def test_zero_signal(self):
test_data_1 = mdtd.MakeTestData(default=False)
assert (test_data_1.signal.data == 0.0).all()
test_data_2 = mdtd.MakeTestData(default=True)
test_data_2.set_signal_zero()
assert (test_data_2.signal.data == 0.0).all()
def test_lw_r(self):
test0 = mdtd.MakeTestData(size_x=120, size_y=100)
test0.add_ring_ellipse(x0=50, y0=50, semi_len0=20, semi_len1=30)
test1 = mdtd.MakeTestData(size_x=120, size_y=100)
test1.add_ring_ellipse(x0=50,
y0=50,
semi_len0=20,
semi_len1=30,
lw_r=3)
assert test0.signal.data.sum() < test1.signal.data.sum()
def setup_method(self):
self.r0, self.r1 = 10, 20
test_data0 = mdtd.MakeTestData(100, 100)
test_data0.add_ring(50, 50, self.r0)
test_data1 = mdtd.MakeTestData(100, 100)
test_data1.add_ring(50, 50, self.r1)
s0, s1 = test_data0.signal, test_data1.signal
s0.axes_manager[0].offset, s0.axes_manager[1].offset = -50, -50
s1.axes_manager[0].offset, s1.axes_manager[1].offset = -50, -50
self.s0, self.s1 = s0, s1
def test_rotation(self):
test0 = mdtd.MakeTestData(size_x=120, size_y=100)
test0.add_ring_ellipse(x0=50, y0=50, semi_len0=20, semi_len1=30)
test1 = mdtd.MakeTestData(size_x=120, size_y=100)
test1.add_ring_ellipse(x0=50,
y0=50,
semi_len0=20,
semi_len1=30,
rotation=1)
assert not (test0.signal.data == test1.signal.data).all()
def test_init(self):
mdtd.MakeTestData(default=True)
mdtd.MakeTestData(size_x=1, size_y=10, scale=0.05)
mdtd.MakeTestData(
size_x=200,
size_y=100,
scale=2,
default=False,
blur=False,
blur_sigma=3.0,
downscale=False,
)
def test_with_downscale_blur_default(self):
test = mdtd.MakeTestData(size_x=120, size_y=100)
test.add_disk_ellipse(x0=50,
y0=50,
semi_len0=10,
semi_len1=13,
intensity=2)
def test_ring_inner_radius(self):
r, lw = 20, 2
x0, y0, scale = 50, 50, 1
test_data = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=False,
downscale=False)
test_data.add_ring(x0=x0, y0=y0, r=r, intensity=10, lw_pix=lw)
r_inner = 20 - 2.5 * scale
s_h0 = test_data.signal.isig[x0, :y0 + 1]
s_h0_edge = s_h0.axes_manager[0].index2value(s_h0.data[::-1].argmax())
r_h0 = s_h0_edge - 0.5 * scale
assert r_h0 == r_inner
s_h1 = test_data.signal.isig[x0, y0:]
s_h1_edge = s_h1.axes_manager[0].index2value(s_h1.data.argmax())
r_h1 = s_h1_edge - 0.5 * scale - 50
assert r_h1 == r_inner
s_h2 = test_data.signal.isig[:x0 + 1, y0]
s_h2_edge = s_h2.axes_manager[0].index2value(s_h2.data[::-1].argmax())
r_h2 = s_h2_edge - 0.5 * scale
assert r_h2 == r_inner
s_h3 = test_data.signal.isig[x0:, y0]
s_h3_edge = s_h3.axes_manager[0].index2value(s_h3.data.argmax())
r_h3 = s_h3_edge - 0.5 * scale - 50
assert r_h3 == r_inner
def test_large_disk(self):
test_data_1 = mdtd.MakeTestData(size_x=10,
size_y=10,
scale=0.01,
default=False)
test_data_1.add_disk(x0=5, y0=5, r=20, intensity=100)
assert (test_data_1.signal.data > 0.0).all()
def get_hot_pixel_signal(lazy=False):
"""Get Diffraction2D signal with a disk in the middle.
Has 4 pixels with value equal to 50000, to simulate hot pixels.
