Adding option to control min_area_factor (#201)

Author: JoOkuma

Diff for: ultrack/config/segmentationconfig.py

@@ -21,12 +21,20 @@ class SegmentationConfig(BaseModel):
 
     min_area: int = 100
     """
-    Minimum segment number of pixels, regions smaller than this value are merged
-    or removed when there is no neighboring region
+    Minimum number of pixels for segmentation hypotheses prunning.
+    Regions smaller than this value are merged or removed when there is no neighboring region
+    """
+
+    min_area_factor: float = 4.0
+    """
+    Objects in the foreground below `min_area / min_area_factor` are removed
+    and not considered as hypotheses.
     """
 
     max_area: int = 1_000_000
-    """Maximum segment's number of pixels, regions larger than this value are removed """
+    """Maximum number of pixels for segmentation hypotheses prunning
+    Regions larger than this value are merged or removed when there is no neighboring region
+    """
 
     n_workers: int = 1
     """Number of worker threads """

Diff for: ultrack/core/segmentation/_test/test_hierarchy.py

@@ -23,6 +23,7 @@ def test_horizontal_cut(
         edge,
         hierarchy_fun=hg.watershed_hierarchy_by_dynamics,
         min_area=0,
+        min_area_factor=1,
         cut_threshold=0.1,
     )
 

Diff for: ultrack/core/segmentation/hierarchy.py

@@ -67,7 +67,9 @@ def create_hierarchies(
         #  Nodes in hierarchies are still filtered by minimum area.
         #  This is mainly for lonely cells.
         morphology.remove_small_objects(
-            labels, min_size=int(kwargs["min_area"] / 4), out=labels
+            labels,
+            min_size=int(kwargs["min_area"] / kwargs.get("min_area_factor", 4.0)),
+            out=labels,
         )
 
     edge = np.asarray(edge)
@@ -81,6 +83,8 @@ def create_hierarchies(
             kwargs.get("anisotropy_pen", 0.0),
         )
 
+    kwargs.pop("min_area_factor")
+
     LOG.info("Creating hierarchies (lazy).")
     for c in measure.regionprops(labels, edge, cache=True):
         yield Hierarchy(c, **kwargs)

Diff for: ultrack/core/segmentation/processing.py

@@ -214,6 +214,7 @@ def _process(
         hierarchy_fun=config.ws_hierarchy,
         max_area=config.max_area,
         min_area=config.min_area,
+        min_area_factor=config.min_area_factor,
         min_frontier=config.min_frontier,
     )