Configuring images

The InstrumentConfig 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.InstrumentConfig

Configuration and utilities for an electron microscopy image.

cryojax.simulator.InstrumentConfig.__init__(shape: tuple[int, int], pixel_size: float | Float[Array, ''], voltage_in_kilovolts: float | Float[Array, ''], electrons_per_angstrom_squared: float | Float[Array, ''] = 100.0, padded_shape: Optional[tuple[int, int]] = None, *, pad_scale: float = 1.0, pad_mode: Union[str, Callable] = 'constant')

Arguments:

• shape: Shape of the imaging plane in pixels.
• pixel_size: The pixel size of the image in angstroms.
• voltage_in_kilovolts: The incident energy of the electron beam.
• electrons_per_angstrom_squared: The integrated dose rate of the electron beam.
• padded_shape: The shape of the image after padding. If this argument is not given, it can be set by the pad_scale argument.
• pad_scale: A scale factor at which to pad the image. This is optionally used to set padded_shape and must be greater than 1. If padded_shape is set, this argument is ignored.
• pad_mode: The method of image padding. By default, "constant". For all options, see jax.numpy.pad.

cryojax.simulator.InstrumentConfig.wavelength_in_angstroms: Float[Array, ''] property

The incident electron wavelength corresponding to the beam energy voltage_in_kilovolts.

cryojax.simulator.InstrumentConfig.wavenumber_in_inverse_angstroms: Float[Array, ''] property

The incident electron wavenumber corresponding to the beam energy voltage_in_kilovolts.

cryojax.simulator.InstrumentConfig.n_pixels: int property

Convenience property for math.prod(shape)

cryojax.simulator.InstrumentConfig.y_dim: int property

Convenience property for shape[0]

cryojax.simulator.InstrumentConfig.x_dim: int property

Convenience property for shape[1]

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

A spatial coordinate system for the shape.

cryojax.simulator.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.padded_n_pixels: int property

Convenience property for math.prod(padded_shape)

cryojax.simulator.InstrumentConfig.padded_y_dim: int property

Convenience property for padded_shape[0]

cryojax.simulator.InstrumentConfig.padded_x_dim: int property

Convenience property for padded_shape[1]

cryojax.simulator.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.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.InstrumentConfig.crop_to_shape(image: Float[Array, 'y_dim x_dim']) -> Float[Array, '{self.y_dim} {self.x_dim}']

Crop an image to shape.

cryojax.simulator.InstrumentConfig.pad_to_padded_shape(image: Float[Array, 'y_dim x_dim'], **kwargs: Any) -> Float[Array, '{self.padded_y_dim} {self.padded_x_dim}']

Pad an image to padded_shape.

cryojax.simulator.InstrumentConfig.crop_or_pad_to_padded_shape(image: Float[Array, 'y_dim x_dim'], **kwargs: Any) -> Float[Array, '{self.padded_y_dim} {self.padded_x_dim}']

Reshape an image to padded_shape using cropping or padding.