Fixed database typo and removed unnecessary class identifier.
This commit is contained in:
parent
00ad49a143
commit
45fb349a7d
5098 changed files with 952558 additions and 85 deletions
|
|
@ -0,0 +1,180 @@
|
|||
import numpy as np
|
||||
from skimage.draw import ellipsoid, ellipsoid_stats
|
||||
from skimage.measure import marching_cubes, mesh_surface_area
|
||||
from skimage._shared import testing
|
||||
from skimage._shared.testing import assert_array_equal
|
||||
import pytest
|
||||
|
||||
def test_marching_cubes_isotropic():
|
||||
ellipsoid_isotropic = ellipsoid(6, 10, 16, levelset=True)
|
||||
_, surf = ellipsoid_stats(6, 10, 16)
|
||||
|
||||
# Classic
|
||||
verts, faces = marching_cubes(ellipsoid_isotropic, 0., method='_lorensen')
|
||||
surf_calc = mesh_surface_area(verts, faces)
|
||||
# Test within 1% tolerance for isotropic. Will always underestimate.
|
||||
assert surf > surf_calc and surf_calc > surf * 0.99
|
||||
|
||||
# Lewiner
|
||||
verts, faces = marching_cubes(ellipsoid_isotropic, 0.)[:2]
|
||||
surf_calc = mesh_surface_area(verts, faces)
|
||||
# Test within 1% tolerance for isotropic. Will always underestimate.
|
||||
assert surf > surf_calc and surf_calc > surf * 0.99
|
||||
|
||||
|
||||
def test_marching_cubes_anisotropic():
|
||||
# test spacing as numpy array (and not just tuple)
|
||||
spacing = np.array([1., 10 / 6., 16 / 6.])
|
||||
ellipsoid_anisotropic = ellipsoid(6, 10, 16, spacing=spacing,
|
||||
levelset=True)
|
||||
_, surf = ellipsoid_stats(6, 10, 16)
|
||||
|
||||
# Classic
|
||||
verts, faces = marching_cubes(ellipsoid_anisotropic, 0.,
|
||||
spacing=spacing, method='_lorensen')
|
||||
surf_calc = mesh_surface_area(verts, faces)
|
||||
# Test within 1.5% tolerance for anisotropic. Will always underestimate.
|
||||
assert surf > surf_calc and surf_calc > surf * 0.985
|
||||
|
||||
# Lewiner
|
||||
verts, faces = marching_cubes(ellipsoid_anisotropic, 0.,
|
||||
spacing=spacing)[:2]
|
||||
surf_calc = mesh_surface_area(verts, faces)
|
||||
# Test within 1.5% tolerance for anisotropic. Will always underestimate.
|
||||
assert surf > surf_calc and surf_calc > surf * 0.985
|
||||
|
||||
# Test marching cube with mask
|
||||
with pytest.raises(ValueError):
|
||||
verts, faces = marching_cubes(
|
||||
ellipsoid_anisotropic, 0., spacing=spacing,
|
||||
mask=np.array([]))[:2]
|
||||
|
||||
# Test spacing together with allow_degenerate=False
|
||||
marching_cubes(ellipsoid_anisotropic, 0, spacing=spacing,
|
||||
allow_degenerate=False)
|
||||
|
||||
|
||||
def test_invalid_input():
|
||||
# Classic
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.zeros((2, 2, 1)), 0, method='_lorensen')
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.zeros((2, 2, 1)), 1, method='_lorensen')
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.ones((3, 3, 3)), 1, spacing=(1, 2), method='_lorensen')
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.zeros((20, 20)), 0, method='_lorensen')
|
||||
|
||||
# Lewiner
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.zeros((2, 2, 1)), 0)
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.zeros((2, 2, 1)), 1)
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.ones((3, 3, 3)), 1, spacing=(1, 2))
|
||||
with testing.raises(ValueError):
|
||||
marching_cubes(np.zeros((20, 20)), 0)
|
||||
|
||||
|
||||
def test_both_algs_same_result_ellipse():
|
||||
# Performing this test on data that does not have ambiguities
|
||||
|
||||
sphere_small = ellipsoid(1, 1, 1, levelset=True)
|
||||
|
||||
vertices1, faces1 = marching_cubes(sphere_small, 0, method='_lorensen')[:2]
|
||||
vertices2, faces2 = marching_cubes(sphere_small, 0,
|
||||
allow_degenerate=False)[:2]
|
||||
vertices3, faces3 = marching_cubes(sphere_small, 0,
|
||||
allow_degenerate=False,
|
||||
method='lorensen')[:2]
|
||||
|
||||
# Order is different, best we can do is test equal shape and same
|
||||
# vertices present
|
||||
assert _same_mesh(vertices1, faces1, vertices2, faces2)
|
||||
assert _same_mesh(vertices1, faces1, vertices3, faces3)
|
||||
|
||||
|
||||
def _same_mesh(vertices1, faces1, vertices2, faces2, tol=1e-10):
|
||||
""" Compare two meshes, using a certain tolerance and invariant to
|
||||
the order of the faces.
