Merge pull request #376 from w-k-jones/add_predictive_tracking_pbc

Uncomment `dist_func` parameter to enable PBCs with predictive tracking

Author: w-k-jones

tobac/tests/test_tracking.py

@@ -650,3 +650,74 @@ def test_time_cell_min(
             np.sum(all_feats_tracked_drop_no_cells["orig_cell_num"] == i)
             == expected_val
         )
+
+
+def test_trackpy_predict_PBC():
+    """Test if predictive tracking with PBCs works correctly"""
+
+    test_features = pd.DataFrame(
+        {
+            "feature": [1, 2, 3, 4, 5, 6, 7, 8],
+            "hdim_1": [85, 15, 95, 5, 5, 95, 15, 85],
+            "hdim_2": [50, 45, 50, 45, 50, 45, 50, 45],
+            "frame": [0, 0, 1, 1, 2, 2, 3, 3],
+            "time": [
+                datetime.datetime(2000, 1, 1),
+                datetime.datetime(2000, 1, 1),
+                datetime.datetime(2000, 1, 1, 0, 5),
+                datetime.datetime(2000, 1, 1, 0, 5),
+                datetime.datetime(2000, 1, 1, 0, 10),
+                datetime.datetime(2000, 1, 1, 0, 10),
+                datetime.datetime(2000, 1, 1, 0, 15),
+                datetime.datetime(2000, 1, 1, 0, 15),
+            ],
+        }
+    )
+
+    output_random_no_pbc = tobac.linking_trackpy(
+        test_features, None, 1, 1, d_max=10, method_linking="random"
+    )
+
+    # Assert cell does not cross border
+    assert output_random_no_pbc["cell"].tolist() == [1, 2, 1, 2, 2, 1, 2, 1]
+
+    output_random_pbc = tobac.linking_trackpy(
+        test_features,
+        None,
+        1,
+        1,
+        d_max=10,
+        method_linking="random",
+        PBC_flag="hdim_1",
+        min_h1=0,
+        max_h1=100,
+        min_h2=0,
+        max_h2=100,
+    )
+
+    # Assert cell does not cross border even with PBC because of random tracking
+    assert output_random_pbc["cell"].tolist() == [1, 2, 1, 2, 2, 1, 2, 1]
+
+    output_predict_no_pbc = tobac.linking_trackpy(
+        test_features, None, 1, 1, d_max=10, method_linking="predict"
+    )
+
+    # Assert that without PBCs predictive tracking creates 4 cells because the d_max criteria is too small
+    assert output_predict_no_pbc["cell"].tolist() == [1, 2, 1, 2, 3, 4, 3, 4]
+
+    output_predict_pbc = tobac.linking_trackpy(
+        test_features,
+        None,
+        1,
+        1,
+        d_max=10,
+        method_linking="predict",
+        PBC_flag="hdim_1",
+        min_h1=0,
+        max_h1=100,
+        min_h2=0,
+        max_h2=100,
+    )
+
+    # Assert with PBCs and prdictive tracking the cells should cross the border
+    assert output_predict_pbc["cell"].tolist() == [1, 2, 1, 2, 1, 2, 1, 2]

tobac/tracking.py

@@ -385,7 +385,7 @@ def linking_trackpy(
             link_strategy="auto",
             adaptive_step=adaptive_step,
             adaptive_stop=adaptive_stop,
-            # dist_func=dist_func
+            dist_func=dist_func
             #                                 copy_features=False, diagnostics=False,
             #                                 hash_size=None, box_size=None, verify_integrity=True,
             #                                 retain_index=False