Merge branch 'master' of github.com:seung-lab/igneous

igneous/tasks/skeleton.py

@@ -332,11 +332,33 @@ def compute_cross_sectional_area(self, vol, bbox, skeletons):
   def repair_cross_sectional_area_contacts(self, vol, bbox, skeletons):
     from dbscan import DBSCAN
 
-    repair_skels = [
-      skel for skel in skeletons.values()
-      if np.any(skel.cross_sectional_area_contacts > 0)
+    boundaries = [
+      bbox.minpt.x == vol.bounds.minpt.x,
+      bbox.maxpt.x == vol.bounds.maxpt.x,
+      bbox.minpt.y == vol.bounds.minpt.y,
+      bbox.maxpt.y == vol.bounds.maxpt.y,
+      bbox.minpt.z == vol.bounds.minpt.z,
+      bbox.maxpt.z == vol.bounds.maxpt.z,
     ]
 
+    if all(boundaries):
+      return skeletons
+
+    invalid_repairs = 0
+    for i, bnd in enumerate(boundaries):
+      invalid_repairs |= (bnd << i)
+
+    invalid_repairs = (~np.uint8(invalid_repairs)) & np.uint8(0b00111111)
+
+    # We want to repair any skeleton that has a contact with the
+    # edge except those that are contacting the volume boundary due to futility
+
+    repair_skels = []
+    for skel in skeletons.values():
+      contacts = skel.cross_sectional_area_contacts & invalid_repairs
+      if np.any(contacts):
+        repair_skels.append(skel)
+
     delta = int(self.cross_sectional_area_shape_delta)
 
     shape = bbox.size3()

igneous_cli/cli.py

@@ -65,12 +65,12 @@ def enqueue_tasks(ctx, queue, tasks):
     tq.insert(tasks, parallel=parallel)
   return tq
 
-class TupleN(click.ParamType):
+class ListN(click.ParamType):
   """A command line option type consisting of 3 comma-separated integers."""
-  name = 'tupleN'
+  name = 'ListN'
   def convert(self, value, param, ctx):
     if isinstance(value, str):
-      value = tuple(map(int, value.split(',')))
+      value = list(map(int, value.split(',')))
     return value
 
 class Tuple34(click.ParamType):
@@ -1236,19 +1236,20 @@ def skeletongroup():
 @click.option('--soma-const', default=300, help="Const factor for soma invalidation.", type=float, show_default=True)
 @click.option('--max-paths', default=None, help="Abort skeletonizing an object after this many paths have been traced.", type=float)
 @click.option('--sharded', is_flag=True, default=False, help="Generate shard fragments instead of outputing skeleton fragments.", show_default=True)
-@click.option('--labels', type=TupleN(), default=None, help="Skeletonize only this comma separated list of labels.", show_default=True)
+@click.option('--labels', type=ListN(), default=None, help="Skeletonize only this comma separated list of labels.", show_default=True)
 @click.option('--cross-section', type=int, default=0, help="Compute the cross sectional area for each skeleton vertex. May add substantial computation time. Integer value is the normal vector rolling average smoothing window over vertices. 0 means off.", show_default=True)
 @click.option('--output', '-o', type=CloudPath(), default=None, help="Output the results to a different place.", show_default=True)
 @click.option('--timestamp', type=int, default=None, help="(graphene) Use the proofreading state at this UNIX timestamp.", show_default=True)
 @click.option('--root-ids', type=CloudPath(), default=None, help="(graphene) If you have a materialization of graphene root ids for this timepoint, it's more efficient to use it than making requests to the graphene server.", show_default=True)
+@click.option('--progress', is_flag=True, default=False, help="Print progress bars.", show_default=True)
 @click.pass_context
 def skeleton_forge(
   ctx, path, queue, mip, shape, 
   fill_missing, dust_threshold, dust_global, spatial_index,
   fix_branching, fix_borders, fix_avocados, fix_autapses,
   fill_holes, scale, const, soma_detect, soma_accept,
   soma_scale, soma_const, max_paths, sharded, labels,
-  cross_section, output, timestamp, root_ids,
+  cross_section, output, timestamp, root_ids, progress,
 ):
   """
   (1) Synthesize skeletons from segmentation cutouts.
@@ -1287,7 +1288,7 @@ def skeleton_forge(
     teasar_params=teasar_params, 
     fix_branching=fix_branching, fix_borders=fix_borders, 
     fix_avocados=fix_avocados, fill_holes=fill_holes,
-    dust_threshold=dust_threshold, progress=False,
+    dust_threshold=dust_threshold, progress=progress,
     parallel=1, fill_missing=fill_missing, 
     sharded=sharded, spatial_index=spatial_index,
     dust_global=dust_global, object_ids=labels,