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if root is None:
if soma_mode:
root = find_soma_root(DBF, dbf_max)
soma_radius = dbf_max * soma_invalidation_scale + soma_invalidation_const
else:
root = find_root(labels, anisotropy)
if root is None:
return PrecomputedSkeleton()
# DBF: Distance to Boundary Field
# DAF: Distance from any voxel Field (distance from root field)
# PDRF: Penalized Distance from Root Field
DBF = kimimaro.skeletontricks.zero2inf(DBF) # DBF[ DBF == 0 ] = np.inf
DAF = dijkstra3d.euclidean_distance_field(labels, root, anisotropy=anisotropy)
DAF = kimimaro.skeletontricks.inf2zero(DAF) # DAF[ DAF == np.inf ] = 0
PDRF = compute_pdrf(dbf_max, pdrf_scale, pdrf_exponent, DBF, DAF)
# Use dijkstra propogation w/o a target to generate a field of
# pointers from each voxel to its parent. Then we can rapidly
# compute multiple paths by simply hopping pointers using path_from_parents
if not fix_branching:
parents = dijkstra3d.parental_field(PDRF, root)
del PDRF
else:
parents = PDRF
if soma_mode:
invalidated, labels = kimimaro.skeletontricks.roll_invalidation_ball(
labels, DBF, np.array([root], dtype=np.uint32),
scale=soma_invalidation_scale,
def find_root(labels, anisotropy):
"""
"4.4 DAF: Compute distance from any voxel field"
Compute DAF, but we immediately convert to the PDRF
The extremal point of the PDRF is a valid root node
even if the DAF is computed from an arbitrary pixel.
"""
any_voxel = kimimaro.skeletontricks.first_label(labels)
if any_voxel is None:
return None
DAF = dijkstra3d.euclidean_distance_field(
np.asfortranarray(labels), any_voxel, anisotropy=anisotropy)
return kimimaro.skeletontricks.find_target(labels, DAF)