Merge branch 'main' into refactor-data-challenge

Author: anna-grim

src/segmentation_skeleton_metrics/__init__.py

@@ -2,4 +2,4 @@
 Package to evaluate a predicted segmentation.
 """
 
-__version__ = "5.5.1"
+__version__ = "5.5.8"

src/segmentation_skeleton_metrics/skeleton_metric.py

@@ -314,6 +314,7 @@ def run(self):
         util.update_txt(path, "  # Splits: " + str(n_splits))
 
         if self.fragment_graphs is not None:
+            self.metrics["# Merges"].fillna(0, inplace=True)
             n_merges = self.metrics["# Merges"].sum()
             util.update_txt(path, "  # Merges: " + str(n_merges))
 
@@ -403,7 +404,7 @@ def count_merges(self, key, kdtree):
         # Iterate over fragments that intersect with GT skeleton
         for label in self.get_node_labels(key):
             nodes = self.graphs[key].nodes_with_label(label)
-            if len(nodes) > 100:
+            if len(nodes) > 70:
                 for label in self.label_handler.get_class(label):
                     if label in self.fragment_ids:
                         self.is_fragment_merge(key, label, kdtree)
@@ -722,3 +723,4 @@ def to_local_voxels(self, key, i, offset):
         voxel = np.array(self.graphs[key].voxels[i])
         offset = np.array(offset)
         return tuple(voxel - offset)
+

src/segmentation_skeleton_metrics/utils/swc_util.py

@@ -65,13 +65,16 @@ def read(self, swc_pointer):
 
         Parameters
         ----------
-        swc_pointer : dict, list, str
+        swc_pointer : str or List[str]
             Object that points to SWC files to be read, must be one of:
-                - swc_dir (str): Path to directory containing SWC files.
                 - swc_path (str): Path to single SWC file.
-                - swc_path_list (List[str]): List of paths to SWC files.
-                - swc_zip (str): Path to a ZIP archive containing SWC files.
-                - swc_zip_dir (str): Path to directory of ZIPs with SWC files.
+                - swc_dir_path (str): Path to local directory containing SWC files.
+                - swc_zip_path (str): Path to a local ZIP archive containing SWC files.
+                - swc_zip_dir_path (str): Path to a local directory of ZIPs with SWC files.
+                - swc_s3_dir_path (str): Path to S3 directory containing SWC files.
+                - swc_gcs_dir_path (str): Path to GCS directory containing SWC files.
+                - swc_gcs_zip_dir_path (str): Path to GCS directory containing ZIP archives of SWC files.
+                - swc_path_list (List[str]): List of paths to local SWC files.
 
         Returns
         -------
@@ -287,7 +290,7 @@ def read_from_gcs(self, gcs_path):
         Returns
         -------
         Dequeue[dict]
-            List of dictionaries whose keys and values are the attribute
+            Dictionaries whose keys and values are the attribute
             names and values from an SWC file.
         """
         # List filenames
@@ -317,7 +320,7 @@ def read_from_gcs_swcs(self, bucket_name, swc_paths):
         Returns
         -------
         Dequeue[dict]
-            List of dictionaries whose keys and values are the attribute
+            Dictionaries whose keys and values are the attribute
             names and values from an SWC file.
         """
         pbar = tqdm(total=len(swc_paths), desc="Read SWCs")
@@ -376,7 +379,7 @@ def read_from_gcs_zips(self, bucket_name, zip_paths):
         Returns
         -------
         Dequeue[dict]
-            List of dictionaries whose keys and values are the attribute
+            Dictionaries whose keys and values are the attribute
             names and values from an SWC file.
         """
         swc_dicts = deque()
@@ -397,7 +400,7 @@ def read_from_gcs_zip(self, bucket_name, path):
         Returns
         -------
         Dequeue[dict]
-            List of dictionaries whose keys and values are the attribute
+            Dictionaries whose keys and values are the attribute
             names and values from an SWC file.
         """
         # Initialize cloud reader