swcgeom 0.14.0__py3-none-any.whl → 0.15.0__py3-none-any.whl

swcgeom/transforms/mst.py

@@ -140,13 +140,8 @@ class PointsToCuntzMST(Transform[npt.NDArray[np.float32], Tree]):
             t = sort_tree(t)
         return t
 
-    def __repr__(self) -> str:
-        return (
-            f"PointsToCuntzMST"
-            f"-bf-{self.bf}"
-            f"-furcations-{self.furcations}"
-            f"-{'exclude-soma' if self.exclude_soma else 'include-soma'}"
-        )  # TODO: names, types
+    def extra_repr(self) -> str:  # TODO: names, types
+        return f"bf={self.bf:.4f}, furcations={self.furcations}, exclude_soma={self.exclude_soma}, sort={self.sort}"
 
 
 class PointsToMST(PointsToCuntzMST):  # pylint: disable=too-few-public-methods
@@ -173,6 +168,7 @@ class PointsToMST(PointsToCuntzMST):  # pylint: disable=too-few-public-methods
         names : SWCNames, optional
         types : SWCTypes, optional
         """
+
         if k_furcations is not None:
             warnings.warn(
                 "`PointsToMST(k_furcations=...)` has been renamed to "
@@ -191,9 +187,5 @@ class PointsToMST(PointsToCuntzMST):  # pylint: disable=too-few-public-methods
             **kwargs,
         )
 
-    def __repr__(self) -> str:
-        return (
-            f"PointsToMST"
-            f"-furcations-{self.furcations}"
-            f"-{'exclude-soma' if self.exclude_soma else 'include-soma'}"
-        )
+    def extra_repr(self) -> str:
+        return f"furcations-{self.furcations}, exclude-soma={self.exclude_soma}"

swcgeom/transforms/population.py

@@ -25,5 +25,5 @@ class PopulationTransform(Transform[Population, Population]):
 
         return Population(trees, root=population.root)
 
-    def __repr__(self) -> str:
-        return f"pop({self.transform})"
+    def extra_repr(self) -> str:
+        return f"transform={self.transform}"

swcgeom/transforms/tree.py

@@ -64,8 +64,8 @@ class TreeSmoother(Transform[Tree, Tree]):  # pylint: disable=missing-class-docs
 
         return x
 
-    def __repr__(self) -> str:
-        return f"TreeSmoother-{self.n_nodes}"
+    def extra_repr(self):
+        return f"n_nodes={self.n_nodes}"
 
 
 class TreeNormalizer(Normalizer[Tree]):
@@ -107,8 +107,8 @@ class CutByType(Transform[Tree, Tree]):
         y = to_subtree(x, removals)
         return y
 
-    def __repr__(self) -> str:
-        return f"CutByType-{self.type}"
+    def extra_repr(self):
+        return f"type={self.type}"
 
 
 class CutAxonTree(CutByType):
@@ -118,9 +118,6 @@ class CutAxonTree(CutByType):
         types = get_types(types)
         super().__init__(type=types.axon)
 
-    def __repr__(self) -> str:
-        return "CutAxonTree"
-
 
 class CutDendriteTree(CutByType):
     """Cut dendrite tree."""
@@ -129,9 +126,6 @@ class CutDendriteTree(CutByType):
         types = get_types(types)
         super().__init__(type=types.basal_dendrite)  # TODO: apical dendrite
 
-    def __repr__(self) -> str:
-        return "CutDenriteTree"
-
 
 class CutByBifurcationOrder(Transform[Tree, Tree]):
     """Cut tree by bifurcation order."""
@@ -177,9 +171,6 @@ class CutShortTipBranch(Transform[Tree, Tree]):
         if callback is not None:
             self.callbacks.append(callback)
 
-    def __repr__(self) -> str:
-        return f"CutShortTipBranch-{self.thre}"
-
     def __call__(self, x: Tree) -> Tree:
         removals: List[int] = []
         self.callbacks.append(lambda br: removals.append(br[1].id))
@@ -187,6 +178,9 @@ class CutShortTipBranch(Transform[Tree, Tree]):
         self.callbacks.pop()
         return to_subtree(x, removals)
 
+    def extra_repr(self):
+        return f"threshold={self.thre}"
+
     def _leave(
         self, n: Tree.Node, children: List[Tuple[float, Tree.Node] | None]
     ) -> Tuple[float, Tree.Node] | None:

swcgeom/transforms/tree_assembler.py

@@ -1,17 +1,22 @@
 """Assemble a tree."""
 
