CTF#
- class abtem.transfer.CTF(semiangle_cutoff=inf, soft=True, focal_spread=0.0, angular_spread=0.0, aberration_coefficients=None, energy=None, extent=None, gpts=None, sampling=None, flip_phase=False, wiener_snr=0.0, **kwargs)[source]#
Bases:
_HasAberrations
,BaseAperture
The contrast transfer function (CTF) describes the aberrations of the objective lens in HRTEM and specifies how the condenser system shapes the probe in STEM.
abTEM implements phase aberrations up to 5th order using polar coefficients. See Eq. 2.22 in the reference [1].
Cartesian coefficients can be converted to polar using the utility function abtem.transfer.cartesian2polar.
Partial coherence is included as envelopes in the quasi-coherent approximation. See Chapter 3.2 in reference [1].
- Parameters:
semiangle_cutoff (float, optional) – The semiangle cutoff describes the sharp reciprocal-space cutoff due to the objective aperture [mrad] (default is no cutoff).
soft (bool, optional) – If True, the edge of the aperture is softened (default is True).
focal_spread (float, optional) – The standard deviation of the focal spread due to chromatic aberration and lens current instability [Å] (default is 0).
angular_spread (float, optional) – The standard deviation of the angular deviations due to source size [Å] (default is 0).
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.
flip_phase (bool, optional) – Changes the sign of all negative parts of the CTF to positive (following doi:10.1016/j.ultramic.2008.03.004) (default is False).
wiener_snr (float, optional) – Applies a Wiener filter to the CTF (following doi:10.1016/j.ultramic.2008.03.004) with a given SNR value. If no value is given, the default value of 0.0 means that no filter is applied.
kwargs (dict, optional) – Optionally provide the aberration coefficients as keyword arguments.
References
- __init__(semiangle_cutoff=inf, soft=True, focal_spread=0.0, angular_spread=0.0, aberration_coefficients=None, energy=None, extent=None, gpts=None, sampling=None, flip_phase=False, wiener_snr=0.0, **kwargs)[source]#
Methods
__init__
([semiangle_cutoff, soft, ...])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.
profiles
([gpts, max_angle, phi])Calculate radial line profiles for each included component (phase aberrations, aperture, temporal and spatial envelopes) of the contrast transfer function.
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.
to_point_spread_functions
(gpts, extent)Attributes
C10
C12
C21
C23
C30
C32
C34
C41
C43
C45
C5
C50
C52
C54
C56
Cs
The aberration coefficients as a dictionary.
Accelerator object describing the acceleration energy.
The sampling in scattering angles of the transfer function [mrad].
The standard deviation of the angular deviations due to source size [mrad].
astigmatism
astigmatism_angle
List of AxisMetadata.
List of AxisMetadata of the base axes.
Shape of the base axes.
coma
coma_angle
The first zero-crossing of the phase at Scherzer defocus [mrad].
Defocus equivalent to negative C10.
distributions
Electron acceleration energy in electron volts.
Axes metadata describing the ensemble axes added to the waves when applying the transform.
The shape of the ensemble axes added to the waves when applying the transform.
Extent of grid for each dimension in Ångstrom.
If true the signs of all negative parts of the CTF are changed to positive.
The standard deviation of the focal spread [Å].
Number of grid points for each dimension.
Simulation grid.
The array representing the waves may be modified in-place.
Metadata added to the waves when applying the transform.
Nyquist sampling corresponding to the semiangle cutoff of the aperture [Å].
phi12
phi21
phi23
phi32
phi34
phi41
phi43
phi45
phi52
phi54
phi56
The Scherzer point resolution [Å].
Reciprocal-space sampling in reciprocal Ångstrom.
Grid sampling for each dimension in Ångstrom per grid point.
The Scherzer defocus [Å].
The semiangle cutoff [mrad].
Shape of the ensemble.
True if the aperture has a soft edge.
Relativistic wavelength in Ångstrom.
If true a Wiener filter is applied to the CTF.
- property aberration_coefficients#
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].
- property angular_spread: float | BaseDistribution#
The standard deviation of the angular deviations due to source size [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:
- 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 crossover_angle#
The first zero-crossing of the phase at Scherzer defocus [mrad].
- property defocus: float | BaseDistribution#
Defocus equivalent to negative C10.
- 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.
- property flip_phase: bool#
If true the signs of all negative parts of the CTF are changed to positive.
- property focal_spread: float | BaseDistribution#
The standard deviation of the focal spread [Å].
- 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#
Metadata added to the waves when applying the transform.
- property nyquist_sampling: float#
Nyquist sampling corresponding to the semiangle cutoff of the aperture [Å].
- property point_resolution#
The Scherzer point resolution [Å].
- profiles(gpts=1000, max_angle=None, phi=0.0)[source]#
Calculate radial line profiles for each included component (phase aberrations, aperture, temporal and spatial envelopes) of the contrast transfer function.
- Parameters:
gpts (int) – Number of grid points along the line profiles.
max_angle (float) – The maximum scattering angle included in the radial line profiles [mrad]. The default is 1.5 times the semiangle cutoff or 50 mrad if no semiangle cutoff is set.
phi (float) – The azimuthal angle of the radial line profiles [rad]. Default is 0.
- Returns:
ctf_profiles – Ensemble of reciprocal space line profiles. The first ensemble dimension represents the different
- Return type:
- 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.
- property scherzer_defocus#
The Scherzer defocus [Å].
- 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: float | BaseDistribution#
The semiangle cutoff [mrad].
- 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.
- property soft: float#
True if the aperture has a soft edge.
- 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:
- property wavelength#
Relativistic wavelength in Ångstrom.
- property wiener_snr: float#
If true a Wiener filter is applied to the CTF.