large_image_source_tiff package

Submodules

large_image_source_tiff.girder_source module

class large_image_source_tiff.girder_source.TiffGirderTileSource(*args, **kwargs)[source]

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'

Name of the tile source

large_image_source_tiff.tiff_reader module

exception large_image_source_tiff.tiff_reader.IOTiffException[source]

Bases: TiffException

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

exception large_image_source_tiff.tiff_reader.InvalidOperationTiffException[source]

Bases: TiffException

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

exception large_image_source_tiff.tiff_reader.TiffException[source]

Bases: Exception

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

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

InvalidOperationTiffException or IOTiffException or ValidationTiffException

CoreFunctions = ['SetDirectory', 'SetSubDirectory', 'GetField', 'LastDirectory', 'GetMode', 'IsTiled', 'IsByteSwapped', 'IsUpSampled', 'IsMSB2LSB', 'NumberOfStrips']
getTile(x, y)[source]

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.

Returns

either a buffer with a JPEG or a PIL image.

Return type

bytes

Raises

InvalidOperationTiffException or IOTiffException

property imageHeight
property imageWidth
parse_image_description(meta=None)[source]
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

exception large_image_source_tiff.tiff_reader.ValidationTiffException[source]

Bases: TiffException

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

large_image_source_tiff.tiff_reader.patchLibtiff()[source]

Module contents

class large_image_source_tiff.TiffFileTileSource(*args, **kwargs)[source]

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 = {None: 4, 'tif': 3, 'tiff': 3, 'ptif': 1, 'ptiff': 1}

A dictionary of known file extensions and the SourcePriority given to each. It must contain a None key with a priority for the tile source when the extension does not match.

getAssociatedImagesList()[source]

Get a list of all associated images.

Returns

the list of image keys.

getInternalMetadata(**kwargs)[source]

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()[source]

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

Returns

metadata dictionary.

getNativeMagnification()[source]

Get the magnification at a particular level.

Returns

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

getPreferredLevel(level)[source]

Given a desired level (0 is minimum resolution, self.levels - 1 is max resolution), return the level that contains actual data that is no lower resolution.

Parameters

level – desired level

Returns level

a level with actual data that is no lower resolution.

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

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.

getTileFromEmptyDirectory(x, y, z, **kwargs)[source]

Given the x, y, z tile location in an unpopulated level, get tiles from higher resolution levels to make the lower-res tile.

Parameters
  • x – location of tile within original level.

  • y – location of tile within original level.

  • z – original level.

Returns

tile in PIL format.

getTileIOTiffError(x, y, z, pilImageAllowed=False, numpyAllowed=False, sparseFallback=False, exception=None, **kwargs)[source]
mimeTypes = {None: 8, 'image/tiff': 3, 'image/x-tiff': 3, 'image/x-ptif': 1}

A dictionary of common mime-types handled by the source and the SourcePriority given to each. This are used in place of or in additional to extensions.

name = 'tifffile'

Name of the tile source

large_image_source_tiff.canRead(*args, **kwargs)[source]

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

large_image_source_tiff.open(*args, **kwargs)[source]

Create an instance of the module class.