swcgeom 0.17.0__py3-none-any.whl → 0.17.2__py3-none-any.whl

swcgeom/core/tree.py

@@ -2,24 +2,13 @@
 
 import itertools
 import os
-import warnings
-from typing import (
-    Callable,
-    Dict,
-    Iterable,
-    Iterator,
-    List,
-    Literal,
-    Optional,
-    Tuple,
-    TypeVar,
-    Union,
-    overload,
-)
+from collections.abc import Callable, Iterable, Iterator
+from typing import Literal, Optional, TypeVar, Union, overload
 
 import numpy as np
 import numpy.typing as npt
 import pandas as pd
+from typing_extensions import deprecated
 
 from swcgeom.core.branch import Branch
 from swcgeom.core.compartment import Compartment, Compartments
@@ -44,17 +33,17 @@ class Tree(DictSWC):
         def parent(self) -> Union["Tree.Node", None]:
             return Tree.Node(self.attach, self.pid) if self.pid != -1 else None
 
-        def children(self) -> List["Tree.Node"]:
+        def children(self) -> list["Tree.Node"]:
             children = self.attach.id()[self.attach.pid() == self.id]
             return [Tree.Node(self.attach, idx) for idx in children]
 
         def branch(self) -> "Tree.Branch":
-            ns: List["Tree.Node"] = [self]
-            while not ns[-1].is_bifurcation() and (p := ns[-1].parent()) is not None:
+            ns: list["Tree.Node"] = [self]
+            while not ns[-1].is_furcation() and (p := ns[-1].parent()) is not None:
                 ns.append(p)
 
             ns.reverse()
-            while not (ns[-1].is_bifurcation() or ns[-1].is_tip()):
+            while not (ns[-1].is_furcation() or ns[-1].is_tip()):
                 ns.append(ns[-1].children()[0])
 
             return Tree.Branch(self.attach, [n.id for n in ns])
@@ -68,7 +57,7 @@ class Tree(DictSWC):
 
             Parameters
             ----------
-            out_mapping : List of int or Dict[int, int], optional
+            out_mapping : List of int or dict[int, int], optional
                 Map from new id to old id.
             """
 
@@ -160,7 +149,7 @@ class Tree(DictSWC):
 
     # fmt:off
     @overload
-    def __getitem__(self, key: slice) -> List[Node]: ...
+    def __getitem__(self, key: slice) -> list[Node]: ...
     @overload
     def __getitem__(self, key: int) -> Node: ...
     @overload
@@ -199,18 +188,30 @@ class Tree(DictSWC):
             raise ValueError(f"no soma found in: {self.source}")
         return n
 
-    def get_bifurcations(self) -> List[Node]:
-        """Get all node of bifurcations."""
-        bifurcations: List[int] = []
+    def get_furcations(self) -> list[Node]:
+        """Get all node of furcations."""
+        furcations: list[int] = []
 
-        def collect_bifurcations(n: Tree.Node, children: List[None]) -> None:
+        def collect_furcations(n: Tree.Node, children: list[None]) -> None:
             if len(children) > 1:
-                bifurcations.append(n.id)
+                furcations.append(n.id)
 
-        self.traverse(leave=collect_bifurcations)
-        return [self.node(i) for i in bifurcations]
+        self.traverse(leave=collect_furcations)
+        return [self.node(i) for i in furcations]
 
-    def get_tips(self) -> List[Node]:
+    @deprecated("Use `get_furcations` instead")
+    def get_bifurcations(self) -> list[Node]:
+        """Get all node of furcations.
+
+        Notes
+        -----
+        Deprecated due to the wrong spelling of furcation. For now, it
+        is just an alias of `get_furcations` and raise a warning. It
+        will be change to raise an error in the future.
+        """
+        return self.get_furcations()
+
+    def get_tips(self) -> list[Node]:
         """Get all node of tips."""
         tip_ids = np.setdiff1d(self.id(), self.pid(), assume_unique=True)
         return [self.node(i) for i in tip_ids]
@@ -221,16 +222,16 @@ class Tree(DictSWC):
     def get_segments(self) -> Compartments[Compartment]:  # Alias
         return self.get_compartments()
 