|
||||
"""
|
||||
# Unwind vertices
|
||||
triangles1 = vertices1[np.array(faces1)]
|
||||
triangles2 = vertices2[np.array(faces2)]
|
||||
# Sort vertices within each triangle
|
||||
triang1 = [np.concatenate(sorted(t, key=lambda x:tuple(x)))
|
||||
for t in triangles1]
|
||||
triang2 = [np.concatenate(sorted(t, key=lambda x:tuple(x)))
|
||||
for t in triangles2]
|
||||
# Sort the resulting 9-element "tuples"
|
||||
triang1 = np.array(sorted([tuple(x) for x in triang1]))
|
||||
triang2 = np.array(sorted([tuple(x) for x in triang2]))
|
||||
return (triang1.shape == triang2.shape and
|
||||
np.allclose(triang1, triang2, 0, tol))
|
||||
|
||||
|
||||
def test_both_algs_same_result_donut():
|
||||
# Performing this test on data that does not have ambiguities
|
||||
n = 48
|
||||
a, b = 2.5/n, -1.25
|
||||
|
||||
vol = np.empty((n, n, n), 'float32')
|
||||
for iz in range(vol.shape[0]):
|
||||
for iy in range(vol.shape[1]):
|
||||
for ix in range(vol.shape[2]):
|
||||
# Double-torii formula by Thomas Lewiner
|
||||
z, y, x = float(iz)*a+b, float(iy)*a+b, float(ix)*a+b
|
||||
vol[iz,iy,ix] = ( (
|
||||
(8*x)**2 + (8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) * ( (8*x)**2 +
|
||||
(8*y-2)**2 + (8*z)**2 + 16 - 1.85*1.85 ) - 64 * ( (8*x)**2 + (8*y-2)**2 )
|
||||
) * ( ( (8*x)**2 + ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2 + 16 - 1.85*1.85 )
|
||||
* ( (8*x)**2 + ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2 + 16 - 1.85*1.85 ) -
|
||||
64 * ( ((8*y-2)+4)*((8*y-2)+4) + (8*z)**2
|
||||
) ) + 1025
|
||||
|
||||
vertices1, faces1 = marching_cubes(vol, 0, method='_lorensen')[:2]
|
||||
vertices2, faces2 = marching_cubes(vol, 0)[:2]
|
||||
vertices3, faces3 = marching_cubes(vol, 0, method='lorensen')[:2]
|
||||
|
||||
# Old and new alg are different
|
||||
assert not _same_mesh(vertices1, faces1, vertices2, faces2)
|
||||
# New classic and new Lewiner are different
|
||||
assert not _same_mesh(vertices2, faces2, vertices3, faces3)
|
||||
# Would have been nice if old and new classic would have been the same
|
||||
# assert _same_mesh(vertices1, faces1, vertices3, faces3, 5)
|
||||
|
||||
|
||||
def test_masked_marching_cubes():
|
||||
|
||||
ellipsoid_scalar = ellipsoid(6, 10, 16, levelset=True)
|
||||
mask = np.ones_like(ellipsoid_scalar, dtype=bool)
|
||||
mask[:10, :, :] = False
|
||||
mask[:, :, 20:] = False
|
||||
ver, faces, _, _ = marching_cubes(ellipsoid_scalar, 0, mask=mask)
|
||||
area = mesh_surface_area(ver, faces)
|
||||
|
||||
np.testing.assert_allclose(area, 299.56878662109375, rtol=.01)
|
||||
|
||||
|
||||
def test_masked_marching_cubes_empty():
|
||||
ellipsoid_scalar = ellipsoid(6, 10, 16, levelset=True)
|
||||
mask = np.array([])
|
||||
with pytest.raises(ValueError):
|
||||
_ = marching_cubes(ellipsoid_scalar, 0, mask=mask)
|
||||
|
||||
|
||||
def test_masked_marching_cubes_old_lewiner():
|
||||
ellipsoid_scalar = ellipsoid(6, 10, 16, levelset=True)
|
||||
mask = np.array([])
|
||||
with pytest.raises(NotImplementedError):
|
||||
_ = marching_cubes(ellipsoid_scalar, 0, mask=mask, method='_lorensen')
|
||||
|
||||
|
||||
def test_masked_marching_cubes_all_true():
|
||||
ellipsoid_scalar = ellipsoid(6, 10, 16, levelset=True)
|
||||
mask = np.ones_like(ellipsoid_scalar, dtype=bool)
|
||||
ver_m, faces_m, _, _ = marching_cubes(ellipsoid_scalar, 0, mask=mask)
|
||||
ver, faces, _, _ = marching_cubes(ellipsoid_scalar, 0, mask=mask)
|
||||
np.testing.assert_allclose(ver_m, ver, rtol=.00001)
|
||||
np.testing.assert_allclose(faces_m, faces, rtol=.00001)
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue