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Classes | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
ome::files::tiff::IFD Class Reference

Image File Directory (IFD). More...

`#include <ome/files/tiff/IFD.h>`

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## Classes
class | Impl
| Internal implementation details of OffsetIFD. More...

## Public Member Functions
virtual | ~IFD ()
| Destructor.
ome::compat::shared_ptr< TIFF > & | getTIFF () const
| Get the source TIFF this descriptor belongs to. More...
void | makeCurrent () const
| Make this IFD the current directory. More...
offset_type | getOffset () const
| Get the directory offset. More...
void | getRawField (tag_type tag,...) const
| Get a field by its tag number. More...
void | setRawField (tag_type tag,...)
| Set a field by its tag number. More...
template<typename TagCategory >
Field< TagCategory > | getField (TagCategory tag)
| Get a Field by its tag enumeration. More...
template<typename TagCategory >
const Field< TagCategory > | getField (TagCategory tag) const
| Get a Field by its tag enumeration. More...
TileType | getTileType () const
| Get the tile type. More...
void | setTileType (TileType type)
| Set the tile type. More...
dimension_size_type | getCurrentTile () const
| Get the current tile being written. More...
void | setCurrentTile (dimension_size_type tile)
| Set the current tile being written. More...
TileInfo | getTileInfo ()
| Get tiling metadata. More...
const TileInfo | getTileInfo () const
| Get tiling metadata. More...
std::vector< TileCoverage > & | getTileCoverage ()
| Get tile coverage cache. More...
const std::vector< TileCoverage > & | getTileCoverage () const
| Get tile coverage cache. More...
uint32_t | getImageWidth () const
| Get the image width. More...
void | setImageWidth (uint32_t width)
| Set the image width. More...
uint32_t | getImageHeight () const
| Get the image height. More...
void | setImageHeight (uint32_t height)
| Set the image height. More...
uint32_t | getTileWidth () const
| Get the tile width. More...
void | setTileWidth (uint32_t width)
| Set the tile width. More...
uint32_t | getTileHeight () const
| Get the tile height. More...
void | setTileHeight (uint32_t height)
| Set the tile height. More...
::ome::xml::model::enums::PixelType | getPixelType () const
| Get the OME data model PixelType. More...
void | setPixelType (::ome::xml::model::enums::PixelType type)
| Set the OME data model PixelType. More...
uint16_t | getBitsPerSample () const
| Get bits per sample. More...
void | setBitsPerSample (uint16_t samples)
| Set bits per sample. More...
uint16_t | getSamplesPerPixel () const
| Get samples per pixel. More...
void | setSamplesPerPixel (uint16_t samples)
| Set samples per pixel. More...
PlanarConfiguration | getPlanarConfiguration () const
| Get planar configuration. More...
void | setPlanarConfiguration (PlanarConfiguration planarconfig)
| Set planar configuration. More...
PhotometricInterpretation | getPhotometricInterpretation () const
| Get photometric interpretation. More...
void | setPhotometricInterpretation (PhotometricInterpretation photometric)
| Set photometric interpretation. More...
void | readImage (VariantPixelBuffer &buf) const
| Read a whole image plane into a pixel buffer. More...
void | readImage (VariantPixelBuffer &buf, dimension_size_type subC) const
| Read a whole image plane into a pixel buffer. More...
void | readImage (VariantPixelBuffer &dest, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h) const
| Read a region of an image plane into a pixel buffer. More...
void | readImage (VariantPixelBuffer &dest, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h, dimension_size_type subC) const
| Read a region of an image plane into a pixel buffer. More...
void | readLookupTable (VariantPixelBuffer &buf) const
| Read a lookup table into a pixel buffer. More...
void | writeImage (const VariantPixelBuffer &buf)
| Write a whole image plane from a pixel buffer. More...
void | writeImage (const VariantPixelBuffer &buf, dimension_size_type subC)
| Write a whole image plane from a pixel buffer. More...
void | writeImage (const VariantPixelBuffer &source, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h)
| Write a whole image plane from a pixel buffer. More...
void | writeImage (const VariantPixelBuffer &source, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h, dimension_size_type subC)
| Write a whole image plane from a pixel buffer. More...
ome::compat::shared_ptr< IFD > | next () const
| Get next directory. More...
bool | last () const
| Check if this is the last directory. More...

