How to use the dijkstra3d.parental_field function in dijkstra3d

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github seung-lab / kimimaro / kimimaro / trace.py View on Github external
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,
      const=soma_invalidation_const, 
      anisotropy=anisotropy
    )

  paths = compute_paths(
    root, labels, DBF, DAF, 
    parents, scale, const, anisotropy, 
    soma_mode, soma_radius, fix_branching,

dijkstra3d

Implementation of Dijkstra's Shortest Path algorithm on 3D images.

GPL-3.0
Latest version published 6 months ago

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