swcgeom 0.16.0__py3-none-any.whl → 0.18.3__py3-none-any.whl

swcgeom/transforms/tree.py

@@ -1,14 +1,31 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Transformation in tree."""
 
-import warnings
-from typing import Callable, List, Optional, Tuple
+from collections.abc import Callable
+from typing import Optional
 
 import numpy as np
+from typing_extensions import deprecated
 
-from swcgeom.core import BranchTree, DictSWC, Path, Tree, cut_tree, to_subtree
+from swcgeom.core import Branch, BranchTree, DictSWC, Path, Tree, cut_tree, to_subtree
 from swcgeom.core.swc_utils import SWCTypes, get_types
 from swcgeom.transforms.base import Transform
-from swcgeom.transforms.branch import BranchConvSmoother
+from swcgeom.transforms.branch import BranchConvSmoother, BranchIsometricResampler
+from swcgeom.transforms.branch_tree import BranchTreeAssembler
 from swcgeom.transforms.geometry import Normalizer
 
 __all__ = [
@@ -19,8 +36,9 @@ __all__ = [
     "CutByType",
     "CutAxonTree",
     "CutDendriteTree",
-    "CutByBifurcationOrder",
+    "CutByFurcationOrder",
     "CutShortTipBranch",
+    "IsometricResampler",
 ]
 
 
@@ -64,10 +82,11 @@ class TreeSmoother(Transform[Tree, Tree]):  # pylint: disable=missing-class-docs
 
         return x
 
-    def extra_repr(self):
+    def extra_repr(self) -> str:
         return f"n_nodes={self.n_nodes}"
 
 
+@deprecated("Use `Normalizer` instead")
 class TreeNormalizer(Normalizer[Tree]):
     """Noramlize coordinates and radius to 0-1.
 
@@ -75,15 +94,6 @@ class TreeNormalizer(Normalizer[Tree]):
         Use :cls:`Normalizer` instead.
     """
 
-    def __init__(self, *args, **kwargs) -> None:
-        warnings.warn(
-            "`TreeNormalizer` has been replaced by `Normalizer` since "
-            "v0.6.0 beacuse it applies more widely, and this will be "
-            "removed in next version",
-            DeprecationWarning,
-        )
-        super().__init__(*args, **kwargs)
-
 
 class CutByType(Transform[Tree, Tree]):
     """Cut tree by type.
@@ -102,7 +112,7 @@ class CutByType(Transform[Tree, Tree]):
     def __call__(self, x: Tree) -> Tree:
         removals = set(x.id()[x.type() != self.type])
 
-        def leave(n: Tree.Node, keep_children: List[bool]) -> bool:
+        def leave(n: Tree.Node, keep_children: list[bool]) -> bool:
             if n.id in removals and any(keep_children):
                 removals.remove(n.id)
             return n.id not in removals
@@ -111,7 +121,7 @@ class CutByType(Transform[Tree, Tree]):
         y = to_subtree(x, removals)
         return y
 
-    def extra_repr(self):
+    def extra_repr(self) -> str:
         return f"type={self.type}"
 
 
@@ -131,28 +141,48 @@ class CutDendriteTree(CutByType):
         super().__init__(type=types.basal_dendrite)  # TODO: apical dendrite
 
 
-class CutByBifurcationOrder(Transform[Tree, Tree]):
-    """Cut tree by bifurcation order."""
+class CutByFurcationOrder(Transform[Tree, Tree]):
+    """Cut tree by furcation order."""
 
-    max_bifurcation_order: int
+    max_furcation_order: int
 
     def __init__(self, max_bifurcation_order: int) -> None:
-        self.max_bifurcation_order = max_bifurcation_order
+        self.max_furcation_order = max_bifurcation_order
 
     def __call__(self, x: Tree) -> Tree:
         return cut_tree(x, enter=self._enter)
 
     def __repr__(self) -> str:
-        return f"CutByBifurcationOrder-{self.max_bifurcation_order}"
+        return f"CutByBifurcationOrder-{self.max_furcation_order}"
 
