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055ab3a2e3
Summary:
Converts the directory specified to use the Ruff formatter in pyfmt
ruff_dog
If this diff causes merge conflicts when rebasing, please run
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That should help reduce or eliminate any merge conflicts.
allow-large-files
Reviewed By: bottler
Differential Revision: D66472063
fbshipit-source-id: 35841cb397e4f8e066e2159550d2f56b403b1bef
975 lines
37 KiB
Python
975 lines
37 KiB
Python
# Copyright (c) Meta Platforms, Inc. and affiliates.
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# All rights reserved.
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#
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# This source code is licensed under the BSD-style license found in the
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# LICENSE file in the root directory of this source tree.
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import os
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import pickle
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import unittest
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import torch
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from pytorch3d.ops.marching_cubes import marching_cubes, marching_cubes_naive
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from .common_testing import get_tests_dir, TestCaseMixin
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USE_SCIKIT = False
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DATA_DIR = get_tests_dir() / "data"
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def convert_to_local(verts, volume_dim):
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return (2 * verts) / (volume_dim - 1) - 1
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class TestCubeConfiguration(TestCaseMixin, unittest.TestCase):
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# Test single cubes. Each case corresponds to the corresponding
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# cube vertex configuration in each case here (0-indexed):
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# https://en.wikipedia.org/wiki/Marching_cubes#/media/File:MarchingCubes.svg
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def test_empty_volume(self): # case 0
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor([[]])
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expected_faces = torch.tensor([[]], dtype=torch.int64)
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self.assertClose(verts, expected_verts)
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self.assertClose(faces, expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts, expected_verts)
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self.assertClose(faces, expected_faces)
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def test_case1(self): # case 1
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0, 0, 0] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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expected_verts = torch.tensor(
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[
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[0.5, 0, 0],
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[0, 0.5, 0],
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[0, 0, 0.5],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2]])
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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expected_verts = convert_to_local(expected_verts, 2)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case2(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0:2, 0, 0] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[1.0000, 0.0000, 0.5000],
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[0.0000, 0.5000, 0.0000],
