swcgeom 0.11.1__py3-none-any.whl → 0.13.0__py3-none-any.whl

swcgeom/core/swc_utils/io.py

@@ -4,25 +4,25 @@ import re
 import warnings
 from typing import Callable, Iterable, List, Literal, Optional, Tuple
 
-import chardet
 import numpy as np
 import numpy.typing as npt
 import pandas as pd
 
-from .base import SWCNames, get_names
-from .checker import is_single_root
-from .normalizer import (
+from swcgeom.core.swc_utils.base import SWCNames, get_names
+from swcgeom.core.swc_utils.checker import is_single_root
+from swcgeom.core.swc_utils.normalizer import (
     link_roots_to_nearest_,
     mark_roots_as_somas_,
     reset_index_,
     sort_nodes_,
 )
+from swcgeom.utils import FileReader, PathOrIO
 
 __all__ = ["read_swc", "to_swc"]
 
 
 def read_swc(
-    swc_file: str,
+    swc_file: PathOrIO,
     extra_cols: Optional[Iterable[str]] = None,
     fix_roots: Literal["somas", "nearest", False] = False,
     sort_nodes: bool = False,
@@ -35,7 +35,7 @@ def read_swc(
 
     Parameters
     ----------
-    swc_file : str
+    swc_file : PathOrIO
         Path of swc file, the id should be consecutively incremented.
     extra_cols : Iterable[str], optional
         Read more cols in swc file.
@@ -47,7 +47,7 @@ def read_swc(
     reset_index : bool, default `True`
         Reset node index to start with zero, DO NOT set to false if
         you are not sure what will happend.
-    encoding : str, default `utf-8`
+    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.
     names : SWCNames, optional
@@ -59,19 +59,6 @@ def read_swc(
     """
 
     names = get_names(names)
-
-    if encoding == "detect":
-        with open(swc_file, "rb") as f:
-            data = f.read()
-
-        result = chardet.detect(data)
-        encoding = result["encoding"] or "utf-8"
-        if result["confidence"] < 0.9:
-            warnings.warn(
-                f"parse as `{encoding}` with low confidence "
-                f"{result['confidence']} in `{swc_file}`"
-            )
-
     df, comments = parse_swc(
         swc_file, names=names, extra_cols=extra_cols, encoding=encoding
     )
@@ -145,14 +132,23 @@ RE_FLOAT = r"([+-]?(?:\d+(?:[.]\d*)?(?:[eE][+-]?\d+)?|[.]\d+(?:[eE][+-]?\d+)?))"
 
 
 def parse_swc(
-    swc_file: str,
+    fname: PathOrIO,
     *,
     names: SWCNames,
     extra_cols: Iterable[str] | None = None,
-    encoding: str = "utf-8",
+    encoding: Literal["detect"] | str = "utf-8",
 ) -> Tuple[pd.DataFrame, List[str]]:
     """Parse swc file.
 
+    Parameters
+    ----------
+    fname : PathOrIO
+    names : SWCNames
+    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.
+
     Returns
     -------
     df : ~pandas.DataFrame
@@ -183,17 +179,19 @@ def parse_swc(
     # neuromorpho.org. More fields at the end is allowed, such as
     # reading eswc as swc, but with a warning.
     re_swc = re.compile(rf"^\s*{re_swc_cols_str}\s*([\s+-.0-9]*)$")
+
     last_group = 7 + len(extras) + 1
+    ignored_comment = f"# {' '.join(names.cols())}"
+    flag = True
 
     comments = []
-    try:
-        with open(swc_file, "r", encoding=encoding) as f:
-            flag = True
+    with FileReader(fname, encoding=encoding) as f:
+        try:
             for i, line in enumerate(f):
                 if (match := re_swc.search(line)) is not None:
                     if flag and match.group(last_group):
                         warnings.warn(
-                            f"some fields are ignored in row {i} of `{swc_file}`"
+                            f"some fields are ignored in row {i+1} of `{fname}`"
                         )
                         flag = False
 