-    def _enter(self, n: Tree.Node, parent_level: int | None) -> Tuple[int, bool]:
+    def _enter(self, n: Tree.Node, parent_level: int | None) -> tuple[int, bool]:
         if parent_level is None:
             level = 0
-        elif n.is_bifurcation():
+        elif n.is_furcation():
             level = parent_level + 1
         else:
             level = parent_level
-        return (level, level >= self.max_bifurcation_order)
+        return (level, level >= self.max_furcation_order)
+
+
+@deprecated("Use CutByFurcationOrder instead")
+class CutByBifurcationOrder(CutByFurcationOrder):
+    """Cut tree by bifurcation order.
+
+    Notes
+    -----
+    Deprecated due to the wrong spelling of furcation. For now, it
+    is just an alias of `CutByFurcationOrder` and raise a warning. It
+    will be change to raise an error in the future.
+    """
+
+    max_furcation_order: int
+
+    def __init__(self, max_bifurcation_order: int) -> None:
+        super().__init__(max_bifurcation_order)
+
+    def __repr__(self) -> str:
+        return f"CutByBifurcationOrder-{self.max_furcation_order}"
 
 
 class CutShortTipBranch(Transform[Tree, Tree]):
@@ -164,7 +194,7 @@ class CutShortTipBranch(Transform[Tree, Tree]):
     """
 
     thre: float
-    callbacks: List[Callable[[Tree.Branch], None]]
+    callbacks: list[Callable[[Tree.Branch], None]]
 
     def __init__(
         self, thre: float = 5, callback: Optional[Callable[[Tree.Branch], None]] = None
@@ -176,18 +206,18 @@ class CutShortTipBranch(Transform[Tree, Tree]):
             self.callbacks.append(callback)
 
     def __call__(self, x: Tree) -> Tree:
-        removals: List[int] = []
+        removals: list[int] = []
         self.callbacks.append(lambda br: removals.append(br[1].id))
         x.traverse(leave=self._leave)
         self.callbacks.pop()
         return to_subtree(x, removals)
 
-    def extra_repr(self):
+    def extra_repr(self) -> str:
         return f"threshold={self.thre}"
 
     def _leave(
-        self, n: Tree.Node, children: List[Tuple[float, Tree.Node] | None]
-    ) -> Tuple[float, Tree.Node] | None:
+        self, n: Tree.Node, children: list[tuple[float, Tree.Node] | None]
+    ) -> tuple[float, Tree.Node] | None:
         if len(children) == 0:  # tip
             return 0, n
 
@@ -214,3 +244,27 @@ class CutShortTipBranch(Transform[Tree, Tree]):
                 cb(br)
 
         return None
+
+
+class Resampler(Transform[Tree, Tree]):
+    def __init__(self, branch_resampler: Transform[Branch, Branch]) -> None:
+        super().__init__()
+        self.resampler = branch_resampler
+        self.assembler = BranchTreeAssembler()
+
+    def __call__(self, x: Tree) -> Tree:
+        t = BranchTree.from_tree(x)
+        t.branches = {
+            k: [self.resampler(br) for br in brs] for k, brs in t.branches.items()
+        }
+        return self.assembler(t)
+
+
+class IsometricResampler(Resampler):
+    def __init__(
+        self, distance: float, *, adjust_last_gap: bool = True, **kwargs
+    ) -> None:
+        branch_resampler = BranchIsometricResampler(
+            distance, adjust_last_gap=adjust_last_gap, **kwargs
+        )
+        super().__init__(branch_resampler)

swcgeom/transforms/tree_assembler.py

@@ -1,7 +1,23 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Assemble a tree."""
 
