Feat s3 loading (#178)

* refactor: improved txt reader

* remove print

* feat: load swcs from s3

* feat: read json

* bug: read local txt

* bug: swc loading, merge sites

* bug: merge site names

---------

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

Author: anna-grim

src/segmentation_skeleton_metrics/data_handling/graph_loading.py

@@ -89,7 +89,7 @@ def load_groundtruth(self, swc_pointer, label_mask):
             use_anisotropy=False,
             verbose=self.verbose
         )
-        return graph_loader.run(swc_pointer)
+        return graph_loader(swc_pointer)
 
     def load_fragments(self, swc_pointer, gt_graphs):
         """
@@ -124,7 +124,7 @@ def load_fragments(self, swc_pointer, gt_graphs):
             use_anisotropy=self.use_anisotropy,
             verbose=self.verbose
         )
-        return graph_loader.run(swc_pointer)
+        return graph_loader(swc_pointer)
 
     # --- Helpers ---
     def get_all_node_labels(self, graphs):
@@ -198,7 +198,7 @@ def __init__(
             anisotropy, selected_ids=selected_ids
         )
 
-    def run(self, swc_pointer):
+    def __call__(self, swc_pointer):
         """
         Builds a graphs by reading SWC files to extract content to load into a
         SkeletonGraph object. Nodes are labeled if a label_mask is provided.

src/segmentation_skeleton_metrics/skeleton_metrics.py

@@ -525,6 +525,7 @@ def verify_site(self, gt_graph, fragment_graph, gt_node, fragment_node):
         self.fragments_with_merge.add(fragment_graph.name)
         self.merge_sites.append(
             {
+                "Fragment_Name": fragment_graph.name,
                 "Segment_ID": fragment_graph.segment_id,
                 "GroundTruth_ID": gt_graph.name,
                 "Voxel": tuple(map(int, voxel)),
@@ -931,17 +932,17 @@ def __call__(self, gt_graphs, fragment_graphs, merge_sites):
         pair_to_length = dict()
         for i in merge_sites.index:
             # Extract site info
-            segment_id = merge_sites["Segment_ID"][i]
+            fragment_name = str(merge_sites["Fragment_Name"][i])
             gt_id = merge_sites["GroundTruth_ID"][i]
-            pair_id = (segment_id, gt_id)
+            pair_id = (fragment_name, gt_id)
 
             # Check wheter to visit
             if pair_id in pair_to_length:
                 merge_sites.loc[i, self.name] = pair_to_length[pair_id]
             else:
                 # Get graphs
                 gt_graph = gt_graphs[gt_id]
-                fragment_graph = deepcopy(fragment_graphs[segment_id])
+                fragment_graph = deepcopy(fragment_graphs[fragment_name])
 
                 # Compute metric
                 pair_to_length[pair_id] = self.compute_added_length(