@@ -201,11 +199,14 @@ def parse_swc(
                         vals[i].append(trans(match.group(i + 1)))
                 elif match := RE_COMMENT.match(line):
                     comment = line[len(match.group(0)) :].removesuffix("\n")
-                    comments.append(comment)
+                    if not comment.startswith(ignored_comment):
+                        comments.append(comment)
                 elif not line.isspace():
-                    raise ValueError(f"invalid row {i} in `{swc_file}`")
-    except UnicodeDecodeError as e:
-        raise ValueError(f"encoding error in `{swc_file}`") from e
+                    raise ValueError(f"invalid row {i+1} in `{fname}`")
+        except UnicodeDecodeError as e:
+            raise ValueError(
+                f"decode failed, try to enable auto detect `encoding='detect'`"
+            ) from e
 
     df = pd.DataFrame.from_dict(dict(zip(keys, vals)))
     return df, comments

swcgeom/core/swc_utils/normalizer.py

@@ -9,7 +9,7 @@ import numpy as np
 import numpy.typing as npt
 import pandas as pd
 
-from .base import SWCNames, Topology, get_dsu, get_names
+from swcgeom.core.swc_utils.base import SWCNames, Topology, get_dsu, get_names
 
 __all__ = [
     "mark_roots_as_somas",

swcgeom/core/swc_utils/subtree.py

@@ -11,7 +11,7 @@ from typing import Tuple, cast
 import numpy as np
 import numpy.typing as npt
 
-from .base import Topology, traverse
+from swcgeom.core.swc_utils.base import Topology, traverse
 
 __all__ = ["REMOVAL", "to_sub_topology", "propagate_removal"]
 

swcgeom/core/tree.py

@@ -22,13 +22,14 @@ import numpy.typing as npt
 import pandas as pd
 from typing_extensions import Self
 
-from ..utils import padding1d
-from .branch import Branch
-from .node import Node
-from .path import Path
-from .segment import Segment, Segments
-from .swc import DictSWC, eswc_cols
-from .swc_utils import SWCNames, get_names, read_swc, traverse
+from swcgeom.core.branch import Branch
+from swcgeom.core.node import Node
+from swcgeom.core.path import Path
+from swcgeom.core.segment import Segment, Segments
+from swcgeom.core.swc import DictSWC, eswc_cols
+from swcgeom.core.swc_utils import SWCNames, get_names, read_swc, traverse
+from swcgeom.core.tree_utils_impl import get_subtree_impl
+from swcgeom.utils import PathOrIO, padding1d
 
 __all__ = ["Tree"]
 
@@ -68,13 +69,21 @@ class Tree(DictSWC):
 
             return Tree.Branch(self.attach, [n.id for n in ns])
 
-        def is_soma(self) -> bool:
-            return self.id == 0
-
         def radial_distance(self) -> float:
             """The end-to-end straight-line distance to soma."""
             return self.distance(self.attach.soma())
 
+        def subtree(self) -> "Tree":
+            """Get subtree from node."""
+            n_nodes, ndata, source, names = get_subtree_impl(self.attach, self.id)
+            return Tree(n_nodes, **ndata, source=source, names=names)
+
+        def is_root(self) -> bool:
+            return self.parent() is None
+
+        def is_soma(self) -> bool:  # TODO: support multi soma, e.g. 3 points
+            return self.type == self.attach.types.soma and self.is_root()
+
         # fmt: off
         @overload
         def traverse(self, *, enter: Callable[[Node, T | None], T], mode: Literal["dfs"] = ...) -> None: ...
@@ -181,8 +190,13 @@ class Tree(DictSWC):
     def node(self, idx: int | np.integer) -> Node:
         return self.Node(self, idx)
 
-    def soma(self) -> Node:
-        return self.node(0)
+    def soma(self, type_check: bool = True) -> Node:
+        """Get soma of neuron."""
+        # TODO: find soma, see also: https://neuromorpho.org/myfaq.jsp
+        n = self.node(0)
+        if type_check and n.type != self.types.soma:
+            raise ValueError(f"no soma found in: {self.source}")
+        return n
 
     def get_bifurcations(self) -> List[Node]:
         """Get all node of bifurcations."""
@@ -246,6 +260,16 @@ class Tree(DictSWC):
         paths = self.traverse(enter=assign_path, leave=collect_path)
         return [self.Path(self, idx) for idx in paths]
 
+    def get_neurites(self, type_check: bool = True) -> Iterable[Self]:
+        """Get neurites from soma."""
+        return (n.subtree() for n in self.soma(type_check).children())
+
+    def get_dendrites(self, type_check: bool = True) -> Iterable[Self]:
+        """Get dendrites."""
+        types = [self.types.apical_dendrite, self.types.basal_dendrite]
+        children = self.soma(type_check).children()
+        return (n.subtree() for n in children if n.type in types)
+
     # fmt: off
     @overload
     def traverse(self, *,
@@ -309,7 +333,7 @@ class Tree(DictSWC):
         return tree
 
     @classmethod
-    def from_swc(cls, swc_file: str, **kwargs) -> Self:
+    def from_swc(cls, swc_file: PathOrIO, **kwargs) -> Self:
         """Read neuron tree from swc file.
 
