def test_non_square1(self):
image = np.zeros((40, 80))
y, x = 38, 11
image[y, x] = 10.
cy, cx = afr.calculate_center_of_mass(image)
assert cy == float(y)
assert cx == float(x)
def _get_center_position_com(
self,
image_data,
percent_to_nn=0.40,
mask_radius=None):
'''Get new atom position based on the center of mass approach
Parameters
----------
image_data : Numpy 2D array
percent_to_nn : float, optional
The percent of the distance to the nearest neighbor atom
in the same sub lattice. The distance times this percentage
defines the mask around the atom where the Gaussian will be
fitted. A smaller value can reduce the effect from
neighboring atoms, but might also decrease the accuracy of
the fitting due to less data to fit to.
Default 0.4 (40%).
mask_radius : float, optional
Radius of the mask around each atom. If this is not set,
the radius will be the distance to the nearest atom in the
same sublattice times the `percent_to_nn` value.
Note: if `mask_radius` is not specified, the Atom_Position objects
must have a populated nearest_neighbor_list.
Returns
-------
new_position : tuple
(new x, new y)
'''
if mask_radius is None:
closest_neighbor = 100000000000000000
for neighbor_atom in self.nearest_neighbor_list:
distance = self.get_pixel_distance_from_another_atom(
neighbor_atom)
if distance < closest_neighbor:
closest_neighbor = distance
mask_radius = closest_neighbor * percent_to_nn
cx, cy = int(round(self.pixel_x)), int(round(self.pixel_y))
crop_radius = np.ceil(mask_radius).astype(int)
data = _crop_array(image_data, cx, cy, crop_radius+1)
edgeX, edgeY = cx - crop_radius, cy - crop_radius
data2 = zero_array_outside_circle(data, mask_radius)
new_y, new_x = calculate_center_of_mass(data2)
new_x, new_y = edgeX + new_x, edgeY + new_y
return new_x, new_y
def test_compare_center_of_mass(self):
from scipy.ndimage import center_of_mass
rand = np.random.random((5, 5))
center_of_mass(rand) == afr.calculate_center_of_mass(rand)
def test_find_center(self):
center = np.zeros((5, 5))
center[1, 1] = 1
assert afr.calculate_center_of_mass(center) == (1, 1)