From d45091a9bdda77289347b8f90f3dcf850fe3ab95 Mon Sep 17 00:00:00 2001 From: Sivert Dagenborg Date: Fri, 1 Nov 2024 15:14:12 +0100 Subject: [PATCH] Updated documentation --- examples/processing/centering_the_zero_beam.py | 14 ++++++++++---- pyxem/signals/beam_shift.py | 17 ++++++++++------- 2 files changed, 20 insertions(+), 11 deletions(-) diff --git a/examples/processing/centering_the_zero_beam.py b/examples/processing/centering_the_zero_beam.py index 401a78cd3..76eb00546 100644 --- a/examples/processing/centering_the_zero_beam.py +++ b/examples/processing/centering_the_zero_beam.py @@ -43,14 +43,15 @@ # Centering the Zero Beam with constant deflection magnitude # ---------------------------------------------------------- # In the presence of electromagnetic fields in the entire sample area, -# the plane fitting can fail. In this case, two seperate effects can be observed: +# the plane fitting can fail. In this case, two separate effects can be observed: # # 1. The zero beam position varies systematically with the scan position due to the effects of descan # 2. The zero beam will be deflected from electromagnetic fields in the sample # -# Assuming that the effects of 1 are systematic and that the electomagnetic fields are -# large we can try to fit a plane to correct for effects of 1 by minimizing the magnitude -# variance. You may need a mask for good performance. +# Assuming that the effects of 1 are systematic and that the electromagnetic fields have +# constant strengths, we can try to fit a plane to correct for effects of 1 by minimizing the +# magnitude variance. You may need use a mask and/or have several electromagnetic +# domains for good performance. s_probes = pxm.data.simulated_constant_shift_magnitude() @@ -76,4 +77,9 @@ s_shifts -= s_linear_plane s_shifts.get_magnitude_phase_signal().plot() +# For more realistic data, the linear plane optimization algorithm can give poor results. In this case, +# you can change the initial values for the optimization algorithm by using the `initial_values` parameter +# in `get_linear_plane`. See the docstring for more information. Try varying this and see if the plane +# changes significantly. + # %% diff --git a/pyxem/signals/beam_shift.py b/pyxem/signals/beam_shift.py index 2e934e874..6d352a2d9 100644 --- a/pyxem/signals/beam_shift.py +++ b/pyxem/signals/beam_shift.py @@ -90,13 +90,16 @@ def get_linear_plane( 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 x- and y-shifts are described by two linear planes with three parameters. - The two first parameters, d/dx and d/dy, are the changes in x- or y-shift - as you move one position in the navigation space in respectively the x- and y- - directions. The third parameter, x_0 or y_0, are respectively the x- and y- - shifts in the (0, 0) navigation position. The parameters are laid out thusly, - with the first three being for the x-shifts and the rest for the y-shifts: - [d/dx, d/dy, x_0, d/dx, d/dy, y_0] + The horizontal- and vertical-shifts are described by two linear planes + with three parameters. The two first parameters, d/dx and d/dy, are the changes + in horizontal-shift as you move one position in the navigation space in + respectively the x- and y-directions. I. e. they are the steps in + horizontal-shift as you change x- or y-coordinates. The third parameter, + shift_0, is the horizontal-shift in the (0, 0) navigation position. The + vertical-shift are described by similar parameters. In this argument + supply the plane parameters in the following way, with the first three + being for the horizontal-shift and the rest for the vertical-shift: + [d/dx, d/dy, shift_0, d/dx, d/dy, shift_0] Currently only implemented for the case when `constrain_magnitude_variance` is `True`. constrain_magnitude_variance : bool, optional