Configuring an image¤
The AbstractConfig
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.AbstractConfig
¤
Configuration and utilities for an electron microscopy image.
cryojax.simulator.AbstractConfig.wavelength_in_angstroms: Float[Array, '']
property
¤
The incident electron wavelength corresponding to the beam
energy voltage_in_kilovolts
.
cryojax.simulator.AbstractConfig.wavenumber_in_inverse_angstroms: Float[Array, '']
property
¤
The incident electron wavenumber corresponding to the beam
energy voltage_in_kilovolts
.
cryojax.simulator.AbstractConfig.n_pixels: int
property
¤
Convenience property for math.prod(shape)
cryojax.simulator.AbstractConfig.y_dim: int
property
¤
Convenience property for shape[0]
cryojax.simulator.AbstractConfig.x_dim: int
property
¤
Convenience property for shape[1]
cryojax.simulator.AbstractConfig.coordinate_grid_in_pixels: Float[Array, '{self.y_dim} {self.x_dim} 2']
cached
property
¤
A spatial coordinate system for the shape
.
cryojax.simulator.AbstractConfig.coordinate_grid_in_angstroms: Float[Array, '{self.y_dim} {self.x_dim} 2']
cached
property
¤
Convenience property for pixel_size * coordinate_grid_in_pixels
cryojax.simulator.AbstractConfig.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.
cryojax.simulator.AbstractConfig.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
cryojax.simulator.AbstractConfig.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.
cryojax.simulator.AbstractConfig.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
cryojax.simulator.AbstractConfig.padded_n_pixels: int
property
¤
Convenience property for math.prod(padded_shape)
cryojax.simulator.AbstractConfig.padded_y_dim: int
property
¤
Convenience property for padded_shape[0]
cryojax.simulator.AbstractConfig.padded_x_dim: int
property
¤
Convenience property for padded_shape[1]
cryojax.simulator.AbstractConfig.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
.
cryojax.simulator.AbstractConfig.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
cryojax.simulator.AbstractConfig.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.
cryojax.simulator.AbstractConfig.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
cryojax.simulator.AbstractConfig.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.
cryojax.simulator.AbstractConfig.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
cryojax.simulator.AbstractConfig.crop_to_shape(image: Inexact[Array, 'y_dim x_dim']) -> Inexact[Array, '{self.y_dim} {self.x_dim}']
¤
Crop an image to shape
.
cryojax.simulator.AbstractConfig.pad_to_padded_shape(image: Inexact[Array, 'y_dim x_dim'], **kwargs: Any) -> Inexact[Array, '{self.padded_y_dim} {self.padded_x_dim}']
¤
Pad an image to padded_shape
.
cryojax.simulator.AbstractConfig.crop_or_pad_to_padded_shape(image: Inexact[Array, 'y_dim x_dim'], **kwargs: Any) -> Inexact[Array, '{self.padded_y_dim} {self.padded_x_dim}']
¤
Reshape an image to padded_shape
using cropping or padding.