## Static Public Member Functions
static ome::compat::shared_ptr< IFD > | openIndex (ome::compat::shared_ptr< TIFF > &tiff, directory_index_type index)
| Open an IFD by index. More...
static ome::compat::shared_ptr< IFD > | openOffset (ome::compat::shared_ptr< TIFF > &tiff, offset_type offset)
| Open an IFD. More...
static ome::compat::shared_ptr< IFD > | current (ome::compat::shared_ptr< TIFF > &tiff)
| Get the current IFD. More...

## Protected Member Functions
| IFD (ome::compat::shared_ptr< TIFF > &tiff, offset_type offset)
| Constructor (not public).
| IFD (ome::compat::shared_ptr< TIFF > &tiff)
| Constructor (not public).

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

## Private Attributes
ome::compat::shared_ptr< Impl > | impl
| Private implementation details.

## Detailed Description

Image File Directory (IFD).

An IFD represents a subfile within a TIFF.

## Member Function Documentation

ome::compat::shared_ptr< IFD > ome::files::tiff::IFD::current | ( | ome::compat::shared_ptr< TIFF > & | tiff | ) |
| static

Get the current IFD.

Parameters

  tiff | the source TIFF.

Returns
  the open IFD.

Referenced by ome::files::tiff::TIFF::getCurrentDirectory().

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uint16_t ome::files::tiff::IFD::getBitsPerSample | ( |  | ) | const

Get bits per sample.

Returns
  the number of bits per sample.

References ome::files::tiff::BITSPERSAMPLE, getField(), and impl.

Referenced by ome::files::tiff::getCoreMetadata(), and getPixelType().

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dimension_size_type ome::files::tiff::IFD::getCurrentTile | ( |  | ) | const

Get the current tile being written.

This is the tile currently being modified pending flush.

Returns
  the current tile.

References impl.

template<typename TagCategory >

Field<TagCategory> ome::files::tiff::IFD::getField | ( | TagCategory | tag | ) |
| inline

Get a Field by its tag enumeration.

Parameters

  tag | the field identifier.

Returns
  the Field corresponding to the tag.

Referenced by getBitsPerSample(), ome::files::tiff::getCoreMetadata(), getImageHeight(), getImageWidth(), getPhotometricInterpretation(), getPixelType(), getPlanarConfiguration(), getSamplesPerPixel(), getTileHeight(), getTileType(), getTileWidth(), ome::files::tiff::ImageJMetadata::ImageJMetadata(), readLookupTable(), setBitsPerSample(), setImageHeight(), setImageWidth(), setPhotometricInterpretation(), setPixelType(), setPlanarConfiguration(), setSamplesPerPixel(), setTileHeight(), and setTileWidth().

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template<typename TagCategory >

const Field<TagCategory> ome::files::tiff::IFD::getField | ( | TagCategory | tag | ) | const
| inline

Get a Field by its tag enumeration.

Parameters

  tag | the field identifier.

Returns
  the Field corresponding to the tag.

uint32_t ome::files::tiff::IFD::getImageHeight | ( |  | ) | const

Get the image height.

Returns
  the image height.

References getField(), ome::files::tiff::IMAGELENGTH, and impl.

Referenced by ome::files::tiff::getCoreMetadata(), readImage(), and writeImage().

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uint32_t ome::files::tiff::IFD::getImageWidth | ( |  | ) | const

Get the image width.

Returns
  the image width.

References getField(), ome::files::tiff::IMAGEWIDTH, and impl.

Referenced by ome::files::tiff::getCoreMetadata(), getTileWidth(), readImage(), and writeImage().

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offset_type ome::files::tiff::IFD::getOffset | ( |  | ) | const

Get the directory offset.

Internally this is simply a call to TIFFCurrentDirOffset.

Returns
  the directory offset.

References impl.

PhotometricInterpretation ome::files::tiff::IFD::getPhotometricInterpretation | ( |  | ) | const

Get photometric interpretation.

Returns
  the photometric interpretation of sample values.

References getField(), impl, and ome::files::tiff::PHOTOMETRIC.

