large_image_source_tiff package

Submodules

large_image_source_tiff.exceptions module

exception large_image_source_tiff.exceptions.IOOpenTiffError

Bases: IOTiffError

An exception caused by an internal failure where the file cannot be opened by the main library.

exception large_image_source_tiff.exceptions.IOTiffError

Bases: TiffError

An exception caused by an internal failure, due to an invalid file or other error.

exception large_image_source_tiff.exceptions.InvalidOperationTiffError

Bases: TiffError

An exception caused by the user making an invalid request of a TIFF file.

exception large_image_source_tiff.exceptions.TiffError

Bases: Exception

exception large_image_source_tiff.exceptions.ValidationTiffError

Bases: TiffError

An exception caused by the TIFF reader not being able to support a given file.

large_image_source_tiff.girder_source module

class large_image_source_tiff.girder_source.TiffGirderTileSource(*args, **kwargs)

Bases: TiffFileTileSource, GirderTileSource

Provides tile access to Girder items with a TIFF file.

Initialize the tile class. See the base class for other available parameters.

Parameters:

path – a filesystem path for the tile source.

cacheName = 'tilesource'

name = 'tiff'

large_image_source_tiff.tiff_reader module

class large_image_source_tiff.tiff_reader.TiledTiffDirectory(filePath, directoryNum, mustBeTiled=True, subDirectoryNum=0, validate=True)

Bases: object

Create a new reader for a tiled image file directory in a TIFF file.

Parameters:

• filePath (str) – A path to a TIFF file on disk.

• directoryNum (int) – The number of the TIFF image file directory to open.

• mustBeTiled (bool) – if True, only tiled images validate. If False, only non-tiled images validate. None validates both.

• subDirectoryNum (int) – if set, the number of the TIFF subdirectory.

• validate – if False, don’t validate that images can be read.

Raises:

InvalidOperationTiffError or IOTiffError or ValidationTiffError

CoreFunctions = ['SetDirectory', 'SetSubDirectory', 'GetField', 'LastDirectory', 'GetMode', 'IsTiled', 'IsByteSwapped', 'IsUpSampled', 'IsMSB2LSB', 'NumberOfStrips']

getTile(x, y, asarray=False)

Get the complete JPEG image from a tile.

Parameters:

• x (int) – The column index of the desired tile.

• y (int) – The row index of the desired tile.

• asarray (boolean) – If True, read jpeg compressed images as arrays.

Returns:

either a buffer with a JPEG or a PIL image.

Return type:

bytes

Raises:

InvalidOperationTiffError or IOTiffError

property imageHeight

property imageWidth

parse_image_description(meta=None)

property pixelInfo

property tileHeight

Get the pixel height of tiles.

Returns:

The tile height in pixels.

Return type:

int

property tileWidth

Get the pixel width of tiles.

Returns:

The tile width in pixels.

Return type:

int

large_image_source_tiff.tiff_reader.patchLibtiff()

Module contents

class large_image_source_tiff.TiffFileTileSource(*args, **kwargs)

Bases: FileTileSource

Provides tile access to TIFF files.

Initialize the tile class. See the base class for other available parameters.

Parameters:

path – a filesystem path for the tile source.

cacheName = 'tilesource'

extensions: Dict[str | None, SourcePriority] = {'ptif': SourcePriority.PREFERRED, 'ptiff': SourcePriority.PREFERRED, 'qptiff': SourcePriority.PREFERRED, 'svs': SourcePriority.MEDIUM, 'tif': SourcePriority.HIGH, 'tiff': SourcePriority.HIGH, None: SourcePriority.MEDIUM}

getAssociatedImagesList()

Get a list of all associated images.

Returns:

the list of image keys.

getInternalMetadata(**kwargs)

Return additional known metadata about the tile source. Data returned from this method is not guaranteed to be in any particular format or have specific values.

Returns:

a dictionary of data or None.

getMetadata()

Return a dictionary of metadata containing levels, sizeX, sizeY, tileWidth, tileHeight, magnification, mm_x, mm_y, and frames.

Returns:

metadata dictionary.

getNativeMagnification()

Get the magnification at a particular level.

Returns:

magnification, width of a pixel in mm, height of a pixel in mm.

getTiffDir(directoryNum, mustBeTiled=True, subDirectoryNum=0, validate=True)

Get a tile tiff directory reader class.

Parameters:

• directoryNum – The number of the TIFF image file directory to open.

• mustBeTiled – if True, only tiled images validate. If False, only non-tiled images validate. None validates both.

• subDirectoryNum – if set, the number of the TIFF subdirectory.

• validate – if False, don’t validate that images can be read.

Returns:

a class that can read from a specific tiff directory.

getTile(x, y, z, pilImageAllowed=False, numpyAllowed=False, sparseFallback=False, **kwargs)

Get a tile from a tile source, returning it as an binary image, a PIL image, or a numpy array.

Parameters:

• x – the 0-based x position of the tile on the specified z level. 0 is left.

• y – the 0-based y position of the tile on the specified z level. 0 is top.

• z – the z level of the tile. May range from [0, self.levels], where 0 is the lowest resolution, single tile for the whole source.

• pilImageAllowed – True if a PIL image may be returned.

• numpyAllowed – True if a numpy image may be returned. ‘always’ to return a numpy array.

• sparseFallback – if False and a tile doesn’t exist, raise an error. If True, check if a lower resolution tile exists, and, if so, interpolate the needed data for this tile.

• frame – the frame number within the tile source. None is the same as 0 for multi-frame sources.

Returns:

either a numpy array, a PIL image, or a memory object with an image file.

getTileIOTiffError(x, y, z, pilImageAllowed=False, numpyAllowed=False, sparseFallback=False, exception=None, **kwargs)

mimeTypes: Dict[str | None, SourcePriority] = {'image/tiff': SourcePriority.HIGH, 'image/x-ptif': SourcePriority.PREFERRED, 'image/x-tiff': SourcePriority.HIGH, None: SourcePriority.FALLBACK}

name = 'tiff'

large_image_source_tiff.canRead(*args, **kwargs)

Check if an input can be read by the module class.

large_image_source_tiff.open(*args, **kwargs)

Create an instance of the module class.