Bug path parser (#152)

* bugs: path parser, write

* bug: skeleton writer:

* bug: write skeleton graph

---------

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

Author: anna-grim

src/segmentation_skeleton_metrics/skeleton_graph.py

@@ -297,24 +297,28 @@ def to_zipped_swc(self, zip_writer):
         def write_entry(node, parent):
             x, y, z = tuple(self.voxels[i] * self.anisotropy)
             r = 2 if self.is_groundtruth else 3
-            node_id = len(node_to_idx) + 1
+            node_id = cnt
+            parent_id = node_to_idx[parent]
             node_to_idx[node] = node_id
-            text_buffer.write("\n" + f"{node_id} 2 {x} {y} {z} {r} {parent}")
+            text_buffer.write(f"\n{node_id} 2 {x} {y} {z} {r} {parent_id}")
 
         # Main
         with StringIO() as text_buffer:
             # Preamble
-            text_buffer.write("\n" + "# id, type, z, y, x, r, pid")
+            text_buffer.write(self.get_color())
+            text_buffer.write("\n# id, type, z, y, x, r, pid")
 
             # Write entries
+            cnt = 1
             node_to_idx = defaultdict(lambda: -1)
             for i, j in nx.dfs_edges(self):
                 # Special Case: Root
                 if len(node_to_idx) == 0:
-                    write_entry(i, node_to_idx[i])
+                    write_entry(i, -1)
 
                 # General Case: Non-Root
-                write_entry(j, node_to_idx[i])
+                cnt += 1
+                write_entry(j, i)
 
             # Finish
             zip_writer.writestr(self.filename, text_buffer.getvalue())

src/segmentation_skeleton_metrics/utils/swc_util.py

@@ -326,10 +326,14 @@ def read_from_gcs_swcs(self, bucket_name, swc_paths):
         with ThreadPoolExecutor() as executor:
             # Assign threads
             threads = list()
+            cnt = 0
             for path in swc_paths:
                 threads.append(
                     executor.submit(self.read_from_gcs_swc, bucket_name, path)
                 )
+                cnt += 1
+                if cnt > 2:
+                    break  # temp
 
             # Store results
             swc_dicts = deque()

src/segmentation_skeleton_metrics/utils/util.py

@@ -533,4 +533,3 @@ def save_results(path, stats):
             sheet.write(i + 1, j + 1, round(stats[swc_id][metric], 4))
 
     wb.save(path)
-