+from collections.abc import Iterable
 from copy import copy
-from typing import Iterable, List, Optional, Tuple
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -18,7 +34,7 @@ from swcgeom.transforms.base import Transform
 EPS = 1e-5
 
 
-class LinesToTree(Transform[List[pd.DataFrame], Tree]):
+class LinesToTree(Transform[list[pd.DataFrame], Tree]):
     """Assemble lines to swc."""
 
     def __init__(self, *, thre: float = 0.2, undirected: bool = True):
@@ -37,7 +53,7 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
 
     def __call__(
         self, lines: Iterable[pd.DataFrame], *, names: Optional[SWCNames] = None
-    ):
+    ):  # TODO check this
         return self.assemble(lines, names=names)
 
     def assemble(
@@ -55,8 +71,8 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
         Parameters
         ----------
         lines : List of ~pd.DataFrame
-            An array of tables containing a line, columns should follwing
-            the swc.
+            An array of tables containing a line, columns should
+            following the swc.
         undirected : bool, default `True`
             Forwarding to `self.try_assemble`.
         names : SWCNames, optional
@@ -97,7 +113,7 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
         undirected: bool = True,
         sort_nodes: bool = True,
         names: Optional[SWCNames] = None,
-    ) -> Tuple[pd.DataFrame, List[pd.DataFrame]]:
+    ) -> tuple[pd.DataFrame, list[pd.DataFrame]]:
         """Trying assemble lines to a tree.
 
         Treat the first line as a tree, find a line whose shortest distance
@@ -169,5 +185,5 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
 
         return tree, lines
 
-    def extra_repr(self):
+    def extra_repr(self) -> str:
         return f"thre={self.thre}, undirected={self.undirected}"

swcgeom/utils/__init__.py

@@ -1,14 +1,29 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Utils."""
 
-from swcgeom.utils.debug import *
-from swcgeom.utils.dsu import *
-from swcgeom.utils.ellipse import *
-from swcgeom.utils.file import *
-from swcgeom.utils.neuromorpho import *
-from swcgeom.utils.numpy_helper import *
-from swcgeom.utils.plotter_2d import *
-from swcgeom.utils.renderer import *
-from swcgeom.utils.sdf import *
-from swcgeom.utils.solid_geometry import *
-from swcgeom.utils.transforms import *
-from swcgeom.utils.volumetric_object import *
+from swcgeom.utils.debug import *  # noqa: F403
+from swcgeom.utils.dsu import *  # noqa: F403
+from swcgeom.utils.ellipse import *  # noqa: F403
+from swcgeom.utils.file import *  # noqa: F403
+from swcgeom.utils.neuromorpho import *  # noqa: F403
+from swcgeom.utils.numpy_helper import *  # noqa: F403
+from swcgeom.utils.plotter_2d import *  # noqa: F403
+from swcgeom.utils.renderer import *  # noqa: F403
+from swcgeom.utils.sdf import *  # noqa: F403
+from swcgeom.utils.solid_geometry import *  # noqa: F403
+from swcgeom.utils.transforms import *  # noqa: F403
+from swcgeom.utils.volumetric_object import *  # noqa: F403

swcgeom/utils/debug.py

@@ -1,3 +1,18 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Debug helpers"""
 
 import time

swcgeom/utils/download.py

@@ -1,3 +1,18 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Download helpers.
 
 Notes
@@ -13,6 +28,7 @@ import itertools
 import logging
 import multiprocessing
 import os
+from functools import partial
 from urllib.parse import urljoin
 
 __all__ = ["download", "fetch_page", "clone_index_page"]
@@ -26,7 +42,7 @@ def download(dst: str, url: str) -> None:
     r = conn.request("GET", url)
 
     dirname = os.path.dirname(dst)
-    if not os.path.exists(dirname):
+    if dirname != "" and not os.path.exists(dirname):
         os.makedirs(dirname)
 
     with open(dst, "wb") as file:
@@ -41,7 +57,7 @@ def fetch_page(url: str):
     conn = connection_from_url(url)
     r = conn.request("GET", url)
     data = r.data.decode("utf-8")
-    return BeautifulSoup(data)
+    return BeautifulSoup(data, features="html.parser")
 
 
 def clone_index_page(
@@ -62,31 +78,35 @@ def clone_index_page(
     multiprocess : int, default `4`
         How many process are available for download.
     """
-    from urllib3.exceptions import HTTPError
-
     files = get_urls_in_index_page(index_url)
     logging.info("downloader: search `%s`, found %s files.", index_url, len(files))
 
