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# Copyright 2018 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS-IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import math
import numpy as np
ENCODE_NEIGHBOURHOOD_3D_KERNEL = np.array([[[128, 64], [32, 16]], [[8, 4],
[2, 1]]])
"""
lookup_tables.py
all of the lookup-tables functions are borrowed from DeepMind surface_distance repository
"""
# _NEIGHBOUR_CODE_TO_NORMALS is a lookup table.
# For every binary neighbour code
# (2x2x2 neighbourhood = 8 neighbours = 8 bits = 256 codes)
# it contains the surface normals of the triangles (called "surfel" for
# "surface element" in the following). The length of the normal
# vector encodes the surfel area.
#
# created using the marching_cube algorithm
# see e.g. https://en.wikipedia.org/wiki/Marching_cubes
# pylint: disable=line-too-long
_NEIGHBOUR_CODE_TO_NORMALS = [
[[0, 0, 0]],
[[0.125, 0.125, 0.125]],
[[-0.125, -0.125, 0.125]],
[[-0.25, -0.25, 0.0], [0.25, 0.25, -0.0]],
[[0.125, -0.125, 0.125]],
[[-0.25, -0.0, -0.25], [0.25, 0.0, 0.25]],
[[0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[0.5, 0.0, -0.0], [0.25, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[-0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, 0.125, 0.125]],
[[-0.25, 0.0, 0.25], [-0.25, 0.0, 0.25]],
[[0.5, 0.0, 0.0], [-0.25, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.25, -0.25, 0.0], [0.25, -0.25, 0.0]],
[[0.5, 0.0, 0.0], [0.25, -0.25, 0.25], [-0.125, 0.125, -0.125]],
[[-0.5, 0.0, 0.0], [-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[0.5, 0.0, 0.0], [0.5, 0.0, 0.0]],
[[0.125, -0.125, -0.125]],
[[0.0, -0.25, -0.25], [0.0, 0.25, 0.25]],
[[-0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, -0.5, 0.0], [0.25, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, 0.0, -0.5], [0.25, 0.25, 0.25], [-0.125, -0.125, -0.125]],
[[-0.125, -0.125, 0.125], [0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[-0.125, -0.125, -0.125], [-0.25, -0.25, -0.25],
[0.25, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, -0.25, -0.25], [0.0, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[-0.25, 0.0, 0.25], [-0.25, 0.0, 0.25], [0.125, -0.125, -0.125]],
[[0.125, 0.125, 0.125], [0.375, 0.375, 0.375],
[0.0, -0.25, 0.25], [-0.25, 0.0, 0.25]],
[[0.125, -0.125, -0.125], [0.25, -0.25, 0.0], [0.25, -0.25, 0.0]],
[[0.375, 0.375, 0.375], [0.0, 0.25, -0.25],
[-0.125, -0.125, -0.125], [-0.25, 0.25, 0.0]],
[[-0.5, 0.0, 0.0], [-0.125, -0.125, -0.125],
[-0.25, -0.25, -0.25], [0.125, 0.125, 0.125]],
[[-0.5, 0.0, 0.0], [-0.125, -0.125, -0.125], [-0.25, -0.25, -0.25]],
[[0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.0, -0.25, 0.25], [0.0, 0.25, -0.25]],
[[0.0, -0.5, 0.0], [0.125, 0.125, -0.125], [0.25, 0.25, -0.25]],
