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

Process=false option

Author: schlegelp

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