Referenced by ome::files::tiff::getCoreMetadata().

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ome::xml::model::enums::PixelType ome::files::tiff::IFD::getPixelType | ( |  | ) | const

Get the OME data model PixelType.

This is computed based upon the SampleFormat and BitsPerSample tags for this IFD.

Returns
  the PixelType.

Exceptions

  an | Exception if there is no corresponding PixelType for the SampleFormat and BitsPerSample in use.

References ome::files::tiff::COMPLEX_FLOAT, ome::files::tiff::FLOAT, getBitsPerSample(), getField(), impl, ome::files::tiff::SAMPLEFORMAT, ome::files::tiff::SIGNED_INT, and ome::files::tiff::UNSIGNED_INT.

Referenced by ome::files::tiff::getCoreMetadata(), readImage(), setBitsPerSample(), and writeImage().

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PlanarConfiguration ome::files::tiff::IFD::getPlanarConfiguration | ( |  | ) | const

Get planar configuration.

Returns
  the number of planar configuration.

References getField(), impl, and ome::files::tiff::PLANARCONFIG.

Referenced by ome::files::tiff::getCoreMetadata(), readImage(), and writeImage().

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void ome::files::tiff::IFD::getRawField | ( | tag_type | tag,
|  |  | ...
| ) |  | const

Get a field by its tag number.

Note
  This should not be used except internally. Use getField(TagCategory) instead which offers a type-safe interface on top of this lower-level TIFFGetField wrapper.

Parameters

  tag | the tag number.
  ... | pointers to variables to store the value(s) in.

References ome::files::tiff::Sentry::error(), getTIFF(), and makeCurrent().

uint16_t ome::files::tiff::IFD::getSamplesPerPixel | ( |  | ) | const

Get samples per pixel.

Returns
  the number of samples per pixel.

References getField(), impl, and ome::files::tiff::SAMPLESPERPIXEL.

Referenced by ome::files::tiff::getCoreMetadata(), readImage(), and writeImage().

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ome::compat::shared_ptr< TIFF > & ome::files::tiff::IFD::getTIFF | ( |  | ) | const

Get the source TIFF this descriptor belongs to.

Returns
  the source TIFF.

References impl.

Referenced by getRawField(), last(), makeCurrent(), next(), and setRawField().

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std::vector< TileCoverage > & ome::files::tiff::IFD::getTileCoverage | ( |  | ) |

Get tile coverage cache.

Returns
  the TileCoverage cache for this IFD.

References impl.

const std::vector< TileCoverage > & ome::files::tiff::IFD::getTileCoverage | ( |  | ) | const

Get tile coverage cache.

Returns
  the TileCoverage cache for this IFD.

References impl.

uint32_t ome::files::tiff::IFD::getTileHeight | ( |  | ) | const

Get the tile height.

Returns
  the tile height.

References getField(), getTileType(), impl, ome::files::tiff::ROWSPERSTRIP, ome::files::tiff::TILE, and ome::files::tiff::TILELENGTH.

TileInfo ome::files::tiff::IFD::getTileInfo | ( |  | ) |

Get tiling metadata.

Returns
  the TileInfo metadata for this IFD.

Exceptions

  an | Exception if tiles are not supported.

Referenced by readImage(), and writeImage().

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const TileInfo ome::files::tiff::IFD::getTileInfo | ( |  | ) | const

Get tiling metadata.

Returns
  the TileInfo metadata for this IFD.

Exceptions

  an | Exception if tiles are not supported.

TileType ome::files::tiff::IFD::getTileType | ( |  | ) | const

Get the tile type.

Returns
  the tile type.

References getField(), impl, ome::files::tiff::ROWSPERSTRIP, ome::files::tiff::STRIP, ome::files::tiff::TILE, ome::files::tiff::TILELENGTH, and ome::files::tiff::TILEWIDTH.

Referenced by getTileHeight(), getTileWidth(), setTileHeight(), and setTileWidth().

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uint32_t ome::files::tiff::IFD::getTileWidth | ( |  | ) | const

Get the tile width.

Returns
  the tile width.