[[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.125, -0.125, 0.125], [-0.25, -0.0, -0.25], [0.25, 0.0, 0.25]],
[[0.0, -0.25, 0.25], [0.0, 0.25, -0.25], [0.125, -0.125, 0.125]],
[[-0.375, -0.375, 0.375], [-0.0, 0.25, 0.25],
[0.125, 0.125, -0.125], [-0.25, -0.0, -0.25]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125], [-0.125, 0.125, 0.125]],
[[-0.0, 0.0, 0.5], [-0.25, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.25, 0.25, -0.25], [0.25, 0.25, -0.25],
[0.125, 0.125, -0.125], [-0.125, -0.125, 0.125]],
[[0.125, -0.125, 0.125], [0.25, -0.25, 0.0], [0.25, -0.25, 0.0]],
[[0.5, 0.0, 0.0], [0.25, -0.25, 0.25],
[-0.125, 0.125, -0.125], [0.125, -0.125, 0.125]],
[[0.0, 0.25, -0.25], [0.375, -0.375, -0.375],
[-0.125, 0.125, 0.125], [0.25, 0.25, 0.0]],
[[-0.5, 0.0, 0.0], [-0.25, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.25, -0.25, 0.0], [-0.25, 0.25, 0.0]],
[[0.0, 0.5, 0.0], [-0.25, 0.25, 0.25], [0.125, -0.125, -0.125]],
[[0.0, 0.5, 0.0], [0.125, -0.125, 0.125], [-0.25, 0.25, -0.25]],
[[0.0, 0.5, 0.0], [0.0, -0.5, 0.0]],
[[0.25, -0.25, 0.0], [-0.25, 0.25, 0.0], [0.125, -0.125, 0.125]],
[[-0.375, -0.375, -0.375], [-0.25, 0.0, 0.25],
[-0.125, -0.125, -0.125], [-0.25, 0.25, 0.0]],
[[0.125, 0.125, 0.125], [0.0, -0.5, 0.0],
[-0.25, -0.25, -0.25], [-0.125, -0.125, -0.125]],
[[0.0, -0.5, 0.0], [-0.25, -0.25, -0.25], [-0.125, -0.125, -0.125]],
[[-0.125, 0.125, 0.125], [0.25, -0.25, 0.0], [-0.25, 0.25, 0.0]],
[[0.0, 0.5, 0.0], [0.25, 0.25, -0.25],
[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.375, 0.375, -0.375], [-0.25, -0.25, 0.0],
[-0.125, 0.125, -0.125], [-0.25, 0.0, 0.25]],
[[0.0, 0.5, 0.0], [0.25, 0.25, -0.25], [-0.125, -0.125, 0.125]],
[[0.25, -0.25, 0.0], [-0.25, 0.25, 0.0],
[0.25, -0.25, 0.0], [0.25, -0.25, 0.0]],
[[-0.25, -0.25, 0.0], [-0.25, -0.25, 0.0], [-0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.25, -0.25, 0.0], [-0.25, -0.25, 0.0]],
[[-0.25, -0.25, 0.0], [-0.25, -0.25, 0.0]],
[[-0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.125, -0.125, 0.125], [-0.25, -0.25, 0.0], [0.25, 0.25, -0.0]],
[[0.0, -0.25, 0.25], [0.0, -0.25, 0.25]],
[[0.0, 0.0, 0.5], [0.25, -0.25, 0.25], [0.125, -0.125, 0.125]],
[[0.0, -0.25, 0.25], [0.0, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.375, -0.375, 0.375], [0.0, -0.25, -0.25],
[-0.125, 0.125, -0.125], [0.25, 0.25, 0.0]],
[[-0.125, -0.125, 0.125], [-0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125], [-0.125, 0.125, 0.125]],
[[-0.125, -0.125, 0.125], [-0.25, 0.0, 0.25], [-0.25, 0.0, 0.25]],
[[0.5, 0.0, 0.0], [-0.25, -0.25, 0.25],
[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.0, 0.5, 0.0], [-0.25, 0.25, -0.25], [0.125, -0.125, 0.125]],
[[-0.25, 0.25, -0.25], [-0.25, 0.25, -0.25],
[-0.125, 0.125, -0.125], [-0.125, 0.125, -0.125]],
[[-0.25, 0.0, -0.25], [0.375, -0.375, -0.375],
