Merge pull request #477 from yfukai/refactor_field_names

Updated overlap tracking field names

src/laptrack/_overlap_tracking.py

@@ -1,10 +1,13 @@
 # from functools import cache
+import warnings
 from functools import partial
+from typing import Any
 from typing import List
 from typing import Tuple
 from typing import Union
 
 from pydantic import Field
+from pydantic import model_validator
 
 from ._tracking import LapTrack
 from ._typing_utils import IntArray
@@ -14,6 +17,13 @@
     float, float, float, float, float
 ]  # offset, overlap, iou, ratio_1, ratio_2
 
+_ALIAS_FIELDS = {
+    "track_dist_metric_coefs": "metric_coefs",
+    "gap_closing_dist_metric_coefs": "gap_closing_metric_coefs",
+    "splitting_dist_metric_coefs": "splitting_metric_coefs",
+    "merging_dist_metric_coefs": "merging_metric_coefs",
+}
+
 
 class OverLapTrack(LapTrack):
     """Tracking by label overlaps."""
@@ -41,6 +51,19 @@ class OverLapTrack(LapTrack):
         + "See `metric_coefs` for details.",
     )
 
+    @model_validator(mode="before")
+    @classmethod
+    def _check_deprecated_names(cls, data: Any) -> Any:
+        if isinstance(data, dict):
+            for old_name, new_name in _ALIAS_FIELDS.items():
+                if old_name in data:
+                    warnings.warn(
+                        f"Use of `{old_name}` is deprecated, use `{new_name}` instead.",
+                        DeprecationWarning,
+                    )
+                    data[new_name] = data.pop(old_name)
+        return data
+
     def predict_overlap_dataframe(self, labels: Union[IntArray, List[IntArray]]):
         """Predicts tracks with label overlaps.
 

tests/test_tracking.py

@@ -12,6 +12,8 @@
 
 from laptrack import LapTrack
 from laptrack import laptrack
+from laptrack import OverLapTrack
+from laptrack._overlap_tracking import _ALIAS_FIELDS as _ALIAS_FIELDS_OVERLAP
 from laptrack._tracking import _ALIAS_FIELDS
 from laptrack.data_conversion import convert_tree_to_dataframe
 
@@ -429,25 +431,32 @@ def test_no_connected_node(tracker_class) -> None:
 
 def test_alias_and_deprecation_warning():
     # Check that the alias works and issues a warning
-    for old_name, new_name in _ALIAS_FIELDS.items():
-        with warnings.catch_warnings(record=True) as w:
-            if "metric" in old_name:
-                test_value = "euclidean"
-            else:
-                test_value = 20**2
-            warnings.simplefilter("always")  # Ensure all warnings are captured
-            lt = LapTrack(**{old_name: test_value})
-            assert (
-                getattr(lt, new_name) == test_value
-            )  # Validate the correct field is populated
-
-            # Check if a DeprecationWarning was raised
-            assert len(w) == 1  # Only one warning should be present
-            assert issubclass(w[0].category, DeprecationWarning)
-            assert (
-                f"Use of `{old_name}` is deprecated, use `{new_name}` instead."
-                == str(w[0].message)
-            )
+    for fields, cls in [
+        (_ALIAS_FIELDS, LapTrack),
+        (_ALIAS_FIELDS_OVERLAP, OverLapTrack),
+    ]:
+        for old_name, new_name in fields.items():
+            with warnings.catch_warnings(record=True) as w:
+                if cls == LapTrack:
+                    if "metric" in old_name:
+                        test_value = "euclidean"
+                    else:
+                        test_value = 20**2
+                else:
+                    test_value = (1.0, 0.0, 0.0, 0.0, -1.0)
+                warnings.simplefilter("always")  # Ensure all warnings are captured
+                lt = cls(**{old_name: test_value})
+                assert (
+                    getattr(lt, new_name) == test_value
+                )  # Validate the correct field is populated
+
+                # Check if a DeprecationWarning was raised
+                assert len(w) == 1  # Only one warning should be present
+                assert issubclass(w[0].category, DeprecationWarning)
+                assert (
+                    f"Use of `{old_name}` is deprecated, use `{new_name}` instead."
+                    == str(w[0].message)
+                )
 
 
 # # %%