

dimension_size_type ome::files::detail::FormatWriter::getSizeT | ( |  | ) | const
| virtual

Get the size of the T dimension.

Returns
  the T dimension size.

References getSeries(), metadataRetrieve, and series.

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

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dimension_size_type ome::files::detail::FormatWriter::getSizeX | ( |  | ) | const
| virtual

Get the size of the X dimension.

Returns
  the X dimension size.

References getSeries(), metadataRetrieve, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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dimension_size_type ome::files::detail::FormatWriter::getSizeY | ( |  | ) | const
| virtual

Get the size of the Y dimension.

Returns
  the Y dimension size.

References getSeries(), metadataRetrieve, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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dimension_size_type ome::files::detail::FormatWriter::getSizeZ | ( |  | ) | const
| virtual

Get the size of the Z dimension.

Returns
  the Z dimension size.

References getSeries(), metadataRetrieve, and series.

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

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const std::vector< boost::filesystem::path > & ome::files::detail::FormatWriter::getSuffixes | ( |  | ) | const
| virtual

Get the default file suffixes for this file format.

Returns
  a list of file suffixes.

Implements ome::files::FormatHandler.

References ome::files::detail::WriterProperties::suffixes, and writerProperties.

bool ome::files::detail::FormatWriter::getWriteSequentially | ( |  | ) | const
| virtual

Check if planes are written sequentially.

Returns
  `true` if sequential, `false` if not.

Implements ome::files::FormatWriter.

References sequential.

ome::compat::array< dimension_size_type, 3 > ome::files::detail::FormatWriter::getZCTCoords | ( | dimension_size_type | index | ) | const
| virtual

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

Parameters

  index | the linear index.

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

Todo:
  unify with the pixel buffer dimension indexes.

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

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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bool ome::files::detail::FormatWriter::isRGB | ( | dimension_size_type | channel | ) | const
| virtual

Does a channel contain subchannels?

Check if the image planes in the file have more than one subchannel per openBytes() call for the specified channel.

Parameters

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

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

References getRGBChannelCount().

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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bool ome::files::detail::FormatWriter::isSupportedType | ( | ome::xml::model::enums::PixelType | type | ) | const
| virtual

Check if the pixel type is supported.

Parameters

  type | the pixel type to check.

Returns
  `true` if supported, `false` otherwise.

Implements ome::files::FormatWriter.

bool ome::files::detail::FormatWriter::isSupportedType | ( | ome::xml::model::enums::PixelType | type,
|  | const std::string & | codec
| ) |  | const
| virtual

Check if the pixel type is supported by the given codex.

Parameters

  type | the pixel type to check.
  codec | the codec to check.

Returns
  `true` if supported, `false` otherwise.

Implements ome::files::FormatWriter.

References getPixelTypes().

bool ome::files::detail::FormatWriter::isThisType | ( | const boost::filesystem::path & | name,
|  | bool | open = `true`
| ) |  | const
| virtual

Check if the given file is a valid instance of this file format.

Parameters

  name | the file to open for checking.
  open | If `true`, and the file extension is insufficient to determine the file type, the file may be opened for further analysis, or other relatively expensive file system operations (such as file existence tests and directory listings) may be performed. If `false`, file system access is not allowed.

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

Todo:
  Could this method be static?

Implements ome::files::FormatHandler.

References ome::files::FormatHandler::checkSuffix(), ome::files::detail::WriterProperties::compression_suffixes, ome::files::detail::WriterProperties::suffixes, and writerProperties.

void ome::files::detail::FormatWriter::saveBytes | ( | dimension_size_type | plane,
|  | VariantPixelBuffer & | buf
| ) |  |
| virtual

Save an image plane.

Write an image plane from a VariantPixelBuffer of size

getSizeX * getSizeY * bytesPerPixel * getRGBChannelCount()

to the current series in the current file.

Parameters

  plane | the plane index within the series.
  buf | the source pixel buffer.

Exceptions

  FormatException | if any of the parameters are invalid.

Implements ome::files::FormatWriter.

References ome::files::FormatHandler::assertId(), currentId, getSeries(), and metadataRetrieve.

void ome::files::detail::FormatWriter::setCompression | ( | const std::string & | compression | ) |
| virtual

Set the compression type to use when writing.

Parameters

  compression | the compression type.

Implements ome::files::FormatWriter.

References compression, ome::files::detail::WriterProperties::compression_types, and writerProperties.

void ome::files::detail::FormatWriter::setFramesPerSecond | ( | frame_rate_type | rate | ) |
| virtual

Set the frame rate to use when writing.

Parameters

  rate | the frame rate (number of frames per second).

Implements ome::files::FormatWriter.

References framesPerSecond.

void ome::files::detail::FormatWriter::setId | ( | const boost::filesystem::path & | id | ) |
| virtual

Set the current file name.

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

Parameters

  id | the filename to open.

Implements ome::files::FormatHandler.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References ome::common::canonical(), currentId, and out.

Referenced by changeOutputFile(), and ome::files::out::OMETIFFWriter::setId().

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void ome::files::detail::FormatWriter::setInterleaved | ( | bool | interleaved | ) |
| virtual

Set subchannel interleaving.

Parameters

  interleaved | `true` to enable interleaving (chunky) or `false` to disable interleaving (planar).

Implements ome::files::FormatWriter.

References interleaved.

void ome::files::detail::FormatWriter::setLookupTable | ( | dimension_size_type | plane,
|  | const VariantPixelBuffer & | buf
| ) |  |
| virtual

Set the color lookup table associated with the current series.

If the pixel type of the lookup table is unsupported by the file format, this method will throw an exception.

Parameters

  plane | the plane index within the series.
  buf | the source pixel buffer.

Implements ome::files::FormatWriter.

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

void ome::files::detail::FormatWriter::setMetadataRetrieve | ( | ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > & | retrieve | ) |
| virtual

Set the default metadata store for this writer.

Parameters

  retrieve | a metadata retrieve implementation.

Implements ome::files::FormatWriter.

References ome::files::FormatHandler::assertId(), currentId, and metadataRetrieve.

void ome::files::detail::FormatWriter::setPlane | ( | dimension_size_type | plane | ) | const
| virtual

Set the active plane.

Parameters

  plane | the plane to activate.

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

Implements ome::files::FormatWriter.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References ome::files::FormatHandler::assertId(), currentId, getImageCount(), getPlane(), and plane.

Referenced by ome::files::out::MinimalTIFFWriter::setPlane(), and ome::files::out::OMETIFFWriter::setPlane().

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void ome::files::detail::FormatWriter::setSeries | ( | dimension_size_type | series | ) | const
| virtual

Set the active series.

Parameters

  series | the series to activate.

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

Implements ome::files::FormatWriter.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References ome::files::FormatHandler::assertId(), currentId, getSeries(), getSeriesCount(), plane, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setSeries(), and ome::files::out::OMETIFFWriter::setSeries().

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void ome::files::detail::FormatWriter::setWriteSequentially | ( | bool | sequential = `true` | ) |
| virtual

Write planes sequentially.

Set if planes will be written sequentially. If planes are written sequentially and this flag is set, then performance will be slightly improved.

Parameters

  sequential | `true` if sequential, `false` if not.

Implements ome::files::FormatWriter.

References sequential.

## Member Data Documentation

ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve> ome::files::detail::FormatWriter::metadataRetrieve
| protected

Current metadata store.

Should never be accessed directly as the semantics of getMetadataRetrieve() prevent "null" access.

Referenced by close(), ome::files::out::OMETIFFWriter::fillMetadata(), getBitsPerPixel(), getDimensionOrder(), getEffectiveSizeC(), getMetadataRetrieve(), getPixelType(), getRGBChannelCount(), getSeriesCount(), getSizeC(), getSizeT(), getSizeX(), getSizeY(), getSizeZ(), saveBytes(), ome::files::out::MinimalTIFFWriter::setId(), ome::files::out::OMETIFFWriter::setId(), and setMetadataRetrieve().

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

- ome/files/detail/FormatWriter.h
- ome/files/detail/FormatWriter.cpp