fix tests to load slp paths in Series

tests/test_angle.py

@@ -140,11 +140,16 @@ def test_get_vector_angle_from_gravity(vector, expected_angle):
 
 
 # test get_node_ind function
-def test_get_node_ind(canola_h5):
+def test_get_node_ind(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_index = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary root points
     primary_points = series.get_primary_points(frame_index)
     # Set the proximal flag to True
@@ -204,11 +209,16 @@ def test_get_node_ind_5node_proximal(pts_nan32_5node):
 
 
 # test canola get_root_angle function (base node to distal node angle)
-def test_get_root_angle_distal(canola_h5):
+def test_get_root_angle_distal(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_index = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary root points
     primary_points = series.get_primary_points(frame_index)
     # Set the proximal flag to False
@@ -221,11 +231,16 @@ def test_get_root_angle_distal(canola_h5):
 
 
 # test rice get_root_angle function (base node to proximal node angle)
-def test_get_root_angle_proximal_rice(rice_h5):
+def test_get_root_angle_proximal_rice(rice_h5, rice_main_slp, rice_long_slp):
     # Set the frame index to 0
     frame_index = 0
     # Load the series from the rice dataset
-    series = Series.load(rice_h5, primary_name="crown", lateral_name="primary")
+    series = Series.load(
+        series_name="rice_test",
+        h5_path=rice_h5,
+        primary_path=rice_long_slp,
+        crown_path=rice_main_slp,
+    )
     # Get the primary root points
     primary_points = series.get_primary_points(frame_index)
     # Set the proximal flag to True

tests/test_bases.py

@@ -215,11 +215,16 @@ def test_get_base_tip_dist_no_roots(pts_no_roots):
 
 
 # test get_base_xs with canola
-def test_get_base_xs_canola(canola_h5):
+def test_get_base_xs_canola(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame idx to 0
     frame_idx = 0
     # Load a series from a canola dataset
-    plant = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    plant = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the labeled frame
     lateral_points = plant.get_lateral_points(frame_idx)
     # Get the lateral root bases
@@ -269,11 +274,16 @@ def test_get_base_ys_no_roots(pts_no_roots):
 
 
 # test get_base_length with canola
-def test_get_base_length_canola(canola_h5):
+def test_get_base_length_canola(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_idx = 0
     # Load a series from a canola dataset
-    plant = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    plant = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the lateral points
     lateral_pts = plant.get_lateral_points(frame_idx)
     # Get the bases of the lateral roots
@@ -309,11 +319,16 @@ def test_get_base_ct_density(primary_pts, lateral_pts):
 
 
 # test get_base_ct_density function with canola example
-def test_get_base_ct_density_canola(canola_h5):
+def test_get_base_ct_density_canola(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_idx = 0
     # Load a series from a canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary and lateral points
     primary_pts = series.get_primary_points(frame_idx)
     lateral_pts = series.get_lateral_points(frame_idx)
@@ -328,11 +343,16 @@ def test_get_base_ct_density_canola(canola_h5):
 
 
 # test get_base_length_ratio with canola
-def test_get_base_length_ratio(canola_h5):
+def test_get_base_length_ratio(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_idx = 0
     # Load a series from a canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary and lateral points
     primary_pts = series.get_primary_points(frame_idx)
     lateral_pts = series.get_lateral_points(frame_idx)
@@ -350,11 +370,16 @@ def test_get_base_length_ratio(canola_h5):
     np.testing.assert_almost_equal(base_length_ratio, 0.086, decimal=3)
 
 
-def test_root_width_canola(canola_h5):
+def test_root_width_canola(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_idx = 0
     # Load a series from a canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary points
     primary_pts = series.get_primary_points(frame_idx)
     # Get the primary points with the maximum length

tests/test_convhull.py

@@ -121,11 +121,16 @@ def lateral_pts():
 
 
 # test get_convhull function using canola
-def test_get_convhull_canola(canola_h5):
+def test_get_convhull_canola(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set frame index to 0
     frame_index = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary and lateral root from the series
     primary_pts = series.get_primary_points(frame_index)
     lateral_pts = series.get_lateral_points(frame_index)
@@ -137,12 +142,19 @@ def test_get_convhull_canola(canola_h5):
     assert type(convex_hull) == ConvexHull
 
 
-# test canola model
-def test_get_convhull_features_canola(canola_h5):
+# test canola convex hull features
+def test_get_convhull_features_canola(
+    canola_h5, canola_primary_slp, canola_lateral_slp
+):
     # Set the frame index to 0
     frame_index = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary and lateral root from the series
     primary_pts = series.get_primary_points(frame_index)
     lateral_pts = series.get_lateral_points(frame_index)
@@ -163,12 +175,17 @@ def test_get_convhull_features_canola(canola_h5):
     np.testing.assert_almost_equal(max_height, 876.5622253417969, decimal=3)
 
