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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.

Mutable morphology copy constructor reindexes sections #416

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@eleftherioszisis

Description

@eleftherioszisis
import morphio
string = """
("CellBody"
  (Color Red)
  (CellBody)
  ( 0.1  0.1 0.0 0.1)
  ( 0.1 -0.1 0.0 0.1)
)

( (Color Cyan)
  (Axon)
  (0.0  0.0 0.0 2.0) ; section 0
  (0.0 -4.0 1.0 2.0)
  (
    (0.0 -4.0 1.0 4.0) ; section 1
    (0.0 -4.0 2.0 4.0)
    (0.0 -4.0 3.0 4.0)
    (
        (6.0 -4.0 0.0 4.0) ; section 2
        (7.0 -5.0 0.0 4.0)
        (
            (8.0 -4.0 0.0 4.0) ; section 3
            (8.0 -5.0 0.0 4.0)
        |
            (8.0 -4.0 0.0 4.0) ; section 4
            (8.0 -5.0 0.0 4.0)
        )
    |
        (6.0 -4.0 0.0 4.0) ; section 5
        (8.0 -4.0 0.0 4.0)
    )
  |
    ( 0.0 -4.0 1.0 4.0) ; section 6
    (-5.0 -4.0 0.0 4.0)
    (
        (3.0 2.0 1.0 4.0) ; section 7
        (3.0 2.0 0.0 4.0)
    |
        (2.0 3.0 1.0 4.0) ; section 8
        (2.0 3.0 0.0 4.0)
    )
  )
)
"""
morph = morphio.Morphology(string, "asc").as_mutable() 

morph.delete_section(morph.section(0), recursive=False)
morph.delete_section(morph.section(1), recursive=False)
morph.delete_section(morph.section(4), recursive=False)
morph.delete_section(morph.section(7), recursive=False)

expected_section_ids = [s.id for s in morph.iter()]

morph2 = morphio.mut.Morphology(morph)
section_ids = [s.id for s in morph2.iter()] 

assert section_ids == expected_section_ids, f"{section_ids}, {expected_section_ids}"

Throws:

AssertionError: [0, 1, 2, 3, 4], [2, 3, 5, 6, 8]

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