+from copy import copy
 from typing import Iterable, List, Optional, Tuple
 
+import numpy as np
 import pandas as pd
 
 from swcgeom.core import Tree
-from swcgeom.core.swc_utils import SWCNames
-from swcgeom.core.swc_utils.assembler import (
-    assemble_lines_impl,
-    try_assemble_lines_impl,
+from swcgeom.core.swc_utils import (
+    SWCNames,
+    get_names,
+    link_roots_to_nearest_,
+    sort_nodes_,
 )
 from swcgeom.transforms.base import Transform
 
+EPS = 1e-5
+
 
 class LinesToTree(Transform[List[pd.DataFrame], Tree]):
     """Assemble lines to swc."""
@@ -35,11 +40,12 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
     ):
         return self.assemble(lines, names=names)
 
-    def __repr__(self) -> str:
-        return f"LinesToTree-thre-{self.thre}-{'undirected' if self.undirected else 'directed'}"
-
     def assemble(
-        self, lines: Iterable[pd.DataFrame], *, names: Optional[SWCNames] = None
+        self,
+        lines: Iterable[pd.DataFrame],
+        *,
+        undirected: bool = True,
+        names: Optional[SWCNames] = None,
     ) -> pd.DataFrame:
         """Assemble lines to a tree.
 
@@ -51,6 +57,8 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
         lines : List of ~pd.DataFrame
             An array of tables containing a line, columns should follwing
             the swc.
+        undirected : bool, default `True`
+            Forwarding to `self.try_assemble`.
         names : SWCNames, optional
             Forwarding to `self.try_assemble`.
 
@@ -60,17 +68,33 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
 
         See Also
         --------
-        self.try_assemble_lines
+        self.try_assemble
         """
-        return assemble_lines_impl(
-            lines, thre=self.thre, undirected=self.undirected, names=names
+
+        tree, lines = self.try_assemble(
+            lines, sort_nodes=False, undirected=undirected, names=names
         )
+        while len(lines) > 0:
+            t, lines = self.try_assemble(
+                lines,
+                id_offset=len(tree),
+                sort_nodes=False,
+                undirected=undirected,
+                names=names,
+            )
+            tree = pd.concat([tree, t])
+
+        tree = tree.reset_index()
+        link_roots_to_nearest_(tree)
+        sort_nodes_(tree)
+        return tree
 
     def try_assemble(
         self,
         lines: Iterable[pd.DataFrame],
         *,
         id_offset: int = 0,
+        undirected: bool = True,
         sort_nodes: bool = True,
         names: Optional[SWCNames] = None,
     ) -> Tuple[pd.DataFrame, List[pd.DataFrame]]:
@@ -88,6 +112,9 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
             the swc.
         id_offset : int, default `0`
             The offset of the line node id.
+        undirected : bool, default `True`
+            Both ends of a line can be considered connection point. If
+            `False`, only the starting point.
         sort_nodes : bool, default `True`
             sort nodes of subtree.
         names : SWCNames, optional
@@ -97,11 +124,50 @@ class LinesToTree(Transform[List[pd.DataFrame], Tree]):
         tree : ~pandas.DataFrame
         remaining_lines : List of ~pandas.DataFrame
         """
-        return try_assemble_lines_impl(
-            lines,
-            undirected=self.undirected,
-            thre=self.thre,
-            id_offset=id_offset,
-            sort_nodes=sort_nodes,
-            names=names,
-        )
+
+        names = get_names(names)
+        lines = copy(list(lines))
+
+        tree = lines[0]
+        tree[names.id] = id_offset + np.arange(len(tree))
+        tree[names.pid] = tree[names.id] - 1
+        tree.at[0, names.pid] = -1
+        del lines[0]
+
+        while True:
+            for i, line in enumerate(lines):
+                for p in [0, -1] if undirected else [0]:
+                    xyz = [names.x, names.y, names.z]
+                    vs = tree[xyz] - line.iloc[p][xyz]
+                    dis = np.linalg.norm(vs, axis=1)
+                    ind = np.argmin(dis)
+                    if dis[ind] > self.thre:
+                        continue
+
+                    if dis[ind] < EPS:
+                        line = line.drop((p + len(line)) % len(line)).reset_index(
+                            drop=True
+                        )
+
+                    line[names.id] = id_offset + len(tree) + np.arange(len(line))
+                    line[names.pid] = line[names.id] + (-1 if p == 0 else 1)
+                    line.at[(p + len(line)) % len(line), names.pid] = tree.iloc[ind][
+                        names.id
+                    ]
+                    tree = pd.concat([tree, line])
+                    del lines[i]
+                    break
+                else:
+                    continue
+
+                break
+            else:
+                break
+
+        if sort_nodes:
+            sort_nodes_(tree)
+
+        return tree, lines
+
+    def extra_repr(self):
+        return f"thre={self.thre}, undirected={self.undirected}"

