def test_ellipsoid_stats():
# Test comparison values generated by Wolfram Alpha
vol, surf = ellipsoid_stats(6, 10, 16)
assert_allclose(1280 * np.pi, vol, atol=1e-4)
assert_allclose(1383.28, surf, atol=1e-2)
# Test when a <= b <= c does not hold
vol, surf = ellipsoid_stats(16, 6, 10)
assert_allclose(1280 * np.pi, vol, atol=1e-4)
assert_allclose(1383.28, surf, atol=1e-2)
# Larger test to ensure reliability over broad range
vol, surf = ellipsoid_stats(17, 27, 169)
assert_allclose(103428 * np.pi, vol, atol=1e-4)
assert_allclose(37426.3, surf, atol=1e-1)
def test_ellipsoid_stats():
# Test comparison values generated by Wolfram Alpha
vol, surf = ellipsoid_stats(6, 10, 16)
assert(round(1280 * np.pi, 4) == round(vol, 4))
assert(1383.28 == round(surf, 2))
# Test when a <= b <= c does not hold
vol, surf = ellipsoid_stats(16, 6, 10)
assert(round(1280 * np.pi, 4) == round(vol, 4))
assert(1383.28 == round(surf, 2))
# Larger test to ensure reliability over broad range
vol, surf = ellipsoid_stats(17, 27, 169)
assert(round(103428 * np.pi, 4) == round(vol, 4))
assert(37426.3 == round(surf, 1))
def test_ellipsoid_stats():
# Test comparison values generated by Wolfram Alpha
vol, surf = ellipsoid_stats(6, 10, 16)
assert (round(1280 * np.pi, 4) == round(vol, 4))
assert (1383.28 == round(surf, 2))
# Test when a <= b <= c does not hold
vol, surf = ellipsoid_stats(16, 6, 10)
assert (round(1280 * np.pi, 4) == round(vol, 4))
assert (1383.28 == round(surf, 2))
# Larger test to ensure reliability over broad range
vol, surf = ellipsoid_stats(17, 27, 169)
assert (round(103428 * np.pi, 4) == round(vol, 4))
assert (37426.3 == round(surf, 1))
def test_ellipsoid_stats():
# Test comparison values generated by Wolfram Alpha
vol, surf = ellipsoid_stats(6, 10, 16)
assert_allclose(1280 * np.pi, vol, atol=1e-4)
assert_allclose(1383.28, surf, atol=1e-2)
# Test when a <= b <= c does not hold
vol, surf = ellipsoid_stats(16, 6, 10)
assert_allclose(1280 * np.pi, vol, atol=1e-4)
assert_allclose(1383.28, surf, atol=1e-2)
# Larger test to ensure reliability over broad range
vol, surf = ellipsoid_stats(17, 27, 169)
assert_allclose(103428 * np.pi, vol, atol=1e-4)
assert_allclose(37426.3, surf, atol=1e-1)
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_classic(ellipsoid_anisotropic,
0.,
spacing=spacing)
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_lewiner(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 spacing together with allow_degenerate=False
marching_cubes_lewiner(ellipsoid_anisotropic,
0,
spacing=spacing,
allow_degenerate=False)
def test_marching_cubes_isotropic():
ellipsoid_isotropic = ellipsoid(6, 10, 16, levelset=True)
_, surf = ellipsoid_stats(6, 10, 16)
verts, faces = marching_cubes(ellipsoid_isotropic, 0.)
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_isotropic():
ellipsoid_isotropic = ellipsoid(6, 10, 16, levelset=True)
_, surf = ellipsoid_stats(6, 10, 16)
verts, faces = marching_cubes(ellipsoid_isotropic, 0.)
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():
spacing = (1.0, 10 / 6.0, 16 / 6.0)
ellipsoid_anisotropic = ellipsoid(6, 10, 16, spacing=spacing, levelset=True)
_, surf = ellipsoid_stats(6, 10, 16)
verts, faces = marching_cubes(ellipsoid_anisotropic, 0.0, spacing=spacing)
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
def test_marching_cubes_anisotropic():
sampling = (1., 10 / 6., 16 / 6.)