References getField(), getImageWidth(), getTileType(), impl, ome::files::tiff::TILE, and ome::files::tiff::TILEWIDTH.

bool ome::files::tiff::IFD::last | ( |  | ) | const

Check if this is the last directory.

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

References getTIFF(), and makeCurrent().

void ome::files::tiff::IFD::makeCurrent | ( |  | ) | const

Make this IFD the current directory.

Internally this is simply a call to TIFFSetDirectory.

References ome::files::tiff::Sentry::error(), getTIFF(), and impl.

Referenced by getRawField(), last(), next(), and setRawField().

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ome::compat::shared_ptr< IFD > ome::files::tiff::IFD::next | ( |  | ) | const

Get next directory.

Returns
  the next directory, or null if this is the last directory.

References getTIFF(), makeCurrent(), and openOffset().

ome::compat::shared_ptr< IFD > ome::files::tiff::IFD::openIndex | ( | ome::compat::shared_ptr< TIFF > & | tiff,
|  | directory_index_type | index
| ) |  |
| static

Open an IFD by index.

Parameters

  tiff | the source TIFF.
  index | the directory index.

Returns
  the open IFD.

References ome::files::tiff::Sentry::error(), and openOffset().

Referenced by ome::files::tiff::TIFF::getDirectoryByIndex().

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ome::compat::shared_ptr< IFD > ome::files::tiff::IFD::openOffset | ( | ome::compat::shared_ptr< TIFF > & | tiff,
|  | offset_type | offset
| ) |  |
| static

Open an IFD.

Parameters

  tiff | the source TIFF.
  offset | the directory offset.

Returns
  the open IFD.

Referenced by ome::files::tiff::TIFF::getDirectoryByOffset(), next(), and openIndex().

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void ome::files::tiff::IFD::readImage | ( | VariantPixelBuffer & | buf | ) | const

Read a whole image plane into a pixel buffer.

Parameters

  buf | the destination pixel buffer.

References getImageHeight(), and getImageWidth().

Referenced by readImage().

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void ome::files::tiff::IFD::readImage | ( | VariantPixelBuffer & | buf,
|  | dimension_size_type | subC
| ) |  | const

Read a whole image plane into a pixel buffer.

Parameters

  buf | the destination pixel buffer.
  subC | the subchannel to read.

References getImageHeight(), getImageWidth(), and readImage().

void ome::files::tiff::IFD::readImage | ( | VariantPixelBuffer & | dest,
|  | dimension_size_type | x,
|  | dimension_size_type | y,
|  | dimension_size_type | w,
|  | dimension_size_type | h
| ) |  | const

Read a region of an image plane into a pixel buffer.

If the destination pixel buffer is of a different size to the region being read, or is of the incorrect pixel type, or has a different storage order, it will be resized using the correct pixel type and storage order.

Parameters

  dest | the destination pixel buffer.
  x | the `X` coordinate of the upper-left corner of the sub-image.
  y | the `Y` coordinate of the upper-left corner of the sub-image.
  w | the width of the sub-image.
  h | the height of the sub-image.

References ome::files::DIM_CHANNEL, ome::files::DIM_MODULO_C, ome::files::DIM_MODULO_T, ome::files::DIM_MODULO_Z, ome::files::DIM_SPATIAL_X, ome::files::DIM_SPATIAL_Y, ome::files::DIM_SPATIAL_Z, ome::files::DIM_SUBCHANNEL, ome::files::DIM_TEMPORAL_T, ome::files::PixelBufferBase::dimensions, getPixelType(), getPlanarConfiguration(), getSamplesPerPixel(), getTileInfo(), ome::files::PixelBufferBase::make_storage_order(), ome::files::VariantPixelBuffer::pixelType(), ome::files::tiff::SEPARATE, ome::files::VariantPixelBuffer::setBuffer(), ome::files::VariantPixelBuffer::shape(), ome::files::VariantPixelBuffer::storage_order(), ome::files::tiff::TileInfo::tileCoverage(), ome::files::VariantPixelBuffer::vbuffer(), and ome::xml::model::enums::DimensionOrder::XYZTC.

void ome::files::tiff::IFD::readImage | ( | VariantPixelBuffer & | dest,
|  | dimension_size_type | x,
|  | dimension_size_type | y,
|  | dimension_size_type | w,
|  | dimension_size_type | h,
|  | dimension_size_type | subC
| ) |  | const

Read a region of an image plane into a pixel buffer.