         See Also
@@ -322,7 +346,7 @@ class Tree(DictSWC):
         except Exception as e:  # pylint: disable=broad-except
             raise ValueError(f"fails to read swc: {swc_file}") from e
 
-        source = os.path.abspath(swc_file)
+        source = os.path.abspath(swc_file) if isinstance(swc_file, str) else ""
         return cls.from_data_frame(df, source=source, comments=comments)
 
     @classmethod

swcgeom/core/tree_utils.py

@@ -5,8 +5,8 @@ from typing import Callable, Dict, Iterable, List, Optional, Tuple, TypeVar, ove
 
 import numpy as np
 
-from .swc import SWCLike
-from .swc_utils import (
+from swcgeom.core.swc import SWCLike
+from swcgeom.core.swc_utils import (
     REMOVAL,
     SWCNames,
     Topology,
@@ -15,9 +15,9 @@ from .swc_utils import (
     propagate_removal,
     sort_nodes_impl,
     to_sub_topology,
-    traverse,
 )
-from .tree import Tree
+from swcgeom.core.tree import Tree
+from swcgeom.core.tree_utils_impl import get_subtree_impl, to_subtree_impl
 
 __all__ = [
     "sort_tree",
@@ -120,8 +120,7 @@ def to_sub_tree(swc_like: SWCLike, sub: Topology) -> Tuple[Tree, Dict[int, int]]
     ndata = {k: swc_like.get_ndata(k)[id_map_arr].copy() for k in swc_like.keys()}
     ndata.update(id=new_id, pid=new_pid)
 
-    subtree = Tree(n_nodes, **ndata, names=swc_like.names)
-    subtree.source = swc_like.source
+    subtree = Tree(n_nodes, **ndata, source=swc_like.source, names=swc_like.names)
 
     id_map = {}
     for i, idx in enumerate(id_map_arr):
@@ -143,7 +142,8 @@ def to_subtree(swc_like: SWCLike, removals: Iterable[int]) -> Tree:
         new_ids[i] = REMOVAL
 
     sub = propagate_removal((new_ids, swc_like.pid()))
-    return _to_subtree(swc_like, sub)
+    n_nodes, ndata, source, names = to_subtree_impl(swc_like, sub)
+    return Tree(n_nodes, **ndata, source=source, names=names)
 
 
 def get_subtree(swc_like: SWCLike, n: int) -> Tree:
@@ -155,14 +155,8 @@ def get_subtree(swc_like: SWCLike, n: int) -> Tree:
     n : int
         Id of the root of the subtree.
     """
-    ids = []
-    topo = (swc_like.id(), swc_like.pid())
-    traverse(topo, enter=lambda n, _: ids.append(n), root=n)
-
-    sub_ids = np.array(ids, dtype=np.int32)
-    sub_pid = swc_like.pid()[sub_ids]
-    sub_pid[0] = -1
-    return _to_subtree(swc_like, (sub_ids, sub_pid))
+    n_nodes, ndata, source, names = get_subtree_impl(swc_like, n)
+    return Tree(n_nodes, **ndata, source=source, names=names)
 
 
 def redirect_tree(tree: Tree, new_root: int, sort: bool = True) -> Tree:
@@ -179,9 +173,11 @@ def redirect_tree(tree: Tree, new_root: int, sort: bool = True) -> Tree:
     """
     tree = tree.copy()
     path = [tree.node(new_root)]
-    while (p := path[-1]).parent() is not None:
+    while (p := path[-1].parent()) is not None:
         path.append(p)
 
+    path[0].pid = -1
+    path[0].type, path[-1].type = path[-1].type, path[0].type
     for n, p in zip(path[1:], path[:-1]):
         n.pid = p.id
 
@@ -194,11 +190,12 @@ def redirect_tree(tree: Tree, new_root: int, sort: bool = True) -> Tree:
 def cat_tree(  # pylint: disable=too-many-arguments
     tree1: Tree,
     tree2: Tree,
-    node1: int,
+    node1: int = 0,
     node2: int = 0,
     *,
-    no_move: bool = False,
+    translate: bool = True,
     names: Optional[SWCNames] = None,
+    no_move: Optional[bool] = None,  # legacy
 ) -> Tree:
     """Concatenates the second tree onto the first one.
 