{swcgeom-0.14.0.dist-info → swcgeom-0.15.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.14.0
+Version: 0.15.0
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: Apache-2.0

{swcgeom-0.14.0.dist-info → swcgeom-0.15.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
 swcgeom/__init__.py,sha256=z88Zwcjv-ii7c7dYd9QPg9XrUVorQjtrgGbQCsEnQhc,265
-swcgeom/_version.py,sha256=9XbM6DRatFmjNkeSNxF4a6enpQeo8nPyAy9RTPPwPpY,413
+swcgeom/_version.py,sha256=oHv-EAjiXbJma3jZ0Tq6UPimiWYyyw2Ao9S8zdq9uWs,413
 swcgeom/analysis/__init__.py,sha256=esL_poW8u-_bmp7vR9ldcumX3_xodtaVfM1USqxQo5w,377
 swcgeom/analysis/branch_features.py,sha256=s6PTMwwvxrVtZXRZlQbUSIw4M9-1IG63kf-Nxc0tMB0,1958
 swcgeom/analysis/feature_extractor.py,sha256=coe07_bJau96BkimcnXzuf4KqjY5_QRLwqaumFsu_tQ,14031
@@ -11,37 +11,37 @@ swcgeom/analysis/visualization.py,sha256=mKOpzTPkLpr1ggGL1MZPZRTG92GEg4idLT4eN5z
 swcgeom/analysis/volume.py,sha256=nWPR7wGOk3Wl5eh97YMws0X-2jk8K7lmFp4-03wL3lY,4628
 swcgeom/core/__init__.py,sha256=ZUudZavxAIUU6Q0lBHrQ4ybmL5lBfvzyYsTtpuih9wg,332
 swcgeom/core/branch.py,sha256=uuJCxaByRu-OdDZVWEffSFcmZWY-6ZWUhHN1M2Awj1s,3980
-swcgeom/core/branch_tree.py,sha256=sN0viBVg5A4r9dMCkGNAaVttrdR4bEoZZBbHZFKdXj4,1892
+swcgeom/core/branch_tree.py,sha256=Ece6q1VNCRLLMj29N_MjXmmlHT8h4tpWCuDE0uSgKJo,1873
 swcgeom/core/node.py,sha256=HvfgsW4WU01hkRIPci8KF4bQMAkwtAxOGfUL4yUbuBs,3623
 swcgeom/core/path.py,sha256=CsEelHiDR0JPBP1dTvoCSRvX3kBlZxkQilosnncV4nQ,4188
-swcgeom/core/population.py,sha256=YZLAtkZKJeErOsE5MwhqieGjoMa7sWjFl5xxmXVPTco,8786
+swcgeom/core/population.py,sha256=I9xSeGUveLhxkOg_5FWLcvf4yJVJ6j9_n03Hna3y_6w,8790
 swcgeom/core/segment.py,sha256=yabRdFj7KlkJP4V67jAlCIRzpHduNnq3bRBIRMuANfA,3158
 swcgeom/core/swc.py,sha256=lSYxAa25l6O8WZ9JtSSET-RZMr6EA1Tq_aXL_x0H9Rc,6795
-swcgeom/core/tree.py,sha256=oAx31r2jFzxSW7vnM17m8sMVVI3_xzxRyDQh19MPTlQ,12126
-swcgeom/core/tree_utils.py,sha256=xPy9b3MO43QR7VSvJvrwioXyQLGAPLotQjekn_-UiLg,7308
-swcgeom/core/tree_utils_impl.py,sha256=5Cb63ziVVLADnkjfuq1T-ePw2TQQ5TKk4gcPZR6f_wY,1123
+swcgeom/core/tree.py,sha256=K2k7o8OZ9r2YeMmIebT8_0qvkwJYtLLzFHECz3fmmts,12365
+swcgeom/core/tree_utils.py,sha256=3aCHghny5Z727sxkt6P8E2MMr34vK6irfPCelMn3vk4,7681
