skeleton postprocessing cosmetic changes

Author: GOESTERN-1107078

examples/skeleton/instance_segmentation.py

@@ -11,7 +11,7 @@
 import numpy as np
 
 from bioimage_cpp.graph import connected_components
-from bioimage_cpp.skeleton import clean_graph, draw_instances, skeleton_to_graph, teasar
+from bioimage_cpp.skeleton import clean_filament_graph, draw_instances, skeleton_to_graph, teasar
 
 
 def parse_args():
@@ -78,7 +78,7 @@ def main():
         number_of_threads=args.number_of_threads,
     )
 
-    vertices, edges, radii = clean_graph(
+    vertices, edges, radii = clean_filament_graph(
         raw_vertices, raw_edges, radii=raw_radii,
         direction_span=args.direction_span, min_through_angle=args.min_through_angle,
         min_branch_angle=args.min_branch_angle, tick_length=args.tick_length,

src/bioimage_cpp/skeleton/__init__.py

@@ -10,7 +10,7 @@
 from .._validation import strict_index
 from ..distance._distance import _as_binary_input, _normalize_sampling, _normalize_threads
 from ._graph import skeleton_to_graph
-from .postprocessing import clean_graph, draw_instances, join_close_components, remove_ticks
+from .postprocessing import clean_filament_graph, draw_instances, join_close_components, remove_ticks
 
 
 _TEASAR_LABELS_BY_DTYPE = {
@@ -206,4 +206,4 @@ def teasar_labels(
 from . import distributed
 
 
-__all__ = ["clean_graph", "distributed", "draw_instances", "join_close_components", "remove_ticks", "skeleton_to_graph", "teasar", "teasar_labels"]
+__all__ = ["clean_filament_graph", "distributed", "draw_instances", "join_close_components", "remove_ticks", "skeleton_to_graph", "teasar", "teasar_labels"]

src/bioimage_cpp/skeleton/postprocessing.py

@@ -45,7 +45,7 @@ def _compact(vertices, edges, radii):
     return vertices[used], remap[edges], radii
 
 
-def split_degree3(v, graph, vertices, direction_span=1, min_branch_angle=30.0):
+def _split_degree3(v, graph, vertices, direction_span=1, min_branch_angle=30.0):
     adj = np.asarray(graph.node_adjacency(int(v)))
     if adj.shape[0] != 3:
         return None
@@ -64,7 +64,7 @@ def split_degree3(v, graph, vertices, direction_span=1, min_branch_angle=30.0):
     return [int(edge_ids[odd])]
 
 
-def split_degree4(v, graph, vertices, direction_span=1, min_through_angle=160.0):
+def _split_degree4(v, graph, vertices, direction_span=1, min_through_angle=160.0):
     adj = np.asarray(graph.node_adjacency(int(v)))
     if adj.shape[0] != 4:
         return None
@@ -81,7 +81,7 @@ def split_degree4(v, graph, vertices, direction_span=1, min_through_angle=160.0)
     return [int(edge_ids[k]) for k in pair_b]
 
 
-def clean_graph(
+def clean_filament_graph(
     vertices: np.ndarray,
     edges: np.ndarray,
     radii: np.ndarray | None = None,
@@ -159,11 +159,11 @@ def _snapshot(name):
 
     splits, prune_edges = [], set()
     for v in np.where(degrees == 3)[0]:
-        ids = split_degree3(v, graph, vertices, direction_span, min_branch_angle)
+        ids = _split_degree3(v, graph, vertices, direction_span, min_branch_angle)
         if ids:
             prune_edges.update(ids)
     for v in np.where(degrees == 4)[0]:
-        ids = split_degree4(v, graph, vertices, direction_span, min_through_angle)
+        ids = _split_degree4(v, graph, vertices, direction_span, min_through_angle)
         if ids:
             splits.append((int(v), ids))
 
@@ -479,4 +479,4 @@ def draw_instances(vertices, edges, labels, shape, radius=1):
     return volume
 
 
-__all__ = ["clean_graph", "draw_instances", "join_close_components", "remove_ticks"]
+__all__ = ["clean_filament_graph", "draw_instances", "join_close_components", "remove_ticks"]

tests/skeleton/test_postprocessing.py

@@ -2,7 +2,7 @@
 import pytest
 
 import bioimage_cpp as bic
-from bioimage_cpp.skeleton.postprocessing import split_degree3, split_degree4
+from bioimage_cpp.skeleton.postprocessing import _split_degree3, _split_degree4
 
 
 def _graph(vertices, edges):
@@ -22,7 +22,7 @@ def test_split_degree3_splits_odd_arm():
         [[0.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, -1.0], [0.0, 1.0, 0.0]],
         [[0, 1], [0, 2], [0, 3]],
     )
-    assert split_degree3(0, graph, vertices, direction_span=1, min_branch_angle=30.0) == [2]
+    assert _split_degree3(0, graph, vertices, direction_span=1, min_branch_angle=30.0) == [2]
 
 
 def test_split_degree3_keeps_collinear_arm():
@@ -31,7 +31,7 @@ def test_split_degree3_keeps_collinear_arm():
         [[0.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, -1.0], [0.0, 1.0, 10.0]],
         [[0, 1], [0, 2], [0, 3]],
     )
-    assert split_degree3(0, graph, vertices, direction_span=1, min_branch_angle=30.0) is None
+    assert _split_degree3(0, graph, vertices, direction_span=1, min_branch_angle=30.0) is None
 
 
 def test_split_degree4_splits_through_pair():
@@ -40,7 +40,7 @@ def test_split_degree4_splits_through_pair():
         [[0.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, -1.0], [0.0, 1.0, 0.0], [0.0, -1.0, 0.0]],
         [[0, 1], [0, 2], [0, 3], [0, 4]],
     )
-    result = split_degree4(0, graph, vertices, direction_span=1, min_through_angle=170.0)
+    result = _split_degree4(0, graph, vertices, direction_span=1, min_through_angle=170.0)
     assert set(result) in ({0, 1}, {2, 3})
 
 
@@ -52,7 +52,7 @@ def test_split_degree4_keeps_non_collinear_crossing():
         np.concatenate([[[0.0, 0.0, 0.0]], arms]),
         [[0, 1], [0, 2], [0, 3], [0, 4]],
     )
-    assert split_degree4(0, graph, vertices, direction_span=1, min_through_angle=170.0) is None
+    assert _split_degree4(0, graph, vertices, direction_span=1, min_through_angle=170.0) is None
 
 
 @pytest.mark.parametrize(
@@ -141,7 +141,7 @@ def test_clean_graph_splits_crossing():
 
     assert _component_count(vertices, edges) == 1
 
-    out_vertices, out_edges, out_radii = bic.skeleton.clean_graph(
+    out_vertices, out_edges, out_radii = bic.skeleton.clean_filament_graph(
         vertices, edges, radii=radii, direction_span=1, tick_length=0.0, join_dist=0.0,
     )