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This repository was archived by the owner on Feb 26, 2025. It is now read-only.
This repository was archived by the owner on Feb 26, 2025. It is now read-only.

Morphology check has_no_narrow_start raises Exception because a neurite's root node has only one point  #1133

@ssssarah

Description

@ssssarah

Reproduction:

from morphio import Morphology
from neurom import load_morphology
from neurom.check import morphology_checks

# morphology_id: https://bbp.epfl.ch/neurosciencegraph/data/neuronmorphologies/ec4d9eae-5e0a-4409-a45d-ec5ec6dc3223
# morphology_self: https://bbp.epfl.ch/nexus/v1/resources/bbp-external/seu/_/https:%2F%2Fbbp.epfl.ch%2Fneurosciencegraph%2Fdata%2Fneuronmorphologies%2Fec4d9eae-5e0a-4409-a45d-ec5ec6dc3223
swc_path = ".../18455_00141.swc"

morphology = load_morphology(Morphology(swc_path), process_subtrees=True)

for neurite in morphology.neurites:
    r = neurite.root_node.points
    print(len(r))

# OUTPUT

# 104
# 9
# 467
# 58
# 6
# 25
# 23
# 1
# 1
# 3
# 132

fail = morphology_checks.has_no_narrow_start(morphology, frac=0.9)

Should all neurites' root node have at least 2 points?

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