If the destination pixel buffer is of a different size to the region being read, or is of the incorrect pixel type, or has a different storage order, it will be resized using the correct pixel type and storage order.

Parameters

  dest | the destination pixel buffer.
  x | the `X` coordinate of the upper-left corner of the sub-image.
  y | the `Y` coordinate of the upper-left corner of the sub-image.
  w | the width of the sub-image.
  h | the height of the sub-image.
  subC | the subchannel to read.

References readImage(), and ome::files::VariantPixelBuffer::vbuffer().

void ome::files::tiff::IFD::readLookupTable | ( | VariantPixelBuffer & | buf | ) | const

Read a lookup table into a pixel buffer.

Parameters

  buf | the destination pixel buffer.

References ome::files::tiff::COLORMAP, ome::files::DIM_CHANNEL, ome::files::DIM_MODULO_C, ome::files::DIM_MODULO_T, ome::files::DIM_MODULO_Z, ome::files::DIM_SPATIAL_X, ome::files::DIM_SPATIAL_Y, ome::files::DIM_SPATIAL_Z, ome::files::DIM_SUBCHANNEL, ome::files::DIM_TEMPORAL_T, getField(), ome::files::PixelBufferBase::make_storage_order(), ome::files::VariantPixelBuffer::setBuffer(), ome::files::VariantPixelBuffer::vbuffer(), and ome::xml::model::enums::DimensionOrder::XYZTC.

void ome::files::tiff::IFD::setBitsPerSample | ( | uint16_t | samples | ) |

Set bits per sample.

Parameters

  samples | the number of bits per sample.

References ome::files::tiff::BITSPERSAMPLE, getField(), getPixelType(), impl, and ome::files::significantBitsPerPixel().

void ome::files::tiff::IFD::setCurrentTile | ( | dimension_size_type | tile | ) |

Set the current tile being written.

This is the tile currently being modified pending flush.

Note
  This should not be set by hand; it will be updated by the code writing out tile data called internally by writeImage().

Parameters

  tile | the current tile.

References impl.

void ome::files::tiff::IFD::setImageHeight | ( | uint32_t | height | ) |

Set the image height.

Parameters

  height | the image height.

References getField(), ome::files::tiff::IMAGELENGTH, and impl.

void ome::files::tiff::IFD::setImageWidth | ( | uint32_t | width | ) |

Set the image width.

Parameters

  width | the image width.

References getField(), ome::files::tiff::IMAGEWIDTH, and impl.

void ome::files::tiff::IFD::setPhotometricInterpretation | ( | PhotometricInterpretation | photometric | ) |

Set photometric interpretation.

Parameters

  photometric | the photometric interpretation of sample values.

References getField(), impl, and ome::files::tiff::PHOTOMETRIC.

void ome::files::tiff::IFD::setPixelType | ( | ::ome::xml::model::enums::PixelType | type | ) |

Set the OME data model PixelType.

This sets the SampleFormat and BitsPerSample tags for this IFD which correspond to the PixelType in use.

Parameters

  type | the PixelType to set.

Exceptions

  an | Exception if the PixelType is invalid.

References ome::files::tiff::COMPLEX_FLOAT, ome::files::tiff::FLOAT, getField(), impl, ome::files::tiff::SAMPLEFORMAT, ome::files::tiff::SIGNED_INT, and ome::files::tiff::UNSIGNED_INT.

void ome::files::tiff::IFD::setPlanarConfiguration | ( | PlanarConfiguration | planarconfig | ) |

Set planar configuration.

Parameters

  planarconfig | the number of planar configuration.

References getField(), impl, and ome::files::tiff::PLANARCONFIG.

void ome::files::tiff::IFD::setRawField | ( | tag_type | tag,
|  |  | ...
| ) |  |

Set a field by its tag number.

Note
  This should not be used except internally. Use getField(TagCategory) instead which offers a type-safe interface on top of this lower-level TIFFSetField wrapper.

Parameters

  tag | the tag number.
  ... | variables containing the value(s) to set.