Example
-------
>>> s = pxm.dummy_data.get_hot_pixel_signal()
Lazy signal
>>> s_lazy = pxm.dummy_data.get_hot_pixel_signal(lazy=True)
"""
data = mdtd.MakeTestData(size_x=128, size_y=128, default=False, blur=True)
data.add_disk(64, 64, r=30, intensity=10000)
s = data.signal
s.change_dtype("int64")
s.data += gaussian_filter(s.data, sigma=50)
s.data[76, 4] = 50000
s.data[12, 102] = 50000
s.data[32, 10] = 50000
s.data[120, 61] = 50000
if lazy:
s = LazyDiffraction2D(s)
s.data = da.from_array(s.data, chunks=(64, 64))
else:
s = Diffraction2D(s)
return s
def test_ring_radius_outside_image(self):
test = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=False,
downscale=False)
test.add_ring(x0=50, y0=50, r=300, intensity=19, lw_pix=1)
assert not test.signal.data.any()
def test_very_large_radius_no_cover(self):
test = mdtd.MakeTestData(size_x=120, size_y=100)
test.add_ring_ellipse(x0=50,
y0=50,
semi_len0=200,
semi_len1=159,
intensity=2)
assert not test.signal.data.any()
def test_ring_cover_whole_image(self):
intensity = 10.0
test = mdtd.MakeTestData(size_x=50,
size_y=100,
default=False,
blur=False,
downscale=False)
test.add_ring(x0=25, y0=200, r=150, intensity=intensity, lw_pix=100)
assert (test.signal.data == intensity).all()
def get_single_ring_diffraction_signal():
"""Get HyperSpy 2D signal with a single ring with centre position.
The ring has a centre at x=105 and y=67, and radius=40.
"""
data = mdtd.MakeTestData(size_x=200, size_y=150, default=False, blur=True)
x, y = 105, 67
data.add_ring(x, y, r=40)
s = data.signal
s.axes_manager[0].offset, s.axes_manager[1].offset = -x, -y
return s
def test_refine_signal_centre_position(self):
test_data = mdtd.MakeTestData(
70, 70, blur=False, downscale=False, default=False
)
x, y, r = 35, 35, 15
test_data.add_ring(x, y, r)
s = test_data.signal
s.axes_manager.signal_axes[0].offset = -x + 1
s.axes_manager.signal_axes[1].offset = -y - 1
ra.refine_signal_centre_position(s, (10.0, 20.0), angleN=6)
assert s.axes_manager.signal_axes[0].offset == -x
assert s.axes_manager.signal_axes[1].offset == -y
def test_get_optimal_centre_position(self):
x0, y0 = 300.0, 300.0
test_data = mdtd.MakeTestData(size_x=600, size_y=600, default=False)
test_data.add_ring(x0=x0, y0=y0, r=200, intensity=10, lw_pix=2)
s = test_data.signal
s.axes_manager[0].offset = -301.0
s.axes_manager[1].offset = -301.0
s_centre_position = ra.get_optimal_centre_position(
s, radial_signal_span=(180, 210), steps=2, step_size=1)
x, y = ra.get_coordinate_of_min(s_centre_position)
assert (x0 - 0.5) <= x and x <= (x0 + 0.5)
assert (x0 - 0.5) <= x and x <= (x0 + 0.5)
def test_disk_cover_all(self):
test = mdtd.MakeTestData(size_x=120,
size_y=100,
default=False,
blur=False,
downscale=False)
test.add_disk_ellipse(x0=50,
y0=50,
semi_len0=100,
semi_len1=130,
intensity=2)
assert (test.signal.data == 2).all()
def test_get_optimal_centre_position_off_centre_non_square(self):
test_data = mdtd.MakeTestData(size_x=300,
size_y=400,
default=False,
blur=True,
downscale=False)
x0, y0 = 150, 170
test_data.add_ring(x0=x0, y0=y0, r=100, intensity=10, lw_pix=1)
s = test_data.signal
s.axes_manager[0].offset = -x0 - 2
s.axes_manager[1].offset = -y0 - 3
s_c = ra.get_optimal_centre_position(
test_data.signal,
radial_signal_span=(90, 110),
steps=3,
step_size=1.0,
angleN=8,
)
min_pos0 = ra.get_coordinate_of_min(s_c)
s.axes_manager[0].offset = -x0 + 2
s.axes_manager[1].offset = -y0 - 3
s_c = ra.get_optimal_centre_position(
test_data.signal,
radial_signal_span=(90, 110),
steps=3,
step_size=1.0,
angleN=8,
)
min_pos1 = ra.get_coordinate_of_min(s_c)
s.axes_manager[0].offset = -x0 - 2
s.axes_manager[1].offset = -y0 + 3
s_c = ra.get_optimal_centre_position(
test_data.signal,
radial_signal_span=(90, 110),
steps=3,
step_size=1.0,
