swcgeom 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

swcgeom/core/swc_utils.py

@@ -1,8 +1,7 @@
-"""SWC format."""
+"""SWC format utils."""
 
-import warnings
 from copy import copy
-from typing import List, Literal, Tuple
+from typing import Any, List, Literal, Tuple
 
 import numpy as np
 import numpy.typing as npt
@@ -13,6 +12,12 @@ __all__ = []  # do not export anything
 
 def mark_roots_as_somas(
     df: pd.DataFrame, update_type: int | Literal[False] = 1
+) -> pd.DataFrame:
+    return _copy_and_apply(mark_roots_as_somas_, df, update_type=update_type)
+
+
+def mark_roots_as_somas_(
+    df: pd.DataFrame, update_type: int | Literal[False] = 1
 ) -> None:
     """Merge multiple roots in swc.
 
@@ -27,7 +32,11 @@ def mark_roots_as_somas(
     df.loc[root_loc, "pid"] = -1
 
 
-def link_roots_to_nearest(df: pd.DataFrame) -> None:
+def link_roots_to_nearest(df: pd.DataFrame) -> pd.DataFrame:
+    return _copy_and_apply(link_roots_to_nearest_, df)
+
+
+def link_roots_to_nearest_(df: pd.DataFrame) -> None:
     """Merge multiple roots in swc.
 
     The first root are reserved, and the others was.
@@ -67,9 +76,11 @@ def assemble_lines(lines: List[pd.DataFrame], **kwargs) -> pd.DataFrame:
     ~swcgeom.core.swc_utils.try_assemble_lines
     """
 
-    tree, lines = try_assemble_lines(lines, sort=False, **kwargs)
+    tree, lines = try_assemble_lines(lines, sort_nodes=False, **kwargs)
     while len(lines) > 0:
-        t, lines = try_assemble_lines(lines, id_offset=len(tree), sort=False, **kwargs)
+        t, lines = try_assemble_lines(
+            lines, id_offset=len(tree), sort_nodes=False, **kwargs
+        )
         tree = pd.concat([tree, t])
 
     tree = tree.reset_index()
@@ -83,7 +94,7 @@ def try_assemble_lines(
     undirected: bool = True,
     thre: float = 0.2,
     id_offset: int = 0,
-    sort: bool = True,
+    sort_nodes: bool = True,
 ) -> Tuple[pd.DataFrame, List[pd.DataFrame]]:
     """Trying assemble lines to a tree.
 
@@ -104,7 +115,7 @@ def try_assemble_lines(
         Connection threshold.
     id_offset : int, default `0`
         The offset of the line node id.
-    sort : bool, default `True`
+    sort_nodes : bool, default `True`
         sort nodes of subtree
 
     Returns
@@ -140,33 +151,33 @@ def try_assemble_lines(
         else:
             break
 
-    if sort:
-        sort_nodes(tree)
+    if sort_nodes:
+        sort_nodes_(tree)
     return tree, lines
 
 
-def sort_swc(df: pd.DataFrame):
-    warnings.warn(
-        "`sort_swc` has been renamed to `sort_nodes`, and will be remove in next version",
-        DeprecationWarning,
-    )
-    return sort_nodes(df)
+def sort_nodes(df: pd.DataFrame) -> pd.DataFrame:
+    """Sort the indices of neuron tree.
+
+    The index for parent are always less than children.
+    """
+    return _copy_and_apply(sort_nodes_, df)
 
 
-def sort_nodes(df: pd.DataFrame):
+def sort_nodes_(df: pd.DataFrame) -> None:
     """Sort the indices of neuron tree.
 
     The index for parent are always less than children.
     """
     ids, pids = df["id"].to_numpy(), df["pid"].to_numpy()
-    indices, new_ids, new_pids = sort_swc_impl(ids, pids)
+    indices, new_ids, new_pids = sort_nodes_impl(ids, pids)
     for col in df.columns:
         df[col] = df[col][indices].to_numpy()
 
     df["id"], df["pid"] = new_ids, new_pids
 
 
-def sort_swc_impl(
+def sort_nodes_impl(
     old_ids: npt.NDArray[np.int32], old_pids: npt.NDArray[np.int32]
 ) -> Tuple[npt.NDArray[np.int32], npt.NDArray[np.int32], npt.NDArray[np.int32]]:
     """Sort the indices of neuron tree."""
@@ -190,8 +201,12 @@ def sort_swc_impl(
     return indices, new_ids, new_pids
 
