swcgeom 0.17.1__tar.gz → 0.17.2__tar.gz

{swcgeom-0.17.1 → swcgeom-0.17.2}/CHANGELOG.md

@@ -1,5 +1,25 @@
 # Changelog
 
+## **0.17.2**&emsp;<sub><sup>2024-08-07 ([9d5347d...59a5cbf](https://github.com/yzx9/swcgeom/compare/9d5347d0a427f460b92fd86c596e40a23812e48d...59a5cbfbe78f18a95ff8f35e72a4a0f0cdbc5009?diff=split))</sup></sub>
+
+### Bug Fixes
+
+##### &ensp;`analysis`
+
+- handle zero partition asymmetry in lmeasure ([1f332f2](https://github.com/yzx9/swcgeom/commit/1f332f22f465ea1ec7ff0b5e4013ddb6d64ffa5d))
+- workaround with angle ([05d2ff7](https://github.com/yzx9/swcgeom/commit/05d2ff77ba5f4b4331daca0bade89e10a56f564d))
+
+##### &ensp;`utils`
+
+- download with multiprocessing should avoid locals func ([6aff3e0](https://github.com/yzx9/swcgeom/commit/6aff3e0ee06fb527f759e6ec9ac09ab1ca745dad))
+
+
+### BREAKING CHANGES
+-  rename bifurcation to furcation ([26e9dec](https://github.com/yzx9/swcgeom/commit/26e9dec2db5b7d457dfe52d9a8e0177d26bc5b07))
+- `core` lazy loading in range indexing ([7d38ea8](https://github.com/yzx9/swcgeom/commit/7d38ea80fefc907c3f55663c052db9b81f144d68))
+<br>
+
+
 ## **0.17.1**&emsp;<sub><sup>2024-04-05 ([a8007ac...0ef3c2b](https://github.com/yzx9/swcgeom/compare/a8007ac6c5eb7de03298dbdcc6be59d3c282e125...0ef3c2b370a570366a79ef456c1125d12f006409?diff=split))</sup></sub>
 
 ### Features

{swcgeom-0.17.1/swcgeom.egg-info → swcgeom-0.17.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.17.1
+Version: 0.17.2
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: Apache-2.0
@@ -20,7 +20,7 @@ Requires-Dist: seaborn>=0.12.0
 Requires-Dist: tifffile>=2022.8.12
 Requires-Dist: typing_extensions>=4.4.0
 Requires-Dist: tqdm>=4.46.1
-Requires-Dist: v3d-py-helper>=0.1.0
+Requires-Dist: v3d-py-helper==0.1.0
 Provides-Extra: all
 Requires-Dist: beautifulsoup4>=4.11.1; extra == "all"
 Requires-Dist: certifi>=2023.5.7; extra == "all"

{swcgeom-0.17.1 → swcgeom-0.17.2}/examples/pytorch/branch_dataset.py

@@ -41,7 +41,7 @@ class BranchDataset(torch.utils.data.Dataset, Generic[T]):
         save : Union[str, bool], default `True`
             Save branch data to file if not False. If `True`, automatically
             generate file name.
-        transfroms : Transfroms[Branch, T], optional
+        transforms : Transforms[Branch, T], optional
             Branch transformations.
 
         See Also

{swcgeom-0.17.1 → swcgeom-0.17.2}/examples/pytorch/tree_folder_dataset.py

@@ -30,7 +30,7 @@ class TreeFolderDataset(torch.utils.data.Dataset, Generic[T]):
         ----------
         swc_dir : str
             Path of SWC file directory.
-        transfroms : Transfroms[Tree, T], optional
+        transforms : Transforms[Tree, T], optional
             Branch transformations.
 
