Refactor optimize merge (#120)

* refactor: optimized merge detection

* bug: removed subroutine

* removed test tqdm

* bug: close zip writer

* refactor: metrics in pandas df

* refactor: detect all sites

* bug: empty merge list

* bug: rescaling swcs

---------

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

Author: anna-grim

src/segmentation_skeleton_metrics/skeleton_metric.py

@@ -69,6 +69,7 @@ def __init__(
         preexisting_merges=None,
         save_merges=False,
         save_fragments=False,
+        use_anisotropy=True,
         valid_labels=None,
     ):
         """
@@ -122,6 +123,7 @@ def __init__(
         self.preexisting_merges = preexisting_merges
         self.save_merges = save_merges
         self.save_fragments = save_fragments
+        self.use_anisotropy = use_anisotropy
 
         # Label handler
         self.label_handler = gutil.LabelHandler(
@@ -201,7 +203,7 @@ def load_fragments(self, swc_pointer):
             graph_builder = gutil.GraphBuilder(
                 anisotropy=self.anisotropy,
                 selected_ids=self.get_all_node_labels(),
-                use_anisotropy=True,
+                use_anisotropy=self.use_anisotropy,
             )
             self.fragment_graphs = graph_builder.run(swc_pointer)
             self.set_fragment_ids()

src/segmentation_skeleton_metrics/utils/swc_util.py

@@ -326,6 +326,7 @@ def read_from_gcs_swcs(self, bucket_name, swc_paths):
                 threads.append(
                     executor.submit(self.read_from_gcs_swc, bucket_name, path)
                 )
+                break
 
             # Store results
             swc_dicts = deque()