Merge pull request #168 from fcollman/process=False-option

Process=false option

navis/utils/cv.py

@@ -56,20 +56,22 @@ def patch_cloudvolume():
 
  # If CV not installed do nothing
  if not cv:
- logger.info('cloud-volume appears to not be installed?')
+ logger.info("cloud-volume appears to not be installed?")
  return
 
- for ds in [cv.datasource.graphene.mesh.sharded.GrapheneShardedMeshSource,
- cv.datasource.graphene.mesh.unsharded.GrapheneUnshardedMeshSource,
- cv.datasource.precomputed.mesh.unsharded.UnshardedLegacyPrecomputedMeshSource,
- cv.datasource.precomputed.mesh.multilod.UnshardedMultiLevelPrecomputedMeshSource,
- cv.datasource.precomputed.mesh.multilod.ShardedMultiLevelPrecomputedMeshSource,
- cv.datasource.precomputed.skeleton.sharded.ShardedPrecomputedSkeletonSource,
- cv.datasource.precomputed.skeleton.unsharded.UnshardedPrecomputedSkeletonSource]:
+ for ds in [
+ cv.datasource.graphene.mesh.sharded.GrapheneShardedMeshSource,
+ cv.datasource.graphene.mesh.unsharded.GrapheneUnshardedMeshSource,
+ cv.datasource.precomputed.mesh.unsharded.UnshardedLegacyPrecomputedMeshSource,
+ cv.datasource.precomputed.mesh.multilod.UnshardedMultiLevelPrecomputedMeshSource,
+ cv.datasource.precomputed.mesh.multilod.ShardedMultiLevelPrecomputedMeshSource,
+ cv.datasource.precomputed.skeleton.sharded.ShardedPrecomputedSkeletonSource,
+ cv.datasource.precomputed.skeleton.unsharded.UnshardedPrecomputedSkeletonSource,
+ ]:
  ds.get_navis = return_navis(ds.get, only_on_kwarg=False)
  ds.get = return_navis(ds.get, only_on_kwarg=True)
 
- logger.info('cloud-volume successfully patched!')
+ logger.info("cloud-volume successfully patched!")
 
 
 def return_navis(func, only_on_kwarg=False):
@@ -82,12 +84,15 @@ def return_navis(func, only_on_kwarg=False):
  only_on_kwarg : bool
  If True, will look for a `as_navis=True` (default=False)
  keyword argument to determine if results should be converted
- to navis neurons.
+ to navis neurons. If 'process' is set to False, the neuron
+ will not be processed by TriMesh (remove nan, duplicate vertices,etc)
 
  """
+
  @functools.wraps(func)
  def wrapper(*args, **kwargs):
- ret_navis = kwargs.pop('as_navis', False)
+ ret_navis = kwargs.pop("as_navis", False)
+ process = kwargs.pop("process", False)
  res = func(*args, **kwargs)
 
  if not only_on_kwarg or ret_navis:
@@ -99,18 +104,20 @@ def wrapper(*args, **kwargs):
 
  for k, v in res.items():
  if isinstance(v, cv.Mesh):
- n = core.MeshNeuron(v, id=k, units='nm')
+ n = core.MeshNeuron(v, id=k, units="nm", process=process)
  neurons.append(n)
  elif isinstance(v, cv.Skeleton):
  swc_str = v.to_swc()
  n = io.read_swc(swc_str)
  n.id = k
- n.units = 'nm'
+ n.units = "nm"
  neurons.append(n)
  else:
- logger.warning(f'Skipped {k}: Unable to convert {type(v)} to '
- 'navis Neuron.')
+ logger.warning(
+ f"Skipped {k}: Unable to convert {type(v)} to " "navis Neuron."
+ )
 
  return core.NeuronList(neurons)
  return res
+
  return wrapper