microscopes module

class PyLorentz.utils.microscopes.Microscope(E=200000.0, Cs=1000000.0, Cc=5000000.0, theta_c=0.0006, Ca=0.0, phi_a=0, def_spr=120.0, scale=None, verbose=False)[source]

Bases: object

Class for Microscope objects.

A class that describes a microscope for image simulation and reconstruction purposes. Along with accelerating voltage, aberrations, and other parameters, this also contains methods for propagating the electron wave and simulating images.

Notes:

When initializing a Microscope you can set verbose=True to get a printout of the parameters.

E

Accelerating voltage (V). Default 200kV.

Type:: float

Cs

Spherical aberration (nm). Default 1mm.

Type:: float

Cc

Chromatic aberration (nm). Default 5mm.

Type:: float

theta_c

Beam coherence (rad). Default 0.6mrad.

Type:: float

Ca

2-fold astigmatism (nm). Default 0.

Type:: float

phi_a

2-fold astigmatism angle (rad). Default 0.

Type:: float

def_spr

Defocus spread (nm). Default 120nm.

Type:: float

defocus

Defocus of the microscope (nm). Default 0nm.

Type:: float

lam

Electron wavelength (nm) calculated from E. Default 2.51pm.

Type:: float

gamma

Relativistic factor (unitless) from E. Default 1.39.

Type:: float

sigma

Interaction constant (1/(V*nm)) from E. Default 0.00729.

Type:: float

__init__(E=200000.0, Cs=1000000.0, Cc=5000000.0, theta_c=0.0006, Ca=0.0, phi_a=0, def_spr=120.0, scale=None, verbose=False)[source]

Constructs the Microscope object.

All arguments are optional. Set verbose=True to print microscope values.

property scale: float

get_scherzer_defocus()[source]: Calculate the Scherzer defocus

get_optimum_defocus()[source]

Calculate the Optimum or Lichte defocus (for holography).

Returns:: Optimum defocus (nm)
Return type:: float

get_transfer_function(scale=None, shape=None)[source]

Generate the full transfer function in reciprocal space

Args:

Returns:: Transfer function. 2D array.
Return type:: ndarray

backpropagate_wave(ImgWave)[source]

Back-propagate an image wave to get the object wave.

This function will back-propagate the image wave function to the object wave plane by convolving with exp(+i*Chiq). The damping envelope is not used for back propagation. Returns ObjWave in real space.

Parameters:: ObjWave (2D array) – Object wave function.
Returns:: Realspace object wave function. Complex 2D array same size as ObjWave.
Return type:: ndarray

compute_image(object_wave, padded_shape=None, pad_mode='reflect', symmetrize=False)[source]

Produce the image at the set defocus using the methods in this class.

Parameters:

ObjWave (2D array) – Object wave function.
padded_shape (tuple | None, optional) – Shape for padding. Default is None.
pad_mode (str, optional) – mode passed to np.pad. Default is “edge”.
sym (bool, optional) – Whether or not to symmetrize the phase

Returns:

Realspace image wave function. Real-valued 2D array same size as ObjWave.

Return type:

ndarray

compute_diffraction_pattern(ObjWave)[source]

Produce the image in the backfocal plane (diffraction)

Parameters:: ObjWave (2D array) – Object wave function.
Returns:: Realspace image wave function. Real-valued 2D array same size as ObjWave.
Return type:: ndarray