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[0.0000, 0.0000, 0.5000],
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[1.0000, 0.5000, 0.0000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [3, 1, 0]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case3(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0, 0, 0] = 0
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volume_data[0, 1, 1, 0] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[1.0000, 0.5000, 0.0000],
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[1.0000, 1.0000, 0.5000],
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[0.5000, 1.0000, 0.0000],
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[0.5000, 0.0000, 0.0000],
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[0.0000, 0.5000, 0.0000],
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[0.0000, 0.0000, 0.5000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [3, 4, 5]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case4(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 1, 0, 0] = 0
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volume_data[0, 1, 0, 1] = 0
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volume_data[0, 0, 0, 1] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[0.0000, 0.0000, 0.5000],
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[1.0000, 0.5000, 0.0000],
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[0.5000, 0.0000, 0.0000],
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[0.0000, 0.5000, 1.0000],
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[1.0000, 0.5000, 1.0000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [0, 3, 1], [3, 4, 1]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case5(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0:2, 0, 0:2] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[1.0000, 0.5000, 0.0000],
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[0.0000, 0.5000, 0.0000],
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[1.0000, 0.5000, 1.0000],
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[0.0000, 0.5000, 1.0000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [2, 1, 3]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case6(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 1, 0, 0] = 0
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volume_data[0, 1, 0, 1] = 0
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volume_data[0, 0, 0, 1] = 0
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volume_data[0, 0, 1, 0] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[0.5000, 1.0000, 0.0000],
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[0.0000, 1.0000, 0.5000],
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[0.0000, 0.5000, 0.0000],
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[1.0000, 0.5000, 0.0000],
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[0.5000, 0.0000, 0.0000],
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[0.0000, 0.5000, 1.0000],
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[1.0000, 0.5000, 1.0000],
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[0.0000, 0.0000, 0.5000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [3, 4, 5], [3, 5, 6], [5, 4, 7]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case7(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0, 0, 0] = 0
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volume_data[0, 1, 0, 1] = 0
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volume_data[0, 1, 1, 0] = 0
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volume_data[0, 0, 1, 1] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[0.5000, 1.0000, 1.0000],
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[0.0000, 0.5000, 1.0000],
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[0.0000, 1.0000, 0.5000],
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[1.0000, 0.0000, 0.5000],
