large_image_source_tifffile package¶
Submodules¶
large_image_source_tifffile.girder_source module¶
- class large_image_source_tifffile.girder_source.TifffileGirderTileSource(*args, **kwargs)[source]¶
Bases:
TifffileFileTileSource
,GirderTileSource
Provides tile access to Girder items with files that tifffile can read.
Initialize the tile class. See the base class for other available parameters.
- Parameters:
path – a filesystem path for the tile source.
- cacheName = 'tilesource'¶
- name = 'tifffile'¶
Module contents¶
- class large_image_source_tifffile.TifffileFileTileSource(*args, **kwargs)[source]¶
Bases:
FileTileSource
Provides tile access to files that the tifffile library can read.
Initialize the tile class. See the base class for other available parameters.
- Parameters:
path – a filesystem path for the tile source.
- cacheName = 'tilesource'¶
- extensions = {'scn': 1, 'tif': 5, 'tiff': 5, None: 5}¶
- 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.
- getTile(x, y, z, pilImageAllowed=False, numpyAllowed=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.
- mimeTypes = {'image/scn': 1, 'image/tiff': 5, 'image/x-tiff': 5, None: 8}¶
- name = 'tifffile'¶
- large_image_source_tifffile.canRead(*args, **kwargs)[source]¶
Check if an input can be read by the module class.