adding bounding-box column (#121)

Author: JoOkuma

src/tracksdata/constants.py

@@ -18,6 +18,10 @@ class DefaultAttrKeys:
         Default key for time information.
     MASK : str
         Default key for node masks.
+    BBOX : str
+        Default key for node bounding boxes.
+        For a 2D image, the bounding box is a tuple of (x_start, y_start, x_end, y_end).
+        For a 3D image, the bounding box is a tuple of (x_start, y_start, z_start, x_end, y_end, z_end).
     SOLUTION : str
         Default key for solution information.
     TRACK_ID : str
@@ -50,6 +54,7 @@ class DefaultAttrKeys:
     NODE_ID = "node_id"
     T = "t"
     MASK = "mask"
+    BBOX = "bbox"
     SOLUTION = "solution"
     TRACK_ID = "track_id"
 

src/tracksdata/nodes/_regionprops.py

@@ -120,8 +120,9 @@ def _init_node_attrs(self, graph: BaseGraph, axis_names: list[str]) -> None:
         """
         Initialize the node attributes for the graph.
         """
-        if DEFAULT_ATTR_KEYS.MASK not in graph.node_attr_keys:
-            graph.add_node_attr_key(DEFAULT_ATTR_KEYS.MASK, None)
+        for attr_key in [DEFAULT_ATTR_KEYS.MASK, DEFAULT_ATTR_KEYS.BBOX]:
+            if attr_key not in graph.node_attr_keys:
+                graph.add_node_attr_key(attr_key, None)
 
         # initialize the attribute keys
         for attr_key in axis_names + self.attrs_keys():
@@ -288,6 +289,7 @@ def _nodes_per_time(
                     attrs[prop] = getattr(obj, prop)
 
             attrs[DEFAULT_ATTR_KEYS.MASK] = Mask(obj.image, obj.bbox)
+            attrs[DEFAULT_ATTR_KEYS.BBOX] = np.asarray(obj.bbox, dtype=int)
             attrs[DEFAULT_ATTR_KEYS.T] = t
 
             nodes_data.append(attrs)

src/tracksdata/nodes/_test/test_regionprops.py

@@ -252,9 +252,11 @@ def test_regionprops_spacing() -> None:
 
     # Check that nodes were added (spacing affects internal calculations)
     nodes_df = graph.node_attrs()
+
     assert len(nodes_df) == 1
     assert "area" in nodes_df.columns
     assert DEFAULT_ATTR_KEYS.MASK in nodes_df.columns
+    assert nodes_df[DEFAULT_ATTR_KEYS.BBOX].to_numpy().ndim == 2
 
 
 def test_regionprops_empty_labels() -> None: