refactor: minor update (#172)

Co-authored-by: anna-grim <anna.grim@alleninstitute.org>

Author: anna-grim

src/segmentation_skeleton_metrics/data_handling/swc_loading.py

@@ -201,8 +201,8 @@ def read_from_zips(self, zip_dir):
         with ProcessPoolExecutor() as executor:
             # Assign threads
             processes = list()
-            for f in zip_names:
-                zip_path = os.path.join(zip_dir, f)
+            for name in zip_names:
+                zip_path = os.path.join(zip_dir, name)
                 processes.append(executor.submit(self.read_from_zip, zip_path))
 
             # Store results
@@ -323,10 +323,6 @@ def read_from_gcs_swcs(self, bucket_name, swc_paths):
             # Assign threads
             threads = list()
             for path in swc_paths:
-
-                if "003" not in path:  # TEMP
-                    continue  # TEMP
-
                 threads.append(
                     executor.submit(self.read_from_gcs_swc, bucket_name, path)
                 )

src/segmentation_skeleton_metrics/evaluate.py

@@ -35,12 +35,12 @@
 
 
 def evaluate(
-    gt_pointer,
+    gt_path,
     segmentation,
     output_dir,
     anisotropy=(1.0, 1.0, 1.0),
     connections_path=None,
-    fragments_pointer=None,
+    fragments_path=None,
     results_filename="results",
     save_merges=False,
     save_fragments=False,
@@ -54,10 +54,9 @@ def evaluate(
 
     Parameters
     ----------
-    gt_pointer : str
-        Pointer to ground truth SWC files, see "swc_util.Reader" for
-        documentation. These SWC files are assumed to be stored in voxel
-        coordinates.
+    gt_path : str
+        Path to ground truth SWC files, see swc_util.Reader for documentation
+        These SWC files are assumed to be stored in voxel coordinates.
     segmentation : ImageReader
         Predicted segmentation.
     anisotropy : Tuple[float], optional
@@ -66,11 +65,11 @@ def evaluate(
     connections_path : str, optional
         Path to a txt file containing pairs of segment IDs that represents
         fragments that were merged. Default is None.
-    fragments_pointer : str, optional
-        Pointer to SWC files corresponding to "segmentation", see
-        "swc_util.Reader" for documentation. Notes: (1) "anisotropy" is
-        applied to these SWC files and (2) these SWC files are required
-        for counting merges. Default is None.
+    fragments_path : str, optional
+        Path to SWC files corresponding to "segmentation", see swc_util.Reader
+        for documentation. Notes: (1) "anisotropy" is applied to these SWC
+        files and (2) these SWC files are required for counting merges.
+        Default is None.
     results_filename : str, optional
         Name of file that skeleton metric results are written to. Default is
         "results".
@@ -97,10 +96,11 @@ def evaluate(
         use_anisotropy=use_anisotropy,
         verbose=verbose
     )
-    gt_graphs = dataloader.load_groundtruth(gt_pointer, segmentation)
-    fragment_graphs = dataloader.load_fragments(fragments_pointer, gt_graphs)
+    gt_graphs = dataloader.load_groundtruth(gt_path, segmentation)
+    fragment_graphs = dataloader.load_fragments(fragments_path, gt_graphs)
 
     # Run evaluation
+    util.mkdir(output_dir)
     evaluator = Evaluator(output_dir, results_filename, verbose)
     evaluator(gt_graphs, fragment_graphs)
 

src/segmentation_skeleton_metrics/skeleton_metrics.py

@@ -570,6 +570,7 @@ def add_merge_site_names(self):
         for i, _ in enumerate(self.merge_sites.index, 1):
             row_names.append(f"merge-{i}.swc")
         self.merge_sites.index = row_names
+        self.merge_sites.index.name = "Merge_ID"
 
     def remove_repeat_merge_sites(self):
         """

src/segmentation_skeleton_metrics/utils/util.py

@@ -38,8 +38,8 @@ def mkdir(path, delete=False):
     """
     if delete:
         rmdir(path)
-    if not os.path.exists(path):
-        os.mkdir(path)
+
+    os.makedirs(path, exist_ok=True)
 
 
 def rmdir(path):
@@ -268,7 +268,7 @@ def is_gcs_path(path):
     return path.startswith("gs://")
 
 
-def list_gcs_filenames(bucket_name, prefix, extension):
+def list_gcs_filenames(bucket_name, prefix, extension=""):
     """
     Lists all files in a GCS bucket with the given extension.
 
@@ -278,8 +278,8 @@ def list_gcs_filenames(bucket_name, prefix, extension):
         Name of bucket to be searched.
     prefix : str
         Path to location within bucket to be searched.
-    extension : str
-        File extension of filenames to be listed.
+    extension : str, optional
+        File extension of filenames to be listed. Default is an empty string.
 
     Returns
     -------