angleN=8,
)
min_pos2 = ra.get_coordinate_of_min(s_c)
s.axes_manager[0].offset = -x0 + 2
s.axes_manager[1].offset = -y0 + 3
s_c = ra.get_optimal_centre_position(
test_data.signal,
radial_signal_span=(90, 110),
steps=3,
step_size=1.0,
angleN=8,
)
min_pos3 = ra.get_coordinate_of_min(s_c)
for min_pos in [min_pos0, min_pos1, min_pos2, min_pos3]:
assert approx(min_pos[0]) == x0
assert approx(min_pos[1]) == y0
def test_disk_cover_nothing(self):
test = mdtd.MakeTestData(size_x=120,
size_y=100,
default=False,
blur=False,
downscale=False)
test.add_disk_ellipse(x0=350,
y0=50,
semi_len0=10,
semi_len1=10,
intensity=2)
assert not test.signal.data.any()
def test_blur(self):
test0 = mdtd.MakeTestData(size_x=120,
size_y=100,
downscale=False,
blur=True,
default=False)
test0.add_ring_ellipse(x0=50,
y0=50,
semi_len0=8,
semi_len1=13,
intensity=2)
test1 = mdtd.MakeTestData(size_x=120,
size_y=100,
downscale=False,
blur=False,
default=False)
test1.add_ring_ellipse(x0=50,
y0=50,
semi_len0=8,
semi_len1=13,
intensity=2)
assert not (test0.signal.data == test1.signal.data).all()
def test_ring_rectangle_image(self):
intensity = 10
test = mdtd.MakeTestData(size_x=100,
size_y=50,
default=False,
blur=False,
downscale=False)
test.add_ring(x0=50, y0=25, r=1, intensity=intensity, lw_pix=0)
assert (test.signal.isig[50, 25].data == 0.0).all()
test.signal.data[25, 50] = intensity
assert (test.signal.isig[49:52, 24:27].data == intensity).all()
test.signal.data[24:27, 49:52] = 0.0
assert not test.signal.data.any()
def test_ring_radius2(self):
intensity = 10
test = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=False,
downscale=False)
test.add_ring(x0=50, y0=50, r=2, intensity=intensity, lw_pix=0)
assert (test.signal.isig[49:52, 49:52].data == 0.0).all()
test.signal.data[49:52, 49:52] = intensity
assert (test.signal.isig[48:53, 48:53].data == intensity).all()
test.signal.data[48:53, 48:53] = 0.0
assert not test.signal.data.any()
def test_ring_outer_radius(self):
r, lw = 20, 1
x0, y0, scale = 0, 0, 1
ring_1 = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=False,
downscale=False)
ring_1.add_ring(x0=x0, y0=y0, r=r, intensity=10, lw_pix=lw)
s_h0 = ring_1.signal.isig[x0, :]
s_h0_edge = s_h0.axes_manager[0].index2value(s_h0.data[::-1].argmax())
r_h0 = s_h0.data.size - s_h0_edge - 0.5 * scale
r_out = r + lw + 0.5 * scale
assert r_h0 == r_out
s_h1 = ring_1.signal.isig[:, y0]
s_h1_edge = s_h1.axes_manager[0].index2value(s_h1.data[::-1].argmax())
r_h1 = s_h1.data.size - s_h1_edge - 0.5 * scale
assert r_h1 == r_out
r, lw = 20, 1
x0, y0, scale = 100, 100, 1
ring_2 = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=False,
downscale=False)
ring_2.add_ring(x0=x0, y0=y0, r=r, intensity=10, lw_pix=lw)
s_h2 = ring_2.signal.isig[-1, :]
s_h2_edge = s_h2.axes_manager[0].index2value(s_h2.data.argmax())
r_h2 = 100 - (s_h2_edge - 0.5 * scale)
r_out = r + lw + 0.5 * scale
assert r_h2 == r_out
s_h3 = ring_2.signal.isig[:, -1]
s_h3_edge = s_h3.axes_manager[0].index2value(s_h3.data.argmax())
r_h3 = 100 - (s_h3_edge - 0.5 * scale)
assert r_h3 == r_out
def test_determine_ellipse(self, rot):
test_data = mdtd.MakeTestData(200, 200, default=False)
test_data.add_disk(x0=100, y0=100, r=5, intensity=30)
test_data.add_ring_ellipse(x0=100, y0=100, semi_len0=63, semi_len1=70, rotation=rot)
s = test_data.signal
s.set_signal_type("electron_diffraction")
mask = np.zeros_like(s.data, dtype=bool)
mask[100 - 20:100 + 20, 100 - 20:100 + 20] = True
center, affine = ret.determine_ellipse(s, mask=mask, use_ransac=False)
s.unit = "k_nm^-1"
s.beam_energy = 200
s.axes_manager.signal_axes[0].scale = 0.1
s.axes_manager.signal_axes[1].scale = 0.1
s.set_ai(center=center, affine=affine)
s_az = s.get_azimuthal_integral2d(npt=100)
assert (np.sum((s_az.sum(axis=0).isig[10:] > 1).data) < 10)