-    def get_branches(self) -> List[Branch]:
+    def get_branches(self) -> list[Branch]:
         def collect_branches(
-            node: "Tree.Node", pre: List[Tuple[List[Tree.Branch], List[int]]]
-        ) -> Tuple[List[Tree.Branch], List[int]]:
+            node: "Tree.Node", pre: list[tuple[list[Tree.Branch], list[int]]]
+        ) -> tuple[list[Tree.Branch], list[int]]:
             if len(pre) == 1:
                 branches, child = pre[0]
                 child.append(node.id)
                 return branches, child
 
-            branches: List[Tree.Branch] = []
+            branches: list[Tree.Branch] = []
 
             for sub_branches, child in pre:
                 child.append(node.id)
@@ -244,19 +245,19 @@ class Tree(DictSWC):
         branches, _ = self.traverse(leave=collect_branches)
         return branches
 
-    def get_paths(self) -> List[Path]:
+    def get_paths(self) -> list[Path]:
         """Get all path from soma to tips."""
-        path_dic: Dict[int, List[int]] = {}
+        path_dic: dict[int, list[int]] = {}
 
-        def assign_path(n: Tree.Node, pre_path: List[int] | None) -> List[int]:
+        def assign_path(n: Tree.Node, pre_path: list[int] | None) -> list[int]:
             path = [] if pre_path is None else pre_path.copy()
             path.append(n.id)
             path_dic[n.id] = path
             return path
 
         def collect_path(
-            n: Tree.Node, children: List[List[List[int]]]
-        ) -> List[List[int]]:
+            n: Tree.Node, children: list[list[list[int]]]
+        ) -> list[list[int]]:
             if len(children) == 0:
                 return [path_dic[n.id]]
 
@@ -283,7 +284,7 @@ class Tree(DictSWC):
     @overload
     def traverse(self, *,
                  enter: Optional[Callable[[Node, T | None], T]] = ...,
-                 leave: Callable[[Node, List[K]], K],
+                 leave: Callable[[Node, list[K]], K],
                  root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> K: ...
     # fmt: on
 
@@ -293,7 +294,7 @@ class Tree(DictSWC):
         Parameters
         ----------
         enter : (n: Node, parent: T | None) => T, optional
-        leave : (n: Node, children: List[T]) => T, optional
+        leave : (n: Node, children: list[T]) => T, optional
 
         See Also
         --------
@@ -355,7 +356,7 @@ class Tree(DictSWC):
 
     @classmethod
     def from_eswc(
-        cls, swc_file: str, extra_cols: Optional[List[str]] = None, **kwargs
+        cls, swc_file: str, extra_cols: Optional[list[str]] = None, **kwargs
     ) -> "Tree":
         """Read neuron tree from eswc file.
 

swcgeom/core/tree_utils.py

@@ -1,9 +1,11 @@
 """SWC util wrapper for tree."""
 
 import warnings
-from typing import Callable, Dict, Iterable, List, Optional, Tuple, TypeVar, overload
+from collections.abc import Callable, Iterable
+from typing import Optional, TypeVar, overload
 
 import numpy as np
+from typing_extensions import deprecated
 
 from swcgeom.core.swc import SWCLike
 from swcgeom.core.swc_utils import (
@@ -50,9 +52,9 @@ def sort_tree(tree: Tree) -> Tree:
 
