def test_get_simple_cubic_signal(self):
s0 = dd.get_simple_cubic_signal()
s0.plot()
s1 = dd.get_simple_cubic_signal(image_noise=False)
s1.plot()
s2 = dd.get_simple_cubic_signal(image_noise=True)
s2.plot()
def test_pca_subtract_background_normalize_intensity(self):
s = dd.get_simple_cubic_signal()
s_fs = afr.get_feature_separation(s,
pca=True,
subtract_background=True,
normalize_intensity=True)
assert hasattr(s_fs, 'data')
def test_detector_normalisation(self):
det_image = get_detector_image_signal()
img = get_simple_cubic_signal(image_noise=True)
img = (img) * 300000 + 4000
image_normalised = quant.detector_normalisation(img, det_image, 60)
assert image_normalised.data.max() < 1
assert image_normalised.data.shape == img.data.shape
def test_separation_step(self):
sr0, sr1, s_step = 10, 16, 2
s = dd.get_simple_cubic_signal()
s_fs = afr.get_feature_separation(s,
separation_range=(sr0, sr1),
separation_step=s_step)
assert s_fs.axes_manager.navigation_size == ((sr1 - sr0) / s_step)
def test_dtypes(self):
dtype_list = [
'float64', 'float32', 'uint64', 'uint32', 'uint16', 'uint8',
'int64', 'int32', 'int16', 'int8'
]
s = dd.get_simple_cubic_signal()
s *= 10**9
for dtype in dtype_list:
print(dtype)
s.change_dtype(dtype)
afr.get_feature_separation(s, separation_range=(10, 15))
s.change_dtype('float16')
with pytest.raises(ValueError):
afr.get_feature_separation(s, separation_range=(10, 15))
overwrite=True)
def plot_planes_figure(sublattice):
s = sublattice.get_all_atom_planes_by_zone_vector()
s.plot()
s.axes_manager.indices = (1, )
s._plot.signal_plot.figure.savefig(os.path.join(my_path,
'zone_axes_sig.png'),
overwrite=True)
s._plot.navigator_plot.figure.savefig(os.path.join(my_path,
'zone_axes_nav.png'),
overwrite=True)
s = dummy_data.get_simple_cubic_signal(image_noise=True)
save_simple_cubic_image(s)
save_s_peaks_image(s)
atom_positions = am.get_atom_positions(s, separation=7)
sublattice = am.Sublattice(atom_positions, image=s.data)
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_center_of_mass()
sublattice.refine_atom_positions_using_2d_gaussian()
plot_position_history(sublattice)
sublattice.construct_zone_axes()
plot_planes_figure(sublattice)
def test_inverted_signal(self):
s = dd.get_simple_cubic_signal()
amm.run_image_filtering(s, invert_signal=True)
def test_standard(self):
s = dd.get_simple_cubic_signal()
amm.run_image_filtering(s)
def test_find_no_peaks(self):
s = dd.get_simple_cubic_signal().isig[:5., :5.]
with pytest.raises(ValueError):
afr.get_feature_separation(s)
def test_small_input_size_large_separation_range(self):
# For small images and large separation, no peaks can be returned.
# This test checks that this doesn't result in an error.
s = dd.get_simple_cubic_signal().isig[:50., :50.]
afr.get_feature_separation(s)
def test_separation_range_bad(self, separation_range):
s = dd.get_simple_cubic_signal()
with pytest.raises(ValueError):
afr.get_feature_separation(s, separation_range)
def test_too_low_separation_low(self, separation_low):
separation_range = (separation_low, 3)
s = dd.get_simple_cubic_signal()
with pytest.raises(ValueError):
afr.get_feature_separation(s, separation_range)
def test_separation_range(self):
sr0, sr1 = 10, 15
s = dd.get_simple_cubic_signal()
s_fs = afr.get_feature_separation(s, separation_range=(sr0, sr1))
assert s_fs.axes_manager.navigation_size == (sr1 - sr0)
assert s_fs.axes_manager.navigation_extent == (sr0, sr1 - 1)
def test_simple(self):
s = dd.get_simple_cubic_signal()
s_fs = afr.get_feature_separation(s)
s_fs.plot()
def test_too_low_separation(self, separation):
s = dd.get_simple_cubic_signal()
with pytest.raises(ValueError):
afr.get_atom_positions(s, separation)