large_image_source_tifffile package

Submodules

large_image_source_tifffile.girder_source module

class large_image_source_tifffile.girder_source.TifffileGirderTileSource(*args, **kwargs)

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)

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()

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.

getTile(x, y, z, pilImageAllowed=False, numpyAllowed=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.

mimeTypes = {'image/scn': 1, 'image/tiff': 5, 'image/x-tiff': 5, None: 8}

name = 'tifffile'

large_image_source_tifffile.canRead(*args, **kwargs)

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

large_image_source_tifffile.et_findall(tag, text)

Find all the child tags in an element tree that end with a specific string.

Parameters:

• tag – the tag to search.

• text – the text to end with.

Returns:

a list of tags.

large_image_source_tifffile.open(*args, **kwargs)

Create an instance of the module class.