From 699cd39f6f2423582fcaf281fa2e8c44bc2f3c7f Mon Sep 17 00:00:00 2001
From: Jason Ken Adhinarta <35003073+jasonkena@users.noreply.github.com>
Date: Tue, 8 Oct 2024 16:25:54 -0400
Subject: [PATCH] make mesh_dir behavior consistent across create_meshing_tasks
 and create_mesh_manifest_tasks (#178)

* typo fix in README, remove duplicate arguments in skeletonization example

* make mesh_dir behavior consistent across create_meshing_tasks and create_mesh_manifest_tasks

* fix vol.mesh.get in bounds_from_mesh
---
 README.md                         | 4 +---
 igneous/task_creation/mesh.py     | 5 ++++-
 igneous/task_creation/skeleton.py | 5 +++--
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index e2180d4..3248e2d 100755
--- a/README.md
+++ b/README.md
@@ -458,7 +458,7 @@ tasks = create_meshing_tasks(             # First Pass
 tasks = create_mesh_manifest_tasks(layer_path, magnitude=3) # Second Pass
 ```
 
-The parameters above are mostly self explainatory, but the magnitude parameter of `create_mesh_manifest_tasks` is a bit odd. What a MeshManifestTask does is iterate through a proportion of the files defined by a filename prefix. `magnitude` splits up the work by 
+The parameters above are mostly self explanatory, but the magnitude parameter of `create_mesh_manifest_tasks` is a bit odd. What a MeshManifestTask does is iterate through a proportion of the files defined by a filename prefix. `magnitude` splits up the work by
 an additional 10^magnitude. A high magnitude (3-5+) is appropriate for horizontal scaling workloads while small magnitudes 
 (1-2) are more suited for small volumes locally processed since there is overhead introduced by splitting up the work.  
 
@@ -515,8 +515,6 @@ tasks = tc.create_skeletonizing_tasks(
     dust_threshold=1000, # Don't skeletonize below this physical distance
     progress=False, # Show a progress bar
     parallel=1, # Number of parallel processes to use (more useful locally)
-    spatial_index=True, # generate a spatial index for querying skeletons by bounding box
-    sharded=False, # generate intermediate shard fragments for later processing into sharded format
     cross_sectional_area=False, # Compute the cross sectional area for each vertex.
     cross_sectional_area_smoothing_window=5, # Rolling average of vertices.
   )
diff --git a/igneous/task_creation/mesh.py b/igneous/task_creation/mesh.py
index 21a8eaa..d18e842 100644
--- a/igneous/task_creation/mesh.py
+++ b/igneous/task_creation/mesh.py
@@ -168,7 +168,10 @@ def create_meshing_tasks(
   vol = CloudVolume(layer_path, mip)
 
   if mesh_dir is None:
-    mesh_dir = 'mesh_mip_{}_err_{}'.format(mip, max_simplification_error)
+    if 'mesh' in vol.info:
+      mesh_dir = vol.info['mesh']
+    else:
+      mesh_dir = 'mesh_mip_{}_err_{}'.format(mip, max_simplification_error)
 
   if not 'mesh' in vol.info:
     vol.info['mesh'] = mesh_dir
diff --git a/igneous/task_creation/skeleton.py b/igneous/task_creation/skeleton.py
index e99ab06..2a38abf 100644
--- a/igneous/task_creation/skeleton.py
+++ b/igneous/task_creation/skeleton.py
@@ -48,8 +48,9 @@ def bounds_from_mesh(
   """Estimate the bounding box of a label from its mesh if available."""
   bbxes = []
   for label in labels:
-    mesh = vol.mesh.get(labels)[label]
-    if mesh is None:
+    try:
+      mesh = vol.mesh.get(label)
+    except ValueError:
       raise ValueError(f"Mesh {label} is not available.")
 
     bounds = Bbox.from_points(mesh.vertices // vol.resolution)