xrheed.xarray_accessors

Xarray accessors for RHEED (Reflection High-Energy Electron Diffraction) data.

Accessors

  • ri: for manipulating and analyzing RHEED images, including plotting and image centering.

  • rp: for manipulating RHEED intensity profiles.

These accessors extend xarray’s DataArray objects with domain-specific methods for RHEED analysis.

Classes

RHEEDAccessor(xarray_obj)

Xarray accessor for RHEED images.

RHEEDProfileAccessor(xarray_obj)

Xarray accessor for RHEED intensity profiles.
class RHEEDAccessor(xarray_obj)[source]

Bases: object

Xarray accessor for RHEED images.

Provides convenient access to RHEED-specific metadata, image manipulation, centering, rotation, and profile extraction methods.

__init__(xarray_obj)[source]
property alpha

Alias for azimuthal_angle (read/write).

property azimuthal_angle

Azimuthal angle in degrees. Stored in attrs as ‘azimuthal_angle’. If present as a coordinate ‘alpha’, returns that instead.

property beam_energy

Beam energy in eV, if set.

property beta

Alias for incident_angle (read/write).

property ewald_radius

Compute the Ewald sphere radius in reciprocal space (k-space).

Returns:

Ewald sphere radius in 1/Å.

Return type:

float

get_profile(center, width, height, stack_index=0, reduce_over='sy', method='mean', show_origin=False, **kwargs)[source]

Extract an intensity profile from the RHEED image or stack.

Parameters:

  • center (tuple[float, float]) – Center coordinates (sx, sy) in mm.

  • width (float) – Width of the profile window in mm.

  • height (float) – Height of the profile window in mm.

  • stack_index (int) – Frame index for stacks (default=0).

  • reduce_over ({'sy', 'sx', 'both'}) – Dimension(s) over which to reduce intensity (default=’sy’).

  • method ({'mean', 'sum'}) – Reduction method (default=’mean’).

  • show_origin (bool) – If True, display a rectangle showing the profile window.

Returns:

Profile data with metadata preserved.

Return type:

xr.DataArray

get_roi_image()[source]

Return a copy of the image restricted to the screen ROI.

The ROI is defined by the attributes ‘screen_roi_width’ and ‘screen_roi_height’ (in mm).

property incident_angle

Incident angle in degrees. Stored in attrs as ‘incident_angle’. If present as a coordinate ‘beta’, returns that instead.

plot_image(ax=None, auto_levels=0.0, show_center_lines=False, show_specular_spot=False, stack_index=0, **kwargs)[source]

Plot a RHEED image or stack frame.

Parameters:

  • ax (matplotlib.axes.Axes, optional) – Axes to plot on. If None, a new figure is created.

  • auto_levels (float) – Automatic contrast adjustment level (default=0.0).

  • show_center_lines (bool) – If True, show horizontal and vertical center lines.

  • show_specular_spot (bool) – If True, highlight the specular spot.

  • stack_index (int) – Frame index for stacks (default=0).

Returns:

The axes containing the plot.

Return type:

matplotlib.axes.Axes

rotate(angle)[source]

Rotate the image or stack of images by a specified angle.

Parameters:

angle (float) – Rotation angle in degrees. Positive values rotate counterclockwise.

property screen_roi_height

Height of the region of interest (ROI) on the screen in mm.

property screen_roi_width

Width of the region of interest (ROI) on the screen in mm.

property screen_sample_distance

1.0 mm.

Type:

Distance between sample and screen in mm. Default

property screen_scale

1.0.

Type:

Screen scale in px/mm. Default

property screen_width

Screen width in mm, if set.

set_center_auto(update_incident_angle=False, stack_index=0)[source]

Automatically determine and apply the image center.

Parameters:

  • update_incident_angle (bool, default False) – If True, recomputes and updates the incident angle after centering.

  • stack_index (int, default 0) – Frame index to use if the data is a stack; ignored otherwise.

set_center_manual(center_x=0.0, center_y=0.0, method='linear')[source]

Manually shift the image center for a single image or a stack.

Parameters:

  • center_x (float or sequence) – Horizontal shift(s). Scalar applied to all frames; array-like must match stack length.

  • center_y (float or sequence) – Vertical shift(s). Same logic as center_x.

  • method ({'linear', 'nearest', 'cubic'}, optional) – Interpolation method for per-frame shifts (default=’linear’).

class RHEEDProfileAccessor(xarray_obj)[source]

Bases: object

Xarray accessor for RHEED intensity profiles.

Provides profile plotting and conversion to reciprocal space.

__init__(xarray_obj)[source]
convert_to_k()[source]

Convert profile coordinates from screen units (sx) to reciprocal space (ky).

Returns:

Profile with ‘sx’ replaced by ‘ky’.

Return type:

xr.DataArray

plot_profile(ax=None, transform_to_k=True, normalize=True, **kwargs)[source]

Plot a RHEED intensity profile.

Parameters:

  • ax (matplotlib.axes.Axes, optional) – Axes to plot on. If None, a new figure is created.

  • transform_to_k (bool) – If True, convert sx to ky using the Ewald sphere.

  • normalize (bool) – If True, normalize intensity to [0, 1].

Returns:

The axes containing the plot.

Return type:

matplotlib.axes.Axes