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[0.5000, 0.0000, 1.0000],
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[1.0000, 0.5000, 1.0000],
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[0.5000, 0.0000, 0.0000],
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[0.0000, 0.5000, 0.0000],
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[0.0000, 0.0000, 0.5000],
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[0.5000, 1.0000, 0.0000],
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[1.0000, 0.5000, 0.0000],
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[1.0000, 1.0000, 0.5000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [3, 4, 5], [6, 7, 8], [9, 10, 11]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case8(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0, 0, 0] = 0
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volume_data[0, 0, 0, 1] = 0
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volume_data[0, 1, 0, 1] = 0
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volume_data[0, 0, 1, 1] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[1.0000, 0.5000, 1.0000],
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[0.0000, 1.0000, 0.5000],
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[0.5000, 1.0000, 1.0000],
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[1.0000, 0.0000, 0.5000],
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[0.0000, 0.5000, 0.0000],
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[0.5000, 0.0000, 0.0000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [3, 1, 0], [3, 4, 1], [3, 5, 4]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case9(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 1, 0, 0] = 0
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volume_data[0, 0, 0, 1] = 0
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volume_data[0, 1, 0, 1] = 0
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volume_data[0, 0, 1, 1] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[0.5000, 0.0000, 0.0000],
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[0.0000, 0.0000, 0.5000],
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[0.0000, 1.0000, 0.5000],
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[1.0000, 0.5000, 1.0000],
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[1.0000, 0.5000, 0.0000],
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[0.5000, 1.0000, 1.0000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [0, 2, 3], [0, 3, 4], [5, 3, 2]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case10(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0, 0, 0] = 0
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volume_data[0, 1, 1, 1] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[0.5000, 0.0000, 0.0000],
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[0.0000, 0.5000, 0.0000],
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[0.0000, 0.0000, 0.5000],
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[1.0000, 1.0000, 0.5000],
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[1.0000, 0.5000, 1.0000],
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[0.5000, 1.0000, 1.0000],
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]
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)
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expected_faces = torch.tensor([[0, 1, 2], [3, 4, 5]])
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=False)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
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expected_verts = convert_to_local(expected_verts, 2)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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verts, faces = marching_cubes(volume_data, return_local_coords=True)
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self.assertClose(verts[0], expected_verts)
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self.assertClose(faces[0], expected_faces)
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def test_case11(self):
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volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
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volume_data[0, 0, 0, 0] = 0
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volume_data[0, 1, 0, 0] = 0
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volume_data[0, 1, 1, 1] = 0
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volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
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verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
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expected_verts = torch.tensor(
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[
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[1.0000, 0.0000, 0.5000],
|
|
[0.0000, 0.5000, 0.0000],
|
|
[0.0000, 0.0000, 0.5000],
|
|
[1.0000, 0.5000, 0.0000],
|
|
[1.0000, 1.0000, 0.5000],
|
|
[1.0000, 0.5000, 1.0000],
|
|
[0.5000, 1.0000, 1.0000],
|
|
]
|
|
)
|
|
|
|
expected_faces = torch.tensor([[0, 1, 2], [0, 3, 1], [4, 5, 6]])
|
|
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
|
|
expected_verts = convert_to_local(expected_verts, 2)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=True)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
def test_case12(self):
|
|
volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
|
|
volume_data[0, 1, 0, 0] = 0
|
|
volume_data[0, 0, 1, 0] = 0
|
|
volume_data[0, 1, 1, 1] = 0
|
|
volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
|
|
|
|
expected_verts = torch.tensor(
|
|
[
|
|
[1.0000, 0.0000, 0.5000],
|
|
[1.0000, 0.5000, 0.0000],
|
|
[0.5000, 0.0000, 0.0000],
|
|
[1.0000, 1.0000, 0.5000],
|
|
[1.0000, 0.5000, 1.0000],
|
|
[0.5000, 1.0000, 1.0000],
|
|
[0.0000, 0.5000, 0.0000],
|
|
[0.5000, 1.0000, 0.0000],
|
|
[0.0000, 1.0000, 0.5000],
|
|
]
|
|
)
|
|
|
|
expected_faces = torch.tensor([[0, 1, 2], [3, 4, 5], [6, 7, 8]])
|
|
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
|
|
expected_verts = convert_to_local(expected_verts, 2)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=True)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
def test_case13(self):
|
|
volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
|
|
volume_data[0, 0, 0, 0] = 0
|
|
volume_data[0, 0, 1, 0] = 0
|
|
volume_data[0, 1, 0, 1] = 0
|
|
volume_data[0, 1, 1, 1] = 0
|
|
volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
|
|
|
|
expected_verts = torch.tensor(
|
|
[
|
|
[1.0000, 0.0000, 0.5000],
|
|
[0.5000, 0.0000, 1.0000],
|
|
[1.0000, 1.0000, 0.5000],
|
|
[0.5000, 1.0000, 1.0000],
|
|
[0.0000, 0.0000, 0.5000],
|
|
[0.5000, 0.0000, 0.0000],
|
|
[0.5000, 1.0000, 0.0000],
|
|
[0.0000, 1.0000, 0.5000],
|
|
]
|
|
)
|
|
|
|
expected_faces = torch.tensor([[0, 1, 2], [2, 1, 3], [4, 5, 6], [4, 6, 7]])
|
|
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
|
|
expected_verts = convert_to_local(expected_verts, 2)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=True)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
def test_case14(self):
|
|
volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D)
|
|
volume_data[0, 0, 0, 0] = 0
|
|
volume_data[0, 0, 0, 1] = 0
|
|
volume_data[0, 1, 0, 1] = 0
|
|
volume_data[0, 1, 1, 1] = 0
|
|
volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
|
|
|
|
expected_verts = torch.tensor(
|
|
[
|
|
[0.5000, 0.0000, 0.0000],
|
|
[0.0000, 0.5000, 0.0000],
|
|
[0.0000, 0.5000, 1.0000],
|
|
[1.0000, 1.0000, 0.5000],
|
|
[1.0000, 0.0000, 0.5000],
|
|
[0.5000, 1.0000, 1.0000],
|
|
]
|
|
)
|
|
|
|
expected_faces = torch.tensor([[0, 1, 2], [0, 2, 3], [0, 3, 4], [3, 2, 5]])
|
|
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
|
|
expected_verts = convert_to_local(expected_verts, 2)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=True)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
|
|
class TestMarchingCubes(TestCaseMixin, unittest.TestCase):
|
|
def test_single_point(self):
|
|
volume_data = torch.zeros(1, 3, 3, 3) # (B, W, H, D)
|
|
volume_data[0, 1, 1, 1] = 1
|
|
volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
|
|
|
|
expected_verts = torch.tensor(
|
|
[
|
|
[1.0000, 0.5000, 1.0000],
|
|
[1.0000, 1.0000, 0.5000],
|
|
[0.5000, 1.0000, 1.0000],
|
|
[1.5000, 1.0000, 1.0000],
|
|
[1.0000, 1.5000, 1.0000],
|
|
[1.0000, 1.0000, 1.5000],
|
|
]
|
|
)
|
|
expected_faces = torch.tensor(
|
|
[
|
|
[0, 1, 2],
|
|
[1, 0, 3],
|
|
[1, 4, 2],
|
|
[1, 3, 4],
|
|
[0, 2, 5],
|
|
[3, 0, 5],
|
|
[2, 4, 5],
|
|
[3, 5, 4],
|
|
]
|
|
)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=True)
|
|
expected_verts = convert_to_local(expected_verts, 3)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
|
|
|
|
verts, faces = marching_cubes(volume_data, return_local_coords=True)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
|
|
|
|
def test_cube(self):
|
|
volume_data = torch.zeros(1, 5, 5, 5) # (B, W, H, D)
|
|
volume_data[0, 1, 1, 1] = 1
|
|
volume_data[0, 1, 1, 2] = 1
|
|
volume_data[0, 2, 1, 1] = 1
|
|
volume_data[0, 2, 1, 2] = 1
|
|
volume_data[0, 1, 2, 1] = 1
|
|
volume_data[0, 1, 2, 2] = 1
|
|
volume_data[0, 2, 2, 1] = 1
|
|
volume_data[0, 2, 2, 2] = 1
|
|
volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
expected_verts = torch.tensor(
|
|
[
|
|
[1.0000, 0.9000, 1.0000],
|
|
[1.0000, 1.0000, 0.9000],
|
|
[0.9000, 1.0000, 1.0000],
|
|
[2.0000, 0.9000, 1.0000],
|
|
[2.0000, 1.0000, 0.9000],
|
|
[2.1000, 1.0000, 1.0000],
|
|
[1.0000, 2.0000, 0.9000],
|
|
[0.9000, 2.0000, 1.0000],
|
|
[2.0000, 2.0000, 0.9000],
|
|
[2.1000, 2.0000, 1.0000],
|
|
[1.0000, 2.1000, 1.0000],
|
|
[2.0000, 2.1000, 1.0000],
|
|
[1.0000, 0.9000, 2.0000],
|
|
[0.9000, 1.0000, 2.0000],
|
|
[2.0000, 0.9000, 2.0000],
|
|
[2.1000, 1.0000, 2.0000],
|
|
[0.9000, 2.0000, 2.0000],
|
|
[2.1000, 2.0000, 2.0000],
|
|
[1.0000, 2.1000, 2.0000],
|
|
[2.0000, 2.1000, 2.0000],
|
|
[1.0000, 1.0000, 2.1000],
|
|
[2.0000, 1.0000, 2.1000],
|
|
[1.0000, 2.0000, 2.1000],
|
|
[2.0000, 2.0000, 2.1000],
|
|
]
|
|
)
|
|
|
|
expected_faces = torch.tensor(
|
|
[
|
|
[0, 1, 2],
|
|
[0, 3, 4],
|
|
[1, 0, 4],
|
|
[4, 3, 5],
|
|
[1, 6, 7],
|
|
[2, 1, 7],
|
|
[4, 8, 1],
|
|
[1, 8, 6],
|
|
[8, 4, 5],
|
|
[9, 8, 5],
|
|
[6, 10, 7],
|
|
[6, 8, 11],
|
|
[10, 6, 11],
|
|
[8, 9, 11],
|
|
[12, 0, 2],
|
|
[13, 12, 2],
|
|
[3, 0, 14],
|
|
[14, 0, 12],
|
|
[15, 5, 3],
|
|
[14, 15, 3],
|
|
[2, 7, 13],
|
|
[7, 16, 13],
|
|
[5, 15, 9],
|
|
[9, 15, 17],
|
|
[10, 18, 16],
|
|
[7, 10, 16],
|
|
[11, 19, 10],
|
|
[19, 18, 10],
|
|
[9, 17, 19],
|
|
[11, 9, 19],
|
|
[12, 13, 20],
|
|
[14, 12, 20],
|
|
[21, 14, 20],
|
|
[15, 14, 21],
|
|
[13, 16, 22],
|
|
[20, 13, 22],
|
|
[21, 20, 23],
|
|
[20, 22, 23],
|
|
[17, 15, 21],
|
|
[23, 17, 21],
|
|
[16, 18, 22],
|
|
[23, 22, 18],
|
|
[19, 23, 18],
|
|
[17, 23, 19],
|
|
]
|
|
)
|
|
verts, faces = marching_cubes_naive(volume_data, 0.9, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, 0.9, return_local_coords=False)
|
|
verts2, faces2 = marching_cubes(volume_data, 0.9, return_local_coords=False)
|
|
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(volume_data, 0.9, return_local_coords=True)
|
|
expected_verts = convert_to_local(expected_verts, 5)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
# Check all values are in the range [-1, 1]
|
|
self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
|
|
|
|
verts, faces = marching_cubes(volume_data, 0.9, return_local_coords=True)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
|
|
|
|
def test_cube_no_duplicate_verts(self):
|
|
volume_data = torch.zeros(1, 5, 5, 5) # (B, W, H, D)
|
|
volume_data[0, 1, 1, 1] = 1
|
|
volume_data[0, 1, 1, 2] = 1
|
|
volume_data[0, 2, 1, 1] = 1
|
|