 # fmt:off
 @overload
-def cut_tree(tree: Tree, *, enter: Callable[[Tree.Node, T | None], Tuple[T, bool]]) -> Tree: ...
+def cut_tree(tree: Tree, *, enter: Callable[[Tree.Node, T | None], tuple[T, bool]]) -> Tree: ...
 @overload
-def cut_tree(tree: Tree, *, leave: Callable[[Tree.Node, List[K]], Tuple[K, bool]]) -> Tree: ...
+def cut_tree(tree: Tree, *, leave: Callable[[Tree.Node, list[K]], tuple[K, bool]]) -> Tree: ...
 # fmt:on
 def cut_tree(tree: Tree, *, enter=None, leave=None):
     """Traverse and cut the tree.
@@ -60,11 +62,11 @@ def cut_tree(tree: Tree, *, enter=None, leave=None):
     Returning a `True` can delete the current node and its children.
     """
 
-    removals: List[int] = []
+    removals: list[int] = []
 
     if enter:
 
-        def _enter(n: Tree.Node, parent: Tuple[T, bool] | None) -> Tuple[T, bool]:
+        def _enter(n: Tree.Node, parent: tuple[T, bool] | None) -> tuple[T, bool]:
             if parent is not None and parent[1]:
                 removals.append(n.id)
                 return parent
@@ -79,7 +81,7 @@ def cut_tree(tree: Tree, *, enter=None, leave=None):
 
     elif leave:
 
-        def _leave(n: Tree.Node, children: List[K]) -> K:
+        def _leave(n: Tree.Node, children: list[K]) -> K:
             res, removal = leave(n, children)
             if removal:
                 removals.append(n.id)
@@ -94,7 +96,8 @@ def cut_tree(tree: Tree, *, enter=None, leave=None):
     return to_subtree(tree, removals)
 
 
-def to_sub_tree(swc_like: SWCLike, sub: Topology) -> Tuple[Tree, Dict[int, int]]:
+@deprecated("Use `to_subtree` instead")
+def to_sub_tree(swc_like: SWCLike, sub: Topology) -> tuple[Tree, dict[int, int]]:
     """Create subtree from origin tree.
 
     You can directly mark the node for removal, and we will remove it,
@@ -107,16 +110,9 @@ def to_sub_tree(swc_like: SWCLike, sub: Topology) -> Tuple[Tree, Dict[int, int]]
     Returns
     -------
     tree : Tree
-    id_map : Dict[int, int]
+    id_map : dict[int, int]
     """
 
-    warnings.warn(
-        "`to_sub_tree` will be removed in v0.6.0, it is replaced by "
-        "`to_subtree` beacuse it is easy to use, and this will be "
-        "removed in next version",
-        DeprecationWarning,
-    )
-
     sub = propagate_removal(sub)
     (new_id, new_pid), id_map_arr = to_sub_topology(sub)
 
@@ -145,7 +141,7 @@ def to_subtree(
     swc_like : SWCLike
     removals : List of int
         A list of id of nodes to be removed.
-    out_mapping: List of int or Dict[int, int], optional
+    out_mapping: List of int or dict[int, int], optional
         Map new id to old id.
     """
 
@@ -170,7 +166,7 @@ def get_subtree(
     swc_like : SWCLike
     n : int
         Id of the root of the subtree.
-    out_mapping: List of int or Dict[int, int], optional
+    out_mapping: List of int or dict[int, int], optional
         Map new id to old id.
     """
 

swcgeom/core/tree_utils_impl.py

@@ -5,7 +5,7 @@ Notes
 Do not import `Tree` and keep this file minimized.
 """
 
-from typing import Any, Dict, List, Optional, Tuple
+from typing import Any, Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -15,8 +15,8 @@ from swcgeom.core.swc_utils import Topology, to_sub_topology, traverse
 
