large_image_source_bioformats package

Submodules

large_image_source_bioformats.girder_source module

class large_image_source_bioformats.girder_source.BioformatsGirderTileSource(*args, **kwargs)

Bases: BioformatsFileTileSource, GirderTileSource

Provides tile access to Girder items that can be read with bioformats.

Initialize the tile class. See the base class for other available parameters.

Parameters:

path – the associated file path.

cacheName = 'tilesource'

levels: int

mayHaveAdjacentFiles(largeImageFile)

name = 'bioformats'

sizeX: int

sizeY: int

tileHeight: int

tileWidth: int

Module contents

class large_image_source_bioformats.BioformatsFileTileSource(*args, **kwargs)

Bases: FileTileSource

Provides tile access to via Bioformats.

Initialize the tile class. See the base class for other available parameters.

Parameters:

path – the associated file path.

classmethod addKnownExtensions()

cacheName = 'tilesource'

extensions: Dict[str | None, SourcePriority] = {'czi': SourcePriority.PREFERRED, 'ets': SourcePriority.LOW, 'lif': SourcePriority.MEDIUM, 'vsi': SourcePriority.PREFERRED, None: SourcePriority.FALLBACK}

getAssociatedImagesList()

Return a list of 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: Dict[str | None, SourcePriority] = {'image/czi': SourcePriority.PREFERRED, 'image/vsi': SourcePriority.PREFERRED, None: SourcePriority.FALLBACK}

name = 'bioformats'

large_image_source_bioformats.canRead(*args, **kwargs)

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

large_image_source_bioformats.open(*args, **kwargs)

Create an instance of the module class.