References ome::files::tiff::Sentry::error(), getTIFF(), and makeCurrent().

void ome::files::tiff::IFD::setSamplesPerPixel | ( | uint16_t | samples | ) |

Set samples per pixel.

Parameters

  samples | the number of samples per pixel.

References getField(), impl, and ome::files::tiff::SAMPLESPERPIXEL.

void ome::files::tiff::IFD::setTileHeight | ( | uint32_t | height | ) |

Set the tile height.

Parameters

  height | the tile height.

References getField(), getTileType(), impl, ome::files::tiff::ROWSPERSTRIP, ome::files::tiff::TILE, and ome::files::tiff::TILELENGTH.

void ome::files::tiff::IFD::setTileType | ( | TileType | type | ) |

Set the tile type.

Parameters

  type | the tile type.

References impl.

void ome::files::tiff::IFD::setTileWidth | ( | uint32_t | width | ) |

Set the tile width.

Parameters

  width | the tile width.

References getField(), getTileType(), impl, ome::files::tiff::TILE, and ome::files::tiff::TILEWIDTH.

void ome::files::tiff::IFD::writeImage | ( | const VariantPixelBuffer & | buf | ) |

Write a whole image plane from a pixel buffer.

Parameters

  buf | the source pixel buffer.

References getImageHeight(), and getImageWidth().

Referenced by writeImage().

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void ome::files::tiff::IFD::writeImage | ( | const VariantPixelBuffer & | buf,
|  | dimension_size_type | subC
| ) |  |

Write a whole image plane from a pixel buffer.

Parameters

  buf | the source pixel buffer.
  subC | the subchannel to write.

References getImageHeight(), getImageWidth(), and writeImage().

void ome::files::tiff::IFD::writeImage | ( | const VariantPixelBuffer & | source,
|  | dimension_size_type | x,
|  | dimension_size_type | y,
|  | dimension_size_type | w,
|  | dimension_size_type | h
| ) |  |

Write a whole image plane from a pixel buffer.

The source pixel buffer must match the size of the region being written, and must also the same pixel type and storage ordering as the TIFF image.

Parameters

  source | the source pixel buffer.
  x | the `X` coordinate of the upper-left corner of the sub-image.
  y | the `Y` coordinate of the upper-left corner of the sub-image.
  w | the width of the sub-image.
  h | the height of the sub-image.

References ome::files::DIM_CHANNEL, ome::files::DIM_MODULO_C, ome::files::DIM_MODULO_T, ome::files::DIM_MODULO_Z, ome::files::DIM_SPATIAL_X, ome::files::DIM_SPATIAL_Y, ome::files::DIM_SPATIAL_Z, ome::files::DIM_SUBCHANNEL, ome::files::DIM_TEMPORAL_T, ome::files::PixelBufferBase::dimensions, getPixelType(), getPlanarConfiguration(), getSamplesPerPixel(), getTileInfo(), impl, ome::files::PixelBufferBase::make_storage_order(), ome::files::VariantPixelBuffer::pixelType(), ome::files::tiff::SEPARATE, ome::files::VariantPixelBuffer::shape(), ome::files::VariantPixelBuffer::storage_order(), ome::files::tiff::TileInfo::tileCoverage(), ome::files::VariantPixelBuffer::vbuffer(), and ome::xml::model::enums::DimensionOrder::XYZTC.

void ome::files::tiff::IFD::writeImage | ( | const VariantPixelBuffer & | source,
|  | dimension_size_type | x,
|  | dimension_size_type | y,
|  | dimension_size_type | w,
|  | dimension_size_type | h,
|  | dimension_size_type | subC
| ) |  |

Write a whole image plane from a pixel buffer.

The source pixel buffer must match the size of the region being written, and must also the same pixel type and storage ordering as the TIFF image.

Parameters

  source | the source pixel buffer.
  x | the `X` coordinate of the upper-left corner of the sub-image.
  y | the `Y` coordinate of the upper-left corner of the sub-image.
  w | the width of the sub-image.
  h | the height of the sub-image.
  subC | the subchannel to write.

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

- ome/files/tiff/IFD.h
- ome/files/tiff/IFD.cpp