 __all__ = ["get_subtree_impl", "to_subtree_impl"]
 
-Mapping = Dict[int, int] | List[int]
-TreeArgs = Tuple[int, Dict[str, npt.NDArray[Any]], str, SWCNames]
+Mapping = dict[int, int] | list[int]
+TreeArgs = tuple[int, dict[str, npt.NDArray[Any]], str, SWCNames]
 
 
 def get_subtree_impl(

swcgeom/images/augmentation.py

@@ -6,7 +6,7 @@ This is expremental code, and the API is subject to change.
 """
 
 import random
-from typing import List, Literal, Optional
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -54,7 +54,7 @@ class Augmentation:
 
     def swapaxes(self, x, mode: Optional[Literal["xy", "xz", "yz"]] = None) -> NDArrf32:
         if mode is None:
-            modes: List[Literal["xy", "xz", "yz"]] = ["xy", "xz", "yz"]
+            modes: list[Literal["xy", "xz", "yz"]] = ["xy", "xz", "yz"]
             mode = modes[self.rand.randint(0, 2)]
 
         match mode:
@@ -69,7 +69,7 @@ class Augmentation:
 
     def flip(self, x, mode: Optional[Literal["xy", "xz", "yz"]] = None) -> NDArrf32:
         if mode is None:
-            modes: List[Literal["xy", "xz", "yz"]] = ["xy", "xz", "yz"]
+            modes: list[Literal["xy", "xz", "yz"]] = ["xy", "xz", "yz"]
             mode = modes[random.randint(0, 2)]
 
         match mode:

swcgeom/images/folder.py

@@ -3,24 +3,14 @@
 import math
 import os
 import re
-import warnings
+from collections.abc import Callable, Iterable
 from dataclasses import dataclass
-from typing import (
-    Callable,
-    Generic,
-    Iterable,
-    List,
-    Literal,
-    Optional,
-    Tuple,
-    TypeVar,
-    overload,
-)
+from typing import Generic, Literal, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
 from tqdm import tqdm
-from typing_extensions import Self
+from typing_extensions import Self, deprecated
 
 from swcgeom.images.io import ScalarType, read_imgs
 from swcgeom.transforms import Identity, Transform
@@ -33,7 +23,7 @@ T = TypeVar("T")
 class ImageStackFolderBase(Generic[ScalarType, T]):
     """Image stack folder base."""
 
-    files: List[str]
+    files: list[str]
     transform: Transform[npt.NDArray[ScalarType], T]
 
     # fmt: off
@@ -61,7 +51,10 @@ class ImageStackFolderBase(Generic[ScalarType, T]):
         return read_imgs(fname, dtype=self.dtype).get_full()  # type: ignore
 
     @staticmethod
-    def scan(root: str, *, pattern: Optional[str] = None) -> List[str]:
+    def scan(root: str, *, pattern: Optional[str] = None) -> list[str]:
+        if not os.path.isdir(root):
+            raise NotADirectoryError(f"not a directory: {root}")
+
         is_valid = re.compile(pattern).match if pattern is not None else truthly
 
         fs = []
@@ -71,6 +64,7 @@ class ImageStackFolderBase(Generic[ScalarType, T]):
         return fs
 
     @staticmethod
+    @deprecated("Use `~swcgeom.images.io.read_imgs(fname).get_full()` instead")
     def read_imgs(fname: str) -> npt.NDArray[np.float32]:
         """Read images.
 
@@ -78,14 +72,6 @@ class ImageStackFolderBase(Generic[ScalarType, T]):
             Use :meth:`~swcgeom.images.io.read_imgs(fname).get_full()` instead.
         """
 
-        warnings.warn(
-            "`ImageStackFolderBase.read_imgs` serves as a "
-            "straightforward wrapper for `~swcgeom.images.io.read_imgs(fname).get_full()`. "
-            "However, as it is not utilized within our internal "
-            "processes, it is scheduled for removal in the "
-            "forthcoming version.",
-            DeprecationWarning,
-        )
         return read_imgs(fname).get_full()
 
 
@@ -168,13 +154,13 @@ class ImageStackFolder(ImageStackFolderBase[ScalarType, T]):
 class LabeledImageStackFolder(ImageStackFolderBase[ScalarType, T]):
     """Image stack folder with label."""
 