@@ -206,31 +203,44 @@ def cat_tree(  # pylint: disable=too-many-arguments
     ---------
     tree1 : Tree
     tree2 : Tree
-    node1 : int
+    node1 : int, default `0`
         The node id of the tree to be connected.
     node2 : int, default `0`
         The node id of the connection point.
-    no_move : bool, default `False`
-        If true, link connection point without move.
+    translate : bool, default `True`
+        Wheather to translate node_2 to node_1. If False, add link
+        between node_1 and node_2 without translate.
     """
+    if no_move is not None:
+        warnings.warn(
+            "`no_move` has been, it is replaced by `translate` in "
+            "v0.12.0, and this will be removed in next version",
+            DeprecationWarning,
+        )
+        translate = not no_move
+
     names = get_names(names)
     tree, tree2 = tree1.copy(), tree2.copy()
-    if not tree2.node(node2).is_soma():
+    if not tree2.node(node2).is_root():
         tree2 = redirect_tree(tree2, node2, sort=False)
 
     c = tree.node(node1)
-    if not no_move:
+    if translate:
         tree2.ndata[names.x] -= tree2.node(node2).x - c.x
         tree2.ndata[names.y] -= tree2.node(node2).y - c.y
         tree2.ndata[names.z] -= tree2.node(node2).z - c.z
 
-    tree2.ndata[names.id] += tree.number_of_nodes()
-    tree2.ndata[names.pid] += tree.number_of_nodes()
+    ns = tree.number_of_nodes()
     if np.linalg.norm(tree2.node(node2).xyz() - c.xyz()) < EPS:
-        for n in tree2.node(node2).children():
-            n.pid = node1
+        remove = [node2 + ns]
+        link_to_root = [n.id + ns for n in tree2.node(node2).children()]
     else:
-        tree2.node(node2).pid = node1
+        remove = None
+        link_to_root = [node2 + ns]
+
+    # APIs of tree2 are no longer available since we modify the topology
+    tree2.ndata[names.id] += ns
+    tree2.ndata[names.pid] += ns
 
     for k, v in tree.ndata.items():  # only keep keys in tree1
         if k in tree2.ndata:
@@ -238,7 +248,15 @@ def cat_tree(  # pylint: disable=too-many-arguments
         else:
             tree.ndata[k] = np.pad(v, (0, tree2.number_of_nodes()))
 
-    return _sort_tree(tree)
+    for n in link_to_root:
+        tree.node(n).pid = node1
+
+    if remove is not None:  # TODO: This should be easy to implement during sort
+        for k, v in tree.ndata.items():
+            tree.ndata[k] = np.delete(v, remove)
+
+    _sort_tree(tree)
+    return tree
 
 
 def _sort_tree(tree: Tree) -> Tree:
@@ -247,15 +265,3 @@ def _sort_tree(tree: Tree) -> Tree:
     tree.ndata = {k: tree.ndata[k][id_map] for k in tree.ndata}
     tree.ndata.update(id=new_ids, pid=new_pids)
     return tree
-
-
-def _to_subtree(swc_like: SWCLike, sub: Topology) -> Tree:
-    (new_id, new_pid), id_map = to_sub_topology(sub)
-
-    n_nodes = new_id.shape[0]
-    ndata = {k: swc_like.get_ndata(k)[id_map].copy() for k in swc_like.keys()}
-    ndata.update(id=new_id, pid=new_pid)
-
-    subtree = Tree(n_nodes, **ndata, names=swc_like.names)
-    subtree.source = swc_like.source
-    return subtree