-    def task(url: str) -> None:
-        filepath = url.removeprefix(index_url)
-        dist = os.path.join(dist_dir, filepath)
-        if os.path.exists(filepath):
-            if not override:
-                logging.info("downloader: file `%s` exits, skiped.", dist)
-                return
+    task = partial(
+        _clone_index_page, index_url=index_url, dist_dir=dist_dir, override=override
+    )
+    with multiprocessing.Pool(multiprocess) as p:
+        p.map(task, files)
 
-            logging.info("downloader: file `%s` exits, deleted.", dist)
-            os.remove(filepath)
 
-        try:
-            logging.info("downloader: downloading `%s` to `%s`", url, dist)
-            download(filepath, url)
-            logging.info("downloader: download `%s` to `%s`", url, dist)
-        except HTTPError as ex:
-            logging.info("downloader: fails to download `%s`, except `%s`", url, ex)
+def _clone_index_page(url: str, index_url: str, dist_dir: str, override: bool) -> None:
+    from urllib3.exceptions import HTTPError
 
-    with multiprocessing.Pool(multiprocess) as p:
-        p.map(task, files)
+    filepath = url.removeprefix(index_url)
+    dist = os.path.join(dist_dir, filepath)
+    if os.path.exists(dist):
+        if not override:
+            logging.info("downloader: file `%s` exits, skiped.", dist)
+            return
+
+        logging.info("downloader: file `%s` exits, deleted.", dist)
+        os.remove(dist)
+
+    try:
+        logging.info("downloader: downloading `%s` to `%s`", url, dist)
+        download(dist, url)
+        logging.info("downloader: download `%s` to `%s`", url, dist)
+    except HTTPError as ex:
+        logging.info("downloader: fails to download `%s`, except `%s`", url, ex)
 
 
 def get_urls_in_index_page(url: str) -> list[str]:
@@ -97,3 +117,21 @@ def get_urls_in_index_page(url: str) -> list[str]:
     dirs = [urljoin(url, a) for a in links if a != "../" and a.endswith("/")]
     files.extend(itertools.chain(*[get_urls_in_index_page(dir) for dir in dirs]))
     return files
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Download files from index page.")
+    parser.add_argument("url", type=str, help="URL of index page.")
+    parser.add_argument("dist", type=str, help="Directory of dist.")
+    parser.add_argument(
+        "--override", type=bool, default=False, help="Override existing file."
+    )
+    parser.add_argument(
+        "--multiprocess", type=int, default=4, help="How many process are available."
+    )
+    args = parser.parse_args()
+
+    logging.basicConfig(level=logging.INFO)
+    clone_index_page(args.url, args.dist, args.override, args.multiprocess)

swcgeom/utils/dsu.py

@@ -1,3 +1,18 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Disjoint Set Union Impl."""
 
 __all__ = ["DisjointSetUnion"]

swcgeom/utils/ellipse.py

@@ -1,9 +1,23 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """Finds the Minimum Volume Enclosing Ellipsoid."""
 
 # pylint: disable=invalid-name
 
 from functools import cached_property
-from typing import Tuple
 
 import numpy as np
 import numpy.linalg as la
@@ -22,7 +36,7 @@ class Ellipse:
         self.centroid = centroid
 
     @property
-    def radii(self) -> Tuple[float, float]:
+    def radii(self) -> tuple[float, float]:
         # x, y radii.
         _U, D, _V = self.svd
         rx, ry = 1.0 / np.sqrt(D)
@@ -39,7 +53,7 @@ class Ellipse:
         return b
 
     @property
-    def axes(self) -> Tuple[float, float]:
+    def axes(self) -> tuple[float, float]:
         # Major and minor semi-axis of the ellipse.
         rx, ry = self.radii
         dx, dy = 2 * rx, 2 * ry
@@ -77,7 +91,7 @@ def mvee(points: npt.NDArray[np.floating], tol: float = 1e-3) -> Ellipse:
 
 def _mvee(
     points: npt.NDArray[np.floating], tol: float = 1e-3
-) -> Tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
+) -> tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
     """Finds the Minimum Volume Enclosing Ellipsoid.
 
     Returns

swcgeom/utils/file.py

@@ -1,3 +1,18 @@
+# Copyright 2022-2025 Zexin Yuan
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 """File related utils.
 
 Notes