Refactor merge detection (#156)

* refactor: dataloading

* refactor: dataloading

* major refactor

* refactor: added swc run length to results csv

---------

Co-authored-by: anna-grim <[email protected]>

Author: anna-grim

demo/results-overview.txt

@@ -1,8 +1,8 @@
 Average Results...
-  # Splits: 7.9680
+  # Splits: 7.2780
   # Merges: 0.0000
-  Split Rate: 114.6940
-  Merge Rate: 0.0000
+  Split Rate: 124.3079
+  Merge Rate: nan
   % Split Edges: 1.1996
   % Omit Edges: 4.5086
   % Merged Edges: 0.0000
@@ -11,20 +11,5 @@ Average Results...
   Normalized ERL: 0.3949
 
 Total Results...
-  # Splits: 31
-  # Merges: 0
-Average Results...
-  # Splits: 7.9680
-  # Merges: 0.0000
-  Split Rate: 114.6940
-  Merge Rate: 0.0000
-  % Split Edges: 1.1996
-  % Omit Edges: 4.5086
-  % Merged Edges: 0.0000
-  Edge Accuracy: 95.4914
-  ERL: 180.8849
-  Normalized ERL: 0.3949
-
-Total Results...
-  # Splits: 31
+  # Splits: 27
   # Merges: 0

demo/results.csv

@@ -1,12 +1,12 @@
-,# Splits,# Merges,Split Rate,Merge Rate,% Split Edges,% Omit Edges,% Merged Edges,Edge Accuracy,ERL,Normalized ERL,GT Run Length
-SNT_Data-002,0,,84.08376161857129,,0.0,0.0,0.0,100.0,84.08,1.0,84.08
-SNT_Data-035,0,,163.37074041968347,,0.0,0.0,0.0,100.0,163.37,1.0,163.37
-SNT_Data-037,1,,211.9805590314331,,0.98,1.96,0.0,98.04,184.57,0.8585,214.98
-SNT_Data-038,1,,251.78664303157595,,0.83,1.65,0.0,98.35,144.38,0.5667,254.79
-SNT_Data-041,4,,55.46881994891758,,2.83,7.55,0.0,92.45,52.62,0.2286,230.17
-SNT_Data-043,2,,46.354813254114404,,1.92,9.62,0.0,90.38,35.32,0.3334,105.96
-SNT_Data-051,0,,106.56843799568803,,0.0,0.0,0.0,100.0,106.57,1.0,106.57
-SNT_Data-052,6,,99.17738848187402,,1.37,6.48,0.0,93.52,265.1,0.4184,633.57
-SNT_Data-053,15,,98.7153068880868,,1.31,4.46,0.0,95.54,207.79,0.1343,1547.45
-SNT_Data-062,2,,105.1897956496423,,0.9,8.11,0.0,91.89,116.9,0.5144,227.24
-SNT_Data-074,0,,80.17991450259146,,0.0,0.0,0.0,100.0,80.18,1.0,80.18
+,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,,

pyproject.toml

@@ -25,7 +25,6 @@ dependencies = [
     "scikit-image",
     "tensorstore",
     "tifffile",
-    "xlwt",
     "zarr",
 ]
 

src/segmentation_skeleton_metrics/evaluate.py

@@ -141,14 +141,24 @@ 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)
 
     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