swcgeom/core/tree_utils_impl.py

@@ -0,0 +1,39 @@
+"""SWC util wrapper for tree, split to avoid circle imports.
+
+Notes
+-----
+Do not import `Tree` and keep this file minimized.
+"""
+
+from typing import Any, Dict, Tuple
+
+import numpy as np
+import numpy.typing as npt
+
+from swcgeom.core.swc import SWCLike, SWCNames
+from swcgeom.core.swc_utils import Topology, to_sub_topology, traverse
+
+__all__ = ["get_subtree_impl", "to_subtree_impl"]
+
+TreeArgs = Tuple[int, Dict[str, npt.NDArray[Any]], str, SWCNames]
+
+
+def get_subtree_impl(swc_like: SWCLike, n: int) -> TreeArgs:
+    ids = []
+    topo = (swc_like.id(), swc_like.pid())
+    traverse(topo, enter=lambda n, _: ids.append(n), root=n)
+
+    sub_ids = np.array(ids, dtype=np.int32)
+    sub_pid = swc_like.pid()[sub_ids]
+    sub_pid[0] = -1
+    return to_subtree_impl(swc_like, (sub_ids, sub_pid))
+
+
+def to_subtree_impl(swc_like: SWCLike, sub: Topology) -> TreeArgs:
+    (new_id, new_pid), id_map = to_sub_topology(sub)
+
+    n_nodes = new_id.shape[0]
+    ndata = {k: swc_like.get_ndata(k)[id_map].copy() for k in swc_like.keys()}
+    ndata.update(id=new_id, pid=new_pid)
+
+    return n_nodes, ndata, swc_like.source, swc_like.names

swcgeom/images/__init__.py

@@ -1,4 +1,4 @@
 """Image Stack Related."""
 
-from .folder import *
-from .io import *
+from swcgeom.images.folder import *
+from swcgeom.images.io import *

swcgeom/images/folder.py

@@ -9,8 +9,8 @@ import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 
-from ..transforms import Identity, Transform
-from .io import read_imgs
+from swcgeom.images.io import read_imgs
+from swcgeom.transforms import Identity, Transform
 
 __all__ = [
     "ImageStackFolder",

swcgeom/images/io.py

@@ -6,12 +6,23 @@ import re
 import warnings
 from abc import ABC, abstractmethod
 from functools import cache, lru_cache
-from typing import Any, Callable, Iterable, List, Literal, Optional, Tuple, overload
+from typing import (
+    Any,
+    Callable,
+    Iterable,
+    List,
+    Literal,
+    Optional,
+    Tuple,
+    cast,
+    overload,
+)
 
 import nrrd
 import numpy as np
 import numpy.typing as npt
 import tifffile
+from v3dpy.loaders import PBD, Raw
 
 __all__ = ["read_imgs", "save_tiff", "read_images"]
 
@@ -20,10 +31,10 @@ RE_TERAFLY_ROOT = re.compile(r"^RES\((\d+)x(\d+)x(\d+)\)$")
 RE_TERAFLY_NAME = re.compile(r"^\d+(_\d+)?(_\d+)?")
 
 UINT_MAX = {
-    np.dtype(np.uint8): (2**8) - 1,
-    np.dtype(np.uint16): (2**16) - 1,
-    np.dtype(np.uint32): (2**32) - 1,
-    np.dtype(np.uint64): (2**64) - 1,
+    np.dtype(np.uint8): (2**8) - 1,  # type: ignore
+    np.dtype(np.uint16): (2**16) - 1,  # type: ignore
+    np.dtype(np.uint32): (2**32) - 1,  # type: ignore
+    np.dtype(np.uint64): (2**64) - 1,  # type: ignore
 }
 
 AXES_ORDER = {
@@ -92,6 +103,10 @@ def read_imgs(fname: str, **kwargs) -> ImageStack:
         return TiffImageStack(fname, **kwargs)
     if ext in [".nrrd"]:
         return NrrdImageStack(fname, **kwargs)
+    if ext in [".v3dpbd"]:
+        return V3dpbdImageStack(fname, **kwargs)
+    if ext in [".v3draw"]:
+        return V3drawImageStack(fname, **kwargs)
     if ext in [".npy", ".npz"]:
         return NDArrayImageStack(np.load(fname), **kwargs)
     if TeraflyImageStack.is_root(fname):
@@ -226,7 +241,7 @@ class NDArrayImageStack(ImageStack):
 
     @property
     def shape(self) -> Tuple[int, int, int, int]:
-        return self.imgs.shape
+        return cast(Tuple[int, int, int, int], self.imgs.shape)
 
 
 class TiffImageStack(NDArrayImageStack):
@@ -268,6 +283,29 @@ class NrrdImageStack(NDArrayImageStack):
         self.header = header
 
 
+class V3dImageStack(NDArrayImageStack):
+    """v3d image stack."""
+
+    def __init__(self, fname: str, loader: Raw | PBD, **kwargs) -> None:
+        r = loader()
+        imgs = r.load(fname)
+        super().__init__(imgs, **kwargs)
+
+
+class V3drawImageStack(V3dImageStack):
+    """v3draw image stack."""
+
+    def __init__(self, fname: str, **kwargs) -> None:
+        super().__init__(fname, loader=Raw, **kwargs)
+
+
+class V3dpbdImageStack(V3dImageStack):
+    """v3dpbd image stack."""
+
+    def __init__(self, fname: str, **kwargs) -> None:
+        super().__init__(fname, loader=PBD, **kwargs)
+
+
 class TeraflyImageStack(ImageStack):
     """TeraFly image stack.
 
