# Copyright (c) Meta Platforms, Inc. and affiliates. # All rights reserved. # # This source code is licensed under the BSD-style license found in the # LICENSE file in the root directory of this source tree. import os import pickle import unittest import torch from pytorch3d.ops.marching_cubes import marching_cubes, marching_cubes_naive from .common_testing import get_tests_dir, TestCaseMixin USE_SCIKIT = False DATA_DIR = get_tests_dir() / "data" def convert_to_local(verts, volume_dim): return (2 * verts) / (volume_dim - 1) - 1 class TestCubeConfiguration(TestCaseMixin, unittest.TestCase): # Test single cubes. Each case corresponds to the corresponding # cube vertex configuration in each case here (0-indexed): # https://en.wikipedia.org/wiki/Marching_cubes#/media/File:MarchingCubes.svg def test_empty_volume(self): # case 0 volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) verts, faces = marching_cubes_naive(volume_data, return_local_coords=False) expected_verts = torch.tensor([[]]) expected_faces = torch.tensor([[]], dtype=torch.int64) self.assertClose(verts, expected_verts) self.assertClose(faces, expected_faces) verts, faces = marching_cubes(volume_data, return_local_coords=False) self.assertClose(verts, expected_verts) self.assertClose(faces, expected_faces) def test_case1(self): # case 1 volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 0, 0, 0] = 0 volume_data = volume_data.permute(0, 3, 2, 1) # (B, D, H, W) expected_verts = torch.tensor( [ [0.5, 0, 0], [0, 0.5, 0], [0, 0, 0.5], ] ) expected_faces = torch.tensor([[0, 1, 2]]) verts, faces = marching_cubes_naive(volume_data, return_local_coords=False) 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) expected_verts = convert_to_local(expected_verts, 2) verts, faces = marching_cubes_naive(volume_data, return_local_coords=True) 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_case2(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 0:2, 0, 0] = 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], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, 0.5000], [1.0000, 0.5000, 0.0000], ] ) expected_faces = torch.tensor([[0, 1, 2], [3, 1, 0]]) 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_case3(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 0, 0, 0] = 0 volume_data[0, 1, 1, 0] = 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, 0.5000, 0.0000], [1.0000, 1.0000, 0.5000], [0.5000, 1.0000, 0.0000], [0.5000, 0.0000, 0.0000], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, 0.5000], ] ) expected_faces = torch.tensor([[0, 1, 2], [3, 4, 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) def test_case4(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 1, 0, 0] = 0 volume_data[0, 1, 0, 1] = 0 volume_data[0, 0, 0, 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( [ [0.0000, 0.0000, 0.5000], [1.0000, 0.5000, 0.0000], [0.5000, 0.0000, 0.0000], [0.0000, 0.5000, 1.0000], [1.0000, 0.5000, 1.0000], ] ) expected_faces = torch.tensor([[0, 1, 2], [0, 3, 1], [3, 4, 1]]) 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_case5(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 0:2, 0, 0:2] = 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, 0.5000, 0.0000], [0.0000, 0.5000, 0.0000], [1.0000, 0.5000, 1.0000], [0.0000, 0.5000, 1.0000], ] ) expected_faces = torch.tensor([[0, 1, 2], [2, 1, 3]]) 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_case6(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 1, 0, 0] = 0 volume_data[0, 1, 0, 1] = 0 volume_data[0, 0, 0, 1] = 0 volume_data[0, 0, 1, 0] = 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, 1.0000, 0.0000], [0.0000, 1.0000, 0.5000], [0.0000, 0.5000, 0.0000], [1.0000, 0.5000, 0.0000], [0.5000, 0.0000, 0.0000], [0.0000, 0.5000, 1.0000], [1.0000, 0.5000, 1.0000], [0.0000, 0.0000, 0.5000], ] ) expected_faces = torch.tensor([[0, 1, 2], [3, 4, 5], [3, 5, 6], [5, 4, 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_case7(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 0, 0, 0] = 0 volume_data[0, 1, 0, 1] = 0 volume_data[0, 1, 1, 0] = 0 volume_data[0, 0, 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, 1.0000, 1.0000], [0.0000, 0.5000, 1.0000], [0.0000, 1.0000, 0.5000], [1.0000, 0.0000, 0.5000], [0.5000, 0.0000, 1.0000], [1.0000, 0.5000, 1.0000], [0.5000, 0.0000, 0.0000], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, 0.5000], [0.5000, 1.0000, 0.0000], [1.0000, 0.5000, 0.0000], [1.0000, 1.0000, 0.5000], ] ) expected_faces = torch.tensor([[0, 1, 2], [3, 4, 5], [6, 7, 8], [9, 10, 11]]) 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_case8(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, 0, 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, 0.5000, 1.0000], [0.0000, 1.0000, 0.5000], [0.5000, 1.0000, 1.0000], [1.0000, 0.0000, 0.5000], [0.0000, 0.5000, 0.0000], [0.5000, 0.0000, 0.0000], ] ) expected_faces = torch.tensor([[0, 1, 2], [3, 1, 0], [3, 4, 1], [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, 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_case9(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 1, 0, 0] = 0 volume_data[0, 0, 0, 1] = 0 volume_data[0, 1, 0, 1] = 0 volume_data[0, 0, 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, 0.0000, 0.5000], [0.0000, 1.0000, 0.5000], [1.0000, 0.5000, 1.0000], [1.0000, 0.5000, 0.0000], [0.5000, 1.0000, 1.0000], ] ) expected_faces = torch.tensor([[0, 1, 2], [0, 2, 3], [0, 3, 4], [5, 3, 2]]) 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_case10(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 0, 0, 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( [ [0.5000, 0.0000, 0.0000], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, 0.5000], [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], [3, 4, 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) def test_case11(self): volume_data = torch.ones(1, 2, 2, 2) # (B, W, H, D) volume_data[0, 0, 0, 0] = 0 volume_data[0, 1, 0, 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], [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) 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