 
-def reset_index(df: pd.DataFrame) -> None:
+def reset_index(df: pd.DataFrame) -> pd.DataFrame:
     """Reset node index to start with zero."""
+    return _copy_and_apply(reset_index_, df)
+
+
+def reset_index_(df: pd.DataFrame) -> None:
     roots = df["pid"] == -1
     root_loc = roots.argmax()
     root_id = df.loc[root_loc, "id"]
@@ -223,3 +238,9 @@ def _get_dsu(df: pd.DataFrame) -> npt.NDArray[np.int32]:
             break
 
     return dsu
+
+
+def _copy_and_apply(fn_: Any, df: pd.DataFrame, *args, **kwargs):
+    df = df.copy()
+    fn_(df, *args, **kwargs)
+    return df

swcgeom/core/tree.py

@@ -19,6 +19,7 @@ from typing import (
 import numpy as np
 import numpy.typing as npt
 import pandas as pd
+from typing_extensions import Self
 
 from ..utils import padding1d
 from .branch import Branch
@@ -73,12 +74,15 @@ class Tree(SWCLike):
             return self.distance(self.attach.soma())
 
     class Path(Path["Tree"]):
+        # TODO: should returns `Tree.Node`
         """Neural path."""
 
     class Segment(Segment["Tree"]):
+        # TODO: should returns `Tree.Node`
         """Neural segment."""
 
     class Branch(Branch["Tree"]):
+        # TODO: should returns `Tree.Node`
         """Neural branch."""
 
     ndata: dict[str, npt.NDArray]
@@ -174,8 +178,7 @@ class Tree(SWCLike):
         return [self.node(i) for i in tip_ids]
 
     def get_segments(self) -> Segments[Segment]:
-        # pylint: disable-next=not-an-iterable
-        return Segments([self.Segment(self, n.pid, n.id) for n in self[1:]])
+        return Segments(self.Segment(self, n.pid, n.id) for n in self[1:])
 
     def get_branches(self) -> List[Branch]:
         Info = Tuple[List[Tree.Branch], List[int]]
@@ -292,15 +295,15 @@ class Tree(SWCLike):
         """Get length of tree."""
         return sum(s.length() for s in self.get_segments())
 
-    @staticmethod
-    def from_data_frame(df: pd.DataFrame, source: str = "") -> "Tree":
+    @classmethod
+    def from_data_frame(cls, df: pd.DataFrame, source: str = "") -> "Tree":
         """Read neuron tree from data frame."""
         tree = Tree(df.shape[0], **{k: df[k].to_numpy() for k, v in swc_cols})
         tree.source = source
         return tree
 
-    @staticmethod
-    def from_swc(swc_file: str, **kwargs) -> "Tree":
+    @classmethod
+    def from_swc(cls, swc_file: str, **kwargs) -> Self:
         """Read neuron tree from swc file.
 
         See Also
@@ -310,10 +313,10 @@ class Tree(SWCLike):
 
         df = read_swc(swc_file, **kwargs)
         source = os.path.abspath(swc_file)
-        return Tree.from_data_frame(df, source)
+        return cls.from_data_frame(df, source)
 
-    @staticmethod
-    def from_eswc(swc_file: str, extra_cols: List[str] = [], **kwargs) -> "Tree":
+    @classmethod
+    def from_eswc(cls, swc_file: str, extra_cols: List[str] = [], **kwargs) -> Self:
         """Read neuron tree from eswc file.
 
         See Also
@@ -323,4 +326,4 @@ class Tree(SWCLike):
         """
 
         extra_cols.extend(k for k, t in eswc_cols)
-        return Tree.from_swc(swc_file, extra_cols=extra_cols, **kwargs)
+        return cls.from_swc(swc_file, extra_cols=extra_cols, **kwargs)

swcgeom/core/tree_utils.py

@@ -6,7 +6,7 @@ import numpy as np
 import numpy.typing as npt
 
 from .swc import SWCLike
-from .swc_utils import sort_swc_impl
+from .swc_utils import sort_nodes_impl
 from .tree import Tree
 
 __all__ = ["REMOVE", "sort_tree", "to_sub_tree", "cut_tree", "propagate_remove"]
@@ -22,7 +22,7 @@ def sort_tree(tree: Tree) -> Tree:
     --------
     ~core.swc.swc_sort_tree
     """
-    indices, new_ids, new_pids = sort_swc_impl(tree.id(), tree.pid())
+    indices, new_ids, new_pids = sort_nodes_impl(tree.id(), tree.pid())
     new_tree = tree.copy()
     new_tree.ndata = {k: tree.ndata[k][indices] for k in tree.ndata}
     new_tree.ndata["id"] = new_ids

swcgeom/utils/numpy.py

@@ -1,13 +1,12 @@
 """Numpy related utils."""
 