volume_data[0, 2, 1, 2] = 1
|
|
volume_data[0, 1, 2, 1] = 1
|
|
volume_data[0, 1, 2, 2] = 1
|
|
volume_data[0, 2, 2, 1] = 1
|
|
volume_data[0, 2, 2, 2] = 1
|
|
volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume_data, 1, return_local_coords=False)
|
|
|
|
expected_verts = torch.tensor(
|
|
[
|
|
[2.0, 1.0, 1.0],
|
|
[2.0, 2.0, 1.0],
|
|
[1.0, 1.0, 1.0],
|
|
[1.0, 2.0, 1.0],
|
|
[2.0, 1.0, 1.0],
|
|
[1.0, 1.0, 1.0],
|
|
[2.0, 1.0, 2.0],
|
|
[1.0, 1.0, 2.0],
|
|
[1.0, 1.0, 1.0],
|
|
[1.0, 2.0, 1.0],
|
|
[1.0, 1.0, 2.0],
|
|
[1.0, 2.0, 2.0],
|
|
[2.0, 1.0, 1.0],
|
|
[2.0, 1.0, 2.0],
|
|
[2.0, 2.0, 1.0],
|
|
[2.0, 2.0, 2.0],
|
|
[2.0, 2.0, 1.0],
|
|
[2.0, 2.0, 2.0],
|
|
[1.0, 2.0, 1.0],
|
|
[1.0, 2.0, 2.0],
|
|
[2.0, 1.0, 2.0],
|
|
[1.0, 1.0, 2.0],
|
|
[2.0, 2.0, 2.0],
|
|
[1.0, 2.0, 2.0],
|
|
]
|
|
)
|
|
|
|
expected_faces = torch.tensor(
|
|
[
|
|
[0, 1, 2],
|
|
[2, 1, 3],
|
|
[4, 5, 6],
|
|
[6, 5, 7],
|
|
[8, 9, 10],
|
|
[9, 11, 10],
|
|
[12, 13, 14],
|
|
[14, 13, 15],
|
|
[16, 17, 18],
|
|
[17, 19, 18],
|
|
[20, 21, 22],
|
|
[21, 23, 22],
|
|
]
|
|
)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume_data, 1, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(volume_data, 1, return_local_coords=True)
|
|
expected_verts = convert_to_local(expected_verts, 5)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
|
|
|
|
def test_sphere(self):
|
|
# (B, W, H, D)
|
|
volume = torch.Tensor(
|
|
[
|
|
[
|
|
[(x - 10) ** 2 + (y - 10) ** 2 + (z - 10) ** 2 for z in range(20)]
|
|
for y in range(20)
|
|
]
|
|
for x in range(20)
|
|
]
|
|
).unsqueeze(0)
|
|
volume = volume.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(
|
|
volume, isolevel=64, return_local_coords=False
|
|
)
|
|
|
|
data_filename = "test_marching_cubes_data/sphere_level64.pickle"
|
|
filename = os.path.join(DATA_DIR, data_filename)
|
|
with open(filename, "rb") as file:
|
|
verts_and_faces = pickle.load(file)
|
|
expected_verts = verts_and_faces["verts"]
|
|
expected_faces = verts_and_faces["faces"]
|
|
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes(volume, 64, return_local_coords=False)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
verts, faces = marching_cubes_naive(
|
|
volume, isolevel=64, return_local_coords=True
|
|
)
|
|
|
|
expected_verts = convert_to_local(expected_verts, 20)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
|
|
# Check all values are in the range [-1, 1]
|
|
self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
|
|
|
|
verts, faces = marching_cubes(volume, 64, return_local_coords=True)
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
|
|
|
|
# Uses skimage.draw.ellipsoid
|
|
def test_double_ellipsoid(self):
|
|
if USE_SCIKIT:
|
|
import numpy as np
|
|
from skimage.draw import ellipsoid
|
|
|
|
ellip_base = ellipsoid(6, 10, 16, levelset=True)
|
|
ellip_double = np.concatenate(
|
|
(ellip_base[:-1, ...], ellip_base[2:, ...]), axis=0
|
|
)
|
|
volume = torch.Tensor(ellip_double).unsqueeze(0)
|
|
volume = volume.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume, isolevel=0.001)
|
|
verts2, faces2 = marching_cubes(volume, isolevel=0.001)
|
|
|
|
data_filename = "test_marching_cubes_data/double_ellipsoid.pickle"
|
|
filename = os.path.join(DATA_DIR, data_filename)
|
|
with open(filename, "rb") as file:
|
|
verts_and_faces = pickle.load(file)
|
|
expected_verts = verts_and_faces["verts"]
|
|
expected_faces = verts_and_faces["faces"]
|
|
|
|
self.assertClose(verts[0], expected_verts)
|
|
self.assertClose(faces[0], expected_faces)
|
|
self.assertClose(verts2[0], expected_verts)
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|
self.assertClose(faces2[0], expected_faces)
|
|
|
|
def test_single_large_ellipsoid(self):
|
|
if USE_SCIKIT:
|
|
from skimage.draw import ellipsoid
|
|
|
|
ellip_base = ellipsoid(50, 60, 16, levelset=True)
|
|
volume = torch.Tensor(ellip_base).unsqueeze(0).cpu()
|
|
verts, faces = marching_cubes_naive(volume, 0)