+swcgeom/core/tree_utils_impl.py,sha256=kN2ByjqqQtZUfmC_ac25tXOaE-CMiV2lP58VxFphLEU,1616
 swcgeom/core/swc_utils/__init__.py,sha256=qghRxjtzvq5KKfN4HhvLpZNsGPfZQu-Jj2x62_5-TbQ,575
-swcgeom/core/swc_utils/assembler.py,sha256=RoMJ3RjLC4O7mk62QxXVTQ5SUHagrFmpEw3nOnnqeJo,4563
+swcgeom/core/swc_utils/assembler.py,sha256=_ByaVFc61rfCS2p9QUw4g40uF4pZ6NJaDc--TcV4jWo,642
 swcgeom/core/swc_utils/base.py,sha256=huVxjuMLlTHbEb-KSEFDLgU0Ss3723t2Gr4Z_gQtl00,4737
 swcgeom/core/swc_utils/checker.py,sha256=E72GtLZ_1IqQQ7aWQGs0dZ3Z609__bw3EYQqeWrk-EI,2657
 swcgeom/core/swc_utils/io.py,sha256=6_--Qoe8kDja4PWsjwqRAvPJZNMFILFgauHaeWeGikU,6444
 swcgeom/core/swc_utils/normalizer.py,sha256=_Ysi8bSJ2JBnIGB8o6BvAg2mcz6xuJp9rgNLZqpLuR8,5083
-swcgeom/core/swc_utils/subtree.py,sha256=bd4XOLmRDfQSn_ktfQM3Hn8ONpCuZ_TdTWhE9-7QXW4,1999
+swcgeom/core/swc_utils/subtree.py,sha256=43QITYvgXu3b_kfIod2Irrj3dSfrA-gTFev5VxzRafI,1995
 swcgeom/images/__init__.py,sha256=QBP1ZGGo2nWAcV7Krz-vbvW_jN4ChqXrrpoScXcUURs,96
 swcgeom/images/augmentation.py,sha256=v9zluYXmBEbafaDBTpvJovi4_KWJmHZZSvcYHzG0oWo,4099
-swcgeom/images/folder.py,sha256=urh60ITreGgEwSbCbgexJFM8_-C9WLAQ9jUN50sox10,4034
-swcgeom/images/io.py,sha256=VZWBq-_TMrKKdMaqpbZWZP6fCGIxWdhdIfb0ePcDy-4,20272
+swcgeom/images/folder.py,sha256=2REkrdNghLm1z8kZ2PDVvtsupzog8kARkeMjLuLiLFo,4955
+swcgeom/images/io.py,sha256=jUyKjtau8_5V-PN1kRsPHtP1OtueJi1zEf5-7PZ_tG8,21226
 swcgeom/transforms/__init__.py,sha256=Mi2mOgkQ50JbZ9LmgXgJIuAA5eio67oe2AOs2CCCxTQ,463
-swcgeom/transforms/base.py,sha256=22kkpQ11YCrH1SWWMHVqYjHp6cAlhslhdi1wKgAnT_s,3416
-swcgeom/transforms/branch.py,sha256=mdrTC9T4zENS9DdwlFaoFHcWDuFAgKgiNicJZ1gLsOc,5445
-swcgeom/transforms/geometry.py,sha256=zPmEf6ApJKzeZBbZ7qJYZXpY3-mrABN2dr7AUNqENiQ,6619
-swcgeom/transforms/image_stack.py,sha256=uJfRhXz86NQUxA3MguCoHpq4WBUAUjgZjMH1n-Wqoiw,5297
-swcgeom/transforms/images.py,sha256=tUl3dtqWfrhWR7WrOUc6LzWHnOzz3fwEgV3mMLRhn0c,908
-swcgeom/transforms/mst.py,sha256=B6ZRqeEfCHLHFu0tdOsOgplbYHra4VPYjnneXMU-cNY,6413
+swcgeom/transforms/base.py,sha256=gN5Iqi-OHkYrsjllSOdxI6Yzav3jJGoi6kUPy-38FAs,4101
+swcgeom/transforms/branch.py,sha256=R0rVti--u70IiUKyHSx6MsDYJyy6zSCf18Uia2Cmh28,5410
+swcgeom/transforms/geometry.py,sha256=XR73fO_8T7otUFIllqKOWW0OnrsXBc7yA01oDT99yMc,7385