[0.0, 0.25, -0.25], [-0.125, 0.125, 0.125]],
[[0.5, 0.0, 0.0], [-0.25, 0.25, -0.25], [0.125, -0.125, 0.125]],
[[-0.25, 0.0, 0.25], [0.25, 0.0, -0.25]],
[[-0.0, 0.0, 0.5], [-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[-0.125, -0.125, 0.125], [-0.25, 0.0, 0.25], [0.25, 0.0, -0.25]],
[[-0.25, -0.0, -0.25], [-0.375, 0.375, 0.375],
[-0.25, -0.25, 0.0], [-0.125, 0.125, 0.125]],
[[0.0, 0.0, -0.5], [0.25, 0.25, -0.25], [-0.125, -0.125, 0.125]],
[[-0.0, 0.0, 0.5], [0.0, 0.0, 0.5]],
[[0.125, 0.125, 0.125], [0.125, 0.125, 0.125],
[0.25, 0.25, 0.25], [0.0, 0.0, 0.5]],
[[0.125, 0.125, 0.125], [0.25, 0.25, 0.25], [0.0, 0.0, 0.5]],
[[-0.25, 0.0, 0.25], [0.25, 0.0, -0.25], [-0.125, 0.125, 0.125]],
[[-0.0, 0.0, 0.5], [0.25, -0.25, 0.25],
[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[-0.25, 0.0, 0.25], [-0.25, 0.0, 0.25],
[-0.25, 0.0, 0.25], [0.25, 0.0, -0.25]],
[[0.125, -0.125, 0.125], [0.25, 0.0, 0.25], [0.25, 0.0, 0.25]],
[[0.25, 0.0, 0.25], [-0.375, -0.375, 0.375],
[-0.25, 0.25, 0.0], [-0.125, -0.125, 0.125]],
[[-0.0, 0.0, 0.5], [0.25, -0.25, 0.25], [0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.25, 0.0, 0.25], [0.25, 0.0, 0.25]],
[[0.25, 0.0, 0.25], [0.25, 0.0, 0.25]],
[[-0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[-0.125, -0.125, 0.125], [0.0, -0.25, 0.25], [0.0, 0.25, -0.25]],
[[0.0, -0.5, 0.0], [0.125, 0.125, -0.125],
[0.25, 0.25, -0.25], [-0.125, -0.125, 0.125]],
[[0.0, -0.25, 0.25], [0.0, -0.25, 0.25], [0.125, -0.125, 0.125]],
[[0.0, 0.0, 0.5], [0.25, -0.25, 0.25],
[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.0, -0.25, 0.25], [0.0, -0.25, 0.25],
[0.0, -0.25, 0.25], [0.0, 0.25, -0.25]],
[[0.0, 0.25, 0.25], [0.0, 0.25, 0.25], [0.125, -0.125, -0.125]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, 0.125],
[-0.125, -0.125, 0.125], [0.125, 0.125, 0.125]],
[[-0.0, 0.0, 0.5], [-0.25, -0.25, 0.25],
[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[-0.0, 0.5, 0.0], [-0.25, 0.25, -0.25],
[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, -0.25, -0.25], [0.0, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.5, 0.0, -0.0], [0.25, -0.25, -0.25], [0.125, -0.125, -0.125]],
[[-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125],
[-0.25, 0.25, 0.25], [0.125, -0.125, -0.125]],
[[0.375, -0.375, 0.375], [0.0, 0.25, 0.25],
[-0.125, 0.125, -0.125], [-0.25, 0.0, 0.25]],
[[0.0, -0.5, 0.0], [-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[-0.375, -0.375, 0.375], [0.25, -0.25, 0.0],
[0.0, 0.25, 0.25], [-0.125, -0.125, 0.125]],
[[-0.125, 0.125, 0.125], [-0.25, 0.25, 0.25], [0.0, 0.0, 0.5]],
[[0.125, 0.125, 0.125], [0.0, 0.25, 0.25], [0.0, 0.25, 0.25]],
[[0.0, 0.25, 0.25], [0.0, 0.25, 0.25]],
[[0.5, 0.0, -0.0], [0.25, 0.25, 0.25],
[0.125, 0.125, 0.125], [0.125, 0.125, 0.125]],
