Merge pull request #155 from Janelia-Trackathon-2023/bugfix_frame_buffer

Fix frame buffer bug where predecessors were not checked properly

src/traccuracy/track_errors/divisions.py

@@ -174,6 +174,9 @@ def _correct_shifted_divisions(matched_data: Matched, n_frames=1):
     fp_divs = g_pred.get_nodes_with_flag(NodeFlag.FP_DIV)
     fn_divs = g_gt.get_nodes_with_flag(NodeFlag.FN_DIV)
 
+    gt_to_pred_dict = dict(mapper)
+    pred_to_gt_dict = {pred: gt for (gt, pred) in mapper}
+
     # Compare all pairs of fp and fn
     for fp_node, fn_node in itertools.product(fp_divs, fn_divs):
         correct = False
@@ -199,7 +202,10 @@ def _correct_shifted_divisions(matched_data: Matched, n_frames=1):
                 for node in g_pred.graph.successors(fp_node)
             ]
             fn_succ = g_gt.graph.successors(fn_node)
-            if Counter(fp_succ) != Counter(fn_succ):
+            fn_succ_mapped = [
+                gt_to_pred_dict[fn] for fn in fn_succ if fn in gt_to_pred_dict
+            ]
+            if Counter(fp_succ) != Counter(fn_succ_mapped):
                 # Daughters don't match so division cannot match
                 continue
 
@@ -220,7 +226,11 @@ def _correct_shifted_divisions(matched_data: Matched, n_frames=1):
                 for node in g_gt.graph.successors(fn_node)
             ]
             fp_succ = g_pred.graph.successors(fp_node)
-            if Counter(fp_succ) != Counter(fn_succ):
+
+            fp_succ_mapped = [
+                pred_to_gt_dict[fp] for fp in fp_succ if fp in pred_to_gt_dict
+            ]
+            if Counter(fp_succ_mapped) != Counter(fn_succ):
                 # Daughters don't match so division cannot match
                 continue
 

tests/metrics/test_divisions.py

@@ -6,7 +6,8 @@
 
 
 def test_DivisionMetrics():
-    g_gt, g_pred, mapper = get_division_graphs()
+    g_gt, g_pred, map_gt, map_pred = get_division_graphs()
+    mapper = list(zip(map_gt, map_pred))
     matched = Matched(
         TrackingGraph(g_gt),
         TrackingGraph(g_pred),

tests/test_utils.py

@@ -116,9 +116,9 @@ def get_division_graphs():
     1_0 -- 1_1 -- 1_2 -- 1_3 -<
                                 3_4
     G2
-                  2_2 -- 2_3 -- 2_4
-    1_0 -- 1_1 -<
-                  3_2 -- 3_3 -- 3_4
+                  5_2 -- 5_3 -- 5_4
+    4_0 -- 4_1 -<
+                  6_2 -- 6_3 -- 6_4
     """
 
     G1 = nx.DiGraph()
@@ -134,21 +134,22 @@ def get_division_graphs():
     nx.set_node_attributes(G1, attrs)
 
     G2 = nx.DiGraph()
-    G2.add_edge("1_0", "1_1")
-    # Divide to generate 2 lineage
-    G2.add_edge("1_1", "2_2")
-    G2.add_edge("2_2", "2_3")
-    G2.add_edge("2_3", "2_4")
-    # Divide to generate 3 lineage
-    G2.add_edge("1_1", "3_2")
-    G2.add_edge("3_2", "3_3")
-    G2.add_edge("3_3", "3_4")
+    G2.add_edge("4_0", "4_1")
+    # Divide to generate 5 lineage
+    G2.add_edge("4_1", "5_2")
+    G2.add_edge("5_2", "5_3")
+    G2.add_edge("5_3", "5_4")
+    # Divide to generate 6 lineage
+    G2.add_edge("4_1", "6_2")
+    G2.add_edge("6_2", "6_3")
+    G2.add_edge("6_3", "6_4")
 
     attrs = {}
     for node in G2.nodes:
         attrs[node] = {"t": int(node[-1:]), "x": 0, "y": 0}
     nx.set_node_attributes(G2, attrs)
 
-    mapper = [("1_0", "1_0"), ("1_1", "1_1"), ("2_4", "2_4"), ("3_4", "3_4")]
+    mapped_g1 = ["1_0", "1_1", "2_4", "3_4"]
+    mapped_g2 = ["4_0", "4_1", "5_4", "6_4"]
 
-    return G1, G2, mapper
+    return G1, G2, mapped_g1, mapped_g2

tests/track_errors/test_divisions.py

@@ -138,18 +138,18 @@ def test__get_pred_by_t(straight_graph):
 
 
 def test__get_succ_by_t():
-    _, g2, _ = get_division_graphs()
+    _, g2, _, _ = get_division_graphs()
     g2 = TrackingGraph(g2)
 
     # Find 2 frames forward correctly
-    start_node = "2_2"
+    start_node = "5_2"
     delta_t = 2
-    end_node = "2_4"
+    end_node = "5_4"
     node = _get_succ_by_t(g2, start_node, delta_t)
     assert node == end_node
 
     # 3 frames forward returns None
-    start_node = "2_2"
+    start_node = "5_2"
     delta_t = 3
     end_node = None
     node = _get_succ_by_t(g2, start_node, delta_t)
@@ -159,8 +159,9 @@ def test__get_succ_by_t():
 class Test_correct_shifted_divisions:
     def test_no_change(self):
         # Early division in gt
-        g_pred, g_gt, mapper = get_division_graphs()
-        g_gt.nodes["1_1"][NodeFlag.FN_DIV] = True
+        g_pred, g_gt, map_pred, map_gt = get_division_graphs()
+        mapper = list(zip(map_gt, map_pred))
+        g_gt.nodes["4_1"][NodeFlag.FN_DIV] = True
         g_pred.nodes["1_3"][NodeFlag.FP_DIV] = True
 
         matched_data = Matched(TrackingGraph(g_gt), TrackingGraph(g_pred), mapper)
@@ -171,13 +172,14 @@ def test_no_change(self):
         ng_gt = new_matched.gt_graph
 
         assert ng_pred.nodes["1_3"][NodeFlag.FP_DIV] is True
-        assert ng_gt.nodes["1_1"][NodeFlag.FN_DIV] is True
+        assert ng_gt.nodes["4_1"][NodeFlag.FN_DIV] is True
         assert len(ng_gt.get_nodes_with_flag(NodeFlag.TP_DIV)) == 0
 
     def test_fn_early(self):
         # Early division in gt
-        g_pred, g_gt, mapper = get_division_graphs()
-        g_gt.nodes["1_1"][NodeFlag.FN_DIV] = True
+        g_pred, g_gt, map_pred, map_gt = get_division_graphs()
+        mapper = list(zip(map_gt, map_pred))
+        g_gt.nodes["4_1"][NodeFlag.FN_DIV] = True
         g_pred.nodes["1_3"][NodeFlag.FP_DIV] = True
 
         matched_data = Matched(TrackingGraph(g_gt), TrackingGraph(g_pred), mapper)
@@ -188,14 +190,15 @@ def test_fn_early(self):
         ng_gt = new_matched.gt_graph
 
         assert ng_pred.nodes["1_3"][NodeFlag.FP_DIV] is False
-        assert ng_gt.nodes["1_1"][NodeFlag.FN_DIV] is False
+        assert ng_gt.nodes["4_1"][NodeFlag.FN_DIV] is False
         assert ng_pred.nodes["1_3"][NodeFlag.TP_DIV] is True
-        assert ng_gt.nodes["1_1"][NodeFlag.TP_DIV] is True
+        assert ng_gt.nodes["4_1"][NodeFlag.TP_DIV] is True
 
     def test_fp_early(self):
         # Early division in pred
-        g_gt, g_pred, mapper = get_division_graphs()
-        g_pred.nodes["1_1"][NodeFlag.FP_DIV] = True
+        g_gt, g_pred, map_gt, map_pred = get_division_graphs()
+        mapper = list(zip(map_gt, map_pred))
+        g_pred.nodes["4_1"][NodeFlag.FP_DIV] = True
         g_gt.nodes["1_3"][NodeFlag.FN_DIV] = True
 
         matched_data = Matched(TrackingGraph(g_gt), TrackingGraph(g_pred), mapper)
@@ -205,14 +208,15 @@ def test_fp_early(self):
         ng_pred = new_matched.pred_graph
         ng_gt = new_matched.gt_graph
 
-        assert ng_pred.nodes["1_1"][NodeFlag.FP_DIV] is False
+        assert ng_pred.nodes["4_1"][NodeFlag.FP_DIV] is False
         assert ng_gt.nodes["1_3"][NodeFlag.FN_DIV] is False
-        assert ng_pred.nodes["1_1"][NodeFlag.TP_DIV] is True
+        assert ng_pred.nodes["4_1"][NodeFlag.TP_DIV] is True
         assert ng_gt.nodes["1_3"][NodeFlag.TP_DIV] is True
 
 
 def test_evaluate_division_events():
-    g_gt, g_pred, mapper = get_division_graphs()
+    g_gt, g_pred, map_gt, map_pred = get_division_graphs()
+    mapper = list(zip(map_gt, map_pred))
     frame_buffer = 2
 
     matched_data = Matched(TrackingGraph(g_gt), TrackingGraph(g_pred), mapper)