def test_2d_gaussian_all_arguments(self):
sublattice = Sublattice(self.xy, self.image_data)
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_2d_gaussian(
image_data=self.image_data,
percent_to_nn=0.3,
rotation_enabled=False)
def setup_method(self):
image_data = np.random.random(size=(100, 100))
position_list = []
for x in range(10, 100, 5):
for y in range(10, 100, 5):
position_list.append([x, y])
sublattice = Sublattice(np.array(position_list), image_data)
sublattice.find_nearest_neighbors()
self.sublattice = sublattice
def test_center_of_mass_dtypes(self):
sublattice = Sublattice(self.xy, self.image_data)
sublattice.find_nearest_neighbors()
image_data = 127 * (self.image_data / self.image_data.max())
dtype_list = [
'float64', 'float32', 'float16', 'int64', 'int32', 'int16', 'int8',
'uint64', 'uint32', 'uint16', 'uint8'
]
for dtype in dtype_list:
sublattice.refine_atom_positions_using_center_of_mass(
image_data=image_data.astype(dtype))
def get_polarised_single_sublattice_rotated(image_noise=False, rotation=45):
sublattice = get_polarised_single_sublattice(image_noise=image_noise)
sig = sublattice.signal
sig.map(scipy.ndimage.rotate, angle=rotation, reshape=False)
# sig.plot()
atom_positions = get_atom_positions(sig, separation=7)
rot_sublattice = Sublattice(atom_positions, image=sig.data)
rot_sublattice.find_nearest_neighbors()
rot_sublattice.refine_atom_positions_using_center_of_mass()
# rot_sublattice.plot()
return rot_sublattice
def make_atom_lattice_dumbbell_structure(
s, position_list, dumbbell_vector, show_progressbar=True):
"""
Make Atom_Lattice object from image of dumbbell structure.
Parameters
----------
s : HyperSpy 2D signal
position_list : list of atomic positions
In the form [[x0, y0], [x1, y1], [x2, y2], ...]
dumbbell_vector : tuple
show_progressbar : bool, default True
Returns
-------
dumbbell_lattice: Atomap Dumbbell_Lattice object
Examples
--------
>>> import temul.external.atomap_devel_012.api as am
>>> import temul.external.atomap_devel_012.initial_position_finding as ipf
>>> from temul.external.atomap_devel_012.atom_finding_refining import get_atom_positions
>>> s = am.dummy_data.get_dumbbell_signal()
>>> position_list = get_atom_positions(s, separation=16)
>>> dumbbell_vector = ipf.find_dumbbell_vector(s, 4)
>>> dumbbell_lattice = ipf.make_atom_lattice_dumbbell_structure(
... s, position_list, dumbbell_vector)
"""
dumbbell_list0, dumbbell_list1 = _get_dumbbell_arrays(
s, position_list, dumbbell_vector,
show_progressbar=show_progressbar)
s_modified = do_pca_on_signal(s)
sublattice0 = Sublattice(
atom_position_list=dumbbell_list0,
original_image=s.data,
image=s_modified.data,
color='blue')
sublattice1 = Sublattice(
atom_position_list=dumbbell_list1,
original_image=s.data,
image=s_modified.data,
color='red')
sublattice0.find_nearest_neighbors()
sublattice1.find_nearest_neighbors()
atom_lattice = Dumbbell_Lattice(
image=sublattice0.image,
name="Dumbbell structure",
sublattice_list=[sublattice0, sublattice1])
return(atom_lattice)
def setup_method(self):
test_data = tt.MakeTestData(520, 520)
x, y = np.mgrid[10:510:20j, 10:510:20j]
x, y = x.flatten(), y.flatten()
test_data.add_atom_list(x, y)
s = test_data.signal
atom_positions = afr.get_atom_positions(
signal=s,
separation=10,
threshold_rel=0.02,
)
sublattice = Sublattice(atom_position_list=atom_positions,
image=s.data)
sublattice.find_nearest_neighbors()
self.sublattice = sublattice
def test_manual_processing(self):
s_adf_filename = os.path.join(my_path, "datasets",
"test_ADF_cropped.hdf5")
s = load(s_adf_filename)
s.change_dtype('float32')
atom_positions = afr.get_atom_positions(
signal=s,
separation=17,
threshold_rel=0.02,
)
sublattice = Sublattice(atom_position_list=atom_positions,
image=s.data)
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_center_of_mass(
sublattice.image, percent_to_nn=0.4)
sublattice.refine_atom_positions_using_2d_gaussian(sublattice.image,
percent_to_nn=0.4)
Atom_Lattice(image=s.data, sublattice_list=[sublattice])
sublattice.construct_zone_axes()
def test_center_of_mass_all_arguments(self):
sublattice = Sublattice(self.xy, self.image_data)
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_center_of_mass(
image_data=self.image_data, percent_to_nn=0.3)
def test_center_of_mass_simple(self):
sublattice = Sublattice(self.xy, self.image_data)
with pytest.raises(ValueError):
sublattice.refine_atom_positions_using_center_of_mass()
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_center_of_mass()
def test_2d_gaussian_simple(self):
sublattice = Sublattice(self.xy, self.image_data)
with pytest.raises(ValueError):
sublattice.refine_atom_positions_using_2d_gaussian()
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_2d_gaussian()