@@ -383,7 +421,8 @@ class TeraflyImageStack(ImageStack):
 
     @property
     def shape(self) -> Tuple[int, int, int, int]:
-        return tuple(self.res[-1])
+        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]]:
@@ -476,13 +515,13 @@ class TeraflyImageStack(ImageStack):
         if shape[1] > lens[1]:
             starts_y = starts + [0, lens[1], 0]
             ends_y = np.array([starts[0], ends[1], ends[2]])
-            ends_y += [min(shape[0], lens[0]), 0, 0]
+            ends_y += [min(shape[0], lens[0]), 0, 0]  # type: ignore
             self._get_range(starts_y, ends_y, res_level, out[:, lens[1] :, :])
 
         if shape[2] > lens[2]:
             starts_z = starts + [0, 0, lens[2]]
             ends_z = np.array([starts[0], starts[1], ends[2]])
-            ends_z += [min(shape[0], lens[0]), min(shape[1], lens[1]), 0]
+            ends_z += [min(shape[0], lens[0]), min(shape[1], lens[1]), 0]  # type: ignore
             self._get_range(starts_z, ends_z, res_level, out[:, :, lens[2] :])
 
     def _find_correspond_imgs(self, p, res_level):

swcgeom/transforms/__init__.py

@@ -1,10 +1,12 @@
 """A series of transformations to compose codes."""
 
-from .base import *
-from .branch import *
-from .geometry import *
-from .image_stack import *
-from .images import *
-from .mst import *
-from .population import *
-from .tree import *
+from swcgeom.transforms.base import *
+from swcgeom.transforms.branch import *
+from swcgeom.transforms.geometry import *
+from swcgeom.transforms.image_stack import *
+from swcgeom.transforms.images import *
+from swcgeom.transforms.mst import *
+from swcgeom.transforms.path import *
+from swcgeom.transforms.population import *
+from swcgeom.transforms.tree import *
+from swcgeom.transforms.tree_assembler import *

swcgeom/transforms/branch.py

@@ -7,8 +7,9 @@ import numpy as np
 import numpy.typing as npt
 from scipy import signal
 
-from ..core import Branch, DictSWC
-from ..utils import (
+from swcgeom.core import Branch, DictSWC
+from swcgeom.transforms.base import Transform
+from swcgeom.utils import (
     angle,
     rotate3d_x,
     rotate3d_y,
@@ -17,7 +18,6 @@ from ..utils import (
     to_homogeneous,
     translate3d,
 )
-from .base import Transform
 
 __all__ = ["BranchLinearResampler", "BranchConvSmoother", "BranchStandardizer"]
 

swcgeom/transforms/geometry.py

@@ -6,10 +6,17 @@ from typing import Generic, Literal, Optional, TypeVar
 import numpy as np
 import numpy.typing as npt
 
-from ..core import DictSWC
-from ..core.swc_utils import SWCNames
-from ..utils import rotate3d, rotate3d_x, rotate3d_y, rotate3d_z, scale3d, translate3d
-from .base import Transform
+from swcgeom.core import DictSWC
+from swcgeom.core.swc_utils import SWCNames
+from swcgeom.transforms.base import Transform
+from swcgeom.utils import (
+    rotate3d,
+    rotate3d_x,
+    rotate3d_y,
+    rotate3d_z,
+    scale3d,
+    translate3d,
+)
 
 __all__ = [
     "Normalizer",

swcgeom/transforms/image_stack.py

@@ -20,9 +20,9 @@ import numpy as np
 import numpy.typing as npt
 import tifffile
 
-from ..core import Population, Tree
-from ..utils import SDF, SDFCompose, SDFRoundCone
-from .base import Transform
+from swcgeom.core import Population, Tree
+from swcgeom.transforms.base import Transform
+from swcgeom.utils import SDF, SDFCompose, SDFRoundCone
 
 __all__ = ["ToImageStack"]