large_image_source_nd2 package

Submodules

large_image_source_nd2.girder_source module

class large_image_source_nd2.girder_source.ND2GirderTileSource(*args, **kwargs)[source]

Bases: ND2FileTileSource, GirderTileSource

Provides tile access to Girder items with an ND2 file or other files that the nd2 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'
name = 'nd2'

Name of the tile source

Module contents

class large_image_source_nd2.ND2FileTileSource(*args, **kwargs)[source]

Bases: FileTileSource

Provides tile access to nd2 files the nd2 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 = {None: 5, 'nd2': 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.

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/nd2': 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 = 'nd2'

Name of the tile source

large_image_source_nd2.canRead(*args, **kwargs)[source]

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

large_image_source_nd2.diffObj(obj1, obj2)[source]

Given two objects, report the differences that exist in the first object that are not in the second object.

Parameters
  • obj1 – the first object to compare. Only values present in this object are returned.

  • obj2 – the second object to compare.

Returns

a subset of obj1.

large_image_source_nd2.namedtupleToDict(obj)[source]

Convert a namedtuple to a plain dictionary.

Parameters

obj – the object to convert

Returns

a dictionary or the original object.

large_image_source_nd2.open(*args, **kwargs)[source]

Create an instance of the module class.