+swcgeom/transforms/image_stack.py,sha256=KhZ26Ps88jk_7NkI9dkS2E7NZXUvMaN3Ln9WzJ-vPu0,5823
+swcgeom/transforms/images.py,sha256=l5Hx8x27zoClUz3s11j2oj0Lt9ROh5JJfjoIU_vd3H8,898
+swcgeom/transforms/mst.py,sha256=ceL_EWpCtoSy9zYD6wPP5zO68eNTrDl9JExoPLcE_Lw,6236
 swcgeom/transforms/path.py,sha256=Gk2iunGQMX7vE83bdo8xoDO-KAT1Vvep0iZs7oFLzFQ,1089
-swcgeom/transforms/population.py,sha256=ZrKfMAMx4l729f-JLgw0dnGIPtPUoV0ZZoNNyA5cBw8,826
-swcgeom/transforms/tree.py,sha256=Q5OnSti0ZeTNb-WpA_UZsDN7dhLN8YweEF_Siyrj66c,6420
-swcgeom/transforms/tree_assembler.py,sha256=UZ9OUg1bQNecYIY_7ippg3S8gpuoi617ZUE0jg6BrQE,3177
+swcgeom/transforms/population.py,sha256=EmZ6ntuOKe8mXJxMW7nCUA-w2DVlEVe2n0IOVz49tCY,833
+swcgeom/transforms/tree.py,sha256=Q45sVA7yi8pINV7ENOWPKz6DnEM3U5uJxwkFKNFS5VE,6262
+swcgeom/transforms/tree_assembler.py,sha256=vi_X9CNo5IxHP5J7bRl2z91PWufU6HmYlz1iyfdPUxE,5121
 swcgeom/utils/__init__.py,sha256=QfezYuQzgmPziNiWz2T1h77V-gjpuBoUi3mC-K-PZlI,427
 swcgeom/utils/debug.py,sha256=qay2qJpViLX82mzxdndxQFn-pi1vaEj9CbLGuGt8Y9k,465
 swcgeom/utils/download.py,sha256=By2qZezo6h1Ke_4YpSIhDgcisOrpjVqRmNzbhynC2xs,2834
@@ -55,8 +55,8 @@ swcgeom/utils/sdf.py,sha256=K-LSnwwNsGF85GW1kNBaqXAAVesxZAEsrn0nvOA2LcA,10614
 swcgeom/utils/solid_geometry.py,sha256=TV02jhcoCLCqtYA9hfE50LFD_VRfixMiOSiHB5Jb2_U,2431
 swcgeom/utils/transforms.py,sha256=PmP5fL_iVguq4GR2aqXhM0TeCsiFVnrPZMZG6zLohrE,6983
 swcgeom/utils/volumetric_object.py,sha256=DVRGGmQrAL0oaW6hbNtp5TStbic9DfyJdCzsv2FNw2c,15134
-swcgeom-0.14.0.dist-info/LICENSE,sha256=JPtohhZ4XURqoKI0ZqnMYb7dobCOoZR_n5EpnaLTp3E,11344
-swcgeom-0.14.0.dist-info/METADATA,sha256=4DWijpWXVwo7_Cf8H-EH9DVDfQ31XoA9wEMhshow_kg,2347
-swcgeom-0.14.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-swcgeom-0.14.0.dist-info/top_level.txt,sha256=hmLyUXWS61Gxl07haswFEKKefYPBVJYlUlol8ghNkjY,8
-swcgeom-0.14.0.dist-info/RECORD,,
+swcgeom-0.15.0.dist-info/LICENSE,sha256=JPtohhZ4XURqoKI0ZqnMYb7dobCOoZR_n5EpnaLTp3E,11344
+swcgeom-0.15.0.dist-info/METADATA,sha256=VJX8KlMJWpYCZ-bMUYy_kL05sAHXmvHLMqUepQaKNTQ,2347
+swcgeom-0.15.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+swcgeom-0.15.0.dist-info/top_level.txt,sha256=hmLyUXWS61Gxl07haswFEKKefYPBVJYlUlol8ghNkjY,8
+swcgeom-0.15.0.dist-info/RECORD,,