-import math
 from contextlib import contextmanager
-from typing import Any, Tuple
+from typing import Any
 
 import numpy as np
 import numpy.typing as npt
 
-__all__ = ["padding1d", "XYPair", "to_distribution", "numpy_printoptions", "numpy_err"]
+__all__ = ["padding1d", "numpy_printoptions", "numpy_err"]
 
 
 def padding1d(
@@ -44,30 +43,6 @@ def padding1d(
     return np.concatenate([v, padding])
 
 
-XYPair = Tuple[npt.NDArray[np.float32], npt.NDArray[np.float32]]
-
-
-def to_distribution(
-    values: npt.NDArray,
-    step: float,
-    vmin: float = 0,
-    vmax: float | None = None,
-    norm: bool = False,
-) -> XYPair:
-    indices = np.floor(values / step - vmin).astype(np.int32)
-    size_min = np.max(indices).item() + 1
-    size = math.ceil((vmax - vmin) / step) + 1 if vmax is not None else size_min
-    y = np.zeros(max(size, size_min), dtype=np.float32)
-    for i in indices:
-        y[i] = y[i] + 1
-
-    if norm:
-        y /= values.shape[0]
-
-    x = vmin + step * np.arange(size, dtype=np.float32)
-    return x, y[:size]
-
-
 @contextmanager
 def numpy_printoptions(*args, **kwargs):
     original_options = np.get_printoptions()

swcgeom/utils/renderer.py

@@ -1,6 +1,6 @@
 """Painter utils."""
 
-from typing import Dict, NamedTuple, Tuple
+from typing import Dict, Literal, NamedTuple, Optional, Tuple
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -20,17 +20,17 @@ from .transforms import (
 )
 
 __all__ = [
-    "Vector3D",
+    "Vec3f",
     "Camera",
     "palette",
     "draw_lines",
-    "draw_xyz_axes",
+    "draw_direction_indicator",
     "draw_circles",
     "get_fig_ax",
 ]
 
-Vector3D = Tuple[float, float, float]
-Camera = NamedTuple("Camera", position=Vector3D, look_at=Vector3D, up=Vector3D)
+Vec3f = Tuple[float, float, float]
+Camera = NamedTuple("Camera", position=Vec3f, look_at=Vec3f, up=Vec3f)
 
 
 class Palette:
@@ -113,17 +113,13 @@ def draw_lines(
     ends = np.dot(T, ends.T).T[:, 0:2]
 
     edges = np.stack([starts, ends], axis=1)
-    collection = LineCollection(edges, **kwargs)  # type: ignore
-    ax.add_collection(collection)  # type: ignore
-    return collection
+    return ax.add_collection(LineCollection(edges, **kwargs))  # type: ignore
 
 
-def draw_xyz_axes(
-    ax: Axes, camera: Camera, position: Tuple[float, float] = (0.8, 0.10)
+def draw_direction_indicator(
+    ax: Axes, camera: Camera, position: Tuple[float, float]
 ) -> None:
     x, y = position
-    arrow_length = 0.05
-
     direction = np.array(
         [
             [1, 0, 0, 1],
@@ -134,29 +130,31 @@ def draw_xyz_axes(
     )
     direction = model_view_trasformation(*camera).dot(direction)
 
-    for (dx, dy, dz, _), (text, color) in zip(
-        direction[:3],
-        [["x", "red"], ["y", "green"], ["z", "blue"]],
-    ):
+    ARROW_LENTH, TEXT_OFFSET = 0.05, 0.05
+    text_colors = [["x", "red"], ["y", "green"], ["z", "blue"]]
+    for (dx, dy, dz, _), (text, color) in zip(direction, text_colors):
         if 1 - abs(dz) < 1e-5:
             continue
 
         ax.arrow(
             x,
             y,
-            arrow_length * dx,
-            arrow_length * dy,
-            head_length=0.04,
-            head_width=0.03,
+            ARROW_LENTH * dx,
+            ARROW_LENTH * dy,
+            head_length=0.02,
+            head_width=0.01,
             color=color,
             transform=ax.transAxes,
         )
+
         ax.text(
-            x + (arrow_length + 0.06) * dx,
-            y + (arrow_length + 0.06) * dy,
+            x + (ARROW_LENTH + TEXT_OFFSET) * dx,
+            y + (ARROW_LENTH + TEXT_OFFSET) * dy,
             text,
             color=color,
             transform=ax.transAxes,
+            horizontalalignment="center",
+            verticalalignment="center",
         )
 
 
@@ -166,8 +164,8 @@ def draw_circles(
     x: npt.NDArray,
     y: npt.NDArray,
     /,
-    y_min: float | None = None,
-    y_max: float | None = None,
+    y_min: Optional[float] = None,
+    y_max: Optional[float] = None,
     cmap: str = "viridis",
 ) -> None:
     """Draw a sequential of circles."""

