large_image_source_ometiff package¶
Submodules¶
large_image_source_ometiff.girder_source module¶
- class large_image_source_ometiff.girder_source.OMETiffGirderTileSource(*args, **kwargs)[source]¶
Bases:
OMETiffFileTileSource
,GirderTileSource
Provides tile access to Girder items with an OMETiff 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 = 'ometiff'¶
Module contents¶
- class large_image_source_ometiff.OMETiffFileTileSource(*args, **kwargs)[source]¶
Bases:
TiffFileTileSource
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: 5, 'tif': 4, 'tiff': 4, 'ome': 1}¶
- 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 for the highest-resolution 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.
- name = 'ometiff'¶