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"].squeeze() expected_faces = verts_and_faces["faces"].squeeze() 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())
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([ [0.5000, 0.0000, 0.0000], [0.0000, 0.0000, 0.5000], [1.0000, 1.0000, 0.5000], [0.5000, 1.0000, 0.0000], [1.0000, 0.5000, 0.0000], [0.0000, 0.5000, 0.0000], ]) expected_faces = torch.tensor([[0, 1, 5], [4, 3, 2]]) 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)
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([ [0.5, 1, 1], [1, 1, 0.5], [1, 0.5, 1], [1, 1, 1.5], [1, 1.5, 1], [1.5, 1, 1], ]) expected_faces = torch.tensor([ [2, 0, 1], [2, 3, 0], [0, 4, 1], [3, 4, 0], [5, 2, 1], [3, 2, 5], [5, 1, 4], [3, 5, 4], ]) 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())
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([ [1.0, 1.0, 1.0], [1.0, 1.0, 2.0], [1.0, 2.0, 1.0], [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], ]) expected_faces = torch.tensor([ [1, 3, 0], [3, 2, 0], [5, 1, 4], [4, 1, 0], [4, 0, 6], [0, 2, 6], [5, 7, 1], [1, 7, 3], [7, 6, 3], [6, 2, 3], [5, 4, 7], [7, 4, 6], ]) 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) # Check all values are in the range [-1, 1] self.assertTrue(verts[0].ge(-1).all() and verts[0].le(1).all())
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)
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_sci, faces_sci = marching_cubes_classic(volume[0], level=64) surf = mesh_surface_area(verts[0], faces[0]) surf_sci = mesh_surface_area(verts_sci, faces_sci) self.assertClose(surf, surf_sci)
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_sci, faces_sci = marching_cubes_classic(volume[0], level=0) surf = mesh_surface_area(verts[0], faces[0]) surf_sci = mesh_surface_area(verts_sci, faces_sci) self.assertClose(surf, surf_sci)
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) 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[0]) self.assertClose(faces[0], expected_faces[0])
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_sci, faces_sci = marching_cubes_classic(volume_data[0]) surf = mesh_surface_area(verts[0], faces[0]) surf_sci = mesh_surface_area(verts_sci, faces_sci) self.assertClose(surf, surf_sci)
def convert(): marching_cubes_naive(volume_data, return_local_coords=False) torch.cuda.synchronize()
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) verts, faces = marching_cubes_naive(volume_data, 0.9, return_local_coords=False) expected_verts = torch.tensor([ [0.9000, 1.0000, 1.0000], [1.0000, 1.0000, 0.9000], [1.0000, 0.9000, 1.0000], [0.9000, 1.0000, 2.0000], [1.0000, 0.9000, 2.0000], [1.0000, 1.0000, 2.1000], [0.9000, 2.0000, 1.0000], [1.0000, 2.0000, 0.9000], [0.9000, 2.0000, 2.0000], [1.0000, 2.0000, 2.1000], [1.0000, 2.1000, 1.0000], [1.0000, 2.1000, 2.0000], [2.0000, 1.0000, 0.9000], [2.0000, 0.9000, 1.0000], [2.0000, 0.9000, 2.0000], [2.0000, 1.0000, 2.1000], [2.0000, 2.0000, 0.9000], [2.0000, 2.0000, 2.1000], [2.0000, 2.1000, 1.0000], [2.0000, 2.1000, 2.0000], [2.1000, 1.0000, 1.0000], [2.1000, 1.0000, 2.0000], [2.1000, 2.0000, 1.0000], [2.1000, 2.0000, 2.0000], ]) expected_faces = torch.tensor([ [2, 0, 1], [2, 4, 3], [0, 2, 3], [4, 5, 3], [0, 6, 7], [1, 0, 7], [3, 8, 0], [8, 6, 0], [5, 9, 8], [3, 5, 8], [6, 10, 7], [11, 10, 6], [8, 11, 6], [9, 11, 8], [13, 2, 1], [12, 13, 1], [14, 4, 13], [13, 4, 2], [4, 14, 15], [5, 4, 15], [12, 1, 16], [1, 7, 16], [15, 17, 5], [5, 17, 9], [16, 7, 10], [18, 16, 10], [19, 18, 11], [18, 10, 11], [9, 17, 19], [11, 9, 19], [20, 13, 12], [20, 21, 14], [13, 20, 14], [15, 14, 21], [22, 20, 12], [16, 22, 12], [21, 20, 23], [23, 20, 22], [17, 15, 21], [23, 17, 21], [22, 16, 18], [23, 22, 18], [19, 23, 18], [17, 23, 19], ]) 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())