{swcgeom-0.4.0.dist-info → swcgeom-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.4.0
+Version: 0.5.0
 Summary: A neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: CC4.0 BY-NC-SA

{swcgeom-0.4.0.dist-info → swcgeom-0.5.0.dist-info}/RECORD

@@ -1,23 +1,23 @@
 swcgeom/__init__.py,sha256=5oZ4DxgA2DHvUiRVqByVLCWkO1RaRyLSzkqYvkkTFyU,122
-swcgeom/_version.py,sha256=QiCQVGOicQZY3DBr4tYPU9egzT1VgzOJGfLt9Q26uyU,160
+swcgeom/_version.py,sha256=o_9FMpKXs1TaEQNOx-A4tDxKLoFOXZyS8RpLoa-PFCI,160
 swcgeom/analysis/__init__.py,sha256=6vlB8YVwpW0YGijdFo8WjgZ4TbcGr8kFVLUF1FTGR-Y,206
 swcgeom/analysis/branch_features.py,sha256=sJPAMTXXId9xyM-s9TmlS24kK65qyZ6Lva4trP816gs,1952
-swcgeom/analysis/feature_extractor.py,sha256=L-W4BwzvtWpowoPYuoejchWBo7O2FPuD_ncWmILMp-I,8830
-swcgeom/analysis/node_features.py,sha256=hsPJy87IyaVP8h8Fy2BvNeYx5ziYm1Ppcg4omY8Emo8,4324
+swcgeom/analysis/feature_extractor.py,sha256=7GTZ5cfqswc8GzMjhzfNpW7oJ5bB9JBRuMhkgjY5CPA,9232
+swcgeom/analysis/node_features.py,sha256=PQTYMk3VL3_HDjB4E0BcaBRn-_LQXXjHzsbvbUPSUiw,1536
 swcgeom/analysis/path_features.py,sha256=i9FHZtU98KnCrfpOp4NwVuXeqjzAzLQ9U__Jl5sdIow,883
-swcgeom/analysis/sholl.py,sha256=v9wzQ7tnN2syrUyivLlBRiIrfC9YZoEKR8NuhFOAfOg,2336
-swcgeom/analysis/visualization.py,sha256=hidgZqKL6DKauBEJ2lJA4KORnCwMhYvuXQbIm-bgfTE,4742
+swcgeom/analysis/sholl.py,sha256=W3B8uuY935DGtnG3G26UFTTXB2cgIBBk5knNygpcq2s,3093
+swcgeom/analysis/visualization.py,sha256=n-zOmHN0y1akQmGPcv-EvCuxlTJAf4HIBXO2vp2kHb4,6046
 swcgeom/core/__init__.py,sha256=BNdRJEsl_ixpuK-sdBIVxb5ZmBP6vAckQdTVREwDkl0,226
 swcgeom/core/branch.py,sha256=Rh_yHphV91omYpa0vN0jj-whCQzjhUHK_JHLxS_IQuo,3712
-swcgeom/core/branch_tree.py,sha256=8o64y_u2JsryzrC_IqDLYZ9aa-S_JjayfR9LgUtwByA,1648
-swcgeom/core/node.py,sha256=cxaism_qv6UmhYFQtrI9XHCibst_HKSTbcYfI2mokTk,3084
+swcgeom/core/branch_tree.py,sha256=HIrpo30kb3gG0ljIBbiefZvx3AlQkxrRy8Oa6eU6fp8,1698
+swcgeom/core/node.py,sha256=nzJjuJ35n9hbRxRICQsUBmJtxKWoyoHvrEoEmuE_JBc,3097
 swcgeom/core/path.py,sha256=aPebspjzAxC30h7U-ZlOmVKArMj6yeXwtxbgd2OBrRs,3764
-swcgeom/core/population.py,sha256=JpDOqr8k3t4GxuMEatte4E6LZfZerM6a6hRBQPdpN5s,2729
+swcgeom/core/population.py,sha256=IqgSs8KvI0rwwX8KmNyDUuma7HiTt6jr_0gV7UC_hVM,5884
 swcgeom/core/segment.py,sha256=q0qKmVs9K6S5M5KH7TaxM69i_lEOXJwLobd4Bkxubqs,2641
-swcgeom/core/swc.py,sha256=5BtVHw3tSgxMc2qDYUx-CkX6aufY2yMu4wCWakxZmHE,7116
-swcgeom/core/swc_utils.py,sha256=85rleBf39Sz3GwswE13rcUst4C3pzoJ8F4q9I1tQ9MI,6821
-swcgeom/core/tree.py,sha256=7k7BMezwfJZ4BhcxYi1RKwn7Z2xoMPL-Giph2EGRUck,10869
-swcgeom/core/tree_utils.py,sha256=zqzNJQsfjCNAgJV4kyVw7PYc38Hvn254aSFyyWu5HsI,3437
+swcgeom/core/swc.py,sha256=WmMego_nskhiYdPOKLCnTnD5UsDPfI0YI2tlcbPF8lM,7106
+swcgeom/core/swc_utils.py,sha256=0zHsbl9Qg6ueI2i8uxijcK1B_J4nk9QMhn-q0fT-Hk0,7412
+swcgeom/core/tree.py,sha256=RxnHlGAuuZ3neGVlumszfF0LpKcpjmywDoxSAeVzffY,10990
+swcgeom/core/tree_utils.py,sha256=QIcxQ-z1uvm2uPG536SYXdh7gwG42DNSoMN1ck7Kd6I,3441
 swcgeom/datasets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 swcgeom/datasets/pytorch/__init__.py,sha256=gF87h_xfCqpRh9KK3rigeamGI1YzbyE_Kouw9bU69J4,99
 swcgeom/datasets/pytorch/branch_dataset.py,sha256=BXemD23W9aON_q4W7fU8HlMS6bcH2WmntxO9DI65iSM,2784
@@ -34,12 +34,12 @@ swcgeom/transforms/pytorch/branch.py,sha256=O0b5U3F4opHV6DwmiYKhUR2LDk7BhMUHhyzL
 swcgeom/utils/__init__.py,sha256=1oqui-U3SNOklQyR9ZpkQrsEnx_vUbuYFByMSJtP0jA,125
 swcgeom/utils/debug.py,sha256=qay2qJpViLX82mzxdndxQFn-pi1vaEj9CbLGuGt8Y9k,465
 swcgeom/utils/download.py,sha256=qFWd6IG4_QAs7cGueMvT_EuuzeV_wXeb15O8_cWnt_E,2699
-swcgeom/utils/numpy.py,sha256=eOB7BgCc1JEhAe8mRjkbRw3iS2JycXImKcz7FUFIULA,2223
-swcgeom/utils/renderer.py,sha256=q6rT0u_t2sjZpFV-ZTpNk-L4rQYbxhw6yia9G2vJiVc,5355
+swcgeom/utils/numpy.py,sha256=A1gwD3GEqNWnbu07gyfJcsE7n_utpLikinjyQrN3U_I,1544
+swcgeom/utils/renderer.py,sha256=5-OSsDmqsE5Uf7kQn6x5RvMAVOgKz8W2mKq1sUc2ESE,5427
 swcgeom/utils/sdf.py,sha256=GUXmmpGcPCnFMmqWZzK9qJMfGKTgw5awJfJCrvMkPkA,5079
 swcgeom/utils/transforms.py,sha256=TBcEOojlw60gY0s2B8ywmkf51kzZ52fYan5yXsmIYuI,6349
-swcgeom-0.4.0.dist-info/LICENSE,sha256=aiTJ_1to1Xx6PaByy-pSXg42VYzE4FvF6GIt69WSDDI,202
-swcgeom-0.4.0.dist-info/METADATA,sha256=ileKjjajS-sw916Aw9s0TGRrg-fDe1gF-23TZAxsqpc,2200
-swcgeom-0.4.0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-swcgeom-0.4.0.dist-info/top_level.txt,sha256=hmLyUXWS61Gxl07haswFEKKefYPBVJYlUlol8ghNkjY,8
-swcgeom-0.4.0.dist-info/RECORD,,
+swcgeom-0.5.0.dist-info/LICENSE,sha256=aiTJ_1to1Xx6PaByy-pSXg42VYzE4FvF6GIt69WSDDI,202
+swcgeom-0.5.0.dist-info/METADATA,sha256=geB5_hdoY1edFmYrl5cs85uIyxZ0EgmASIFYEMUnPPg,2200
+swcgeom-0.5.0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+swcgeom-0.5.0.dist-info/top_level.txt,sha256=hmLyUXWS61Gxl07haswFEKKefYPBVJYlUlol8ghNkjY,8
+swcgeom-0.5.0.dist-info/RECORD,,