FsspecJsonWSIReader¶

class FsspecJsonWSIReader(input_img, mpp=None, power=None, cache_size=268435456)[source]¶

Reader for fsspec zarr json generated by: tiatoolbox/utils/tiff_to_fsspec.py.

The fsspec zarr json file represents a SVS or TIFF file that be accessed using byte range HTTP API.

All the information on the chunk locations in the SVS or TIFF file is outlined as byte-ranges in the JSON, so the reader requests only chunks that are needed to display requested tiles, rather than the entire SVS or TIFF file.

Initialize FsspecJsonWSIReader.

Methods

is_valid_zarr_fsspec

Check if the input path is a valid Zarr fsspec JSON file.

read_bounds

See TIFFWSIReaderDelegate.read_bounds docs for details.

read_rect

See TIFFWSIReaderDelegate.read_rect docs for details.

Attributes

Parameters:

  • input_img (str | Path | np.ndarray)

  • mpp (tuple[Number, Number] | None)

  • power (Number | None)

  • cache_size (int)

static is_valid_zarr_fsspec(file_path)[source]¶

Check if the input path is a valid Zarr fsspec JSON file.

Checks if the file_path is a valid Zarr fsspec JSON file generated by: tiatoolbox/utils/tiff_to_fsspec.py

Parameters:

file_path (str) – str Path to the file to check.

Returns:

True if the file is a valid Zarr fsspec JSON file

Return type:

bool

read_bounds(bounds, resolution=0, units='level', interpolation='optimise', pad_mode='constant', pad_constant_values=0, coord_space='baseline', **kwargs)[source]¶

See TIFFWSIReaderDelegate.read_bounds docs for details.

Parameters:

  • self (FsspecJsonWSIReader)

  • bounds (IntBounds)

  • resolution (Resolution)

  • units (Units)

  • interpolation (str)

  • pad_mode (str)

  • pad_constant_values (int | IntPair)

  • coord_space (str)

  • kwargs (dict)

Return type:

np.ndarray

read_rect(location, size, resolution=0, units='level', interpolation='optimise', pad_mode='constant', pad_constant_values=0, coord_space='baseline', **kwargs)[source]¶

See TIFFWSIReaderDelegate.read_rect docs for details.

Parameters:

  • self (FsspecJsonWSIReader)

  • location (IntPair)

  • size (IntPair)

  • resolution (Resolution)

  • units (Units)

  • interpolation (str)

  • pad_mode (str)

  • pad_constant_values (int | IntPair)

  • coord_space (str)

  • kwargs (dict)

Return type:

np.ndarray