def add_graph(
self,
name: str,
color: Optional[Union[Vector4, Vector3]] = None,
_enforced_id: Optional[int] = None,
) -> Tree:
"""Deprecated, please use `add_tree`."""
warn_deprecated("add_graph()", "add_tree()")
return self.add_tree(name=name, color=color, _enforced_id=_enforced_id)
def open_annotation(annotation_path: Union[str, PathLike]) -> "Annotation":
"""Deprecated."""
if Path(annotation_path).exists():
warn_deprecated("open_annotation", "Annotation.load")
return Annotation.load(annotation_path)
else:
assert isinstance(
annotation_path, str
), f"Called open_annotation with a path-like, but {annotation_path} does not exist."
warn_deprecated("open_annotation", "Annotation.download")
return Annotation.download(annotation_path)
def __init__(
self,
name: str,
group: "Group",
skeleton: "Skeleton",
color: Optional[Vector4] = None,
enforced_id: Optional[int] = None,
) -> None:
warn_deprecated("Graph", "Tree")
super().__init__(
name=name,
group=group,
skeleton=skeleton,
color=color,
enforced_id=enforced_id,
)
def download_dataset(
dataset_name: str,
organization_name: str,
bbox: Optional[BoundingBox] = None,
layers: Optional[List[str]] = None,
mags: Optional[List[Mag]] = None,
path: Optional[Union[PathLike, str]] = None,
exist_ok: bool = False,
) -> Dataset:
warn_deprecated("download_dataset", "Dataset.download")
return actual_download_dataset(
dataset_name,
organization_id=organization_name,
bbox=bbox,
layers=layers,
mags=mags,
path=path,
exist_ok=exist_ok,
)
"""
# Dataset API
Please use the Dataset API at `webknossos.dataset`.
"""
from webknossos.utils import warn_deprecated
from .bounding_box import BoundingBox
from .dataset import Dataset
from .layer import Layer
from .mag_view import MagView
from .view import View
warn_deprecated("wkcuber.api", "webknossos")
def resolutions(self) -> List[MagViewProperties]:
warn_deprecated("resolutions", "mags")
return self.mags
def resolution(self) -> Mag:
warn_deprecated("resolution", "mag")
return self.mag
def scale(self, scale: Tuple[float, float, float]) -> None:
"""Deprecated, please use `voxel_size`."""
warn_deprecated("scale", "voxel_size")
self.voxel_size = scale
def write(self, out_path: PathLike) -> None:
"""Deprecated. Use Skeleton.save instead."""
warn_deprecated("Skeleton.write", "skeleton.save")
self.save(out_path)
def scale(self) -> Tuple[float, float, float]:
"""Deprecated, please use `voxel_size`."""
warn_deprecated("scale", "voxel_size")
return self.voxel_size
def open_nml(file_path: Union[PathLike, str]) -> Skeleton:
"""open_nml is deprecated, please use Skeleton.load instead."""
warn_deprecated("open_nml", "Skeleton.load")
return Skeleton.load(file_path)
def graphs(self) -> Iterator[Tree]:
"""Deprecated, please use `trees`."""
warn_deprecated("graphs", "trees")
return self.trees
def username(self, username: str) -> None:
warn_deprecated("username", "owner_name")
self.owner_name = username
def username(self) -> Optional[str]:
"""Deprecated, use `owner_name` instead."""
warn_deprecated("username", "owner_name")
return self.owner_name
def get_max_graph_id(self) -> int:
"""Deprecated, please use `get_max_tree_id`."""
warn_deprecated("get_max_graph_id()", "get_max_tree_id()")
return self.get_max_tree_id()
def get_graph_by_id(self, graph_id: int) -> Tree:
"""Deprecated, please use `get_tree_by_id`."""
warn_deprecated("get_graph_by_id()", "get_tree_by_id()")
return self.get_tree_by_id(graph_id)
def flattened_graphs(self) -> Iterator[Tree]:
"""Deprecated, please use `flattened_trees`."""
warn_deprecated("flattened_graphs()", "flattened_trees()")
return self.flattened_trees()
def from_path(file_path: Union[PathLike, str]) -> "Skeleton":
"""Deprecated. Use Skeleton.load instead."""
warn_deprecated("Skeleton.from_path", "Skeleton.load")
return Skeleton.load(file_path)
def user_id(self) -> Optional[str]:
warn_deprecated("user_id", "owner_id")
return self.owner_id