large_image_source_tiff package¶
Submodules¶
large_image_source_tiff.exceptions module¶
- exception large_image_source_tiff.exceptions.IOOpenTiffError[source]¶
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[source]¶
Bases:
TiffError
An exception caused by an internal failure, due to an invalid file or other error.
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'¶
large_image_source_tiff.tiff_reader module¶
- 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:
InvalidOperationTiffError or IOTiffError or ValidationTiffError
- 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:
InvalidOperationTiffError or IOTiffError
- property imageHeight¶
- property imageWidth¶
- 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
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, 'qptiff': 1}¶
- 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}¶
- name = 'tiff'¶