def test_flat_image(self):
image_data = np.ones((100, 100)) * 10
atom = Atom_Position(20, 10)
distortion_x, distortion_y = atom.estimate_local_scanning_distortion(
image_data, radius=6, edge_skip=2)
assert approx(distortion_x, 0)
assert approx(distortion_y, 0)
def test_set_mask_radius_atom(self):
atom_list = [Atom_Position(2, 2), Atom_Position(4, 4)]
image = np.random.random((20, 20))
model, mask = afr._make_model_from_atom_list(atom_list=atom_list,
image_data=image,
mask_radius=3)
assert len(model) == 2
def test_value(self):
image_data = np.zeros((100, 100))
x, y, distance, value = 20, 49, 4, 10
image_data[y, x] = value
atom = Atom_Position(x, y)
image_slice, x0, y0 = atom._get_image_slice_around_atom(
image_data, distance)
assert image_slice[distance, distance] == value
def test_close_to_edge_corner(self):
image_data = np.random.random((50, 60))
x, y, distance = 0, 0, 9
atom = Atom_Position(x, y)
image_slice, x0, y0 = atom._get_image_slice_around_atom(
image_data, distance)
assert image_slice.shape == (10, 10)
assert x0 == 0
assert y0 == 0
def test_image_border_y_max(self, im_y):
x, y, sigma, sigma_quantile = 50, 95, 3, 3
atom_position = Atom_Position(x, y, sigma_x=sigma, sigma_y=sigma)
slice_y, slice_x = atom_position._get_atom_slice(
100, im_y, sigma_quantile=sigma_quantile)
assert slice_x.start == x - sigma * sigma_quantile
assert slice_x.stop == x + sigma * sigma_quantile
assert slice_y.start == y - sigma * sigma_quantile
assert slice_y.stop == im_y
def test_image_border_y_0(self):
x, y, sigma, sigma_quantile = 50, 0, 3, 3
atom_position = Atom_Position(x, y, sigma_x=sigma, sigma_y=sigma)
slice_y, slice_x = atom_position._get_atom_slice(
100, 100, sigma_quantile=sigma_quantile)
assert slice_x.start == x - sigma * sigma_quantile
assert slice_x.stop == x + sigma * sigma_quantile
assert slice_y.start == 0
assert slice_y.stop == y + sigma * sigma_quantile
def test_close_to_edge_y1(self):
image_data = np.random.random((50, 50))
x, y, distance = 20, 49, 4
atom = Atom_Position(x, y)
image_slice, x0, y0 = atom._get_image_slice_around_atom(
image_data, distance)
assert image_slice.shape == (5, 9)
assert x0 == (x - distance)
assert y0 == (y - distance)
def test_simple(self):
image_data = np.random.random((50, 50))
x, y, distance = 10, 15, 4
atom = Atom_Position(x, y)
distance = 4
image_slice, x0, y0 = atom._get_image_slice_around_atom(
image_data, distance)
assert image_slice.shape == (9, 9)
assert x0 == (x - distance)
assert y0 == (y - distance)
def test_sigma_quantile(self, quantile):
x, y, sx, sy, sigma_quantile = 25, 30, 2, 4, quantile
atom_position = Atom_Position(x=x, y=y, sigma_x=sx, sigma_y=sy)
slice_y, slice_x = atom_position._get_atom_slice(
100, 100, sigma_quantile=sigma_quantile)
smax = max(sx, sy)
assert slice_x.start == x - smax * sigma_quantile
assert slice_x.stop == x + smax * sigma_quantile
assert slice_y.start == y - smax * sigma_quantile
assert slice_y.stop == y + smax * sigma_quantile
def test_sigma(self):
sigma_x, sigma_y = 2, 3
atom_position = Atom_Position(1, 2, sigma_x=sigma_x, sigma_y=sigma_y)
assert atom_position.sigma_x == sigma_x
assert atom_position.sigma_y == sigma_y
sigma_x, sigma_y = -5, -6
atom_position = Atom_Position(1, 2, sigma_x=sigma_x, sigma_y=sigma_y)
assert atom_position.sigma_x == abs(sigma_x)
assert atom_position.sigma_y == abs(sigma_y)
def test_create_atom_plane_object(self):
atom_list = [
Atom_Position(1, 2),
Atom_Position(2, 4),
]
zone_vector = (1, 2)
atom_list[0]._start_atom = [zone_vector]
atom_list[1]._end_atom = [zone_vector]
atom_lattice = Atom_Lattice()
Atom_Plane(atom_list, zone_vector, atom_lattice)
def test_elliptical_atom(self):
image = np.zeros((100, 100))
atom = Atom_Position(17, 75)
image[77, 15] = 10
image[76, 16] = 10
image[75, 17] = 10
image[74, 18] = 10
image[73, 19] = 10
scanning_distortions = atom.estimate_local_scanning_distortion(
image, radius=4, edge_skip=2)
assert approx(scanning_distortions) == (0.0, 0.0)
def test_values(self):
image_data = np.zeros((100, 100))
image_data[77, 20] = 10
image_data[76, 21] = 10
image_data[75, 20] = 10
image_data[74, 21] = 10
image_data[73, 20] = 10
atom = Atom_Position(20.5, 75)
distortion_x, distortion_y = atom.estimate_local_scanning_distortion(
image_data, radius=4, edge_skip=2)
assert approx(distortion_y, np.std((20, 21, 20, 21, 20)))
def test_as_gaussian(self):
x, y, sx, sy, A, r = 10., 5., 2., 3.5, 9.9, 1.5
atom_position = Atom_Position(x=x,
y=y,
sigma_x=sx,
sigma_y=sy,
amplitude=A,
rotation=r)
g = atom_position.as_gaussian()
assert g.centre_x.value == x
assert g.centre_y.value == y
assert g.sigma_x.value == sx
assert g.sigma_y.value == sy
assert g.A.value == A
assert g.rotation.value == r
def setup_method(self):
atom_lattice = Atom_Lattice()
atom_plane_list = []
for i in range(2):
atom_list = [
Atom_Position(1, 2),
Atom_Position(2, 4),
]
zone_vector = (1, 2)
atom_list[0]._start_atom = [zone_vector]
atom_list[1]._end_atom = [zone_vector]
atom_plane = Atom_Plane(
atom_list, (1, 2), atom_lattice)
atom_plane_list.append(atom_plane)
self.atom_plane_list = atom_plane_list
def add_atom(self, x, y, sigma_x=1, sigma_y=1, amplitude=1, rotation=0):
"""
Add a single atom to the test data.
Parameters
----------
x, y : numbers
Position of the atom.
sigma_x, sigma_y : numbers, default 1
amplitude : number, default 1
rotation : number, default 0
Examples
--------
>>> from atomap.testing_tools import MakeTestData
>>> test_data = MakeTestData(200, 200)
>>> test_data.add_atom(x=10, y=20)
>>> test_data.signal.plot()
"""
atom = Atom_Position(x=x,
y=y,
sigma_x=sigma_x,
sigma_y=sigma_y,
rotation=rotation,
amplitude=amplitude)
self.__sublattice.atom_list.append(atom)
def test_edge_skip_x(self):
image = np.zeros((100, 100))
image[75, 13] = 100
image[77, 15] = 10
image[76, 16] = 10
image[75, 17] = 10
image[74, 18] = 10
image[73, 19] = 10
atom = Atom_Position(17, 75)
scanning_distortions = atom.estimate_local_scanning_distortion(
image, radius=4, edge_skip=0)
assert approx(scanning_distortions[0]) != 0.0
assert approx(scanning_distortions[1]) != 0.0
scanning_distortions = atom.estimate_local_scanning_distortion(
image, radius=4, edge_skip=1)
assert approx(scanning_distortions[0]) == 0.0
assert approx(scanning_distortions[1]) != 0.0
def test_radius(self):
image = np.zeros((100, 100))
image[79, 17] = 100
image[77, 15] = 10
image[76, 16] = 10
image[75, 17] = 10
image[74, 18] = 10
image[73, 19] = 10
atom = Atom_Position(17, 75)
scanning_distortions = atom.estimate_local_scanning_distortion(
image, radius=2, edge_skip=0)
assert approx(scanning_distortions) == (0.0, 0.0)
scanning_distortions = atom.estimate_local_scanning_distortion(
image, radius=3, edge_skip=0)
assert approx(scanning_distortions) == (0.0, 0.0)
scanning_distortions = atom.estimate_local_scanning_distortion(
image, radius=4, edge_skip=0)
assert approx(scanning_distortions) != (0.0, 0.0)
def test_rotation(self):
rotation0 = 0.0
atom_position = Atom_Position(1, 2, rotation=rotation0)
assert atom_position.rotation == rotation0
rotation1 = math.pi / 2
atom_position = Atom_Position(1, 2, rotation=rotation1)
assert atom_position.rotation == rotation1
rotation2 = math.pi
atom_position = Atom_Position(1, 2, rotation=rotation2)
assert atom_position.rotation == 0
rotation3 = math.pi * 3 / 2
atom_position = Atom_Position(1, 2, rotation=rotation3)
assert atom_position.rotation == math.pi / 2
rotation4 = math.pi * 2
atom_position = Atom_Position(1, 2, rotation=rotation4)
assert atom_position.rotation == 0
def setup_method(self):
x, y = [1, 2], [2, 4]
sX, sY, r = [3.1, 1.2], [2.2, 1.1], [0.5, 0.4]
A_g = [10.2, 5.2]
atom_list = [
Atom_Position(x[0], y[0], sX[0], sY[0], r[0]),
Atom_Position(x[1], y[1], sX[1], sY[1], r[1]),
]
atom_list[0].amplitude_gaussian = A_g[0]
atom_list[1].amplitude_gaussian = A_g[1]
zone_vector = (1, 2)
atom_list[0]._start_atom = [zone_vector]
atom_list[1]._end_atom = [zone_vector]
self.atom_plane = Atom_Plane(
atom_list,
zone_vector,
Atom_Lattice())
self.x, self.y, self.sX, self.sY, self.r = x, y, sX, sY, r
self.A_g = A_g
def test_get_atom_angle(self):
atom_position0 = Atom_Position(1, 2)
atom_position1 = Atom_Position(3, 1)
atom_position2 = Atom_Position(1, 0)
atom_position3 = Atom_Position(5, 1)
atom_position4 = Atom_Position(2, 2)
angle90 = self.atom_position.get_angle_between_atoms(
atom_position0, atom_position1)
angle180 = self.atom_position.get_angle_between_atoms(
atom_position0, atom_position2)
angle0 = self.atom_position.get_angle_between_atoms(
atom_position1, atom_position3)
angle45 = self.atom_position.get_angle_between_atoms(
atom_position1, atom_position4)
assert approx(angle90) == pi / 2
assert approx(angle180) == pi
assert approx(angle0) == 0
assert approx(angle45) == pi / 4
