def test_properties():
g = Gaussian2D(add_rotation=True)
angle = np.radians(20)
g.rotation_angle.value = angle
np.testing.assert_allclose(g.rotation_angle_wrapped, angle)
angle = np.radians(380)
g.rotation_angle.value = angle
np.testing.assert_allclose(g.rotation_angle_wrapped,
math.fmod(angle, 2 * np.pi))
g = Gaussian2D(add_rotation=True)
g.sigma_x.value = 0.5
g.sigma_y.value = 0.1
assert g.ellipticity == 5.0
assert g.rotation_angle.value == 0
assert g.sigma_major == 0.5
assert g.sigma_minor == 0.1
angle = np.radians(20)
g.rotation_angle.value = angle
np.testing.assert_allclose(g.rotation_angle_wrapped, angle)
np.testing.assert_allclose(g.rotation_major_axis, angle)
g = Gaussian2D(add_rotation=True)
g.sigma_x.value = 0.1
g.sigma_y.value = 0.5
assert g.ellipticity == 5.0
assert g.rotation_angle.value == 0
assert g.sigma_major == 0.5
assert g.sigma_minor == 0.1
angle = np.radians(20)
g.rotation_angle.value = angle
np.testing.assert_allclose(g.rotation_angle_wrapped, angle)
np.testing.assert_allclose(g.rotation_major_axis, angle - np.pi / 2)
def test_model2D_linear_many_gaussians(self, nav2d):
mesh, x, y = self.mesh, self.x, self.y
gausslow, gausshigh = -8, 8
gauss_step = 8
X, Y = mesh
z = np.zeros(X.shape)
g = Gaussian2D()
for i in np.arange(gausslow, gausshigh + 1, gauss_step):
for j in np.arange(gausslow, gausshigh + 1, gauss_step):
g.centre_x.value = i
g.centre_y.value = j
g.A.value = 10
z += g.function(X, Y)
s = Signal2D(z)
s.axes_manager[-2].offset = x[0]
s.axes_manager[-1].offset = y[0]
s.axes_manager[-2].scale = x[1] - x[0]
s.axes_manager[-1].scale = y[1] - y[0]
if nav2d:
s = hs.stack([s] * 2)
s = hs.stack([s] * 3)
m = s.create_model()
for i in np.arange(gausslow, gausshigh + 1, gauss_step):
for j in np.arange(gausslow, gausshigh + 1, gauss_step):
g = Gaussian2D(centre_x=i, centre_y=j)
g.set_parameters_not_free()
g.A.free = True
m.append(g)
m.fit(optimizer='lstsq')
np.testing.assert_allclose(s.data, m.as_signal().data)
def test_util_fwhm_set():
g1 = Gaussian2D()
g1.fwhm_x = 0.33
g1.fwhm_y = 0.33
g1.A.value = 1.0
np.testing.assert_allclose(g1.fwhm_x, g1.sigma_x.value * sigma2fwhm)
np.testing.assert_allclose(g1.fwhm_y, g1.sigma_y.value * sigma2fwhm)
def test_model2D_one_component(self, nav2d):
mesh, x, y = self.mesh, self.x, self.y
G1 = Gaussian2D(30, 5.0, 4.0, 0, 0)
data = G1.function(*mesh)
s = Signal2D(data)
s.axes_manager[-2].offset = x[0]
s.axes_manager[-1].offset = y[0]
s.axes_manager[-2].scale = x[1] - x[0]
s.axes_manager[-1].scale = y[1] - y[0]
if nav2d:
s = hs.stack([s] * 2)
s = hs.stack([s] * 3)
m = s.create_model()
m.append(G1)
G1.set_parameters_not_free()
G1.A.free = True
m.multifit(optimizer='lstsq', calculate_errors=True)
diff = (s - m.as_signal(show_progressbar=False))
np.testing.assert_allclose(diff.data, 0.0, atol=1E-7)
np.testing.assert_allclose(m.p_std[0], 0.0, atol=1E-7)
def test_height_value():
g = Gaussian2D()
g.sigma_x.value = 0.1
g.sigma_y.value = 0.5
g.A.value = 99
x = np.arange(-2, 2, 0.01)
y = np.arange(-2, 2, 0.01)
xx, yy = np.meshgrid(x, y)
g_image = g.function(xx, yy)
assert approx(g_image.max()) == g.height
def test_function():
g = Gaussian2D()
g.A.value = 14
g.sigma_x.value = 1.
g.sigma_y.value = 2.
g.centre_x.value = -5.
g.centre_y.value = -5.
np.testing.assert_allclose(g.function(-5, -5), 1.1140846)
np.testing.assert_allclose(g.function(-2, -3), 0.007506643)
assert g._is2D
assert g._position_x == g.centre_x
assert g._position_y == g.centre_y
def test_util_height_getset():
g = Gaussian2D()
g.height = 0.165
assert g.height == 0.165
def test_util_height_get():
g = Gaussian2D(A=55)
np.testing.assert_allclose(
g.height, g.A.value / (2 * np.pi * g.sigma_x.value * g.sigma_y.value))
def test_util_fwhm_getset():
g1 = Gaussian2D()
g1.fwhm_x = 0.33
g1.fwhm_y = 0.33
assert g1.fwhm_x == 0.33
assert g1.fwhm_y == 0.33
def test_util_fwhm_get():
g1 = Gaussian2D(sigma_x=0.33, sigma_y=0.33)
g1.A.value = 1.0
assert_allclose(g1.fwhm_x, g1.sigma_x.value * sigma2fwhm)
assert_allclose(g1.fwhm_y, g1.sigma_y.value * sigma2fwhm)