-    labels: List[int]
+    labels: list[int]
 
     def __init__(self, files: Iterable[str], labels: Iterable[int], **kwargs):
         super().__init__(files, **kwargs)
         self.labels = list(labels)
 
-    def __getitem__(self, idx: int) -> Tuple[T, int]:
+    def __getitem__(self, idx: int) -> tuple[T, int]:
         return self._get(self.files[idx]), self.labels[idx]
 
     @classmethod
@@ -205,7 +191,7 @@ class PathImageStackFolder(ImageStackFolderBase[ScalarType, T]):
         super().__init__(files, **kwargs)
         self.root = root
 
-    def __getitem__(self, idx: int) -> Tuple[T, str]:
+    def __getitem__(self, idx: int) -> tuple[T, str]:
         relpath = os.path.relpath(self.files[idx], self.root)
         return self._get(self.files[idx]), relpath
 

swcgeom/images/io.py

@@ -4,30 +4,20 @@ import os
 import re
 import warnings
 from abc import ABC, abstractmethod
+from collections.abc import Callable, Iterable
 from functools import cache, lru_cache
-from typing import (
-    Any,
-    Callable,
-    Generic,
-    Iterable,
-    List,
-    Literal,
-    Optional,
-    Tuple,
-    TypeVar,
-    cast,
-    overload,
-)
+from typing import Any, Generic, Literal, Optional, TypeVar, cast, overload
 
 import nrrd
 import numpy as np
 import numpy.typing as npt
 import tifffile
+from typing_extensions import deprecated
 from v3dpy.loaders import PBD, Raw
 
 __all__ = ["read_imgs", "save_tiff", "read_images"]
 
-Vec3i = Tuple[int, int, int]
+Vec3i = tuple[int, int, int]
 ScalarType = TypeVar("ScalarType", bound=np.generic, covariant=True)
 
 RE_TERAFLY_ROOT = re.compile(r"^RES\((\d+)x(\d+)x(\d+)\)$")
@@ -58,17 +48,17 @@ class ImageStack(ABC, Generic[ScalarType]):
     def __getitem__(self, key: int) -> npt.NDArray[ScalarType]: ...                     # array of shape (Y, Z, C)
     @overload
     @abstractmethod
-    def __getitem__(self, key: Tuple[int, int]) -> npt.NDArray[ScalarType]: ...         # array of shape (Z, C)
+    def __getitem__(self, key: tuple[int, int]) -> npt.NDArray[ScalarType]: ...         # array of shape (Z, C)
     @overload
     @abstractmethod
-    def __getitem__(self, key: Tuple[int, int, int]) -> npt.NDArray[ScalarType]: ...    # array of shape (C,)
+    def __getitem__(self, key: tuple[int, int, int]) -> npt.NDArray[ScalarType]: ...    # array of shape (C,)
     @overload
     @abstractmethod
-    def __getitem__(self, key: Tuple[int, int, int, int]) -> ScalarType: ...            # value
+    def __getitem__(self, key: tuple[int, int, int, int]) -> ScalarType: ...            # value
     @overload
     @abstractmethod
     def __getitem__(
-        self, key: slice | Tuple[slice, slice] | Tuple[slice, slice, slice] |  Tuple[slice, slice, slice, slice],
+        self, key: slice | tuple[slice, slice] | tuple[slice, slice, slice] |  tuple[slice, slice, slice, slice],
     ) -> npt.NDArray[ScalarType]: ... # array of shape (X, Y, Z, C)
     @overload
     @abstractmethod
@@ -95,7 +85,7 @@ class ImageStack(ABC, Generic[ScalarType]):
         return self[:, :, :, :]
 
     @property
-    def shape(self) -> Tuple[int, int, int, int]:
+    def shape(self) -> tuple[int, int, int, int]:
         raise NotImplementedError()
 