ellipsoid_anisotropic = ellipsoid(6, 10, 16, sampling=sampling,
levelset=True)
_, surf = ellipsoid_stats(6, 10, 16, sampling=sampling)
verts, faces = marching_cubes(ellipsoid_anisotropic, 0.,
sampling=sampling)
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
def test_marching_cubes_anisotropic():
spacing = (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_classic(ellipsoid_anisotropic, 0.,
spacing=spacing)
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_lewiner(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 spacing together with allow_degenerate=False
marching_cubes_lewiner(ellipsoid_anisotropic, 0, spacing=spacing,
allow_degenerate=False)
def gen3d(shape,
r_range,
h_range,
n_ell=1,
noise=False,
label=False,
ell_stats=False):
'''
3-dimensional image generator for hsi images
:param shape:
:param r_range:
:param h_range:
:param n_ell:
:param noise:
:return:
'''
data = np.zeros(shape)
if noise:
data = random_noise(data)
data *= 200
ells = []
r1 = np.random.randint(r_range[0], r_range[1], n_ell)
r2 = np.random.randint(r_range[0], r_range[1], n_ell)
h = np.random.randint(h_range[0], h_range[1], n_ell)
# assuming shape is 240, 200, 200
# and r_range max val < 30
# and h_range max val < 240
# and 1 <= n_ell <= 6
centers = [
[120, 40, 40],
[120, 40, 80],
[120, 40, 120],
[120, 80, 40],
[120, 80, 80],
[120, 80, 120],
[120, 120, 40],
[120, 120, 80],
[120, 120, 120],
]
for i in range(0, n_ell):
ell = ellipsoid(h[i], r1[i], r2[i], levelset=True)
ell *= -500
ell += 500
# c = centers[i]
# xL = c[1] - r1[i] - 3
# xR = c[1] + r1[i] - 3
# yL = c[1] - r2[i] - 3
# yR = c[1] + r2[i] - 3
# bL = c[0] - h[i]
# bR = c[0] + h[i]
# data[bL:bR, xL:xR, yL:yR] += ell
# ells.append(ell)
data = add_ell(data, ell)
if ell_stats:
stats = []
for i in range(0, n_ell):
stat = ellipsoid_stats(h[i], r1[i], r2[i])
stats.append(stat)
return data
def add_ellipsoid(self,
center,
a,
b,
c,
scale,
bands=None,
rot=0.0,
cut=None,
stats=False,
name=None):
'''
Adds ellipsoid structure in simulated HSI.
:param center: tuple of 2 ints centering structure in image
:param a: length of ellipsoid semi-major x-axis
- currently used for bands
:param b: length of ellipsoid semi-major y-axis
- currently used for x-axis in image
:param c: length of ellipsoid semi-major z-axis
- currently used for y-axis in image
- will be switching to kwargs or other method of creating ellipsoids
:param scale: tuple of 2 ints/floats to alter reflectance of structure across pixels/bands
- typically (-a, b) such that levelset of ellipsoid is flipped by X *= (-a)
- and raised by X += b
:param bands: tuple of 2 ints the band range to add structure
:param rot: rotation elliptical structures in image
- currently only multiples of pi/2 accepted for rotations
:param cut: cut a subsection of ellipsoid structure
- not implemented at the moment
:param stats: bool (T/F) of whether or not to collect ellipsoid stats
:param name: unique string for dict key of ellipsoid stats
- must have valid string if stats==True
:return: None, alters base image from self
'''
ell = ellipsoid(
a,
b,
c,
levelset=True,
)
ell *= scale[0]
ell += scale[1]
d1, d2, d3 = self._s
ed1, ed2, ed3 = ell.shape
c1 = int(ed2 / 2) + 1
c2 = int(ed3 / 2) + 1
rr, cc = ellipse(c1, c2, b, c, shape=(ed2, ed3))
rr1, cc1 = ellipse(center[0],
center[1],
b,
c,
shape=(d2, d3),
rotation=rot)
if d1 < ed1:
self._img[:d1, rr1, cc1] += ell[:d1, rr, cc]
else:
self._img[:ed1, rr1, cc1] += ell[:ed1, rr, cc]
if stats:
stat = ellipsoid_stats(a, b, c)
try:
self.obs[name] = [center, stat]
except ValueError:
raise Exception(
"if stats=True, name must be a unique string not in self.obs"
)
def gen_ell_stats(self):
a, b, c = self.axes
self.stats = ellipsoid_stats(a, b, c)
def gen_ellipsoid(self, a, b, c, stats=False, **kwargs):
self.axes = (a, b, c)
self.structure = ellipsoid(a, b, c, **kwargs, levelset=True)
if stats:
self.stats = ellipsoid_stats(a, b, c)
