Probe

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: _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, ...])
`apply_transform`(transform[, max_batch, lazy])
`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.
`transition_potential_scan`(potential, ...[, ...])	type potential: BasePotential \| Atoms

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: Aberrations#: Phase aberrations of the probe wave functions.

property accelerator: Accelerator#: Accelerator object describing the acceleration energy.

property angular_sampling: tuple[float, float]#: Reciprocal-space sampling in units of scattering angles [mrad].

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.

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.

property aperture: Aperture#: Condenser or probe-forming aperture.

property axes_metadata: AxesMetadataList#: List of AxisMetadata.

property base_axes_metadata: list[AxisMetadata]#: List of AxisMetadata for the base axes in real space.

property base_shape: tuple[int, int]#: Shape of the base axes of the waves.

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].

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[AxisMetadata]#: List of AxisMetadata of the ensemble axes.

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.

property full_cutoff_angles: tuple[float, float]#: Scattering angles corresponding to the full wave function size [mrad].

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.

property grid: Grid#: Simulation 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.

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: BaseScan#: The position(s) of the probe.

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[AxisMetadata]#: List of AxisMetadata for base axes in reciprocal space.

property reciprocal_space_sampling: tuple[float] | tuple[float, float] | tuple[float, ...]#: Reciprocal-space sampling in reciprocal Ångstrom.

property rectangle_cutoff_angles: tuple[float, float]#: Scattering angles corresponding to the sides of the largest rectangle within the antialias cutoff [mrad].

property sampling: tuple[float] | tuple[float, float] | tuple[float, ...]#: Grid sampling for each dimension in Ångstrom per grid point.

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].

transition_potential_scan(potential, transition_potentials, scan=None, detectors=None, sites=None, double_channel=True, threshold=1.0, max_batch='auto', lazy=None)[source]#

Parameters:

potential (BasePotential | Atoms) – The potential to be used for calculating the transition potentials. It can be an instance of BasePotential or an Atoms object.
transition_potentials (BaseTransitionPotential | list[BaseTransitionPotential]) – The transition potentials to be used for multislice calculations. It can be an instance of BaseTransitionPotential or a list of BaseTransitionPotential objects.
scan (tuple | BaseScan, optional) – The scan parameters. It can be a tuple or an instance of BaseScan. Defaults to None.
detectors (BaseDetector | list[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. Defaults to None, which
sites (SliceIndexedAtoms | Atoms, optional) – The slice indexed atoms to be used for multislice calculations. It can be an instance of SliceIndexedAtoms or an Atoms object. Defaults to None.
detectors_elastic (BaseDetector | list[BaseDetector], optional) – The elastic detectors to be used for recording the measurements. It can be an instance of BaseDetector or a list of BaseDetector objects. Defaults to None.
double_channel (bool, optional) – A boolean indicating whether to use double channel for recording the measurements. Defaults to True.
max_batch (int | str, optional) – The maximum batch size for parallel processing. It can be an integer or the string “auto”. Defaults to “auto”.
lazy (bool, optional) – A boolean indicating whether to use lazy evaluation for the calculations. Defaults to None.

Returns:

The calculated waves or measurements, depending on the value of lazy.

Return type:

Waves | BaseMeasurements

property wavelength#: Relativistic wavelength in Ångstrom.

Probe

Contents

Probe#