Probe#

class abtem.waves.Probe(semiangle_cutoff=None, extent=None, gpts=None, sampling=None, energy=None, soft=True, tilt=(0.0, 0.0), device=None, aperture=None, aberrations=None, positions=None, metadata=None, **kwargs)[source]#

Bases: abtem.waves._WavesBuilder

Represents electron-probe wave functions for simulating experiments with a convergent beam, such as CBED and STEM.

Parameters

semiangle_cutoff (float, optional) – The cutoff semiangle of the aperture [mrad]. Ignored if a custom aperture is given.
extent (float or two float, optional) – Lateral extent of wave functions [Å] in x and y directions. If a single float is given, both are set equal.
gpts (two ints, optional) – Number of grid points describing the wave functions.
sampling (two float, optional) – Lateral sampling of wave functions [1 / Å]. If ‘gpts’ is also given, will be ignored.
energy (float, optional) – Electron energy [eV]. If not provided, inferred from the wave functions.
soft (float, optional) – Taper the edge of the default aperture [mrad] (default is 2.0). Ignored if a custom aperture is given.
tilt (two float, two 1D BaseDistribution, 2D BaseDistribution, optional) – Small-angle beam tilt [mrad]. This value should generally not exceed one degree.
device (str, optional) – The probe wave functions will be build and stored on this device (‘cpu’ or ‘gpu’). The default is determined by the user configuration.
aperture (BaseAperture, optional) – An optional custom aperture. The provided aperture should be a subtype of BaseAperture.
aberrations (dict or Aberrations) – The phase aberrations as a dictionary.
transforms (list of WaveTransform) – A list of additional wave function transforms which will be applied after creation of the probe wave functions.
kwargs – Provide the aberrations as keyword arguments, forwarded to the Aberrations.

__init__(semiangle_cutoff=None, extent=None, gpts=None, sampling=None, energy=None, soft=True, tilt=(0.0, 0.0), device=None, aperture=None, aberrations=None, positions=None, metadata=None, **kwargs)[source]#

Methods

`__init__`([semiangle_cutoff, extent, gpts, ...])
`build`([scan, max_batch, lazy])	Build probe wave functions at the provided positions.
`check_can_build`([potential])	Check whether the wave functions can be built.
`copy`()	Make a copy.
`ensemble_blocks`([chunks])	Split the ensemble into an array of smaller ensembles.
`generate_blocks`([chunks])	Generate chunks of the ensemble.
`match_grid`(other[, check_match])	Match the grid to another object with a Grid.
`multislice`(potential[, scan, detectors, ...])	Run the multislice algorithm for probe wave functions at the provided positions.
`profiles`([angle])	Create a line profile through the center of the probe.
`scan`(potential[, scan, detectors, ...])	Run the multislice algorithm from probe wave functions over the provided scan.
`select_block`(index, chunks)	Select a block from the ensemble.
`show`([complex_images])	Show the intensity of the probe wave function.

Attributes

`aberrations`	Phase aberrations of the probe wave functions.
`accelerator`	Accelerator object describing the acceleration energy.
`angular_sampling`	Reciprocal-space sampling in units of scattering angles [mrad].
`antialias_cutoff_gpts`	The number of grid points along the x and y direction in the simulation grid at the antialiasing cutoff scattering angle.
`antialias_valid_gpts`	The number of grid points along the x and y direction in the simulation grid for the largest rectangle that fits within antialiasing cutoff scattering angle.
`aperture`	Condenser or probe-forming aperture.
`axes_metadata`	List of AxisMetadata.
`base_axes_metadata`	List of AxisMetadata for the base axes in real space.
`base_shape`	Shape of the base axes of the waves.
`ctf`	Contrast transfer function describing the probe.
`cutoff_angles`	Scattering angles at the antialias cutoff [mrad].
`device`	The device where the waves are created.
`dtype`	The datatype of waves.
`energy`	Electron acceleration energy in electron volts.
`ensemble_axes_metadata`	List of AxisMetadata of the ensemble axes.
`ensemble_shape`	Shape of the ensemble axes of the waves.
`extent`	Extent of grid for each dimension in Ångstrom.
`full_cutoff_angles`	Scattering angles corresponding to the full wave function size [mrad].
`gpts`	Number of grid points for each dimension.
`grid`	Simulation grid.
`metadata`	Metadata describing the probe wave functions.
`positions`	The position(s) of the probe.
`reciprocal_space_axes_metadata`	List of AxisMetadata for base axes in reciprocal space.
`reciprocal_space_sampling`	Reciprocal-space sampling in reciprocal Ångstrom.
`rectangle_cutoff_angles`	Scattering angles corresponding to the sides of the largest rectangle within the antialias cutoff [mrad].
`sampling`	Grid sampling for each dimension in Ångstrom per grid point.
`semiangle_cutoff`	The semiangle cutoff [mrad].
`shape`	Shape of the waves.
`soft`	True if the aperture has a soft edge.
`tilt`	The small-angle tilt of applied to the Fresnel propagator [mrad].
`wavelength`	Relativistic wavelength in Ångstrom.

