Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fit linear plane in pyxem.signals.BeamShift.get_linear_plane by minimising magnitude variance #1116

Open
wants to merge 13 commits into
base: main
Choose a base branch
from
Open

Fit linear plane in pyxem.signals.BeamShift.get_linear_plane by minimising magnitude variance #1116

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
13 commits
Select commit Hold shift click to select a range
00c0ca6
Added constrain_magnitude linear plane fitting
sivborg Sep 16, 2024
0b106c0
Updated tokens
sivborg Sep 16, 2024
e5f052b
Exposed initial values
sivborg Sep 17, 2024
12af338
Added test
sivborg Sep 17, 2024
e317ccb
Added more test cases
sivborg Sep 17, 2024
c82353a
More tests and formatting
sivborg Sep 17, 2024
335a39c
Updated changelog
sivborg Sep 17, 2024
a9871d9
Documentation fix
sivborg Sep 17, 2024
09b5371
Documentation
sivborg Sep 17, 2024
c66bbcd
Update variable names and docstring
sivborg Sep 27, 2024
9dcfc5b
Updated tests
sivborg Sep 27, 2024
427afee
Expanded beam centering example
sivborg Sep 27, 2024
16c3c17
Fixes in center direct beam example
sivborg Sep 27, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Exposed initial values
  • Loading branch information
@sivborg
sivborg committed Sep 17, 2024
commit e5f052bc7fc3c014e12ef2b2323820f464f9bb99
11 changes: 9 additions & 2 deletions pyxem/signals/beam_shift.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 43,7 @@ def make_linear_plane(self, **kwargs):
self.data = s_linear_plane.data
self.events.data_changed.trigger(None)

def get_linear_plane(self, mask=None, fit_corners=None, constrain_magnitude=False):
def get_linear_plane(self, mask=None, fit_corners=None, initial_values=None, constrain_magnitude=False):
"""Fit linear planes to the beam shifts, and returns a BeamShift signal
with the planes.

Expand Down Expand Up @@ -81,6 81,13 @@ def get_linear_plane(self, mask=None, fit_corners=None, constrain_magnitude=Fals
fit_corners : float, optional
Make a mask so that the planes are fitted to the corners of the
signal. This mush be set with a number, like 0.05 (5%) or 0.10 (10%).
initial_values : array of floats, optional
Initial guess for the plane parameters. Useful to vary if the plane fitting
does not give desirable results. The parameters are as follows:
[d/dx, d/dy, x_0, d/dx, d/dy, y_0]
where the first three entries are for the x-shift, being in order the
step in x, step in y and the initial value at (0, 0). Similarly for the
last three entries for the y-shift.
constrain_magnitude : bool, optional
Fits the linear planes so there are deflection with constant magnitude.
In the presence of electromagnetic fields in the sample area, least squares
Expand Down Expand Up @@ -128,7 135,7 @@ def get_linear_plane(self, mask=None, fit_corners=None, constrain_magnitude=Fals
if mask.dtype != bool:
raise ValueError("mask needs to be an array of bools")
if constrain_magnitude:
plane_image = bst._get_linear_plane_by_minimizing_magnitude_variance(self, mask=mask)
plane_image = bst._get_linear_plane_by_minimizing_magnitude_variance(self, mask=mask, initial_values=initial_values)
else:
plane_image_x = bst._get_linear_plane_from_signal2d(s_shift_x, mask=mask)
plane_image_y = bst._get_linear_plane_from_signal2d(s_shift_y, mask=mask)
Expand Down
22 changes: 22 additions & 0 deletions pyxem/tests/signals/test_beam_shift.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 65,28 @@ def test_mask(self):
s_lp = s.get_linear_plane(mask=s_mask)
assert s_lp.data == approx(s_orig.data, abs=1e-7)

def test_constrain_magnitude(self):

p = [0.5]*6 # Plane parameters
x, y = np.meshgrid(np.arange(256), np.arange(256))
base_plane_x = p[0] * x p[1] * y p[2]
base_plane_y = p[3] * x p[4] * y p[5]

base_plane = np.stack((base_plane_x,base_plane_y)).T
data = base_plane.copy()

shifts = np.zeros_like(data)
shifts[:128,128:] =(10,10)
shifts[:128,:128] =(-10,-10)
shifts[128:,128:] =(-10,10)
shifts[128:,:128] =(10,10)
data = shifts

s = BeamShift(data)

s_lp = s.get_linear_plane(constrain_magnitude=True)
assert s_lp.data == approx(base_plane.data, abs=1e-7)

def test_lazy_input_error(self):
s = LazyBeamShift(da.zeros((50, 40, 2)))
with pytest.raises(ValueError):
Expand Down