|
|
verts2, faces2 = marching_cubes(volume, 0)
|
|
|
|
self.assertClose(verts[0], verts2[0], atol=1e-6)
|
|
self.assertClose(faces[0], faces2[0], atol=1e-6)
|
|
|
|
def test_cube_surface_area(self):
|
|
if USE_SCIKIT:
|
|
from skimage.measure import marching_cubes_classic, mesh_surface_area
|
|
|
|
volume_data = torch.zeros(1, 5, 5, 5)
|
|
volume_data[0, 1, 1, 1] = 1
|
|
volume_data[0, 1, 1, 2] = 1
|
|
volume_data[0, 2, 1, 1] = 1
|
|
volume_data[0, 2, 1, 2] = 1
|
|
volume_data[0, 1, 2, 1] = 1
|
|
volume_data[0, 1, 2, 2] = 1
|
|
volume_data[0, 2, 2, 1] = 1
|
|
volume_data[0, 2, 2, 2] = 1
|
|
volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume_data, return_local_coords=False)
|
|
verts_c, faces_c = marching_cubes(volume_data, return_local_coords=False)
|
|
verts_sci, faces_sci = marching_cubes_classic(volume_data[0])
|
|
|
|
surf = mesh_surface_area(verts[0], faces[0])
|
|
surf_c = mesh_surface_area(verts_c[0], faces_c[0])
|
|
surf_sci = mesh_surface_area(verts_sci, faces_sci)
|
|
|
|
self.assertClose(surf, surf_sci)
|
|
self.assertClose(surf, surf_c)
|
|
|
|
def test_sphere_surface_area(self):
|
|
if USE_SCIKIT:
|
|
from skimage.measure import marching_cubes_classic, mesh_surface_area
|
|
|
|
# (B, W, H, D)
|
|
volume = torch.Tensor(
|
|
[
|
|
[
|
|
[
|
|
(x - 10) ** 2 + (y - 10) ** 2 + (z - 10) ** 2
|
|
for z in range(20)
|
|
]
|
|
for y in range(20)
|
|
]
|
|
for x in range(20)
|
|
]
|
|
).unsqueeze(0)
|
|
volume = volume.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume, isolevel=64)
|
|
verts_c, faces_c = marching_cubes(volume, isolevel=64)
|
|
verts_sci, faces_sci = marching_cubes_classic(volume[0], level=64)
|
|
|
|
surf = mesh_surface_area(verts[0], faces[0])
|
|
surf_c = mesh_surface_area(verts_c[0], faces_c[0])
|
|
surf_sci = mesh_surface_area(verts_sci, faces_sci)
|
|
|
|
self.assertClose(surf, surf_sci)
|
|
self.assertClose(surf, surf_c)
|
|
|
|
def test_double_ellipsoid_surface_area(self):
|
|
if USE_SCIKIT:
|
|
import numpy as np
|
|
from skimage.draw import ellipsoid
|
|
from skimage.measure import marching_cubes_classic, mesh_surface_area
|
|
|
|
ellip_base = ellipsoid(6, 10, 16, levelset=True)
|
|
ellip_double = np.concatenate(
|
|
(ellip_base[:-1, ...], ellip_base[2:, ...]), axis=0
|
|
)
|
|
volume = torch.Tensor(ellip_double).unsqueeze(0)
|
|
volume = volume.permute(0, 3, 2, 1) # (B, D, H, W)
|
|
verts, faces = marching_cubes_naive(volume, isolevel=0)
|
|
verts_c, faces_c = marching_cubes(volume, isolevel=0)
|
|
verts_sci, faces_sci = marching_cubes_classic(volume[0], level=0)
|
|
|
|
surf = mesh_surface_area(verts[0], faces[0])
|
|
surf_c = mesh_surface_area(verts_c[0], faces_c[0])
|
|
surf_sci = mesh_surface_area(verts_sci, faces_sci)
|
|
|
|
self.assertClose(surf, surf_sci)
|
|
self.assertClose(surf, surf_c)
|
|
|
|
def test_ball_example(self):
|
|
N = 30
|
|
axis_tensor = torch.arange(0, N)
|
|
X, Y, Z = torch.meshgrid(axis_tensor, axis_tensor, axis_tensor, indexing="ij")
|
|
u = (X - 15) ** 2 + (Y - 15) ** 2 + (Z - 15) ** 2 - 8**2
|
|
u = u[None].float()
|
|
verts, faces = marching_cubes_naive(u, 0, return_local_coords=False)
|
|
verts2, faces2 = marching_cubes(u, 0, return_local_coords=False)
|
|
self.assertClose(verts2[0], verts[0])
|
|
self.assertClose(faces2[0], faces[0])
|
|
verts3, faces3 = marching_cubes(u.cuda(), 0, return_local_coords=False)
|
|
self.assertEqual(len(verts3), len(verts))
|
|
self.assertEqual(len(faces3), len(faces))
|
|
|
|
@staticmethod
|
|
def marching_cubes_with_init(algo_type: str, batch_size: int, V: int, device: str):
|
|
device = torch.device(device)
|
|
volume_data = torch.rand(
|
|
(batch_size, V, V, V), dtype=torch.float32, device=device
|
|
)
|
|
algo_table = {
|
|
"naive": marching_cubes_naive,
|
|
"extension": marching_cubes,
|
|
}
|
|
|
|
def convert():
|
|
algo_table[algo_type](volume_data, return_local_coords=False)
|
|
torch.cuda.synchronize()
|
|
|
|
return convert
|