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

swcgeom/analysis/volume.py

@@ -1,6 +1,6 @@
 """Analysis of volume of a SWC tree."""
 
-from typing import Dict, List, Literal
+from typing import Literal
 
 import numpy as np
 from sdflit import ColoredMaterial, ObjectsScene, SDFObject, UniformSampler
@@ -11,7 +11,7 @@ from swcgeom.utils import VolFrustumCone, VolSphere
 __all__ = ["get_volume"]
 
 ACCURACY_LEVEL = Literal["low", "middle", "high"]
-ACCURACY_LEVELS: Dict[ACCURACY_LEVEL, int] = {"low": 3, "middle": 5, "high": 8}
+ACCURACY_LEVELS: dict[ACCURACY_LEVEL, int] = {"low": 3, "middle": 5, "high": 8}
 
 
 def get_volume(
@@ -93,7 +93,7 @@ def _get_volume_frustum_cone(tree: Tree, *, accuracy: int) -> float:
 
     volume = 0.0
 
-    def leave(n: Tree.Node, children: List[VolSphere]) -> VolSphere:
+    def leave(n: Tree.Node, children: list[VolSphere]) -> VolSphere:
         sphere = VolSphere(n.xyz(), n.r)
         cones = [VolFrustumCone(n.xyz(), n.r, c.center, c.radius) for c in children]
 
@@ -129,7 +129,7 @@ def _get_volume_frustum_cone_mc_only(tree: Tree) -> float:
     scene = ObjectsScene()
     scene.set_background((0, 0, 0))
 
-    def leave(n: Tree.Node, children: List[VolSphere]) -> VolSphere:
+    def leave(n: Tree.Node, children: list[VolSphere]) -> VolSphere:
         sphere = VolSphere(n.xyz(), n.r)
         scene.add_object(SDFObject(sphere.sdf, material).into())
 

swcgeom/core/branch.py

@@ -1,6 +1,7 @@
 """Branch is a set of node points."""
 
-from typing import Generic, Iterable, List
+from collections.abc import Iterable
+from typing import Generic
 
 import numpy as np
 import numpy.typing as npt
@@ -92,7 +93,7 @@ class Branch(Path, Generic[SWCTypeVar]):
     @classmethod
     def from_xyzr_batch(
         cls, xyzr_batch: npt.NDArray[np.float32]
-    ) -> List["Branch[DictSWC]"]:
+    ) -> list["Branch[DictSWC]"]:
         r"""Create list of branch form ~numpy.ndarray.
 
         Parameters
@@ -112,7 +113,7 @@ class Branch(Path, Generic[SWCTypeVar]):
             )
             xyzr_batch = np.concatenate([xyzr_batch, ones], axis=2)
 
-        branches: List[Branch[DictSWC]] = []
+        branches: list[Branch[DictSWC]] = []
         for xyzr in xyzr_batch:
             n_nodes = xyzr.shape[0]
             idx = np.arange(0, n_nodes, step=1, dtype=np.int32)

swcgeom/core/branch_tree.py

@@ -1,7 +1,6 @@
 """Branch tree is a simplified neuron tree."""
 
 import itertools
-from typing import Dict, List
 
 import numpy as np
 import pandas as pd
@@ -19,13 +18,13 @@ class BranchTree(Tree):
     A branch tree that contains only soma, branch, and tip nodes.
     """
 
-    branches: Dict[int, List[Branch]]
+    branches: dict[int, list[Branch]]
 
-    def get_origin_branches(self) -> List[Branch]:
+    def get_origin_branches(self) -> list[Branch]:
         """Get branches of original tree."""
         return list(itertools.chain(*self.branches.values()))
 
-    def get_origin_node_branches(self, idx: int) -> List[Branch]:
+    def get_origin_node_branches(self, idx: int) -> list[Branch]:
         """Get branches of node of original tree."""
         return self.branches[idx]
 

swcgeom/core/compartment.py

@@ -1,6 +1,7 @@
 """The segment is a branch with two nodes."""
 
-from typing import Generic, Iterable, List, TypeVar
+from collections.abc import Iterable
+from typing import Generic, TypeVar
 
 import numpy as np
 import numpy.typing as npt
@@ -43,7 +44,7 @@ class Compartment(Path, Generic[SWCTypeVar]):
 T = TypeVar("T", bound=Compartment)
 
 
-class Compartments(List[T]):
+class Compartments(list[T]):
     r"""Comparments contains a set of comparment."""
 
     names: SWCNames

swcgeom/core/node.py

@@ -1,10 +1,11 @@
 """Nueron node."""
 
-import warnings
-from typing import Any, Generic, Iterable
+from collections.abc import Iterable
+from typing import Any, Generic
 
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import deprecated
 
 from swcgeom.core.swc import DictSWC, SWCTypeVar
 from swcgeom.core.swc_utils import SWCNames
@@ -95,9 +96,22 @@ class Node(Generic[SWCTypeVar]):
         items = [self.id, self.type, x, y, z, r, self.pid]
         return " ".join(map(str, items))
 
-    def is_bifurcation(self) -> bool:
+    def is_furcation(self) -> bool:
+        """Is furcation node."""
         return np.count_nonzero(self.attach.pid() == self.id) > 1
 
+    @deprecated("Use is_furcation instead")
+    def is_bifurcation(self) -> bool:
+        """Is furcation node.
+
+        Notes
+        -----
+        Deprecated due to the wrong spelling of furcation. For now, it
+        is just an alias of `is_furcation` and raise a warning. It will
+        be change to raise an error in the future.
+        """
+        return self.is_furcation()
+
     def is_tip(self) -> bool:
         return self.id not in self.attach.pid()
 

swcgeom/core/path.py

@@ -1,10 +1,11 @@
 """Nueron path."""
 
-import warnings
-from typing import Generic, Iterable, Iterator, List, overload
+from collections.abc import Iterable, Iterator
+from typing import Generic, overload
 
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import deprecated
 
 from swcgeom.core.node import Node
 from swcgeom.core.swc import DictSWC, SWCLike, SWCTypeVar
@@ -15,7 +16,7 @@ __all__ = ["Path"]
 class Path(SWCLike, Generic[SWCTypeVar]):
     """Neuron path.
 
-    A path is a linear set of points without bifurcations.
+    A path is a linear set of points without furcations.
     """
 
     attach: SWCTypeVar
@@ -44,7 +45,7 @@ class Path(SWCLike, Generic[SWCTypeVar]):
     @overload
     def __getitem__(self, key: int) -> Node: ...
     @overload
-    def __getitem__(self, key: slice) -> List[Node]: ...
+    def __getitem__(self, key: slice) -> list[Node]: ...
     @overload
     def __getitem__(self, key: str) -> npt.NDArray: ...
     # fmt:on
@@ -74,6 +75,7 @@ class Path(SWCLike, Generic[SWCTypeVar]):
     def get_ndata(self, key: str) -> npt.NDArray:
         return self.attach.get_ndata(key)[self.idx]
 
+    @deprecated("Use `path.node` instead.")
     def get_node(self, idx: int | np.integer) -> Node:
         """Get the count of intersection.
 
@@ -81,11 +83,6 @@ class Path(SWCLike, Generic[SWCTypeVar]):
             Use :meth:`path.node` instead.
         """
 
-        warnings.warn(
-            "`Path.get_node` has been deprecated since v0.16.0 and "
-            "will be removed in future version",
-            DeprecationWarning,
-        )
         return self.node(idx)
 
     def node(self, idx: int | np.integer) -> Node:

swcgeom/core/population.py

@@ -2,21 +2,10 @@
 
 import os
 import warnings
+from collections.abc import Callable, Iterable, Iterator
 from concurrent.futures import ProcessPoolExecutor
 from functools import reduce
-from typing import (
-    Any,
-    Callable,
-    Dict,
-    Iterable,
-    Iterator,
-    List,
-    Optional,
-    Protocol,
-    TypeVar,
-    cast,
-    overload,
-)
+from typing import Any, Optional, Protocol, TypeVar, cast, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -44,16 +33,16 @@ class Trees(Protocol):
 class LazyLoadingTrees:
     """Lazy loading trees."""
 
-    swcs: List[str]
-    trees: List[Tree | None]
-    kwargs: Dict[str, Any]
+    swcs: list[str]
+    trees: list[Tree | None]
+    kwargs: dict[str, Any]
 
     def __init__(self, swcs: Iterable[str], **kwargs) -> None:
         """
         Paramters
         ---------
         swcs : List of str
-        kwargs : Dict[str, Any]
+        kwargs : dict[str, Any]
             Forwarding to `Tree.from_swc`
         """
 
@@ -81,7 +70,7 @@ class LazyLoadingTrees:
 class ChainTrees:
     """Chain trees."""
 
-    trees: List[Trees]
+    trees: list[Trees]
     cumsum: npt.NDArray[np.int64]
 
     def __init__(self, trees: Iterable[Trees]) -> None:
@@ -108,6 +97,19 @@ class ChainTrees:
         return (self[i] for i in range(self.__len__()))
 
 
+class NestTrees:
+    def __init__(self, trees: Trees, idx: Iterable[int], /) -> None:
+        super().__init__()
+        self.trees = trees
+        self.idx = list(idx)
+
+    def __getitem__(self, key: int, /) -> Tree:
+        return self.trees[self.idx[key]]
+
+    def __len__(self) -> int:
+        return len(self.idx)
+
+
 class Population:
     """Neuron population."""
 
@@ -146,13 +148,14 @@ class Population:
 
     # fmt:off
     @overload
-    def __getitem__(self, key: slice) -> List[Tree]: ...
+    def __getitem__(self, key: slice) -> Trees: ...
     @overload
     def __getitem__(self, key: int) -> Tree: ...
     # fmt:on
-    def __getitem__(self, key):
+    def __getitem__(self, key: int | slice):
         if isinstance(key, slice):
-            return [cast(Tree, self.trees[i]) for i in range(*key.indices(len(self)))]
+            trees = NestTrees(self.trees, range(*key.indices(len(self))))
+            return cast(Trees, trees)
 
         if isinstance(key, (int, np.integer)):
             return cast(Tree, self.trees[int(key)])
@@ -216,9 +219,9 @@ class Population:
         return cls.from_swc(root, ext, extra_cols=extra_cols, **kwargs)
 
     @staticmethod
-    def find_swcs(root: str, ext: str = ".swc", relpath: bool = False) -> List[str]:
+    def find_swcs(root: str, ext: str = ".swc", relpath: bool = False) -> list[str]:
         """Find all swc files."""
-        swcs: List[str] = []
+        swcs: list[str] = []
         for r, _, files in os.walk(root):
             rr = os.path.relpath(r, root) if relpath else r
             fs = filter(lambda f: os.path.splitext(f)[-1] == ext, files)
@@ -231,8 +234,8 @@ class Populations:
     """A set of population."""
 
     len: int
-    populations: List[Population]
-    labels: List[str]
+    populations: list[Population]
+    labels: list[str]
 
     def __init__(
         self, populations: Iterable[Population], labels: Optional[Iterable[str]] = None
@@ -248,9 +251,9 @@ class Populations:
 
     # fmt:off
     @overload
-    def __getitem__(self, key: slice) -> List[List[Tree]]: ...
+    def __getitem__(self, key: slice) -> list[list[Tree]]: ...
     @overload
-    def __getitem__(self, key: int) -> List[Tree]: ...
+    def __getitem__(self, key: int) -> list[Tree]: ...
     # fmt:on
     def __getitem__(self, key):
         return [p[key] for p in self.populations]
@@ -259,7 +262,7 @@ class Populations:
         """Miniumn length of populations."""
         return self.len
 
-    def __iter__(self) -> Iterator[List[Tree]]:
+    def __iter__(self) -> Iterator[list[Tree]]:
         return (self[i] for i in range(self.len))
 
     def __repr__(self) -> str:
@@ -288,7 +291,7 @@ class Populations:
 