 
@@ -118,7 +108,7 @@ def read_imgs(fname: str, **kwargs):  # type: ignore
         Casting data to specified dtype. If integer and float
         conversions occur, they will be scaled (assuming floats are
         between 0 and 1).
-    **kwargs : Dict[str, Any]
+    **kwargs : dict[str, Any]
         Forwarding to the corresponding reader.
     """
 
@@ -169,7 +159,7 @@ def save_tiff(
         Compression algorithm, forwarding to `tifffile.imwrite`. If no
         algorithnm is specify specified, we will use the zlib algorithm
         with compression level 6 by default.
-    **kwargs : Dict[str, Any]
+    **kwargs : dict[str, Any]
         Forwarding to `tifffile.imwrite`
     """
     if isinstance(data, ImageStack):
@@ -245,8 +235,8 @@ class NDArrayImageStack(ImageStack[ScalarType]):
         return self.imgs
 
     @property
-    def shape(self) -> Tuple[int, int, int, int]:
-        return cast(Tuple[int, int, int, int], self.imgs.shape)
+    def shape(self) -> tuple[int, int, int, int]:
+        return cast(tuple[int, int, int, int], self.imgs.shape)
 
 
 class TiffImageStack(NDArrayImageStack[ScalarType]):
@@ -324,7 +314,7 @@ class TeraflyImageStack(ImageStack[ScalarType]):
     use its coordinate system, remember to FLIP Y-AXIS BACK.
     """
 
-    _listdir: Callable[[str], List[str]]
+    _listdir: Callable[[str], list[str]]
     _read_patch: Callable[[str], npt.NDArray]
 
     def __init__(
@@ -350,7 +340,7 @@ class TeraflyImageStack(ImageStack[ScalarType]):
         self.res, self.res_dirs, self.res_patch_sizes = self.get_resolutions(root)
 
         @cache
-        def listdir(path: str) -> List[str]:
+        def listdir(path: str) -> list[str]:
             return os.listdir(path)
 
         @lru_cache(maxsize=lru_maxsize)
@@ -429,19 +419,19 @@ class TeraflyImageStack(ImageStack[ScalarType]):
         raise NotImplementedError()  # TODO
 
     @property
-    def shape(self) -> Tuple[int, int, int, int]:
+    def shape(self) -> tuple[int, int, int, int]:
         res_max = self.res[-1]
         return res_max[0], res_max[1], res_max[2], 1
 
     @classmethod
-    def get_resolutions(cls, root: str) -> Tuple[List[Vec3i], List[str], List[Vec3i]]:
+    def get_resolutions(cls, root: str) -> tuple[list[Vec3i], list[str], list[Vec3i]]:
         """Get all resolutions.
 
         Returns
         -------
         resolutions : List of (int, int, int)
             Sequence of sorted resolutions (from small to large).
-        roots : List[str]
+        roots : list[str]
             Sequence of root of resolutions respectively.
         patch_sizes : List of (int, int, int)
             Sequence of patch size of resolutions respectively.
@@ -581,7 +571,7 @@ class GrayImageStack:
     @overload
     def __getitem__(self, key: npt.NDArray[np.integer[Any]]) -> np.float32: ...
     @overload
-    def __getitem__(self, key: slice | Tuple[slice, slice] | Tuple[slice, slice, slice]) -> npt.NDArray[np.float32]: ...
+    def __getitem__(self, key: slice | tuple[slice, slice] | tuple[slice, slice, slice]) -> npt.NDArray[np.float32]: ...
     # fmt: on
     def __getitem__(self, key):
         """Get pixel/patch of image stack."""
@@ -608,10 +598,11 @@ class GrayImageStack:
         return self.imgs.get_full()[:, :, :, 0]
 
     @property
-    def shape(self) -> Tuple[int, int, int]:
+    def shape(self) -> tuple[int, int, int]:
         return self.imgs.shape[:-1]
 
 
+@deprecated("Use `read_imgs` instead")
 def read_images(*args, **kwargs) -> GrayImageStack:
     """Read images.
 
