Aberrations

Aberrations#

class abtem.transfer.Aberrations(aberration_coefficients=None, energy=None, extent=None, gpts=None, sampling=None, **kwargs)[source]#

Bases: BaseTransferFunction, _HasAberrations

Phase aberrations.

Parameters:

aberration_coefficients (dict, optional) – Mapping from aberration symbols to their corresponding values. All aberration magnitudes should be given in [Å] and angles should be given in [radian].
energy (float, optional) – Electron energy [eV]. If not provided, inferred from the wave functions.
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.
kwargs (dict, optional) – Optionally provide the aberration coefficients as keyword arguments.

__init__(aberration_coefficients=None, energy=None, extent=None, gpts=None, sampling=None, **kwargs)[source]#

Methods

`__init__`([aberration_coefficients, energy, ...])
`apply`(waves)	Apply the transform to the given waves.
`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.
`select_block`(index, chunks)	Select a block from the ensemble.
`set_aberrations`(aberration_coefficients)	Set the phase of the phase aberration.
`show`(**kwargs)
`to_diffraction_patterns`([max_angle, gpts])	Converts the transfer function instance to DiffractionPatterns.

Attributes

`C10`
`C12`
`C21`
`C23`
`C30`
`C32`
`C34`
`C41`
`C43`
`C45`
`C5`
`C50`
`C52`
`C54`
`C56`
`Cs`
`aberration_coefficients`	The aberration coefficients as a dictionary.
`accelerator`	Accelerator object describing the acceleration energy.
`angular_sampling`	The sampling in scattering angles of the transfer function [mrad].
`astigmatism`
`astigmatism_angle`
`axes_metadata`	List of AxisMetadata.
`base_axes_metadata`	List of AxisMetadata of the base axes.
`base_shape`	Shape of the base axes.
`coma`
`coma_angle`
`defocus`	The defocus [Å].
`distributions`
`energy`	Electron acceleration energy in electron volts.
`ensemble_axes_metadata`	Axes metadata describing the ensemble axes added to the waves when applying the transform.
`ensemble_shape`	The shape of the ensemble axes added to the waves when applying the transform.
`extent`	Extent of grid for each dimension in Ångstrom.
`gpts`	Number of grid points for each dimension.
`grid`	Simulation grid.
`in_place`	The array representing the waves may be modified in-place.
`metadata`	Metadata added to the waves when applying the transform.
`phi12`
`phi21`
`phi23`
`phi32`
`phi34`
`phi41`
`phi43`
`phi45`
`phi52`
`phi54`
`phi56`
`reciprocal_space_sampling`	Reciprocal-space sampling in reciprocal Ångstrom.
`sampling`	Grid sampling for each dimension in Ångstrom per grid point.
`shape`	Shape of the ensemble.
`wavelength`	Relativistic wavelength in Ångstrom.

property aberration_coefficients: dict[str, float | BaseDistribution]#: The aberration coefficients as a dictionary.

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

property angular_sampling: tuple[float, float]#: The sampling in scattering angles of the transfer function [mrad].

apply(waves)#

Apply the transform to the given waves.

Parameters:: array_object (ArrayObject) – The array object to transform.
Returns:: transformed_array_object
Return type:: ArrayObject

property axes_metadata: AxesMetadataList#: List of AxisMetadata.

property base_axes_metadata: list[AxisMetadata]#: List of AxisMetadata of the base axes.

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

copy()#: Make a copy.

property defocus: float | BaseDistribution#: The defocus [Å].

property energy#: Electron acceleration energy in electron volts.

property ensemble_axes_metadata#: Axes metadata describing the ensemble axes added to the waves when applying the transform.

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#: The shape of the ensemble axes added to the waves when applying the transform.

property extent: tuple[float] | tuple[float, float] | tuple[float, ...]#: Extent of grid for each dimension in Ångstrom.

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.

property in_place: bool#: The array representing the waves may be modified in-place.

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

property metadata: dict#: Metadata added to the waves when applying the transform.

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

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

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.

set_aberrations(aberration_coefficients)#

Set the phase of the phase aberration.

Parameters:: aberration_coefficients (dict) – Mapping from aberration symbols to their corresponding values.

property shape#: Shape of the ensemble.

to_diffraction_patterns(max_angle=None, gpts=None)#

Converts the transfer function instance to DiffractionPatterns.

Parameters:

max_angle (float, optional) – The maximum diffraction angle in radians. If not provided, the maximum angle will be determined based on the self._max_semiangle_cutoff attribute of the instance. If neither max_angle nor self._max_semiangle_cutoff is available, a RuntimeError will be raised.
gpts (int | tuple[int, int], optional) – The number of grid points in reciprocal space for performing Fourier Transform. If not provided, a default value of 128 will be used.

Returns:

The diffraction patterns obtained from the conversion.

Return type:

abtem.measurements.DiffractionPatterns

property wavelength#: Relativistic wavelength in Ångstrom.

Aberrations

Contents

Aberrations#