def test_make_atom_position_marker_list(self):
atom_position_list = []
for i in range(20):
atom_position = Atom_Position(i, i)
atom_position_list.append(atom_position)
marker_list = pl._make_atom_position_marker_list(
atom_position_list,
scale=0.2,
markersize=30,
color='black',
add_numbers=True)
assert len(marker_list) == 40
class TestAtomPositionObjectTools:
def setup_method(self):
self.atom_position = Atom_Position(1, 1)
def test_get_atom_angle(self):
atom_position0 = Atom_Position(1, 2)
atom_position1 = Atom_Position(3, 1)
atom_position2 = Atom_Position(1, 0)
atom_position3 = Atom_Position(5, 1)
atom_position4 = Atom_Position(2, 2)
angle90 = self.atom_position.get_angle_between_atoms(
atom_position0, atom_position1)
angle180 = self.atom_position.get_angle_between_atoms(
atom_position0, atom_position2)
angle0 = self.atom_position.get_angle_between_atoms(
atom_position1, atom_position3)
angle45 = self.atom_position.get_angle_between_atoms(
atom_position1, atom_position4)
assert approx(angle90) == pi / 2
assert approx(angle180) == pi
assert approx(angle0) == 0
assert approx(angle45) == pi / 4
def test_as_gaussian(self):
x, y, sx, sy, A, r = 10., 5., 2., 3.5, 9.9, 1.5
atom_position = Atom_Position(x=x,
y=y,
sigma_x=sx,
sigma_y=sy,
amplitude=A,
rotation=r)
g = atom_position.as_gaussian()
assert g.centre_x.value == x
assert g.centre_y.value == y
assert g.sigma_x.value == sx
assert g.sigma_y.value == sy
assert g.A.value == A
assert g.rotation.value == r
def test_simple(self):
x, y, sX, sY, r = 7.1, 2.8, 2.1, 3.3, 1.9
atom_position = Atom_Position(x=x,
y=y,
sigma_x=sX,
sigma_y=sY,
rotation=r)
gaussian = afr._atom_to_gaussian_component(atom_position)
assert x == gaussian.centre_x.value
assert y == gaussian.centre_y.value
assert sX == gaussian.sigma_x.value
assert sY == gaussian.sigma_y.value
assert r == gaussian.rotation.value
def test_mask_radius(self):
atom_position0 = Atom_Position(15, 20)
atom_position1 = Atom_Position(15, 20)
image = np.random.randint(1000, size=(30, 30))
x0, y0 = atom_position0._get_center_position_com(image, mask_radius=5)
x1, y1 = atom_position1._get_center_position_com(image, mask_radius=10)
assert x0 != x1
assert y0 != y1
def test_outside_high_x(self):
im_x, im_y = 90, 100
test_data = MakeTestData(im_x, im_y)
test_data.add_atom(100, 50, amplitude=200, sigma_x=10, sigma_y=10)
image = test_data.signal.data
atom_position = Atom_Position(80, 50)
gaussian_list = afr._fit_atom_positions_with_gaussian_model(
[atom_position], image, mask_radius=30)
if gaussian_list is not False:
gaussian = gaussian_list[0]
assert gaussian.centre_x.value > 0
assert gaussian.centre_x.value < im_x
assert gaussian.centre_y.value > 0
assert gaussian.centre_y.value < im_y
def sublattice(self):
atom_list = []
for atom in self.__sublattice.atom_list:
new_atom = Atom_Position(x=atom.pixel_x,
y=atom.pixel_y,
sigma_x=atom.sigma_x,
sigma_y=atom.sigma_y,
rotation=atom.rotation,
amplitude=atom.amplitude_gaussian)
atom_list.append(new_atom)
if self._sublattice_generate_image:
image = self.signal.data
else:
image = np.zeros(self.data_extent[::-1])
sublattice = Sublattice([], image)
sublattice.atom_list = atom_list
return sublattice
def setup_method(self):
self.atom_position = Atom_Position(1, 1)
def test_position(self):
atom_x, atom_y = 10, 20
atom_position = Atom_Position(atom_x, atom_y)
assert atom_position.pixel_x == 10
assert atom_position.pixel_y == 20
def test_amplitude(self):
amplitude = 30
atom_position = Atom_Position(1, 2, amplitude=amplitude)
assert atom_position.amplitude_gaussian == amplitude