@@ -619,9 +610,4 @@ def read_images(*args, **kwargs) -> GrayImageStack:
         Use :meth:`read_imgs` instead.
     """
 
-    warnings.warn(
-        "`read_images` has been replaced by `read_imgs` because it"
-        "provide rgb support, and this will be removed in next version",
-        DeprecationWarning,
-    )
     return GrayImageStack(read_imgs(*args, **kwargs))

swcgeom/transforms/image_stack.py

@@ -12,7 +12,8 @@ pip install swcgeom[all]
 import os
 import re
 import time
-from typing import Iterable, List, Optional, Tuple
+from collections.abc import Iterable
+from typing import Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -26,6 +27,7 @@ from sdflit import (
     SDFObject,
 )
 from tqdm import tqdm
+from typing_extensions import deprecated
 
 from swcgeom.core import Population, Tree
 from swcgeom.transforms.base import Transform
@@ -62,14 +64,14 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
         ONLY works for small image stacks, use :meth`transform_and_save`
         for big image stack.
         """
-        return np.stack(list(self.transfrom(x, verbose=False)), axis=0)
+        return np.stack(list(self.transform(x, verbose=False)), axis=0)
 
-    def transfrom(
+    def transform(
         self,
         x: Tree,
         verbose: bool = True,
         *,
-        ranges: Optional[Tuple[npt.ArrayLike, npt.ArrayLike]] = None,
+        ranges: Optional[tuple[npt.ArrayLike, npt.ArrayLike]] = None,
     ) -> Iterable[npt.NDArray[np.uint8]]:
         if verbose:
             print("To image stack: " + x.source)
@@ -101,10 +103,20 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
             frame = (255 * voxel[..., 0, 0]).astype(np.uint8)
             yield frame
 
+    @deprecated("Use transform instead")
+    def transfrom(
+        self,
+        x: Tree,
+        verbose: bool = True,
+        *,
+        ranges: Optional[tuple[npt.ArrayLike, npt.ArrayLike]] = None,
+    ) -> Iterable[npt.NDArray[np.uint8]]:
+        return self.transform(x, verbose, ranges=ranges)
+
     def transform_and_save(
         self, fname: str, x: Tree, verbose: bool = True, **kwargs
     ) -> None:
-        self.save_tif(fname, self.transfrom(x, verbose=verbose, **kwargs))
+        self.save_tif(fname, self.transform(x, verbose=verbose, **kwargs))
 
     def transform_population(
         self, population: Population | str, verbose: bool = True
@@ -133,7 +145,7 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
         scene = ObjectsScene()
         scene.set_background((0, 0, 0))
 
-        def leave(n: Tree.Node, children: List[Tree.Node]) -> Tree.Node:
+        def leave(n: Tree.Node, children: list[Tree.Node]) -> Tree.Node:
             for c in children:
                 sdf = RoundCone(_tp3f(n.xyz()), _tp3f(c.xyz()), n.r, c.r).into()
                 scene.add_object(SDFObject(sdf, material).into())
@@ -175,7 +187,7 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
     def save_tif(
         fname: str,
         frames: Iterable[npt.NDArray[np.uint8]],
-        resolution: Tuple[float, float] = (1, 1),
+        resolution: tuple[float, float] = (1, 1),
     ) -> None:
         with tifffile.TiffWriter(fname) as tif:
             for frame in frames:
@@ -191,7 +203,7 @@ class ToImageStack(Transform[Tree, npt.NDArray[np.uint8]]):
                 )
 
 
-def _tp3f(x: npt.NDArray) -> Tuple[float, float, float]:
+def _tp3f(x: npt.NDArray) -> tuple[float, float, float]:
     """Convert to tuple of 3 floats."""
     assert len(x) == 3
     return (float(x[0]), float(x[1]), float(x[2]))