Simple-Track 2.2.0__tar.gz → 2.2.1__tar.gz

{simple_track-2.2.0 → simple_track-2.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Simple-Track
-Version: 2.2.0
+Version: 2.2.1
 Summary: Threshold-based object tracking algorithm for 2D data 
 Author-email: Adam Gainford <adam.gainford@reading.ac.uk>, Thorwald Stein <t.h.m.stein@reading.ac.uk>
 License-Expression: MPL-2.0

{simple_track-2.2.0 → simple_track-2.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "Simple-Track"
-version = "2.2.0"
+version = "2.2.1"
 authors = [
   { name="Adam Gainford", email="adam.gainford@reading.ac.uk" },
   { name="Thorwald Stein", email="t.h.m.stein@reading.ac.uk"} 
@@ -43,4 +43,4 @@ testpaths = ["tests"]
 
 [tool.ruff.lint]
 select = ["E", "F", "B", "I", "UP", "SIM", "D101"]
-ignore = ["SIM102"]
+ignore = ["SIM102"]

{simple_track-2.2.0 → simple_track-2.2.1}/src/Simple_Track.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Simple-Track
-Version: 2.2.0
+Version: 2.2.1
 Summary: Threshold-based object tracking algorithm for 2D data 
 Author-email: Adam Gainford <adam.gainford@reading.ac.uk>, Thorwald Stein <t.h.m.stein@reading.ac.uk>
 License-Expression: MPL-2.0

{simple_track-2.2.0 → simple_track-2.2.1}/src/simpletrack/feature.py

@@ -311,11 +311,12 @@ class Feature:
 
         # Reverse eigenvectors to be in (y,x) format, consistent with rest of package
         # Native converts from numpy type to python type
+        # Real ensures types are not complex, which can happen with PCA decomposition
         return (
-            native(major_unit_vector[::-1]),
-            native(minor_unit_vector[::-1]),
-            native(major_diameter / 2),
-            native(minor_diameter / 2),
+            native(np.real(major_unit_vector[::-1])),
+            native(np.real(minor_unit_vector[::-1])),
+            native(np.real(major_diameter / 2)),
+            native(np.real(minor_diameter / 2)),
         )
 
     def calculate_centroid(self) -> tuple:

{simple_track-2.2.0 → simple_track-2.2.1}/src/simpletrack/frame_tracker.py

@@ -768,13 +768,13 @@ class FrameTracker:
         # Set the first value of the hist to 0 since this represents the background
         overlap_hist[0] = 0
 
-        # Normalise overlap histogram by size of each feature in advected field only
-        norm_sizes = np.array(
-            [
-                np.count_nonzero(advected_feature_field == idx)
-                for idx in range(len(overlap_hist))
-            ]
-        )
+        # Normalise overlap histogram by size of each feature in advected field only.
+        # bincount computes all per-id pixel counts in a single pass; the previous
+        # per-id np.count_nonzero loop was O(max_id * domain) and dominated runtime
+        # for long sequences (feature_field holds persistent ids, which grow large).
+        norm_sizes = np.bincount(
+            advected_feature_field.ravel(), minlength=len(overlap_hist)
+        )[: len(overlap_hist)]
         # Replace any zero sizes with 1 to avoid division by zero
         norm_sizes = np.where(norm_sizes == 0, 1, norm_sizes)
         overlap_normed = overlap_hist / norm_sizes

{simple_track-2.2.0 → simple_track-2.2.1}/src/simpletrack/track.py

@@ -152,8 +152,15 @@ class Tracker:
 
             # Now run flow solver between previous and current frame
             prev_frame = self.timeline.get_previous_frame(frame.time)
-            # Set max id for assigning to new features
-            frame.max_id = prev_frame.max_id
+            # Set max id for assigning to new features.
+            # An all-quiet first frame leaves prev_frame.max_id None
+            # (identify_features returns early without setting it when no
+            # features are above threshold). Skip the carry-forward then;
+            # get_next_available_feature_id lazily initialises max_id from the
+            # frame's own feature_field, and there are no earlier ids to collide
+            # with.
+            if prev_frame.max_id is not None:
+                frame.max_id = prev_frame.max_id
             # Get the flow field that translates features between the two frames
             y_flow, x_flow = self.flow_solver.analyse_flow(prev_frame, frame)
 

{simple_track-2.2.0 → simple_track-2.2.1}/tests/test_flow_solver.py

@@ -573,7 +573,9 @@ def test_multiple_unequal_feature_unequal_flow_advection(
 @pytest.mark.parametrize(
     "test_dy_f0, test_dx_f0, test_dy_f1, test_dx_f1, f1_y_growth, expected_dy, expected_dx",
     [
-        [10, 0, 0, 0, 7, 7, 0],  # F0 advects, F1 grows by 7 -> expected dy = 7 (?)
+        # First test shows inconsistent behaviour between different architectures (Linux vs MacOS), needs further refinement
+        # [10, 0, 0, 0, 7, 7, 0],  # F0 advects, F1 grows by 7 -> expected dy = 7 (?)
+        # All other tests do not show the expected outcome on any architecture.
         # [10, 0, 10, 0, 7, 17, 0],  # F1 grows by 7 advects by 10, should get dy = 17, get 0
         # [0, 0, 0, 5, 7, 7, 5], # F1 grows by 7 and dx=5, expect dy=7 and dx=5. get dy=0
         # [0, 0, 5, 5, 7, 12, 5],  # Expect dy=12, get 0
@@ -621,7 +623,8 @@ def test_growing_feature(
         [10, 0, 15, 0, 10, 10, 0],  # F1 advects 15 but shrinks 10. Expect dy=10 from f0
         [0, 10, 0, 15, 5, 0, 10],  # Similar behaviour if just dx rather than just dy
         [10, 10, 15, 15, 5, 10, 10],  # Also works if features move in diagonal
-        [0, 0, 10, 10, 5, 0, 0],  # If f0 is stationary but f1 moves, solver picks f0
+        # Inconsistent behaviour between different architectures (Linux vs MacOS), needs further refinement
+        # [0, 0, 10, 10, 5, 0, 0],  # If f0 is stationary but f1 moves, solver picks f0
         [10, 10, 0, 0, 5, 10, 10],  # If f0 moves and f1 is stationary, solver picks f0
     ],
 )

{simple_track-2.2.0 → simple_track-2.2.1}/tests/test_frame_tracker.py

@@ -446,7 +446,8 @@ def test_overlap_histogram_with_multiple_overlaps_and_different_labels(
         ],
         [np.zeros((10), dtype=int), np.zeros((10), dtype=int), 1, 0, ArrayShapeError],
         [np.zeros((5, 10), dtype=int), zero_arr, 1, 0, ArrayShapeError],
-        [np.zeros((10, 10), dtype=float), np.zeros((10, 10)), 1, 0, ArrayTypeError],
+        # This test should pass now that check_arrays converts to int type if values don't change
+        # [np.zeros((10, 10), dtype=float), np.zeros((10, 10)), 1, 0, ArrayTypeError],
         [zero_arr, zero_arr, -1, 0, NegativeIDError],
         [zero_arr, zero_arr, 1.5, 0, FloatIDError],
         [zero_arr, zero_arr, 0, 0, ZeroIDError],