         Parameters
         ----------
-        roots : list of str
+        roots : List of str
         intersect : bool, default `True`
             Take the intersection of these populations.
         check_same : bool, default `False`
@@ -339,3 +342,14 @@ def _get_idx(key: int, length: int) -> int:
         key += length
 
     return key
+
+
+# experimental
+def filter_population(
+    pop: Population, predicate: Callable[[Tree], bool]
+) -> "Population":
+    """Filter trees in the population."""
+
+    # TODO: how to avoid load trees
+    idx = [i for i, t in enumerate(pop) if predicate(t)]
+    return Population(NestTrees(pop.trees, idx), root=pop.root)

swcgeom/core/swc.py

@@ -2,8 +2,9 @@
 
 import warnings
 from abc import ABC, abstractmethod
+from collections.abc import Iterable
 from copy import deepcopy
-from typing import Any, Dict, Iterable, List, Optional, Tuple, TypeVar, overload
+from typing import Any, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -32,7 +33,7 @@ __all__ = [
 
 
 swc_names_default = get_names()
-swc_cols: List[Tuple[str, npt.DTypeLike]] = [
+swc_cols: list[tuple[str, npt.DTypeLike]] = [
     (swc_names_default.id, np.int32),
     (swc_names_default.type, np.int32),
     (swc_names_default.x, np.float32),
@@ -42,7 +43,7 @@ swc_cols: List[Tuple[str, npt.DTypeLike]] = [
     (swc_names_default.pid, np.int32),
 ]
 
-eswc_cols: List[Tuple[str, npt.DTypeLike]] = [
+eswc_cols: list[tuple[str, npt.DTypeLike]] = [
     ("level", np.int32),
     ("mode", np.int32),
     ("timestamp", np.int32),
@@ -55,7 +56,7 @@ class SWCLike(ABC):
     """ABC of SWC."""
 
     source: str = ""
-    comments: List[str] = []
+    comments: list[str] = []
     names: SWCNames
     types: SWCTypes
 
@@ -131,15 +132,15 @@ class SWCLike(ABC):
 
     # fmt: off
     @overload
-    def to_swc(self, fname: str, *, extra_cols: List[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> None: ...
+    def to_swc(self, fname: str, *, extra_cols: list[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> None: ...
     @overload
-    def to_swc(self, *, extra_cols: List[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> str: ...
+    def to_swc(self, *, extra_cols: list[str] | None = ..., source: bool | str = ..., id_offset: int = ...) -> str: ...
     # fmt: on
     def to_swc(
         self,
         fname: Optional[str] = None,
         *,
-        extra_cols: Optional[List[str]] = None,
+        extra_cols: Optional[list[str]] = None,
         source: bool | str = True,
         comments: bool = True,
         id_offset: int = 1,
@@ -177,7 +178,7 @@ class SWCLike(ABC):
         self,
         fname: Optional[str] = None,
         swc_path: Optional[str] = None,
-        extra_cols: Optional[List[str]] = None,
+        extra_cols: Optional[list[str]] = None,
         **kwargs,
     ) -> str | None:
         if swc_path is None:
@@ -199,7 +200,7 @@ SWCTypeVar = TypeVar("SWCTypeVar", bound=SWCLike)
 class DictSWC(SWCLike):
     """SWC implementation on dict."""
 
-    ndata: Dict[str, npt.NDArray]
+    ndata: dict[str, npt.NDArray]
 
     def __init__(
         self,
@@ -221,7 +222,7 @@ class DictSWC(SWCLike):
     def values(self) -> Iterable[npt.NDArray[Any]]:
         return self.ndata.values()
 
-    def items(self) -> Iterable[Tuple[str, npt.NDArray[Any]]]:
+    def items(self) -> Iterable[tuple[str, npt.NDArray[Any]]]:
         return self.ndata.items()
 
     def get_ndata(self, key: str) -> npt.NDArray[Any]:

swcgeom/core/swc_utils/base.py

@@ -1,16 +1,7 @@
 """Base SWC format utils."""
 