[[0.125, -0.125, 0.125], [-0.125, -0.125, 0.125], [0.125, 0.125, 0.125]],
[[-0.25, -0.0, -0.25], [0.25, 0.0, 0.25], [0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125]],
[[-0.25, -0.25, 0.0], [0.25, 0.25, -0.0], [0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.25, -0.25, 0.0], [0.25, 0.25, -0.0], [0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125]],
[[-0.25, -0.0, -0.25], [0.25, 0.0, 0.25], [0.125, 0.125, 0.125]],
[[0.125, -0.125, 0.125], [-0.125, -0.125, 0.125], [0.125, 0.125, 0.125]],
[[0.5, 0.0, -0.0], [0.25, 0.25, 0.25],
[0.125, 0.125, 0.125], [0.125, 0.125, 0.125]],
[[0.0, 0.25, 0.25], [0.0, 0.25, 0.25]],
[[0.125, 0.125, 0.125], [0.0, 0.25, 0.25], [0.0, 0.25, 0.25]],
[[-0.125, 0.125, 0.125], [-0.25, 0.25, 0.25], [0.0, 0.0, 0.5]],
[[-0.375, -0.375, 0.375], [0.25, -0.25, 0.0],
[0.0, 0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.0, -0.5, 0.0], [-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[0.375, -0.375, 0.375], [0.0, 0.25, 0.25],
[-0.125, 0.125, -0.125], [-0.25, 0.0, 0.25]],
[[-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125],
[-0.25, 0.25, 0.25], [0.125, -0.125, -0.125]],
[[0.5, 0.0, -0.0], [0.25, -0.25, -0.25], [0.125, -0.125, -0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, -0.25, -0.25], [0.0, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[-0.0, 0.5, 0.0], [-0.25, 0.25, -0.25],
[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[-0.0, 0.0, 0.5], [-0.25, -0.25, 0.25],
[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, 0.125],
[-0.125, -0.125, 0.125], [0.125, 0.125, 0.125]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[0.0, 0.25, 0.25], [0.0, 0.25, 0.25], [0.125, -0.125, -0.125]],
[[0.0, -0.25, -0.25], [0.0, 0.25, 0.25], [0.0, 0.25, 0.25], [0.0, 0.25, 0.25]],
[[0.0, 0.0, 0.5], [0.25, -0.25, 0.25],
[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.0, -0.25, 0.25], [0.0, -0.25, 0.25], [0.125, -0.125, 0.125]],
[[0.0, -0.5, 0.0], [0.125, 0.125, -0.125],
[0.25, 0.25, -0.25], [-0.125, -0.125, 0.125]],
[[-0.125, -0.125, 0.125], [0.0, -0.25, 0.25], [0.0, 0.25, -0.25]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[-0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.25, 0.0, 0.25], [0.25, 0.0, 0.25]],
[[0.125, 0.125, 0.125], [0.25, 0.0, 0.25], [0.25, 0.0, 0.25]],
[[-0.0, 0.0, 0.5], [0.25, -0.25, 0.25], [0.125, -0.125, 0.125]],
[[0.25, 0.0, 0.25], [-0.375, -0.375, 0.375],
[-0.25, 0.25, 0.0], [-0.125, -0.125, 0.125]],
[[0.125, -0.125, 0.125], [0.25, 0.0, 0.25], [0.25, 0.0, 0.25]],
[[-0.25, -0.0, -0.25], [0.25, 0.0, 0.25],
[0.25, 0.0, 0.25], [0.25, 0.0, 0.25]],
[[-0.0, 0.0, 0.5], [0.25, -0.25, 0.25],
[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[-0.25, 0.0, 0.25], [0.25, 0.0, -0.25], [-0.125, 0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.25, 0.25, 0.25], [0.0, 0.0, 0.5]],
