large_image_source_bioformats package

Submodules

large_image_source_bioformats.girder_source module

class large_image_source_bioformats.girder_source.BioformatsGirderTileSource(*args, **kwargs)[source]

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'
mayHaveAdjacentFiles(largeImageFile)[source]
name = 'bioformats'

Name of the tile source

Module contents

class large_image_source_bioformats.BioformatsFileTileSource(*args, **kwargs)[source]

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.

cacheName = 'tilesource'
extensions = {None: 8, 'czi': 1, 'vsi': 1}

A dictionary of known file extensions and the SourcePriority given to each. It must contain a None key with a priority for the tile source when the extension does not match.

getAssociatedImagesList()[source]

Return a list of 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 = {None: 8, 'image/czi': 1, 'image/vsi': 1}

A dictionary of common mime-types handled by the source and the SourcePriority given to each. This are used in place of or in additional to extensions.

name = 'bioformats'

Name of the tile source

large_image_source_bioformats.canRead(*args, **kwargs)[source]

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

large_image_source_bioformats.open(*args, **kwargs)[source]

Create an instance of the module class.