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

cryojax.simulator.AbstractImageConfig

Configuration and utilities for an electron microscopy image.

__abstractclassvars__ class

__abstractclassvars__

frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object

Build an immutable unordered collection of unique elements.

__abstractmethods__ class

__abstractmethods__

frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object

Build an immutable unordered collection of unique elements.

__abstractvars__ class

__abstractvars__

frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object

Build an immutable unordered collection of unique elements.

__annotations__ class

__annotations__

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list. For example: dict(one=1, two=2)

__dataclass_fields__ class

__dataclass_fields__

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list. For example: dict(one=1, two=2)

__dataclass_params__ class

__dataclass_params__

__doc__ class

__doc__

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

__match_args__ class

__match_args__

Built-in immutable sequence.

If no argument is given, the constructor returns an empty tuple. If iterable is specified the tuple is initialized from iterable's items.

If the argument is a tuple, the return value is the same object.

__module__ class

__module__

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

coordinate_grid_in_angstroms cached property

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

Convenience property for pixel_size * coordinate_grid_in_pixels

coordinate_grid_in_pixels cached property

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

A spatial coordinate system for the shape.

frequency_grid_in_angstroms cached property

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

Convenience property for frequency_grid_in_pixels / pixel_size

frequency_grid_in_pixels cached property

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

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

full_frequency_grid_in_angstroms cached property

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

Convenience property for full_frequency_grid_in_pixels / pixel_size

full_frequency_grid_in_pixels cached property

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

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

interaction_constant property

interaction_constant

The electron interaction constant at the given voltage_in_kilovolts.

lorentz_factor property

lorentz_factor

The lorenz factor at the given voltage_in_kilovolts.

n_pixels property

n_pixels

Convenience property for math.prod(shape)

padded_coordinate_grid_in_angstroms cached property

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

Convenience property for pixel_size * padded_coordinate_grid_in_pixels

padded_coordinate_grid_in_pixels cached property

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

A spatial coordinate system for the padded_shape.

padded_frequency_grid_in_angstroms cached property

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

Convenience property for padded_frequency_grid_in_pixels / pixel_size

padded_frequency_grid_in_pixels cached property

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

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

padded_full_frequency_grid_in_angstroms cached property

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

Convenience property for padded_full_frequency_grid_in_pixels / pixel_size

padded_full_frequency_grid_in_pixels cached property

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

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

padded_n_pixels property

padded_n_pixels

Convenience property for math.prod(padded_shape)

padded_shape property

padded_shape

padded_x_dim property

padded_x_dim

Convenience property for padded_shape[1]

padded_y_dim property

padded_y_dim

Convenience property for padded_shape[0]

wavelength_in_angstroms property

wavelength_in_angstroms

The incident electron wavelength corresponding to the beam energy voltage_in_kilovolts.

x_dim property

x_dim

Convenience property for shape[1]

y_dim property

y_dim

Convenience property for shape[0]

__check_init__

__check_init__()

__init__

__init__()

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

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cryojax.simulator.BasicImageConfig(cryojax.simulator.AbstractImageConfig)

Configuration and utilities for a basic electron microscopy image.

__init__

__init__(shape: tuple[int, int], pixel_size: cryojax.jax_util.FloatLike, voltage_in_kilovolts: cryojax.jax_util.FloatLike, *, grid_helper: cryojax.simulator.GridHelper | None = None, pad_options: dict[str, Any] = {})

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.
• grid_helper: The GridHelper object, which stores the coordinate grids for image shape shape. If not passed, grid are computed at run-time.
• pad_options: Options that control image padding.
  • shape: The shape of the image after padding. By default, equal to shape.
  • grid_helper: The GridHelper object, which stores coordinate grids for the padded shape. If not passed, grid are computed at run-time. By default, equal to None.

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cryojax.simulator.DoseImageConfig(cryojax.simulator.AbstractImageConfig)

Configuration and utilities for an electron microscopy image, including the electron dose.

__init__

__init__(shape: tuple[int, int], pixel_size: cryojax.jax_util.FloatLike, voltage_in_kilovolts: cryojax.jax_util.FloatLike, electron_dose: cryojax.jax_util.FloatLike, *, grid_helper: cryojax.simulator.GridHelper | None = None, pad_options: dict[str, Any] = {})

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.
• electron_dose: The integrated dose rate of the electron beam in \(e^-/A^2\)
• grid_helper: The GridHelper object, which stores the coordinate grids for image shape shape. If not passed, grid are computed at run-time.
• pad_options: Options that control image padding.
  • shape: The shape of the image after padding. By default, equal to shape.
  • grid_helper: The GridHelper object, which stores coordinate grids for the padded shape. If not passed, grid are computed at run-time. By default, equal to None.

cryojax.simulator.GridHelper

GridHelper(shape: tuple[int, int], only_rfft: bool = True)

__init__

__init__(shape: tuple[int, int], only_rfft: bool = True)