minor upds

AllenInstitute · Oct 30, 2024 · 97d94d6 · 97d94d6
1 parent 4ffe02f
commit 97d94d6
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Showing 4 changed files with 7 additions and 7 deletions.
diff --git a/src/deep_neurographs/config.py b/src/deep_neurographs/config.py
@@ -60,7 +60,7 @@ class GraphConfig:
     min_size: float = 30.0
     node_spacing: int = 1
     proposals_per_leaf: int = 2
-    prune_depth: float = 25.0
+    prune_depth: float = 20.0
     remove_doubles_bool: bool = False
     search_radius: float = 20.0
     smooth_bool: bool = True

diff --git a/src/deep_neurographs/inference.py b/src/deep_neurographs/inference.py
@@ -218,10 +218,11 @@ def build_graph(self, fragments_pointer):
             min_size=self.graph_config.min_size,
             node_spacing=self.graph_config.node_spacing,
             progress_bar=True,
+            prune_depth=self.graph_config.prune_depth,
         )
         self.graph = graph_builder.run(fragments_pointer)
 
-        # Remove doubles (if applicable)
+        # Filter fragments
         n_curvy = fragment_filtering.remove_curvy(self.graph, 200)
         n_curvy = util.reformat_number(n_curvy)
         if self.graph_config.remove_doubles_bool:

diff --git a/src/deep_neurographs/neurograph.py b/src/deep_neurographs/neurograph.py
@@ -715,8 +715,6 @@ def merge_proposal(self, proposal):
             self.upd_ids(swc_id, j if swc_id == swc_id_i else i)
             self.__add_edge((i, j), attrs, swc_id)
             self.proposals.remove(proposal)
-        else:
-            print("Skip! -- Failed Degree Check")
 
     def check_proposal_degrees(self, i, j):
         one_leaf = self.degree[i] == 1 or self.degree[j] == 1

diff --git a/src/deep_neurographs/utils/graph_util.py b/src/deep_neurographs/utils/graph_util.py
@@ -162,7 +162,7 @@ def schedule_processes(self, swc_dicts):
             pbar = tqdm(total=len(swc_dicts), desc="Extract Graphs")
 
         # Main
-        with ProcessPoolExecutor(max_workers=1) as executor:
+        with ProcessPoolExecutor() as executor:
             # Assign Processes
             i = 0
             processes = [None] * len(swc_dicts)
@@ -273,8 +273,9 @@ def prune_branches(self, graph):
                         break
 
                     # Check whether to stop
-                    if length > self.prune_depth or n_passes == 1:
-                        graph.remove_nodes_from(branch[0:min(3, len(branch))])
+                    if length > self.prune_depth:
+                        if n_passes == 1:
+                            graph.remove_nodes_from(branch[0:min(3, len(branch))])
                         break
 
     def get_component_irreducibles(self, graph, swc_dict):