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

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

Build an immutable unordered collection of unique elements.

__abstractmethods__ class

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

Build an immutable unordered collection of unique elements.

__abstractvars__ class

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

Build an immutable unordered collection of unique elements.

__annotations__ class

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

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

__doc__ class

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

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

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 property

coordinate_grid_in_pixels property

frequency_grid_in_angstroms property

frequency_grid_in_pixels property

full_frequency_grid_in_angstroms property

full_frequency_grid_in_pixels property

interaction_constant property

The electron interaction constant at the given voltage_in_kilovolts.

lorentz_factor property

The lorenz factor at the given voltage_in_kilovolts.

n_pixels property

Convenience property for math.prod(shape)

padded_coordinate_grid_in_angstroms property

padded_coordinate_grid_in_pixels property

padded_frequency_grid_in_angstroms property

padded_frequency_grid_in_pixels property

padded_full_frequency_grid_in_angstroms property

padded_full_frequency_grid_in_pixels property

padded_n_pixels property

Convenience property for math.prod(padded_shape)

padded_x_dim property

Convenience property for padded_shape[1]

padded_y_dim property

Convenience property for padded_shape[0]

wavelength_in_angstroms property

The incident electron wavelength corresponding to the beam energy voltage_in_kilovolts.

x_dim property

Convenience property for shape[1]

y_dim property

Convenience property for shape[0]

__check_init__()

__init__()

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

get_coordinate_grid(*, padding: bool = False, physical: bool = True)

Return the image coordinate system. See cryojax.ndimage.make_coordinate_grid for more information.

Arguments:

• padding: If True, return coordinates with shape image_config.padded_shape. Otherwise, return with shape image_config.shape.
• physical: If True, return coordinates in units of angstroms. Otherwise, return on the unit box.

Returns:

The coordinate grid.

get_frequency_grid(*, padding: bool = False, physical: bool = True, full: bool = False)

Return a grid of FFT frequencies. See [cryojax.ndimage.make_frequency_grid] for more information.

Arguments:

• padding: If True, return frequencies corresponding to shape image_config.padded_shape. Otherwise, use image_config.shape.
• physical: If True, return frequencies in units of inverse angstroms. Otherwise, return unitless where Nyquist is equal to 0.5.
• full: If True, return the full plane of frequencies for usage with jax.numpy.fft.fftn. Otherwise, return the half plane for usage with jax.numpy.fft.rfftn.

Returns:

The frequency grid.

---

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

Configuration and utilities for a basic electron microscopy image.

wavelength_in_angstroms property

The incident electron wavelength 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]

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]

__init__(shape: tuple[int, int], pixel_size: cryojax.jax_util.FloatLike, voltage_in_kilovolts: cryojax.jax_util.FloatLike, *, padded_shape: tuple[int, int] | None = None, precompute_mode: Literal['none', 'rfft', 'fft', 'all', 'compile_time_eval'] = 'none')

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.
• padded_shape: The shape of the image after padding. By default, equal to shape.
• precompute_mode: How to pre-compute coordinate and frequency grids stored in the image_config. Options are
  • 'none': Compute grids at runtime and cache the result.
  • 'rfft': Only precompute frequencies in the Fourier domain for a real-valued function (i.e. for use with jax.numpy.fft.rfftn). This is the best option for most use cases.
  • 'fft': Precompute frequencies in the Fourier domain for both real and complex-valued functions (i.e. for use with jax.numpy.fft.rfftn and jax.numpy.fft.fftn). Relevant for use with Ewald sphere extraction.
  • 'all': Precompute all grids in both real-space and frequency-space.
  • 'compile_time_eval': Evaluate grids as needed at compile time using jax.ensure_compile_time_eval.

get_coordinate_grid(*, padding: bool = False, physical: bool = True)

Return the image coordinate system. See cryojax.ndimage.make_coordinate_grid for more information.

Arguments:

• padding: If True, return coordinates with shape image_config.padded_shape. Otherwise, return with shape image_config.shape.
• physical: If True, return coordinates in units of angstroms. Otherwise, return on the unit box.

Returns:

The coordinate grid.

get_frequency_grid(*, padding: bool = False, physical: bool = True, full: bool = False)

Return a grid of FFT frequencies. See [cryojax.ndimage.make_frequency_grid] for more information.

Arguments:

• padding: If True, return frequencies corresponding to shape image_config.padded_shape. Otherwise, use image_config.shape.
• physical: If True, return frequencies in units of inverse angstroms. Otherwise, return unitless where Nyquist is equal to 0.5.
• full: If True, return the full plane of frequencies for usage with jax.numpy.fft.fftn. Otherwise, return the half plane for usage with jax.numpy.fft.rfftn.

Returns:

The frequency grid.

---

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

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

wavelength_in_angstroms property

The incident electron wavelength 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]

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]

__init__(shape: tuple[int, int], pixel_size: cryojax.jax_util.FloatLike, voltage_in_kilovolts: cryojax.jax_util.FloatLike, electron_dose: cryojax.jax_util.FloatLike, *, padded_shape: tuple[int, int] | None = None, precompute_mode: Literal['none', 'rfft', 'fft', 'all', 'compile_time_eval'] = 'none')

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 \(e^-/A^2\)
• padded_shape: The shape of the image after padding. By default, equal to shape.
• precompute_mode: How to pre-compute coordinate and frequency grids stored in the image_config. Options are
  • 'none': Compute grids at runtime and cache the result.
  • 'rfft': Only precompute frequencies in the Fourier domain for a real-valued function (i.e. for use with jax.numpy.fft.rfftn). This is the best option for most use cases.
  • 'fft': Precompute frequencies in the Fourier domain for both real and complex-valued functions (i.e. for use with jax.numpy.fft.rfftn and jax.numpy.fft.fftn). Relevant for use with Ewald sphere extraction.
  • 'all': Precompute all grids in both real-space and frequency-space.
  • 'compile_time_eval': Evaluate grids as needed at compile time using jax.ensure_compile_time_eval.

get_coordinate_grid(*, padding: bool = False, physical: bool = True)

Return the image coordinate system. See cryojax.ndimage.make_coordinate_grid for more information.

Arguments:

• padding: If True, return coordinates with shape image_config.padded_shape. Otherwise, return with shape image_config.shape.
• physical: If True, return coordinates in units of angstroms. Otherwise, return on the unit box.

Returns:

The coordinate grid.

get_frequency_grid(*, padding: bool = False, physical: bool = True, full: bool = False)

Return a grid of FFT frequencies. See [cryojax.ndimage.make_frequency_grid] for more information.

Arguments:

• padding: If True, return frequencies corresponding to shape image_config.padded_shape. Otherwise, use image_config.shape.
• physical: If True, return frequencies in units of inverse angstroms. Otherwise, return unitless where Nyquist is equal to 0.5.
• full: If True, return the full plane of frequencies for usage with jax.numpy.fft.fftn. Otherwise, return the half plane for usage with jax.numpy.fft.rfftn.

Returns:

The frequency grid.