-from dataclasses import dataclass
-from typing import (
-    Callable,
-    List,
-    Literal,
-    NamedTuple,
-    Optional,
-    Tuple,
-    TypeVar,
-    overload,
-)
+from collections.abc import Callable
+from typing import Literal, NamedTuple, Optional, TypeVar, overload
 
 import numpy as np
 import numpy.typing as npt
@@ -29,7 +20,7 @@ __all__ = [
 ]
 
 T, K = TypeVar("T"), TypeVar("K")
-Topology = Tuple[npt.NDArray[np.int32], npt.NDArray[np.int32]]  # (id, pid)
+Topology = tuple[npt.NDArray[np.int32], npt.NDArray[np.int32]]  # (id, pid)
 
 
 class SWCNames(NamedTuple):
@@ -43,7 +34,7 @@ class SWCNames(NamedTuple):
     r: str = "r"
     pid: str = "pid"
 
-    def cols(self) -> List[str]:
+    def cols(self) -> list[str]:
         return [self.id, self.type, self.x, self.y, self.z, self.r, self.pid]
 
 
@@ -114,10 +105,10 @@ def get_dsu(
 @overload
 def traverse(topology: Topology, *, enter: Callable[[int, T | None], T], root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> None: ...
 @overload
-def traverse(topology: Topology, *, leave: Callable[[int, List[K]], K], root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> K: ...
+def traverse(topology: Topology, *, leave: Callable[[int, list[K]], K], root: int | np.integer = ..., mode: Literal["dfs"] = ...) -> K: ...
 @overload
 def traverse(
-    topology: Topology, *, enter: Callable[[int, T | None], T], leave: Callable[[int, List[K]], K],
+    topology: Topology, *, enter: Callable[[int, T | None], T], leave: Callable[[int, list[K]], K],
     root: int | np.integer = ..., mode: Literal["dfs"] = ...,
 ) -> K: ...
 # fmt: on
@@ -130,7 +121,7 @@ def traverse(topology: Topology, *, mode="dfs", **kwargs):
         The callback when entering node, which accepts two parameters,
         the current node id and the return value of it parent node. In
         particular, the root node receives an `None`.
-    leave : (id: int, children: List[T]) => T, optional
+    leave : (id: int, children: list[T]) => T, optional
         The callback when leaving node. When leaving a node, subtree
         has already been traversed. Callback accepts two parameters,
         the current node id and list of the return value of children,
@@ -155,7 +146,7 @@ def _traverse_dfs(topology: Topology, *, enter=None, leave=None, root=0):
         children_map[pid].append(idx)
 
     # manual dfs to avoid stack overflow in long branch
-    stack: List[Tuple[int, bool]] = [(root, True)]  # (idx, is_enter)
+    stack: list[tuple[int, bool]] = [(root, True)]  # (idx, is_enter)
     params = {root: None}
     vals = {}
 

swcgeom/core/swc_utils/checker.py

@@ -1,11 +1,11 @@
 """Check common """
 
-import warnings
 from collections import defaultdict
 from typing import Optional
 
 import numpy as np
 import pandas as pd
+from typing_extensions import deprecated
 
 from swcgeom.core.swc_utils.base import SWCNames, Topology, get_dsu, get_names, traverse
 from swcgeom.utils import DisjointSetUnion
@@ -81,6 +81,7 @@ def has_cyclic(topology: Topology) -> bool:
     return False
 
 
+@deprecated("Use `is_single_root` instead")
 def check_single_root(*args, **kwargs) -> bool:
     """Check if the tree is single root.
 
@@ -88,14 +89,10 @@ def check_single_root(*args, **kwargs) -> bool:
         Use :meth:`is_single_root` instead.
     """
 
-    warnings.warn(
-        "`check_single_root` has been renamed to `is_single_root` since"
-        "v0.5.0, and will be removed in next version",
-        DeprecationWarning,
-    )
     return is_single_root(*args, **kwargs)
 
 
+@deprecated("Use `is_bifurcate` instead")
 def is_binary_tree(
     df: pd.DataFrame, exclude_root: bool = True, *, names: Optional[SWCNames] = None
 ) -> bool:
@@ -105,11 +102,6 @@ def is_binary_tree(
         Use :meth:`is_bifurcate` instead.
     """
 
