feat: add junction cleanup

Author: 404Simon

pyproject.toml

@@ -7,6 +7,7 @@ readme = "README.md"
 requires-python = ">=3.13"
 dependencies = [
     "argcomplete>=3.6.0",
+    "networkx>=3.4",
     "numba>=0.65.0",
     "numpy>=2.4.4",
     "pillow>=12.2.0",

uv.lock

@@ -46,6 +46,8 @@ def _extraction_params(
             extract_summary: bool = True,
             include_fractal: bool = False,
             include_vessel_radius: bool = False,
+            junction_cleanup: bool = False,
+            cleanup_threshold_factor: float = 2.5,
         ) -> None:
             return None
 
@@ -56,6 +58,15 @@ def _extraction_params(
             extract_branch_text={"annotation": bool, "value": True},
             extract_summary={"annotation": bool, "value": True},
             include_fractal={"annotation": bool, "value": False},
+            junction_cleanup={"annotation": bool, "value": False},
+            cleanup_threshold_factor={
+                "annotation": float,
+                "value": 2.5,
+                "widget_type": "FloatSpinBox",
+                "min": 1.0,
+                "max": 10.0,
+                "step": 0.1,
+            },
         )
 
         # ---------- output parameters (magicgui) ----------
@@ -109,6 +120,15 @@ def _output_params(
 
         advanced_group.append(self.include_vessel_radius_widget)
 
+        self.junction_cleanup_widget = extraction_gui.junction_cleanup
+        self.junction_cleanup_widget.label = "Collapse triangle junction artifacts"
+
+        self.cleanup_threshold_widget = extraction_gui.cleanup_threshold_factor
+        self.cleanup_threshold_widget.label = "Cleanup threshold factor"
+
+        advanced_group.append(self.junction_cleanup_widget)
+        advanced_group.append(self.cleanup_threshold_widget)
+
         # ============================================================
         # Output Settings (CLI file export options)
         # ============================================================
@@ -172,13 +192,16 @@ def _output_params(
     # ------------------------------------------------------------------
 
     def _get_current_pipeline_config(self) -> PipelineConfig:
+        junction_cleanup = self.junction_cleanup_widget.value
         return PipelineConfig(
             extraction=ExtractionConfig(
                 branches=self.extract_branches_widget.value,
                 branch_text=self.extract_branch_text_widget.value,
                 summary=self.extract_summary_widget.value,
                 fractal_dimension=self.include_fractal_widget.value,
                 vessel_radius=self.include_vessel_radius_widget.value,
+                junction_cleanup=junction_cleanup,
+                cleanup_threshold_factor=self.cleanup_threshold_widget.value,
             ),
             output=OutputConfig(
                 write_skeleton_npy=self.write_skeleton_npy_widget.value,
@@ -196,6 +219,8 @@ def _set_pipeline_config(self, config: PipelineConfig) -> None:
         self.extract_summary_widget.value = e.summary
         self.include_fractal_widget.value = e.fractal_dimension
         self.include_vessel_radius_widget.value = e.vessel_radius
+        self.junction_cleanup_widget.value = e.junction_cleanup
+        self.cleanup_threshold_widget.value = e.cleanup_threshold_factor
 
         o = config.output
         self.write_skeleton_npy_widget.value = o.write_skeleton_npy

vesskel/_napari.py

@@ -29,6 +29,8 @@ class ExtractionConfig:
     summary: bool = True
     fractal_dimension: bool = False
     vessel_radius: bool = False
+    junction_cleanup: bool = False
+    cleanup_threshold_factor: float = 2.5
 
     def to_dict(self) -> dict[str, Any]:
         return {
@@ -37,6 +39,8 @@ def to_dict(self) -> dict[str, Any]:
             "summary": self.summary,
             "fractal_dimension": self.fractal_dimension,
             "vessel_radius": self.vessel_radius,
+            "junction_cleanup": self.junction_cleanup,
+            "cleanup_threshold_factor": self.cleanup_threshold_factor,
         }
 
     @classmethod
@@ -48,6 +52,8 @@ def from_dict(cls, data: dict[str, Any]) -> ExtractionConfig:
             summary=data.get("summary", True),
             fractal_dimension=data.get("fractal_dimension", False),
             vessel_radius=data.get("vessel_radius", False),
+            junction_cleanup=data.get("junction_cleanup", False),
+            cleanup_threshold_factor=data.get("cleanup_threshold_factor", 2.5),
         )