def test_disk_semi_len1_very_small(self):
test = mdtd.MakeTestData(size_x=120,
size_y=100,
default=False,
blur=False,
downscale=False)
x0, y0 = 50, 40
intensity = 2
test.add_disk_ellipse(x0=x0,
y0=y0,
semi_len0=1000,
semi_len1=0.1,
intensity=intensity,
rotation=0)
data = test.signal.data
assert (data[y0, :] == intensity).all()
data[y0, :] = 0
assert not data.any()
def test_get_radius_vs_angle(self):
test_data = mdtd.MakeTestData(
101, 121, blur=False, downscale=False, default=False
)
x, y, r0, r1 = 51, 55, 21, 35
test_data.add_ring(x, y, r0)
test_data.add_ring(x, y, r1)
s = test_data.signal
s.axes_manager.signal_axes[0].offset = -x
s.axes_manager.signal_axes[1].offset = -y
s_ar0 = ra.get_radius_vs_angle(
s, radial_signal_span=(15, 25), show_progressbar=False
)
s_ar1 = ra.get_radius_vs_angle(
s, radial_signal_span=(28, 40), show_progressbar=False
)
np.testing.assert_allclose(s_ar0.data, r0, 3)
np.testing.assert_allclose(s_ar1.data, r1, 3)
def test_ring_position_downscale_and_blur(self):
x0, y0, r = 50, 50, 18
test = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=True,
downscale=True)
test.add_ring(x0=x0, y0=y0, r=r, intensity=20, lw_pix=1)
s_h0 = test.signal.isig[x0, 0:y0]
max_h0 = s_h0.axes_manager[0].index2value(s_h0.data.argmax())
assert max_h0 == y0 - r
s_h1 = test.signal.isig[x0, y0:]
max_h1 = s_h1.axes_manager[0].index2value(s_h1.data.argmax())
assert max_h1 == y0 + r
s_v0 = test.signal.isig[0:x0, y0]
max_v0 = s_v0.axes_manager[0].index2value(s_v0.data.argmax())
assert max_v0 == x0 - r
s_v1 = test.signal.isig[x0:, y0]
max_v1 = s_v1.axes_manager[0].index2value(s_v1.data.argmax())
assert max_v1 == x0 + r
def test_repr(self):
test = mdtd.MakeTestData(size_x=250)
repr_string = test.__repr__()
assert str(250) in repr_string
def test_repr(self):
test = mdtd.MakeTestData()
test.add_ring_ellipse(x0=70)
repr_string = test.z_list[0].__repr__()
assert str(70) in repr_string
def test_different_signal_size(self):
s0 = mdtd.MakeTestData(100, 100).signal
s1 = mdtd.MakeTestData(100, 150).signal
with pytest.raises(ValueError):
ra.get_angle_image_comparison(s0, s1)
def test_simple_disks(self):
test0 = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=False,
downscale=False)
test0.add_disk(50, 50, 1, 20)
assert (test0.signal.isig[49:52, 49:52].data == 20).all()
test0.signal.data[49:52, 49:52] = 0
assert not test0.signal.data.any()
test1 = mdtd.MakeTestData(size_x=100,
size_y=100,
default=False,
blur=False,
downscale=False)
test1.add_disk(20, 40, 2, 30)
assert (test1.signal.isig[18:23, 38:43].data == 30).all()
test1.signal.data[38:43, 18:23] = 0
assert not test1.signal.data.any()
test2 = mdtd.MakeTestData(size_x=80,
size_y=120,
default=False,
blur=False,
downscale=False)
test2.add_disk(50, 40, 1, 10)
test2.add_disk(20, 30, 2, 30)
assert (test2.signal.isig[49:52, 39:42].data == 10).all()
assert (test2.signal.isig[19:22, 29:32].data == 30).all()
test2.signal.data[39:42, 49:52] = 0
test2.signal.data[28:33, 18:23] = 0
assert not test2.signal.data.any()
test3 = mdtd.MakeTestData(size_x=150,
size_y=50,
default=False,
blur=False,
downscale=False)
test3.add_disk(200, 400, 2, 30)
assert not test3.signal.data.any()
test4 = mdtd.MakeTestData(size_x=150,
size_y=50,
default=False,
blur=False,
downscale=False)
test4.add_disk(50, 50, 500, 500)
assert (test4.signal.data == 500).all()
test5 = mdtd.MakeTestData(size_x=100,
size_y=200,
default=False,
blur=False,
downscale=True)
test5.add_disk(50, 50, 500, 10)
assert (test5.signal.data == 10).all()
test6 = mdtd.MakeTestData(size_x=100,
size_y=200,
default=False,
blur=True,
downscale=False)
test6.add_disk(50, 30, 500, 10)
test6_ref = np.full_like(test6.signal.data, 10.0)
np.testing.assert_allclose(test6.signal.data, test6_ref, rtol=1e-05)