         See Also

{swcgeom-0.17.1 → swcgeom-0.17.2}/pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
     "tifffile>=2022.8.12",
     "typing_extensions>=4.4.0",
     "tqdm>=4.46.1",
-    "v3d-py-helper>=0.1.0",
+    "v3d-py-helper==0.1.0",
 ]
 
 [project.optional-dependencies]

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.17.1'
-__version_tuple__ = version_tuple = (0, 17, 1)
+__version__ = version = '0.17.2'
+__version_tuple__ = version_tuple = (0, 17, 2)

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/analysis/feature_extractor.py

@@ -19,8 +19,8 @@ import seaborn as sns
 from matplotlib.axes import Axes
 
 from swcgeom.analysis.features import (
-    BifurcationFeatures,
     BranchFeatures,
+    FurcationFeatures,
     NodeFeatures,
     PathFeatures,
     TipFeatures,
@@ -40,6 +40,9 @@ Feature = Literal[
     "node_count",
     "node_radial_distance",
     "node_branch_order",
+    # furcation nodes
+    "furcation_count",
+    "furcation_radial_distance",
     # bifurcation nodes
     "bifurcation_count",
     "bifurcation_radial_distance",
@@ -57,7 +60,7 @@ Feature = Literal[
 NDArrayf32 = npt.NDArray[np.float32]
 FeatAndKwargs = Feature | tuple[Feature, dict[str, Any]]
 
-Feature1D = set(["length", "volume", "node_count", "bifurcation_count", "tip_count"])
+Feature1D = set(["length", "volume", "node_count", "furcation_count", "tip_count"])
 
 
 class Features:
@@ -70,7 +73,7 @@ class Features:
     @cached_property
     def node_features(self) -> NodeFeatures: return NodeFeatures(self.tree)
     @cached_property
-    def bifurcation_features(self) -> BifurcationFeatures: return BifurcationFeatures(self.node_features)
+    def furcation_features(self) -> FurcationFeatures: return FurcationFeatures(self.node_features)
     @cached_property
     def tip_features(self) -> TipFeatures: return TipFeatures(self.node_features)
     @cached_property
@@ -214,6 +217,12 @@ class FeatureExtractor(ABC):
     ) -> Axes:
         raise NotImplementedError()
 
+    def get_bifurcation_count(self, **kwargs):
+        raise DeprecationWarning("Use `furcation_count` instead.")
+
+    def get_bifurcation_radial_distance(self, **kwargs):
+        raise DeprecationWarning("Use `furcation_radial_distance` instead.")
+
 
 class TreeFeatureExtractor(FeatureExtractor):
     """Extract feature from tree."""

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/analysis/features.py

@@ -6,7 +6,7 @@ from typing import TypeVar
 
 import numpy as np
 import numpy.typing as npt
-from typing_extensions import Self
+from typing_extensions import Self, deprecated
 
 from swcgeom.core import Branch, BranchTree, Tree
 
@@ -121,12 +121,24 @@ class _SubsetNodesFeatures(ABC):
         return cls(NodeFeatures(tree))
 
 
-class BifurcationFeatures(_SubsetNodesFeatures):
-    """Evaluate bifurcation node feature of tree."""
+class FurcationFeatures(_SubsetNodesFeatures):
+    """Evaluate furcation node feature of tree."""
 
     @cached_property
     def nodes(self) -> npt.NDArray[np.bool_]:
-        return np.array([n.is_bifurcation() for n in self._features.tree])
+        return np.array([n.is_furcation() for n in self._features.tree])
+
+
+@deprecated("Use FurcationFeatures instead")
+class BifurcationFeatures(FurcationFeatures):
+    """Evaluate bifurcation node feature of tree.
+
+    Notes
+    -----
+    Deprecated due to the wrong spelling of furcation. For now, it
+    is just an alias of `FurcationFeatures` and raise a warning. It
+    will be change to raise an error in the future.
+    """
 
 
 class TipFeatures(_SubsetNodesFeatures):

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/analysis/lmeasure.py

@@ -5,9 +5,7 @@ from typing import Literal
 
 import numpy as np
 import numpy.typing as npt
-
 from swcgeom.core import Branch, Compartment, Node, Tree
-from swcgeom.utils import angle
 
 __all__ = ["LMeasure"]
 
@@ -69,7 +67,7 @@ class LMeasure:
         --------
         L-Measure: http://cng.gmu.edu:8080/Lm/help/N_bifs.htm
         """
-        return len(tree.get_bifurcations())
+        return len(tree.get_furcations())
 
     def n_branch(self, tree: Tree) -> int:
         """Number of branches.
@@ -163,12 +161,15 @@ class LMeasure:
         --------
         L-Measure: http://cng.gmu.edu:8080/Lm/help/Partition_asymmetry.htm
         """
+
         children = n.children()
         assert (
             len(children) == 2
         ), "Partition asymmetry is only defined for bifurcations"
         n1 = len(children[0].subtree().get_tips())
         n2 = len(children[1].subtree().get_tips())
+        if n1 == n2:
+            return 0
         return abs(n1 - n2) / (n1 + n2 - 2)
 
     def fractal_dim(self):
@@ -336,7 +337,7 @@ class LMeasure:
         return (da**rall_power + db**rall_power) / dp**rall_power
 
     def bif_ampl_local(self, bif: Tree.Node) -> float:
-        """Bifuraction angle.
+        """Bifurcation angle.
 
         Given a bifurcation, this function returns the angle between
         the first two compartments (in degree).
@@ -350,7 +351,7 @@ class LMeasure:
         return np.degrees(angle(v1, v2))
 
     def bif_ampl_remote(self, bif: Tree.Node) -> float:
-        """Bifuraction angle.
+        """Bifurcation angle.
 
         This function returns the angle between two bifurcation points
         or between bifurcation point and terminal point or between two
@@ -361,7 +362,7 @@ class LMeasure:
         L-Measure: http://cng.gmu.edu:8080/Lm/help/Bif_ampl_remote.htm
         """
 
-        v1, v2 = self._bif_vector_local(bif)
+        v1, v2 = self._bif_vector_remote(bif)
         return np.degrees(angle(v1, v2))
 
     def bif_tilt_local(self, bif: Tree.Node) -> float:
@@ -665,7 +666,7 @@ class LMeasure:
         n = node
         order = 0
         while n is not None:
-            if n.is_bifurcation():
+            if n.is_furcation():
                 order += 1
             n = n.parent()
         return order
@@ -819,3 +820,23 @@ def pill_surface_area(ra: float, rb: float, h: float) -> float:
     bottom_hemisphere_area = 2 * math.pi * rb**2
     total_area = lateral_area + top_hemisphere_area + bottom_hemisphere_area
     return total_area
+
+
+# TODO: move to `utils`
+def angle(a: npt.ArrayLike, b: npt.ArrayLike) -> float:
+    """Get the angle of vectors.
+
+    Returns
+    -------
+    angle : float
+        Angle [0, PI) in radians.
+    """
+
+    a, b = np.array(a), np.array(b)
+    if np.linalg.norm(a) == 0 or np.linalg.norm(b) == 0:
+        raise ValueError("Input vectors must not be zero vectors.")
+
+    costheta = np.dot(a, b) / (np.linalg.norm(a) * np.linalg.norm(b))
+    costheta = np.clip(costheta, -1, 1)  # avoid numerical errors
+    theta = np.arccos(costheta)
+    return theta

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/analysis/sholl.py

@@ -8,6 +8,7 @@ import numpy.typing as npt
 import seaborn as sns
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
+from typing_extensions import deprecated
 
 from swcgeom.analysis.visualization import draw
 from swcgeom.core import Tree
@@ -160,20 +161,17 @@ class Sholl:
 
         return self.get_rs(self.rmax, steps)
 
+    @deprecated("Use `Sholl.get(x)` instead")
     def get_count(self) -> npt.NDArray[np.int32]:
         """Get the count of intersection.
 
