refactor: added swc run length to results csv

Author: anna-grim

demo/demo.py

@@ -20,7 +20,7 @@ def main():
     """
     # Initializations
     pred_labels = TiffReader(pred_labels_path, swap_axes=False)
-    skeleton_metric = evaluate(
+    evaluate(
         groundtruth_pointer,
         pred_labels,
         output_dir,

demo/results.csv

@@ -1,12 +1,12 @@
-# Splits,# Merges,% Split Edges,% Omit Edges,% Merged Edges,ERL,Normalized ERL,Edge Accuracy,Split Rate,Merge Rate
-0.0,,0.0,0.0,0.0,84.08,1.0,100.0,,
-0.0,,0.0,0.0,0.0,163.37,1.0,100.0,,
-1.0,,0.9803921568627451,0.9803921568627451,0.0,40.27,0.1873,98.04,62.82,
-1.0,,0.8264462809917356,5.785123966942149,0.0,146.36,0.5744,93.39,224.52,
-3.0,,2.830188679245283,0.0,0.0,45.66,0.1984,97.17,51.2,
-1.0,,1.9230769230769231,1.9230769230769231,0.0,30.3,0.286,96.15,51.19,
-0.0,,0.0,0.0,0.0,106.57,1.0,100.0,,
-5.0,,1.3651877133105803,2.3890784982935154,0.0,293.17,0.4627,96.25,103.53,
-14.0,,1.3123359580052494,0.7874015748031497,0.0,217.71,0.1407,97.9,92.8,
-2.0,,0.9009009009009009,4.504504504504505,0.0,116.9,0.5144,94.59,105.19,
-0.0,,0.0,0.0,0.0,80.18,1.0,100.0,,
+,SWC Run Length,# Splits,# Merges,% Split Edges,% Omit Edges,% Merged Edges,ERL,Normalized ERL,Edge Accuracy,Split Rate,Merge Rate
+SNT_Data-002,84.0837616185713,0.0,,0.0,0.0,0.0,84.08,1.0,100.0,,
+SNT_Data-035,163.37074041968341,0.0,,0.0,0.0,0.0,163.37,1.0,100.0,,
+SNT_Data-037,214.98055903143316,1.0,,0.9803921568627451,0.9803921568627451,0.0,40.27,0.1873,98.04,62.82,
+SNT_Data-038,254.78664303157612,1.0,,0.8264462809917356,5.785123966942149,0.0,146.36,0.5744,93.39,224.52,
+SNT_Data-041,230.16780853555437,3.0,,2.830188679245283,0.0,0.0,45.66,0.1984,97.17,51.2,
+SNT_Data-043,105.95635789438495,1.0,,1.9230769230769231,1.9230769230769231,0.0,30.3,0.286,96.15,51.19,
+SNT_Data-051,106.56843799568803,0.0,,0.0,0.0,0.0,106.57,1.0,100.0,,
+SNT_Data-052,633.5729425811579,5.0,,1.3651877133105803,2.3890784982935154,0.0,293.17,0.4627,96.25,103.53,
+SNT_Data-053,1547.4466172913558,14.0,,1.3123359580052494,0.7874015748031497,0.0,217.71,0.1407,97.9,92.8,
+SNT_Data-062,227.24329460444093,2.0,,0.9009009009009009,4.504504504504505,0.0,116.9,0.5144,94.59,105.19,
+SNT_Data-074,80.17991450259146,0.0,,0.0,0.0,0.0,80.18,1.0,100.0,,

src/segmentation_skeleton_metrics/evaluate.py

@@ -80,26 +80,24 @@ def evaluate(
     fragment_graphs = dataloader.load_fragments(fragments_pointer, gt_graphs)
 
     # Run evaluation
-    evaluator = Evaluator(output_dir, save_merges, save_fragments, verbose)
+    evaluator = Evaluator(output_dir, results_filename, verbose)
     evaluator.run(gt_graphs, fragment_graphs)
 
+    # Optional saves
+    if save_merges:
+        evaluator.save_merge_results()
+
+    if save_fragments and fragment_graphs:
+        evaluator.save_fragments(gt_graphs, fragment_graphs)
+
 
 # --- Evaluator ---
 class Evaluator:
 
-    def __init__(
-        self,
-        output_dir,
-        results_filename,
-        save_merges,
-        save_fragments,
-        verbose=True
-    ):
+    def __init__(self, output_dir, results_filename, verbose=True):
         # Instance attributes
         self.output_dir = output_dir
         self.results_filename = results_filename
-        self.save_merges = save_merges
-        self.save_fragments = save_fragments
         self.verbose = verbose
 
         # Set core metrics
@@ -131,9 +129,9 @@ def run(self, gt_graphs, fragment_graphs=None):
         for name, metric in self.metrics.items():
             if name == "# Merges" and fragment_graphs:
                 results[name] = metric.compute(gt_graphs, fragment_graphs)
+                print(results[name])
             elif name != "# Merges":
                 results.update(metric.compute(gt_graphs))
-        print(results["# Merges"])
 
         # Compute derived metrics
         for name, metric in self.derived_metrics.items():
@@ -144,27 +142,30 @@ def run(self, gt_graphs, fragment_graphs=None):
 
         # Save report
         path = f"{self.output_dir}/{self.results_filename}.csv"
-        results.to_csv(path, index=False)
+        results.to_csv(path, index=True)
         self.report_summary(results)
 
-        # Optional saves
-        if self.save_merges:
-            self.save_merge_results()
-
-        if self.save_fragments and fragment_graphs:
-            self.save_intersecting_fragments(gt_graphs, fragment_graphs)
-
     def init_results(self, gt_graphs):
-        cols = list(self.metrics.keys()) + list(self.derived_metrics.keys())
+        # Create dataframe
+        cols = (
+            ["SWC Run Length"] +
+            list(self.metrics.keys()) +
+            list(self.derived_metrics.keys())
+        )
         index = list(gt_graphs.keys())
         index.sort()
-        return pd.DataFrame(np.nan, index=index, columns=cols)
+        results = pd.DataFrame(np.nan, index=index, columns=cols)
+
+        # Populate SWC Run Length column
+        for key, graph in gt_graphs.items():
+            results.loc[key, "SWC Run Length"] = graph.run_length
+        return results
 
     def report_summary(self, results):
         pass
 
     # --- Writers ---
-    def save_intersecting_fragments(self):
+    def save_fragments(self):
         pass
 
     def save_merge_results(self, gt_graphs, fragment_graphs, output_dir):