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Neuclease

Miscellaneous Python utilities for interacting with DVID and assisting with proofreading infrastructure.

Most users will only be interested in the neuclease.dvid subpackage, which provides Python bindings for most of DVID's REST API. Eventually, that subpackage will be migrated into its own Python package.

Unfortunately, there is no web-based documentation at the moment. But each function has a docstring. Try your Python interpreter's built-in help feature.

Install

conda install -c flyem-forge -c conda-forge neuclease

Example

In [1]: from neuclease.dvid import *

In [2]: server = 'http://hemibrain-dvid.janelia.org'

In [3]: find_master('http://hemibrain-dvid.janelia.org')
Out[3]: '20631f94c3f446d7864bc55bf515706e'

In [4]: x, y, z = 17019, 21341, 20789

In [5]: # Note: neuclease uses Z,Y,X order for all image volumes, coordinates, and bounding-boxes.
   ...: fetch_label(server, '20631f', 'segmentation', (z,y,x))
Out[5]: 5812980291

In [6]: fetch_label(server, '20631f', 'segmentation', (z,y,x), supervoxels=True)
Out[6]: 1351718075

In [7]: box_zyx = [[20789, 21341, 17019], [20889, 21441, 17119]]
   ...: subvol = fetch_labelmap_voxels(server, '20631f', 'segmentation', box)
   ...: subvol.shape
Out[7]: (100, 100, 100)

In [8]: # Read the docstring
   ...: fetch_labelmap_voxels?
Signature:
fetch_labelmap_voxels(
    server,
    uuid,
    instance,
    box_zyx,
    scale=0,
    throttle=False,
    supervoxels=False,
    *,
    format='array',
    session=None,
)
Docstring:
Fetch a volume of voxels from the given instance.

Args:
    server:
        dvid server, e.g. 'emdata3:8900'

    uuid:
        dvid uuid, e.g. 'abc9'

    instance:
        dvid instance name, e.g. 'segmentation'

    box_zyx:
        The bounds of the volume to fetch in the coordinate system for the requested scale.
        Given as a pair of coordinates (start, stop), e.g. [(0,0,0), (10,20,30)], in Z,Y,X order.
        The box need not be block-aligned, but the request to DVID will be block aligned
        to 64px boundaries, and the retrieved volume will be truncated as needed before
        it is returned.

    scale:
        Which downsampling scale to fetch from

    throttle:
        If True, passed via the query string to DVID, in which case DVID might return a '503' error
        if the server is too busy to service the request.
        It is your responsibility to catch DVIDExceptions in that case.

    supervoxels:
        If True, request supervoxel data from the given labelmap instance.

    format:
        If 'array', inflate the compressed voxels from DVID and return an ordinary ndarray
        If 'lazy-array', return a callable proxy that stores the compressed data internally,
        and that will inflate the data when called.
        If 'raw-response', return DVID's raw /blocks response buffer without inflating it.

Returns:
    ndarray, with shape == (box[1] - box[0])