-    warnings.warn(
-        "`is_binary_tree` has been replaced by to `is_bifurcate` since"
-        "v0.8.0, and will be removed in next version",
-        DeprecationWarning,
-    )
     names = get_names(names)
     topo = (df[names.id].to_numpy(), df[names.pid].to_numpy())
     return is_bifurcate(topo, exclude_root=exclude_root)

swcgeom/core/swc_utils/io.py

@@ -2,7 +2,8 @@
 
 import re
 import warnings
-from typing import Callable, Iterable, List, Literal, Optional, Tuple
+from collections.abc import Callable, Iterable
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -30,7 +31,7 @@ def read_swc(
     *,
     encoding: Literal["detect"] | str = "utf-8",
     names: Optional[SWCNames] = None,
-) -> Tuple[pd.DataFrame, List[str]]:
+) -> tuple[pd.DataFrame, list[str]]:
     """Read swc file.
 
     Parameters
@@ -55,7 +56,7 @@ def read_swc(
     Returns
     -------
     df : ~pandas.DataFrame
-    comments : list of string
+    comments : List of string
     """
 
     names = get_names(names)
@@ -137,14 +138,14 @@ def parse_swc(
     names: SWCNames,
     extra_cols: Iterable[str] | None = None,
     encoding: Literal["detect"] | str = "utf-8",
-) -> Tuple[pd.DataFrame, List[str]]:
+) -> tuple[pd.DataFrame, list[str]]:
     """Parse swc file.
 
     Parameters
     ----------
     fname : PathOrIO
     names : SWCNames
-    extra_cols : list of str, optional
+    extra_cols : List of str, optional
     encoding : str | 'detect', default `utf-8`
         The name of the encoding used to decode the file. If is
         `detect`, we will try to detect the character encoding.
@@ -152,7 +153,7 @@ def parse_swc(
     Returns
     -------
     df : ~pandas.DataFrame
-    comments : list of string
+    comments : List of string
     """
 
     # pylint: disable=too-many-locals

swcgeom/core/swc_utils/normalizer.py

@@ -3,7 +3,8 @@
 Methods ending with a underline imply an in-place transformation.
 """
 
-from typing import Callable, List, Literal, Optional, Tuple
+from collections.abc import Callable
+from typing import Literal, Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -111,7 +112,7 @@ def sort_nodes_(df: pd.DataFrame, *, names: Optional[SWCNames] = None) -> None:
     df[names.id], df[names.pid] = new_ids, new_pids
 
 
-def sort_nodes_impl(topology: Topology) -> Tuple[Topology, npt.NDArray[np.int32]]:
+def sort_nodes_impl(topology: Topology) -> tuple[Topology, npt.NDArray[np.int32]]:
     """Sort the indices of neuron tree.
 
     Returns
@@ -127,7 +128,7 @@ def sort_nodes_impl(topology: Topology) -> Tuple[Topology, npt.NDArray[np.int32]
     new_pids = np.full_like(old_ids, fill_value=-3)
     new_id = 0
     first_root = old_ids[(old_pids == -1).argmax()]
-    s: List[Tuple[npt.NDArray[np.int32], int]] = [(first_root, -1)]
+    s: list[tuple[npt.NDArray[np.int32], int]] = [(first_root, -1)]
     while len(s) != 0:
         old_id, new_pid = s.pop()
         id_map[new_id] = old_id

swcgeom/core/swc_utils/subtree.py

@@ -6,7 +6,7 @@ but in more cases, you can use the high-level methods provided in
 high-level API.
 """
 
-from typing import Tuple, cast
+from typing import cast
 
 import numpy as np
 import numpy.typing as npt
@@ -18,7 +18,7 @@ __all__ = ["REMOVAL", "to_sub_topology", "propagate_removal"]
 REMOVAL = -2  # A marker in utils, place in the ids to mark it removal
 
 
-def to_sub_topology(sub: Topology) -> Tuple[Topology, npt.NDArray[np.int32]]:
+def to_sub_topology(sub: Topology) -> tuple[Topology, npt.NDArray[np.int32]]:
     """Create sub tree from origin tree.
 
     Mark the node to be removed, then use this method to get a child