nyxus.Nested

class Nested

Bases: object

Nyxus image feature extraction library / ROI hierarchy analyzer

Example

from nyxus import Nested nn = Nested() segPath = ‘/home/data/6234838c6b123e21c8b736f5/tissuenet_tif/seg’ fPat = ‘.*’ cnlSig = ‘_c’ parCnl = ‘1’ chiCnl = ‘0’ rels = nn.findrelations (segPath, fPat, cnlSig, parCnl, chiCnl)

__init__()

Methods

__init__()

findrelations(label_dir, file_pattern, ...)

Finds parent-child relationships.
findrelations(label_dir, file_pattern, channel_signature, parent_channel, child_channel)

Finds parent-child relationships.

Find parent-child relationships assuming that images ending <channel_signature><parent_channel> contain parent ROIs and images ending <channel_signature><child_channel> contain child ROIs.

Parameters

  • label_dir (str) – Path to directory containing label images.

  • file_pattern (str) – Regular expression used to filter the images present in label_dir.

  • channel_signature (str) – Characters preceding the channel identifier e.g. “_c”.

  • parent_channel (str) – Identifier of the parent channel e.g. “1”.

  • child_channel (str) – Identifier of the child channel e.g. “0”.

Returns

rel – array of <parent label>,<child label> structure

Return type

array