property aberrations: abtem.transfer.Aberrations#

Phase aberrations of the probe wave functions.

Return type: Aberrations

property accelerator: abtem.core.energy.Accelerator#

Accelerator object describing the acceleration energy.

Return type: Accelerator

property angular_sampling: tuple[float, float]#

Reciprocal-space sampling in units of scattering angles [mrad].

Return type: tuple[float, float]

property antialias_cutoff_gpts: tuple[int, int]#

The number of grid points along the x and y direction in the simulation grid at the antialiasing cutoff scattering angle.

Return type: tuple[int, int]

property antialias_valid_gpts: tuple[int, int]#

The number of grid points along the x and y direction in the simulation grid for the largest rectangle that fits within antialiasing cutoff scattering angle.

Return type: tuple[int, int]

property aperture: abtem.transfer.Aperture#

Condenser or probe-forming aperture.

Return type: Aperture

property axes_metadata: abtem.core.axes.AxesMetadataList#

List of AxisMetadata.

Return type: AxesMetadataList

property base_axes_metadata: list[abtem.core.axes.AxisMetadata]#

List of AxisMetadata for the base axes in real space.

Return type: list[AxisMetadata]

property base_shape: tuple[int, int]#

Shape of the base axes of the waves.

Return type: tuple[int, int]

build(scan=None, max_batch='auto', lazy=None)[source]#

Build probe wave functions at the provided positions.

Parameters

scan (array of xy-positions or BaseScan, optional) – Positions of the probe wave functions. If not given, scans across the entire potential at Nyquist sampling.
max_batch (int, optional) – The number of wave functions in each chunk of the Dask array. If ‘auto’ (default), the batch size is automatically chosen based on the abtem user configuration settings “dask.chunk-size” and “dask.chunk-size-gpu”.
lazy (bool, optional) – If True, create the wave functions lazily, otherwise, calculate instantly. If not given, defaults to the setting in the user configuration file.

Returns

probe_wave_functions – The built probe wave functions.

Return type

Waves

check_can_build(potential=None)#: Check whether the wave functions can be built.

copy()#: Make a copy.

property ctf#: Contrast transfer function describing the probe.

property cutoff_angles: tuple[float, float]#

Scattering angles at the antialias cutoff [mrad].

Return type: tuple[float, float]

property device#: The device where the waves are created.

property dtype#: The datatype of waves.

property energy#: Electron acceleration energy in electron volts.

property ensemble_axes_metadata: list[abtem.core.axes.AxisMetadata]#

List of AxisMetadata of the ensemble axes.

Return type: list[AxisMetadata]

ensemble_blocks(chunks=None)#

Split the ensemble into an array of smaller ensembles.

Parameters: chunks (iterable of tuples) – Block sizes along each dimension.
Return type: Array

property ensemble_shape#: Shape of the ensemble axes of the waves.

property extent: tuple[float] | tuple[float, float] | tuple[float, ...]#

Extent of grid for each dimension in Ångstrom.

Return type: tuple[float] | tuple[float, float] | tuple[float, …]

property full_cutoff_angles: tuple[float, float]#

Scattering angles corresponding to the full wave function size [mrad].

Return type: tuple[float, float]

generate_blocks(chunks=1)#

Generate chunks of the ensemble.

Parameters: chunks (iterable of tuples) – Block sizes along each dimension.

property gpts: tuple[int] | tuple[int, int] | tuple[int, ...]#

Number of grid points for each dimension.

Return type: tuple[int] | tuple[int, int] | tuple[int, …]

property grid: abtem.core.grid.Grid#

Simulation grid.

Return type: Grid

match_grid(other, check_match=False)#: Match the grid to another object with a Grid.

property metadata: dict#

Metadata describing the probe wave functions.

Return type: dict

multislice(potential, scan=None, detectors=None, max_batch='auto', lazy=None)[source]#

Run the multislice algorithm for probe wave functions at the provided positions.

Parameters

potential (BasePotential or Atoms) – The scattering potential. Optionally atoms can be directly given.
scan (array of xy-positions or BaseScan, optional) – Positions of the probe wave functions. If not given, scans across the entire potential at Nyquist sampling.
detectors (BaseDetector or list of BaseDetector, optional) – A detector or a list of detectors defining how the wave functions should be converted to measurements after running the multislice algorithm. If not given, defaults to the flexible annular detector.
max_batch (int, optional) – The number of wave functions in each chunk of the Dask array. If ‘auto’ (default), the batch size is automatically chosen based on the abtem user configuration settings “dask.chunk-size” and “dask.chunk-size-gpu”.
lazy (bool, optional) – If True, create the wave functions lazily, otherwise, calculate instantly. If None, this defaults to the setting in the user configuration file.

Returns

measurements

Return type

BaseMeasurements or Waves or list of BaseMeasurement

property positions: abtem.scan.BaseScan#

The position(s) of the probe.

Return type: BaseScan

profiles(angle=0.0)[source]#

Create a line profile through the center of the probe.

Parameters: angle (float, optional) – Angle with respect to the x-axis of the line profile [degree].
Return type: RealSpaceLineProfiles

property reciprocal_space_axes_metadata: list[abtem.core.axes.AxisMetadata]#

List of AxisMetadata for base axes in reciprocal space.

Return type: list[AxisMetadata]

property reciprocal_space_sampling: tuple[float] | tuple[float, float] | tuple[float, ...]#

Reciprocal-space sampling in reciprocal Ångstrom.

Return type: tuple[float] | tuple[float, float] | tuple[float, …]

property rectangle_cutoff_angles: tuple[float, float]#

Scattering angles corresponding to the sides of the largest rectangle within the antialias cutoff [mrad].

Return type: tuple[float, float]

property sampling: tuple[float] | tuple[float, float] | tuple[float, ...]#

Grid sampling for each dimension in Ångstrom per grid point.

Return type: tuple[float] | tuple[float, float] | tuple[float, …]

scan(potential, scan=None, detectors=None, max_batch='auto', lazy=None)[source]#

Run the multislice algorithm from probe wave functions over the provided scan.

Parameters

potential (BasePotential or Atoms) – The scattering potential.
scan (BaseScan) – Positions of the probe wave functions. If not given, scans across the entire potential at Nyquist sampling.
detectors (BaseDetector, list of BaseDetector, optional) – A detector or a list of detectors defining how the wave functions should be converted to measurements after running the multislice algorithm. See abtem.measurements.detect for a list of implemented detectors.
max_batch (int, optional) – The number of wave functions in each chunk of the Dask array. If ‘auto’ (default), the batch size is automatically chosen based on the abtem user configuration settings “dask.chunk-size” and “dask.chunk-size-gpu”.
lazy (bool, optional) – If True, create the measurements lazily, otherwise, calculate instantly. If None, this defaults to the value set in the configuration file.

Return type

BaseMeasurements | Waves | list[BaseMeasurements | Waves]

Returns

detected_waves (BaseMeasurements or list of BaseMeasurement) – The detected measurement (if detector(s) given).
exit_waves (Waves) – Wave functions at the exit plane(s) of the potential (if no detector(s) given).

select_block(index, chunks)#

Select a block from the ensemble.

Parameters

index (tuple of ints) – Index of selected block.
chunks (iterable of tuples) – Block sizes along each dimension.

property semiangle_cutoff#: The semiangle cutoff [mrad].

property shape#: Shape of the waves.

show(complex_images=False, **kwargs)[source]#

Show the intensity of the probe wave function.

Parameters

complex_images (bool) – If true shows complex images using domain-coloring instead of the intensity.
kwargs (Keyword arguments for the Images.show() function.) –

property soft#: True if the aperture has a soft edge.

property tilt#: The small-angle tilt of applied to the Fresnel propagator [mrad].

property wavelength#: Relativistic wavelength in Ångstrom.