def test_xy_errors_in_conventional_xc_method_as_per_issue_490():
""" This was the MWE example code for the issue """
dp = get_simulated_disc(100, 20)
# translate y by +4
shifted = np.pad(dp, ((0, 4), (0, 0)), "constant")[4:].reshape(1, 1, *dp.shape)
signal = ElectronDiffraction2D(shifted)
spg = SubpixelrefinementGenerator(signal, np.array([[0, 0]]))
peaks = spg.conventional_xc(100, 20, 1).data[0, 0, 0] # as quoted in the issue
np.testing.assert_allclose([0, -4], peaks)
""" we also test com method for clarity """
peaks = spg.center_of_mass_method(60).data[0, 0, 0]
np.testing.assert_allclose([0, -4], peaks, atol=1.5)
""" we also test reference_xc """
peaks = spg.reference_xc(100, dp, 1).data[0, 0, 0] # as quoted in the issue
np.testing.assert_allclose([0, -4], peaks)
def test_out_of_range_vectors_DiffractionVectors(self):
"""Test that putting vectors that lie outside of the
diffraction patterns raises a ValueError"""
vectors = DiffractionVectors(np.array([[1, -100]]))
dp = ElectronDiffraction2D(np.ones((20, 20)))
with pytest.raises(ValueError):
_ = SubpixelrefinementGenerator(dp, vectors)
def test_out_of_range_vectors_numpy(self):
"""Test that putting vectors that lie outside of the
diffraction patterns raises a ValueError"""
vector = np.array([[1, -100]])
dp = ElectronDiffraction2D(np.ones((20, 20)))
with pytest.raises(
ValueError,
match="Some of your vectors do not lie within your diffraction pattern",
):
_ = SubpixelrefinementGenerator(dp, vector)
def test_wrong_navigation_dimensions(self):
"""Tests that navigation dimensions must be appropriate too."""
dp = ElectronDiffraction2D(np.zeros((2, 2, 8, 8)))
vectors = DiffractionVectors(np.zeros((1, 2)))
dp.axes_manager.set_signal_dimension(2)
vectors.axes_manager.set_signal_dimension(0)
# Note - uses regex via re.search()
with pytest.raises(
ValueError,
match=r"Vectors with shape .* must have the same navigation shape as .*",
):
_ = SubpixelrefinementGenerator(dp, vectors)
def get_spr(self, diffraction_vectors):
dp = set_up_for_subpixelpeakfinders().create_spot()
return SubpixelrefinementGenerator(dp, diffraction_vectors)
def setup_method(self):
self.create_dp()
self.create_diffraction_vectors()
self.sprg = SubpixelrefinementGenerator(self.dp, self.diffraction_vectors)
class TestSubpixelPeakFinders:
"""Tests the various peak finders have the correct x,y conventions for
both the vectors and the shifts, in both the numpy and the DiffractionVectors
cases as well as confirming we have avoided 'off by one' errors"""
def create_dp(self):
z1, z1a = np.zeros((128, 128)), np.zeros((128, 128))
z2, z2a = np.zeros((128, 128)), np.zeros((128, 128))
rr, cc = draw.disk((30, 90), radius=4, shape=z1.shape) # 30 is y!
z1[rr, cc], z2[rr, cc] = 1, 1
rr2, cc2 = draw.disk((100, 60), radius=4, shape=z2.shape)
z2[rr2, cc2] = 1
rr, cc = draw.disk((30, 90 + 3), radius=4, shape=z1.shape) # 30 is y!
z1a[rr, cc], z2a[rr, cc] = 1, 1
rr2, cc2 = draw.disk((100 - 2, 60), radius=4, shape=z2.shape)
z2a[rr2, cc2] = 1
# marks centers for local com and local_gaussian_method
z1[30, 90], z2[30, 90], z2[100, 60] = 2, 2, 2
z1a[30, 93], z2a[30, 93], z2a[98, 60] = 10, 10, 10
self.dp = ElectronDiffraction2D(
np.asarray([[z1, z1a], [z2, z2a]])
) # this needs to be in 2x2
def create_diffraction_vectors(self):
v1 = np.array([[90 - 64, 30 - 64]])
v2 = np.array([[90 - 64, 30 - 64], [100 - 64, 60 - 64]])
self.diffraction_vectors = DiffractionVectors(
np.array([[v1, v1], [v2, v2]], dtype=object),
ragged=True,
)
def setup_method(self):
self.create_dp()
self.create_diffraction_vectors()
self.sprg = SubpixelrefinementGenerator(self.dp, self.diffraction_vectors)
def no_shift_case(self, s):
error = s.data[0, 0] - np.asarray([[90 - 64, 30 - 64]])
rms_error = np.sqrt(error[0, 0] ** 2 + error[0, 1] ** 2)
assert rms_error < 1e-5 # perfect detection for this trivial case
def x_shift_case(self, s):
error = s.data[0, 1] - np.asarray([[93 - 64, 30 - 64]])
rms_error = np.sqrt(error[0, 0] ** 2 + error[0, 1] ** 2)
assert rms_error < 0.5 # correct to within a pixel
@pytest.mark.skip(reason="Broken downstream in scikit image")
def test_assertioned_xc(self):
sprg = self.sprg
subpixelsfound = sprg.conventional_xc(12, 4, 8)
self.no_shift_case(subpixelsfound)
self.x_shift_case(subpixelsfound)
def test_assertioned_com(self):
sprg = self.sprg
vector_refine = sprg.center_of_mass_method(12)
self.no_shift_case(vector_refine)
self.x_shift_case(vector_refine)
def test_log(self):
with pytest.raises(
NotImplementedError,
match="This functionality was removed in v.0.13.0",
):
_ = self.sprg.local_gaussian_method(12)