talmolab · andrewjoc · Mar 19, 2025 · Mar 4, 2025 · Mar 5, 2025 · Mar 5, 2025
diff --git a/sleap_roots/convhull.py b/sleap_roots/convhull.py
@@ -607,7 +607,7 @@ def get_chull_intersection_vectors(
 
 
 def get_chull_intersection_vectors_left(
-    vectors: Tuple[np.ndarray, np.ndarray]
+    vectors: Tuple[np.ndarray, np.ndarray],
 ) -> np.ndarray:
     """Get the vector from the top left point to the left intersection point.
 
@@ -623,7 +623,7 @@ def get_chull_intersection_vectors_left(
 
 
 def get_chull_intersection_vectors_right(
-    vectors: Tuple[np.ndarray, np.ndarray]
+    vectors: Tuple[np.ndarray, np.ndarray],
 ) -> np.ndarray:
     """Get the vector from the top right point to the right intersection point.
 

diff --git a/sleap_roots/networklength.py b/sleap_roots/networklength.py
@@ -36,7 +36,7 @@ def get_bbox(pts: np.ndarray) -> Tuple[float, float, float, float]:
 
 
 def get_network_width_depth_ratio(
-    pts: Union[np.ndarray, Tuple[float, float, float, float]]
+    pts: Union[np.ndarray, Tuple[float, float, float, float]],
 ) -> float:
     """Return width to depth ratio of bounding box for root network.
 

diff --git a/sleap_roots/points.py b/sleap_roots/points.py
@@ -264,7 +264,7 @@ def get_left_right_normalized_vectors(
 
 
 def get_left_normalized_vector(
-    normalized_vectors: Tuple[np.ndarray, np.ndarray]
+    normalized_vectors: Tuple[np.ndarray, np.ndarray],
 ) -> np.ndarray:
     """Get the normalized vector from r0 to r1 on the left side of a crown root system.
 
@@ -283,7 +283,7 @@ def get_left_normalized_vector(
 
 
 def get_right_normalized_vector(
-    normalized_vectors: Tuple[np.ndarray, np.ndarray]
+    normalized_vectors: Tuple[np.ndarray, np.ndarray],
 ) -> np.ndarray:
     """Get the normalized vector from r0 to r1 on the right side of a crown root system.
 

diff --git a/tests/data/canola_7do/919QDUH.batch_traits.csv b/tests/data/canola_7do/919QDUH.batch_traits.csv
diff --git a/tests/data/canola_7do/919QDUH.traits.csv b/tests/data/canola_7do/919QDUH.traits.csv
diff --git a/tests/data/soy_6do/6PR6AA22JK.batch_traits.csv b/tests/data/soy_6do/6PR6AA22JK.batch_traits.csv
diff --git a/tests/data/soy_6do/6PR6AA22JK.traits.csv b/tests/data/soy_6do/6PR6AA22JK.traits.csv
diff --git a/tests/fixtures/data.py b/tests/fixtures/data.py
@@ -25,6 +25,18 @@ def canola_lateral_slp():
     return "tests/data/canola_7do/919QDUH.lateral.predictions.slp"
 
 
+@pytest.fixture
+def canola_traits_csv():
+    """Path to computed traits csv for 7 day old canola."""
+    return "tests/data/canola_7do/919QDUH.traits.csv"
+
+
+@pytest.fixture
+def canola_batch_traits_csv():
+    """Path to computed batch traits csv for 7 day old canola."""
+    return "tests/data/canola_7do/919QDUH.batch_traits.csv"
+
+
 @pytest.fixture
 def rice_pipeline_output_folder():
     """Path to the folder with the output of the rice pipeline."""
@@ -109,6 +121,18 @@ def soy_lateral_slp():
     return "tests/data/soy_6do/6PR6AA22JK.lateral.predictions.slp"
 
 
+@pytest.fixture
+def soy_traits_csv():
+    """Path to computed traits csv for 6 day old soy."""
+    return "tests/data/soy_6do/6PR6AA22JK.traits.csv"
+
+
+@pytest.fixture
+def soy_batch_traits_csv():
+    """Path to computed batch traits csv for 6 day old soy."""
+    return "tests/data/soy_6do/6PR6AA22JK.batch_traits.csv"
+
+
 @pytest.fixture
 def multiple_arabidopsis_11do_folder():
     """Path to a folder with the predictions for 3, 11 day old arabidopsis."""

diff --git a/tests/test_series.py b/tests/test_series.py
@@ -280,9 +280,39 @@ def test_get_frame_rice_10do(
     # Get the crown labeled frame
     crown_lf = frames.get("crown")
 
+    # Compare instances
+    for i in range(len(expected_labeled_frame.instances)):
+
+        crown_instance = crown_lf.instances[i]
+        expected_labeled_frame_instance = expected_labeled_frame.instances[i]
+
+        assert np.allclose(
+            crown_instance.numpy(),
+            expected_labeled_frame_instance.numpy(),
+            atol=1e-7,
+            equal_nan=True,
+        )
+
+        assert (
+            (crown_instance.track is None)
+            and (expected_labeled_frame_instance.track is None)
+        ) or (crown_instance.track is expected_labeled_frame_instance.track)
+
+        assert np.isclose(
+            crown_instance.score,
+            expected_labeled_frame_instance.score,
+            atol=1e-7,
+            equal_nan=True,
+        )
+        assert np.isclose(
+            crown_instance.tracking_score,
+            expected_labeled_frame_instance.tracking_score,
+            atol=1e-7,
+            equal_nan=True,
+        )
+
     # Compare the attributes of the labeled frames
     assert crown_lf.frame_idx == expected_labeled_frame.frame_idx
-    assert crown_lf.instances == expected_labeled_frame.instances
     assert crown_lf.video.filename == expected_labeled_frame.video.filename
     assert crown_lf.video.shape == expected_labeled_frame.video.shape
     assert crown_lf.video.backend == expected_labeled_frame.video.backend
@@ -307,9 +337,39 @@ def test_get_frame_rice_10do_no_video(
     # Get the crown labeled frame
     crown_lf = frames.get("crown")
 
+    # Compare instances
+    for i in range(len(expected_labeled_frame.instances)):
+
+        crown_instance = crown_lf.instances[i]
+        expected_labeled_frame_instance = expected_labeled_frame.instances[i]
+
+        assert np.allclose(
+            crown_instance.numpy(),
+            expected_labeled_frame_instance.numpy(),
+            atol=1e-7,
+            equal_nan=True,
+        )
+
+        assert (
+            (crown_instance.track is None)
+            and (expected_labeled_frame_instance.track is None)
+        ) or (crown_instance.track is expected_labeled_frame_instance.track)
+
+        assert np.isclose(
+            crown_instance.score,
+            expected_labeled_frame_instance.score,
+            atol=1e-7,
+            equal_nan=True,
+        )
+        assert np.isclose(
+            crown_instance.tracking_score,
+            expected_labeled_frame_instance.tracking_score,
+            atol=1e-7,
+            equal_nan=True,
+        )
+
     # Compare the attributes of the labeled frames
     assert crown_lf.frame_idx == expected_labeled_frame.frame_idx
-    assert crown_lf.instances == expected_labeled_frame.instances
     assert crown_lf.video.filename == expected_labeled_frame.video.filename
     assert crown_lf.video.shape == expected_labeled_frame.video.shape
     assert crown_lf.video.backend == expected_labeled_frame.video.backend