feat: log results overview

Author: anna-grim

demo/pred_labels.tif demo/data/pred_labels.tifdemo/pred_labels.tif renamed to demo/data/pred_labels.tif

@@ -29,23 +29,22 @@ def evaluate():
 
     """
     # Initializations
-    path = f"{output_dir}/results.xls"
     pred_labels = TiffReader(pred_labels_path)
     skeleton_metric = SkeletonMetric(
         groundtruth_pointer,
         pred_labels,
         fragments_pointer=fragments_pointer,
         output_dir=output_dir,
     )
-    full_results, avg_results = skeleton_metric.run(path)
+    skeleton_metric.run(output_dir)
 
 
 if __name__ == "__main__":
     # Initializations
     output_dir = "./"
-    pred_labels_path = "./pred_labels.tif"
-    fragments_pointer = "./pred_swcs.zip"
-    groundtruth_pointer = "./target_swcs.zip"
+    pred_labels_path = "./data/pred_labels.tif"
+    fragments_pointer = "./data/pred_swcs.zip"
+    groundtruth_pointer = "./data/target_swcs.zip"
 
     # Run
     evaluate()

demo/pred_swcs.zip demo/data/pred_swcs.zipdemo/pred_swcs.zip renamed to demo/data/pred_swcs.zip

@@ -0,0 +1 @@
+ Label   -   Physical Coordinate

demo/target_swcs.zip demo/data/target_swcs.zipdemo/target_swcs.zip renamed to demo/data/target_swcs.zip

@@ -0,0 +1,13 @@
+Average Results...
+   # splits: 7.6878
+   # merges: 0.0
+   % omit: 0.0514
+   % split: 0.0158
+   % merged: 0.0
+   edge accuracy: 0.9486
+   erl: 173.2351
+   normalized erl: 0.3895
+
+Total Results...
+# splits: 36
+# merges: 0

demo/demo.py

@@ -59,10 +59,10 @@ def __init__(
         self,
         gt_pointer,
         label_mask,
+        output_dir,
         anisotropy=(1.0, 1.0, 1.0),
         connections_path=None,
         fragments_pointer=None,
-        output_dir=None,
         preexisting_merges=None,
         save_merges=False,
         valid_labels=None,
@@ -79,6 +79,8 @@ def __init__(
             coordinates.
         label_mask : ImageReader
             Predicted segmentation mask.
+         output_dir : str
+            Path to directory wehere results are written.
         anisotropy : Tuple[float], optional
             Image to physical coordinate scaling factors applied to SWC files
             stored at "fragments_pointer". The default is (1.0, 1.0, 1.0).
@@ -90,8 +92,6 @@ def __init__(
             "swc_util.Reader" for documentation. Notes: (1) "anisotropy" is
             applied to these SWC files and (2) these SWC files are required
             for counting merges. The default is None.
-        output_dir : str, optional
-            Path to directory wehere results are written. The default is None.
         preexisting_merges : List[int], optional
             List of segment IDs that are known to contain a merge mistake. The
             default is None.
@@ -346,29 +346,28 @@ def init_zip_writer(self):
 
         """
         # Initialize output directory
-        output_dir = os.path.join(self.output_dir, "projections")
-        util.mkdir(output_dir)
+        projections_dir = os.path.join(self.output_dir, "projections")
+        util.mkdir(projections_dir)
 
         # Save intial graphs
         self.zip_writer = dict()
         for key in self.graphs.keys():
-            self.zip_writer[key] = ZipFile(f"{output_dir}/{key}.zip", "w")
+            zip_path = f"{projections_dir}/{key}.zip"
+            self.zip_writer[key] = ZipFile(zip_path, "w")
             self.graphs[key].to_zipped_swc(self.zip_writer[key])
 
     # -- Main Routine --
-    def run(self, path=None):
+    def run(self):
         """
         Computes skeleton-based metrics.
 
         Parameters
         ----------
-        path : str, optional
-            Path where the results will be saved. The default is None.
+        None
 
         Returns
         -------
-        tuple
-            ...
+        None
 
         """
         print("\n(3) Evaluation")
@@ -381,21 +380,23 @@ def run(self, path=None):
         self.detect_merges()
         self.quantify_merges()
 
-        # Report results
+        # Compute metrics
         full_results, avg_results = self.compile_results()
-        print(f"\nAverage Results...")
-        for key in avg_results.keys():
-            print(f"   {key}: {round(avg_results[key], 4)}")
 
-        print(f"\nTotal Results...")
-        print("# splits:", self.count_total_splits())
-        print("# merges:", self.count_total_merges())
+        # Report full results
+        prefix = "corrected-" if self.connections_path else ""
+        path = f"{self.output_dir}/{prefix}results.xls"
+        util.save_results(path, full_results)
 
-        # Save results (if applicable)
-        if path:
-            util.save_results(path, full_results)
+        # Report results overview
+        path = os.path.join(self.output_dir, f"{prefix}results-overview.txt")
+        util.update_txt(path, "Average Results...")
+        for key in avg_results.keys():
+            util.update_txt(path, f"   {key}: {round(avg_results[key], 4)}")
 
-        return full_results, avg_results
+        util.update_txt(path, "\nTotal Results...")
+        util.update_txt(path, f"   # splits: {self.count_total_splits()}")
+        util.update_txt(path, f"   # merges: {self.count_total_merges()}")
 
     # -- Split Detection --
     def detect_splits(self):
@@ -695,7 +696,7 @@ def save_merged_labels(self):
         """
         # Save detected merges
         prefix = "corrected_" if self.connections_path else ""
-        filename = f"merged_{prefix}_segment_ids.txt"
+        filename = f"merged_{prefix}segment_ids.txt"
         with open(os.path.join(self.output_dir, filename), "w") as f:
             f.write(f" Label   -   Physical Coordinate\n")
             for _, label, xyz in self.merged_labels:

demo/evaluation_results.xls

@@ -148,6 +148,27 @@ def read_txt(path):
         return f.read().splitlines()
 
 
+def update_txt(path, text):
+    """
+    Appends the given text to a specified text file and prints the text.
+
+    Parameters
+    ----------
+    path : str
+        Path to txt file where the text will be appended.
+    text : str
+        Text to be written to the file.
+
+    Returns
+    -------
+    None
+
+    """
+    print(text)
+    with open(path, 'a') as file:
+        file.write(text + "\n")
+
+
 # --- Miscellaneous ---
 def get_segment_id(filename):
     """