 
-# test rice model
-def test_get_convhull_features_rice(rice_h5):
+# test rice convex hull features
+def test_get_convhull_features_rice(rice_h5, rice_long_slp, rice_main_slp):
     # Set the frame index to 0
     frame_index = 0
     # Load the series from the rice dataset
-    series = Series.load(rice_h5, primary_name="primary", crown_name="crown")
+    series = Series.load(
+        series_name="rice_test",
+        h5_path=rice_h5,
+        primary_path=rice_long_slp,
+        crown_path=rice_main_slp,
+    )
     # Get the crown root from the series
     crown_pts = series.get_crown_points(frame_index)
     # Get the convex hull from the points
@@ -221,11 +238,16 @@ def test_get_chull_perimeter(lateral_pts):
 
 
 # test get_chull_line_lengths with canola
-def test_get_chull_line_lengths(canola_h5):
+def test_get_chull_line_lengths(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_index = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary and lateral root from the series
     primary_pts = series.get_primary_points(frame_index)
     lateral_pts = series.get_lateral_points(frame_index)

tests/test_ellipse.py

@@ -11,11 +11,24 @@
 from typing import Literal
 
 
-def test_get_ellipse(canola_h5: Literal["tests/data/canola_7do/919QDUH.h5"]):
+def test_get_ellipse(
+    canola_h5: Literal["tests/data/canola_7do/919QDUH.h5"],
+    canola_primary_slp: Literal[
+        "tests/data/canola_7do/919QDUH.primary.predictions.slp"
+    ],
+    canola_lateral_slp: Literal[
+        "tests/data/canola_7do/919QDUH.lateral.predictions.slp"
+    ],
+):
     # Set the frame index = 0
     frame_index = 0
     # Load the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     primary_pts = series.get_primary_points(frame_index)
     # only test ellipse for primary root points
     a, b, ratio = fit_ellipse(primary_pts)
@@ -34,11 +47,24 @@ def test_get_ellipse(canola_h5: Literal["tests/data/canola_7do/919QDUH.h5"]):
     assert np.isnan(ratio)
 
 
-def test_get_ellipse_all_points(canola_h5: Literal["tests/data/canola_7do/919QDUH.h5"]):
+def test_get_ellipse_all_points(
+    canola_h5: Literal["tests/data/canola_7do/919QDUH.h5"],
+    canola_primary_slp: Literal[
+        "tests/data/canola_7do/919QDUH.primary.predictions.slp"
+    ],
+    canola_lateral_slp: Literal[
+        "tests/data/canola_7do/919QDUH.lateral.predictions.slp"
+    ],
+):
     # Set the frame index = 0
     frame_index = 0
     # Load the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     primary_pts = series.get_primary_points(frame_index)
     primary_max_length_pts = get_max_length_pts(primary_pts)
     lateral_pts = series.get_lateral_points(frame_index)

tests/test_lengths.py

@@ -171,11 +171,16 @@ def test_min_distance_line_to_line():
 
 
 # tests for get_curve_index function
-def test_get_curve_index_canola(canola_h5):
+def test_get_curve_index_canola(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_idx = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary points from the first frame
     primary_pts = series.get_primary_points(frame_idx)
     # Get the points from the root with maximum length
@@ -310,11 +315,16 @@ def test_curve_index_mixed_invalid():
     )
 
 
-def test_get_root_lengths(canola_h5):
+def test_get_root_lengths(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_idx = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary points from the first frame
     primary_pts = series.get_primary_points(frame_idx)
     assert primary_pts.shape == (1, 6, 2)
@@ -347,11 +357,16 @@ def test_get_root_lengths_one_point(pts_one_base):
     )
 
 
-def test_get_max_length_pts(canola_h5):
+def test_get_max_length_pts(canola_h5, canola_primary_slp, canola_lateral_slp):
     # Set the frame index to 0
     frame_idx = 0
     # Load the series from the canola dataset
-    series = Series.load(canola_h5, primary_name="primary", lateral_name="lateral")
+    series = Series.load(
+        series_name="canola_test",
+        h5_path=canola_h5,
+        primary_path=canola_primary_slp,
+        lateral_path=canola_lateral_slp,
+    )
     # Get the primary points from the first frame
     primary_pts = series.get_primary_points(frame_idx)
     # Get the points from the root with maximum length