Skip to content

webknossos.annotation

SegmentGroup

Bases: _BaseGroup

A hierarchical container for organizing segments of a volume layer.

Segment groups can be nested. A segment is assigned to a group by setting SegmentInformation.group; segments with group=None are top-level.

Attributes:

  • name (str) –

    Name of the group.

  • id (int) –

    Read-only unique identifier for the group within its volume layer.

  • groups (Iterator[_GroupT]) –

    Iterator over immediate subgroups.

  • segments (dict[int, SegmentInformation]) –

    Immediate segments of this group.

Examples:

volume_layer = annotation.get_volume_layer("segmentation")
neuron = volume_layer.add_segment_group("neuron_42")
dendrites = neuron.add_group("dendrites")

volume_layer.segments[1] = wk.SegmentInformation(
    name="dendrite fragment",
    anchor_position=None,
    color=None,
    metadata={},
    group=dendrites,
)

print(neuron.flattened_segments())
Notes
  • Groups should be created with VolumeLayer.add_segment_group or add_group rather than directly.
See Also
  • VolumeLayer: Volume annotation layer owning the groups and segments
  • SegmentInformation: Per-segment information, including its group

groups property 

groups: Iterator[_GroupT]

Returns all (immediate) group children as an iterator. Use flattened_groups if you also need groups within subgroups.

id property 

id: int

Read-only property.

name instance-attribute 

name: str

segments property 

segments: dict[int, SegmentInformation]

Returns the (immediate) segments of this group, keyed by segment id. Use flattened_segments if you also need segments within subgroups.

add_group 

add_group(
    name: str, _enforced_id: int | None = None
) -> SegmentGroup

Creates and adds a new subgroup to this group.

Parameters:

  • name (str) –

    Name for the new group.

  • _enforced_id (int | None, default: None ) –

    Optional specific ID for the group (internal use).

Returns:

  • SegmentGroup ( SegmentGroup ) –

    The newly created group.

Raises:

  • ValueError –

    If _enforced_id is negative or already used by another group of the layer.

as_nml_group 

as_nml_group() -> Group

Converts this group to its NML representation.

flattened_groups 

flattened_groups() -> Iterator[_GroupT]

Returns an iterator of all groups within this group (and its subgroups).

flattened_segments 

flattened_segments() -> dict[int, SegmentInformation]

Returns all segments of this group and its subgroups, keyed by segment id.

get_group_by_id 

get_group_by_id(group_id: int) -> _GroupT

Returns the group within this group (and its subgroups) which has the specified id.