From 12637931373aa4cd5a77619256bd3cbb87f0ad98 Mon Sep 17 00:00:00 2001
From: anna-grim <anna.grim@alleninstitute.org>
Date: Fri, 12 Jan 2024 04:42:25 +0000
Subject: [PATCH] bug : parse swc

---
 src/deep_neurographs/graph_utils.py |  1 +
 src/deep_neurographs/intake.py      | 15 +++++++++++++--
 src/deep_neurographs/swc_utils.py   | 12 ++++++------
 3 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/src/deep_neurographs/graph_utils.py b/src/deep_neurographs/graph_utils.py
index d82c084..3ad9e21 100644
--- a/src/deep_neurographs/graph_utils.py
+++ b/src/deep_neurographs/graph_utils.py
@@ -65,6 +65,7 @@ def get_irreducibles(swc_dict, swc_id=None, prune=True, depth=16, smooth=True):
 
     # Extract irreducibles
     leafs, junctions = get_irreducible_nodes(dense_graph)
+    assert len(leafs) > 0, "Error: swc with no leaf nodes!"
     source = sample(leafs, 1)[0]
     root = None
     edges = dict()
diff --git a/src/deep_neurographs/intake.py b/src/deep_neurographs/intake.py
index 989c33e..8f9e5b8 100644
--- a/src/deep_neurographs/intake.py
+++ b/src/deep_neurographs/intake.py
@@ -28,10 +28,10 @@
 N_PROPOSALS_PER_LEAF = 3
 OPTIMIZE_PROPOSALS = False
 OPTIMIZATION_DEPTH = 15
-PRUNE = True
+PRUNE = False
 PRUNE_DEPTH = 16
 SEARCH_RADIUS = 0
-MIN_SIZE = 30
+MIN_SIZE = 35
 SMOOTH = True
 
 
@@ -281,6 +281,8 @@ def build_neurograph(
 ):
     # Extract irreducibles
     irreducibles = dict()
+    """
+    -- asynchronous --
     with ProcessPoolExecutor() as executor:
         # Assign Processes
         processes = [None] * len(swc_dicts)
@@ -296,6 +298,15 @@ def build_neurograph(
         for process in as_completed(processes):
             process_id, result = process.result()
             irreducibles[process_id] = result
+    """
+    for key in swc_dicts.keys():
+        _, irreducibles[key] = gutils.get_irreducibles(
+                swc_dicts[key],
+                swc_id=key,
+                prune=prune,
+                depth=prune_depth,
+                smooth=smooth
+        )
 
     # Build neurograph
     t0 = time()
diff --git a/src/deep_neurographs/swc_utils.py b/src/deep_neurographs/swc_utils.py
index a234808..ea58f94 100644
--- a/src/deep_neurographs/swc_utils.py
+++ b/src/deep_neurographs/swc_utils.py
@@ -21,15 +21,15 @@
 def process_local_paths(paths, min_size, bbox=None):
     swc_dicts = dict()
     for path in paths:
-        swc_id = utils.get_swc_id(path)
-        swc_dicts[swc_id] = parse_local_swc(path, bbox=bbox)
+        swc_dicts.update(parse_local_swc(path, bbox=bbox, min_size=min_size))
     return swc_dicts
 
 
-def parse_local_swc(path, bbox=None, min_size=0):
+def parse_local_swc(path, bbox=None, min_size=25):
+    swc_id = utils.get_swc_id(path)
     swc_contents = read_from_local(path)
-    parse_bool = len(swc_contents) > min_size
-    return parse(swc_contents, bbox=bbox) if parse_bool else []
+    swc_dict = parse(swc_contents, bbox=bbox)
+    return {swc_id: swc_dict} if len(swc_dict["id"]) > min_size else dict()
 
 
 def parse_gcs_zip(zip_file, path, min_size=0):
@@ -61,7 +61,7 @@ def parse(swc_contents, bbox=None):
         if line.startswith("# OFFSET"):
             parts = line.split()
             offset = read_xyz(parts[2:5])
-        if not line.startswith("#") and len(line) > 0:
+        if not line.startswith("#"):
             parts = line.split()
             xyz = read_xyz(parts[2:5], offset=offset)
             if bbox: