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webknossos.skeleton.skeleton

Representation of the skeleton of an Annotation. It contains metadata to identify the related dataset and is the root-group of sub-groups and trees. See the parent class Group for methods about group and tree handling. To upload a skeleton to webknossos, please create an Annotation() with it.

A small usage example:

annotation = Annotation("my_annotation", voxel_size=(11, 11, 24))
group = annotation.skeleton.add_group("a group")
tree = group.add_tree("a tree")
node_1 = tree.add_node(position=(0, 0, 0), comment="node 1")
node_2 = tree.add_node(position=(100, 100, 100), comment="node 2")

tree.add_edge(node_1, node_2)

Also see this example for a more complex interaction.

#   Skeleton( voxel_size: Tuple[float, float, float], dataset_name: str, organization_id: Union[str, NoneType] = None, description: Union[str, NoneType] = None, enforced_id: Union[int, NoneType] = None )

To initialize a skeleton, setting the following parameters is required (or recommended):

  • voxel_size
  • dataset_name
  • organization_id
  • description
#   voxel_size: Tuple[float, float, float]
#   dataset_name: str
#   organization_id: Union[str, NoneType]
#   description: Union[str, NoneType]
#   name: str

Should not be used with Skeleton, this attribute is only useful for sub-groups. Set to Root.

#   scale: Tuple[float, float, float]

Deprecated, please use voxel_size.

#  
@staticmethod
def load( file_path: Union[os.PathLike, str] ) -> webknossos.skeleton.skeleton.Skeleton:

Loads a .nml file or a .zip file containing an NML (and possibly also volume layers). Returns the Skeleton object. Also see Annotation.load if you want to have the annotation which wraps the skeleton.

#   def save(self, out_path: Union[str, os.PathLike]) -> None:

Stores the skeleton as a zip or nml at the given path.

#  
@staticmethod
def from_path( file_path: Union[os.PathLike, str] ) -> webknossos.skeleton.skeleton.Skeleton:

Deprecated. Use Skeleton.load instead.

#   def write(self, out_path: os.PathLike) -> None:

Deprecated. Use Skeleton.save instead.

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