Physics

The physics module includes functionality for modeling and treating various signal related to X-ray physics. In particular, we offer modeling of X-ray fluorescence (XRF) emission and X-ray attenuation, and some useful tools for X-ray phase contrast. The back-end of this module is the famous X-ray physics package called xraylib.

Attenuation

The physics.attenuation sub-module offers support for attenuation correction in tomographic reconstructions, as well as some plotting functions of the different attenuation effects. For a dedicated walk-through on attenuation correction, we refer to the attenuation tutorial.

X-ray Fluorescence

The physics.xrf sub-module offers support for working with X-ray fluorescence (XRF), and contains mainly two classes: physics.xrf.LinesSiegbahn and physics.xrf.DetectorXRF. The former exposes a simplified interface for handling XRF emission lines, using the Siegbahn nomenclature. The latter allows one to describe the position and geometry of a XRF detector, that is used in the VolumeMaterial class of the physics.materials sub-module.

The module exposes two important functions: a static method of the physics.xrf.LinesSiegbahn class, and a function:

class LinesSiegbahn:
    """Siegbahn fluorescence lines collection class."""

    @staticmethod
    def get_lines(line: str) -> Sequence[FluoLine]:
        ...

def get_energy(
    element: Union[str, int],
    lines: Union[str, FluoLine, Sequence[FluoLine]],
    compute_average: bool = False,
    verbose: bool = False,
) -> Union[float, NDArray]:
    ...

The method corrct.physics.xrf.LinesSiegbahn.get_lines returns the list of available lines for a given line family, e.g. the K_α and K_β lines for the K line family. The function corrct.physics.xrf.get_energy, instead, returns the energy(ies) of the requested line(s) for a given element. If the requested expression matches more than one line, it can either be the list of all the line energies, or their average.

Material modeling

The main class of the physics.materials sub-module is []VolumeMaterial, that allows one to model heterogeneous material compositions in the reconstruction volume, with the aim of generating:

1. Attenuation maps (local linear attenuation coefficient).

2. Emission cross-sections maps for XRF and Compton.

X-ray Phase Contrast

The physics.phase sub-module contains functions to model the delta-over-beta value and transfer functions encountered in phase contrast problems:

1. physics.phase.get_delta_beta: Computes the delta-over-beta parameter for a specific compound given its molar composition, energy, and density.

2. physics.phase.get_delta_beta_curves: Computes and optionally plots the delta-over-beta curves for a list of compounds over a specified energy range.

3. physics.phase.plot_filter_responses: Plots the frequency response of the wave propagation for both TIE and CTF filters in either Fourier or direct space.

4. physics.phase.get_propagation_filter: Computes the phase contrast propagation filter for given parameters, returning both Fourier-space and real-space filters.

5. physics.phase.apply_propagation_filter: Applies a requested propagation filter (either TIE or CTF) to an image or stack of images.

Unit conversion

The physics.units sub-module provides a small list of conversion functions and classes to deal with conversions between different physical scales (e.g. converting between m and nm) and different units of the electromagnetic radiation (e.g. converting from energy to wavelength and vice versa). In particular, here we find the classes physics.units.ConversionMetric and physics.units.ConversionEnergy, which provide the following functionality:

1. ConversionMetric: This class defines conversion factors between orders of magnitude of metric units such as kilometers, meters, centimeters, etc. It includes a convert method to convert numbers from a source unit to a destination unit.

2. ConversionEnergy: Similar to ConversionMetric, this class handles conversion factors between orders of magnitude of energy units like GeV, MeV, keV, eV, etc. It also provides a convert method for converting energy from a source unit to a destination unit.

The two functions physics.units.energy_to_wlength and physics.units.wlength_to_energy convert energy to wavelength and wavelength to energy, respectively.