Configuring an image

The AbstractImageConfig is an object at the core of simulating images in cryojax. It stores a configuration for the simulated image and the electron microscope, such as the shape of the desired image and the wavelength of the incident electron beam.

cryojax.simulator.AbstractImageConfig

Configuration and utilities for an electron microscopy image.

wavelength_in_angstroms property

The incident electron wavelength corresponding to the beam energy voltage_in_kilovolts.

wavenumber_in_inverse_angstroms property

The incident electron wavenumber corresponding to the beam energy voltage_in_kilovolts.

lorentz_factor property

The lorenz factor at the given voltage_in_kilovolts.

interaction_constant property

The electron interaction constant at the given voltage_in_kilovolts.

n_pixels property

Convenience property for math.prod(shape)

y_dim property

Convenience property for shape[0]

x_dim property

Convenience property for shape[1]

coordinate_grid_in_pixels: Float[Array, '{self.y_dim} {self.x_dim} 2'] cached property

A spatial coordinate system for the shape.

coordinate_grid_in_angstroms: Float[Array, '{self.y_dim} {self.x_dim} 2'] cached property

Convenience property for pixel_size * coordinate_grid_in_pixels

frequency_grid_in_pixels: Float[Array, '{self.y_dim} {self.x_dim//2+1} 2'] cached property

A spatial frequency coordinate system for the shape, with hermitian symmetry.

frequency_grid_in_angstroms: Float[Array, '{self.y_dim} {self.x_dim//2+1} 2'] cached property

Convenience property for frequency_grid_in_pixels / pixel_size

full_frequency_grid_in_pixels: Float[Array, '{self.y_dim} {self.x_dim} 2'] cached property

A spatial frequency coordinate system for the shape, without hermitian symmetry.

full_frequency_grid_in_angstroms: Float[Array, '{self.y_dim} {self.x_dim} 2'] cached property

Convenience property for full_frequency_grid_in_pixels / pixel_size

padded_n_pixels property

Convenience property for math.prod(padded_shape)

padded_y_dim property

Convenience property for padded_shape[0]

padded_x_dim property

Convenience property for padded_shape[1]

padded_coordinate_grid_in_pixels: Float[Array, '{self.padded_y_dim} {self.padded_x_dim} 2'] cached property

A spatial coordinate system for the padded_shape.

padded_coordinate_grid_in_angstroms: Float[Array, '{self.padded_y_dim} {self.padded_x_dim} 2'] cached property

Convenience property for pixel_size * padded_coordinate_grid_in_pixels

padded_frequency_grid_in_pixels: Float[Array, '{self.padded_y_dim} {self.padded_x_dim//2+1} 2'] cached property

A spatial frequency coordinate system for the padded_shape, with hermitian symmetry.

padded_frequency_grid_in_angstroms: Float[Array, '{self.padded_y_dim} {self.padded_x_dim//2+1} 2'] cached property

Convenience property for padded_frequency_grid_in_pixels / pixel_size

padded_full_frequency_grid_in_pixels: Float[Array, '{self.padded_y_dim} {self.padded_x_dim} 2'] cached property

A spatial frequency coordinate system for the padded_shape, without hermitian symmetry.

padded_full_frequency_grid_in_angstroms: Float[Array, '{self.padded_y_dim} {self.padded_x_dim} 2'] cached property

Convenience property for padded_full_frequency_grid_in_pixels / pixel_size

__init__()

Initialize self. See help(type(self)) for accurate signature.

crop_to_shape(image: Inexact[Array, 'y_dim x_dim']) -> Inexact[Array, '{self.y_dim} {self.x_dim}']

Crop an image to shape.

pad_to_padded_shape(image: Inexact[Array, 'y_dim x_dim'], **kwargs: typing.Any) -> Inexact[Array, '{self.padded_y_dim} {self.padded_x_dim}']

Pad an image to padded_shape.

crop_or_pad_to_padded_shape(image: Inexact[Array, 'y_dim x_dim'], **kwargs: typing.Any) -> Inexact[Array, '{self.padded_y_dim} {self.padded_x_dim}']

Reshape an image to padded_shape using cropping or padding.