[[0.125, 0.125, 0.125], [0.125, 0.125, 0.125],
[0.25, 0.25, 0.25], [0.0, 0.0, 0.5]],
[[-0.0, 0.0, 0.5], [0.0, 0.0, 0.5]],
[[0.0, 0.0, -0.5], [0.25, 0.25, -0.25], [-0.125, -0.125, 0.125]],
[[-0.25, -0.0, -0.25], [-0.375, 0.375, 0.375],
[-0.25, -0.25, 0.0], [-0.125, 0.125, 0.125]],
[[-0.125, -0.125, 0.125], [-0.25, 0.0, 0.25], [0.25, 0.0, -0.25]],
[[-0.0, 0.0, 0.5], [-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[-0.25, 0.0, 0.25], [0.25, 0.0, -0.25]],
[[0.5, 0.0, 0.0], [-0.25, 0.25, -0.25], [0.125, -0.125, 0.125]],
[[-0.25, 0.0, -0.25], [0.375, -0.375, -0.375],
[0.0, 0.25, -0.25], [-0.125, 0.125, 0.125]],
[[-0.25, 0.25, -0.25], [-0.25, 0.25, -0.25],
[-0.125, 0.125, -0.125], [-0.125, 0.125, -0.125]],
[[-0.0, 0.5, 0.0], [-0.25, 0.25, -0.25], [0.125, -0.125, 0.125]],
[[0.5, 0.0, 0.0], [-0.25, -0.25, 0.25],
[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.125, -0.125, 0.125], [-0.25, 0.0, 0.25], [-0.25, 0.0, 0.25]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125], [-0.125, 0.125, 0.125]],
[[-0.125, -0.125, 0.125], [-0.125, 0.125, 0.125]],
[[0.375, -0.375, 0.375], [0.0, -0.25, -0.25],
[-0.125, 0.125, -0.125], [0.25, 0.25, 0.0]],
[[0.0, -0.25, 0.25], [0.0, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.0, 0.0, 0.5], [0.25, -0.25, 0.25], [0.125, -0.125, 0.125]],
[[0.0, -0.25, 0.25], [0.0, -0.25, 0.25]],
[[-0.125, -0.125, 0.125], [-0.25, -0.25, 0.0], [0.25, 0.25, -0.0]],
[[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.125, -0.125, 0.125]],
[[-0.25, -0.25, 0.0], [-0.25, -0.25, 0.0]],
[[0.125, 0.125, 0.125], [-0.25, -0.25, 0.0], [-0.25, -0.25, 0.0]],
[[-0.25, -0.25, 0.0], [-0.25, -0.25, 0.0], [-0.125, -0.125, 0.125]],
[[-0.25, -0.25, 0.0], [-0.25, -0.25, 0.0],
[-0.25, -0.25, 0.0], [0.25, 0.25, -0.0]],
[[0.0, 0.5, 0.0], [0.25, 0.25, -0.25], [-0.125, -0.125, 0.125]],
[[-0.375, 0.375, -0.375], [-0.25, -0.25, 0.0],
[-0.125, 0.125, -0.125], [-0.25, 0.0, 0.25]],
[[0.0, 0.5, 0.0], [0.25, 0.25, -0.25],
[-0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.125, 0.125, 0.125], [0.25, -0.25, 0.0], [-0.25, 0.25, 0.0]],
[[0.0, -0.5, 0.0], [-0.25, -0.25, -0.25], [-0.125, -0.125, -0.125]],
[[0.125, 0.125, 0.125], [0.0, -0.5, 0.0],
[-0.25, -0.25, -0.25], [-0.125, -0.125, -0.125]],
[[-0.375, -0.375, -0.375], [-0.25, 0.0, 0.25],
[-0.125, -0.125, -0.125], [-0.25, 0.25, 0.0]],
[[0.25, -0.25, 0.0], [-0.25, 0.25, 0.0], [0.125, -0.125, 0.125]],
[[0.0, 0.5, 0.0], [0.0, -0.5, 0.0]],
[[0.0, 0.5, 0.0], [0.125, -0.125, 0.125], [-0.25, 0.25, -0.25]],
[[0.0, 0.5, 0.0], [-0.25, 0.25, 0.25], [0.125, -0.125, -0.125]],
[[0.25, -0.25, 0.0], [-0.25, 0.25, 0.0]],
[[-0.5, 0.0, 0.0], [-0.25, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.0, 0.25, -0.25], [0.375, -0.375, -0.375],
[-0.125, 0.125, 0.125], [0.25, 0.25, 0.0]],
[[0.5, 0.0, 0.0], [0.25, -0.25, 0.25],