         .. deprecated:: 0.5.0
-            Use :meth:`Sholl.get` instead.
+            Use :meth:`Sholl(x).get()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.get_count` has been renamed to `get` since v0.5.0, "
-            "and will be removed in next version",
-            DeprecationWarning,
-        )
         return self.get().astype(np.int32)
 
+    @deprecated("Use `Shool(x).get().mean()` instead")
     def avg(self) -> float:
         """Get the average of the count of intersection.
 
@@ -181,14 +179,9 @@ class Sholl:
             Use :meth:`Shool(x).get().mean()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.avg` has been deprecated since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().mean()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().mean()
 
+    @deprecated("Use `Shool(x).get().std()` instead")
     def std(self) -> float:
         """Get the std of the count of intersection.
 
@@ -196,14 +189,9 @@ class Sholl:
             Use :meth:`Shool(x).get().std()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.std` has been deprecate since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().std()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().std()
 
+    @deprecated("Use `Shool(x).get().sum()` instead")
     def sum(self) -> int:
         """Get the sum of the count of intersection.
 
@@ -211,10 +199,4 @@ class Sholl:
             Use :meth:`Shool(x).get().sum()` instead.
         """
 
-        warnings.warn(
-            "`Sholl.sum` has been deprecate since v0.6.0 and will be "
-            "removed in next version, use `Shool(x).get().sum()` "
-            "instead",
-            DeprecationWarning,
-        )
         return self.get().sum()

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/core/node.py

@@ -5,6 +5,7 @@ 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-0.17.1 → swcgeom-0.17.2}/swcgeom/core/path.py

@@ -1,11 +1,11 @@
 """Nueron path."""
 
-import warnings
 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
@@ -16,7 +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
@@ -75,6 +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.
 
@@ -82,11 +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-0.17.1 → swcgeom-0.17.2}/swcgeom/core/population.py

@@ -97,6 +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."""
 
@@ -135,13 +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)])
@@ -328,3 +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-0.17.1 → swcgeom-0.17.2}/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-0.17.1 → swcgeom-0.17.2}/swcgeom/core/tree.py

@@ -8,6 +8,7 @@ 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
@@ -38,11 +39,11 @@ class Tree(DictSWC):
 
         def branch(self) -> "Tree.Branch":
             ns: list["Tree.Node"] = [self]
-            while not ns[-1].is_bifurcation() and (p := ns[-1].parent()) is not None:
+            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])
@@ -187,16 +188,28 @@ 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_furcations)
+        return [self.node(i) for i in furcations]
 
-        self.traverse(leave=collect_bifurcations)
-        return [self.node(i) for i in bifurcations]
+    @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."""

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/core/tree_utils.py

@@ -5,6 +5,7 @@ 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 (
@@ -95,6 +96,7 @@ def cut_tree(tree: Tree, *, enter=None, leave=None):
     return to_subtree(tree, removals)
 
 
+@deprecated("Use `to_subtree` instead")
 def to_sub_tree(swc_like: SWCLike, sub: Topology) -> tuple[Tree, dict[int, int]]:
     """Create subtree from origin tree.
 
@@ -111,13 +113,6 @@ def to_sub_tree(swc_like: SWCLike, sub: Topology) -> tuple[Tree, 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)
 

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/images/folder.py

@@ -3,7 +3,6 @@
 import math
 import os
 import re
-import warnings
 from collections.abc import Callable, Iterable
 from dataclasses import dataclass
 from typing import Generic, Literal, Optional, TypeVar, overload
@@ -11,7 +10,7 @@ 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
@@ -65,6 +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.
 
@@ -72,14 +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()
 
 

{swcgeom-0.17.1 → swcgeom-0.17.2}/swcgeom/images/io.py

@@ -12,6 +12,7 @@ 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"]
@@ -601,6 +602,7 @@ class GrayImageStack:
         return self.imgs.shape[:-1]
 
 
+@deprecated("Use `read_imgs` instead")
 def read_images(*args, **kwargs) -> GrayImageStack:
     """Read images.
 
@@ -608,9 +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))