large_image_source_zarr package

Submodules

large_image_source_zarr.girder_source module

class large_image_source_zarr.girder_source.ZarrGirderTileSource(*args, **kwargs)

Bases: ZarrFileTileSource, GirderTileSource

Provides tile access to Girder items with files that OME Zarr 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'

levels: int

name = 'zarr'

sizeX: int

sizeY: int

tileHeight: int

tileWidth: int

Module contents

class large_image_source_zarr.ZarrFileTileSource(*args, **kwargs)

Bases: FileTileSource

Provides tile access to files that the zarr library can read.

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

Parameters:

path – a filesystem path for the tile source.

addAssociatedImage(image, imageKey=None)

Add an associated image to this source.

Parameters:

image – a numpy array, PIL Image, or a binary string with an image. The numpy array can have 2 or 3 dimensions.

addTile(tile, x=0, y=0, mask=None, axes=None, **kwargs)

Add a numpy or image tile to the image, expanding the image as needed to accommodate it. Note that x and y can be negative. If so, the output image (and internal memory access of the image) will act as if the 0, 0 point is the most negative position. Cropping is applied after this offset.

Parameters:

• tile – a numpy array, PIL Image, or a binary string with an image. The numpy array can have 2 or 3 dimensions.

• x – location in destination for upper-left corner.

• y – location in destination for upper-left corner.

• mask – a 2-d numpy array (or 3-d if the last dimension is 1). If specified, areas where the mask is false will not be altered.

• axes – a string or list of strings specifying the names of axes in the same order as the tile dimensions.

• kwargs – start locations for any additional axes. Note that level is a reserved word and not permitted for an axis name.

cacheName = 'tilesource'

property channelColors

property channelNames

property crop

Crop only applies to the output file, not the internal data access.

It consists of x, y, w, h in pixels.

extensions: Dict[str | None, SourcePriority] = {'db': SourcePriority.MEDIUM, 'zarr': SourcePriority.PREFERRED, 'zarray': SourcePriority.PREFERRED, 'zattrs': SourcePriority.PREFERRED, 'zgroup': SourcePriority.PREFERRED, 'zip': SourcePriority.LOWER, None: SourcePriority.LOW}

property frameAxes

property frameUnits

property frameValues

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.

getState()

Return a string reflecting the state of the tile source. This is used as part of a cache key when hashing function return values.

Returns:

a string hash value of the source state.

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.

property imageDescription

mimeTypes: Dict[str | None, SourcePriority] = {'application/vnd+zarr': SourcePriority.PREFERRED, 'application/x-zarr': SourcePriority.PREFERRED, 'application/zip+zarr': SourcePriority.PREFERRED, None: SourcePriority.FALLBACK}

property mm_x

property mm_y

name = 'zarr'

newPriority: SourcePriority | None = 3

write(path, lossy=True, alpha=True, overwriteAllowed=True, resample=None, **converterParams)

Output the current image to a file.

Parameters:

• path – output path.

• lossy – if false, emit a lossless file.

• alpha – True if an alpha channel is allowed.

• overwriteAllowed – if False, raise an exception if the output path exists.

• resample – one of the ResampleMethod enum values. Defaults to NP_NEAREST for lossless and non-uint8 data and to PIL_LANCZOS for lossy uint8 data.

• converterParams – options to pass to the large_image_converter if the output is not a zarr variant.

large_image_source_zarr.canRead(*args, **kwargs)

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

large_image_source_zarr.new(*args, **kwargs)

Create a new image, collecting the results from patches of numpy arrays or smaller images.

large_image_source_zarr.open(*args, **kwargs)

Create an instance of the module class.