[-0.125, 0.125, -0.125], [0.125, -0.125, 0.125]],
[[0.125, -0.125, 0.125], [0.25, -0.25, 0.0], [0.25, -0.25, 0.0]],
[[0.25, 0.25, -0.25], [0.25, 0.25, -0.25],
[0.125, 0.125, -0.125], [-0.125, -0.125, 0.125]],
[[-0.0, 0.0, 0.5], [-0.25, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125], [-0.125, 0.125, 0.125]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, 0.125]],
[[-0.375, -0.375, 0.375], [-0.0, 0.25, 0.25],
[0.125, 0.125, -0.125], [-0.25, -0.0, -0.25]],
[[0.0, -0.25, 0.25], [0.0, 0.25, -0.25], [0.125, -0.125, 0.125]],
[[0.125, -0.125, 0.125], [-0.25, -0.0, -0.25], [0.25, 0.0, 0.25]],
[[0.125, -0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.0, -0.5, 0.0], [0.125, 0.125, -0.125], [0.25, 0.25, -0.25]],
[[0.0, -0.25, 0.25], [0.0, 0.25, -0.25]],
[[0.125, 0.125, 0.125], [0.125, -0.125, 0.125]],
[[0.125, -0.125, 0.125]],
[[-0.5, 0.0, 0.0], [-0.125, -0.125, -0.125], [-0.25, -0.25, -0.25]],
[[-0.5, 0.0, 0.0], [-0.125, -0.125, -0.125],
[-0.25, -0.25, -0.25], [0.125, 0.125, 0.125]],
[[0.375, 0.375, 0.375], [0.0, 0.25, -0.25],
[-0.125, -0.125, -0.125], [-0.25, 0.25, 0.0]],
[[0.125, -0.125, -0.125], [0.25, -0.25, 0.0], [0.25, -0.25, 0.0]],
[[0.125, 0.125, 0.125], [0.375, 0.375, 0.375],
[0.0, -0.25, 0.25], [-0.25, 0.0, 0.25]],
[[-0.25, 0.0, 0.25], [-0.25, 0.0, 0.25], [0.125, -0.125, -0.125]],
[[0.0, -0.25, -0.25], [0.0, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[-0.125, 0.125, 0.125], [0.125, -0.125, -0.125]],
[[-0.125, -0.125, -0.125], [-0.25, -0.25, -0.25],
[0.25, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[-0.125, -0.125, 0.125], [0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, 0.0, -0.5], [0.25, 0.25, 0.25], [-0.125, -0.125, -0.125]],
[[0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, -0.5, 0.0], [0.25, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[-0.125, -0.125, 0.125], [0.125, -0.125, -0.125]],
[[0.0, -0.25, -0.25], [0.0, 0.25, 0.25]],
[[0.125, -0.125, -0.125]],
[[0.5, 0.0, 0.0], [0.5, 0.0, 0.0]],
[[-0.5, 0.0, 0.0], [-0.25, 0.25, 0.25], [-0.125, 0.125, 0.125]],
[[0.5, 0.0, 0.0], [0.25, -0.25, 0.25], [-0.125, 0.125, -0.125]],
[[0.25, -0.25, 0.0], [0.25, -0.25, 0.0]],
[[0.5, 0.0, 0.0], [-0.25, -0.25, 0.25], [-0.125, -0.125, 0.125]],
[[-0.25, 0.0, 0.25], [-0.25, 0.0, 0.25]],
[[0.125, 0.125, 0.125], [-0.125, 0.125, 0.125]],
[[-0.125, 0.125, 0.125]],
[[0.5, 0.0, -0.0], [0.25, 0.25, 0.25], [0.125, 0.125, 0.125]],
[[0.125, -0.125, 0.125], [-0.125, -0.125, 0.125]],
[[-0.25, -0.0, -0.25], [0.25, 0.0, 0.25]],
[[0.125, -0.125, 0.125]],
[[-0.25, -0.25, 0.0], [0.25, 0.25, -0.0]],
[[-0.125, -0.125, 0.125]],
[[0.125, 0.125, 0.125]],
[[0, 0, 0]]]
# pylint: enable=line-too-long
def create_table_neighbour_code_to_surface_area(spacing_mm):
"""Returns an array mapping neighbourhood code to the surface elements area.
Note that the normals encode the initial surface area. This function computes
the area corresponding to the given `spacing_mm`.
Args:
spacing_mm: 3-element list-like structure. Voxel spacing in x0, x1 and x2
direction.
"""
# compute the area for all 256 possible surface elements
# (given a 2x2x2 neighbourhood) according to the spacing_mm
neighbour_code_to_surface_area = np.zeros([256])
for code in range(256):
normals = np.array(_NEIGHBOUR_CODE_TO_NORMALS[code])
sum_area = 0
for normal_idx in range(normals.shape[0]):
# normal vector
n = np.zeros([3])
n[0] = normals[normal_idx, 0] * spacing_mm[1] * spacing_mm[2]
n[1] = normals[normal_idx, 1] * spacing_mm[0] * spacing_mm[2]
n[2] = normals[normal_idx, 2] * spacing_mm[0] * spacing_mm[1]
area = np.linalg.norm(n)
sum_area += area
neighbour_code_to_surface_area[code] = sum_area
return neighbour_code_to_surface_area
# In the neighbourhood, points are ordered: top left, top right, bottom left,
# bottom right.
ENCODE_NEIGHBOURHOOD_2D_KERNEL = np.array([[8, 4], [2, 1]])
def create_table_neighbour_code_to_contour_length(spacing_mm):
"""Returns an array mapping neighbourhood code to the contour length.
For the list of possible cases and their figures, see page 38 from:
https://nccastaff.bournemouth.ac.uk/jmacey/MastersProjects/MSc14/06/thesis.pdf
In 2D, each point has 4 neighbors. Thus, are 16 configurations. A
configuration is encoded with '1' meaning "inside the object" and '0' "outside
the object". The points are ordered: top left, top right, bottom left, bottom
right.
The x0 axis is assumed vertical downward, and the x1 axis is horizontal to the
right:
(0, 0) --> (0, 1)
|
(1, 0)
Args:
spacing_mm: 2-element list-like structure. Voxel spacing in x0 and x1
directions.
"""
neighbour_code_to_contour_length = np.zeros([16])
vertical = spacing_mm[0]
horizontal = spacing_mm[1]
diag = 0.5 * math.sqrt(spacing_mm[0]**2 + spacing_mm[1]**2)
# pyformat: disable
neighbour_code_to_contour_length[int("00"
"01", 2)] = diag
neighbour_code_to_contour_length[int("00"
"10", 2)] = diag
neighbour_code_to_contour_length[int("00"
"11", 2)] = horizontal
neighbour_code_to_contour_length[int("01"
"00", 2)] = diag
neighbour_code_to_contour_length[int("01"
"01", 2)] = vertical
neighbour_code_to_contour_length[int("01"
"10", 2)] = 2*diag
neighbour_code_to_contour_length[int("01"
"11", 2)] = diag
neighbour_code_to_contour_length[int("10"
"00", 2)] = diag
neighbour_code_to_contour_length[int("10"
"01", 2)] = 2*diag
neighbour_code_to_contour_length[int("10"
"10", 2)] = vertical
neighbour_code_to_contour_length[int("10"
"11", 2)] = diag
neighbour_code_to_contour_length[int("11"
"00", 2)] = horizontal
neighbour_code_to_contour_length[int("11"
"01", 2)] = diag
neighbour_code_to_contour_length[int("11"
"10", 2)] = diag
# pyformat: enable
return neighbour_code_to_contour_length |