multiel-spectra 0.0.26

Multi-Element Fluorescence Xray Spectra Generator

Multiel_spectra

Multiel_spectra ("Multi element spectra generator") is a pyhton package for creating fluorescence X-ray spectra that simulates photon transmission through several material layers created by a source spectra and with detector effects.

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Name

Highly scalable Multielement Fluorescence Xray Spectra measure simulation.

Description

Spectra_gen is a package that approximately simulates all steps in an Xray-Fluorescence measure. That is, it simulates the whole photon path from the x-ray source to the detector, and the transmission throuh several diverse element layers. The main goal of the package was to generate a more accurate approximation of the X-ray computer simulated spectra in order to be more similar to actual Xray detected spectra. ( As a consequence this spectra could efficiently be used in order to train an artificial neural netwok for several tasks such as automatic element detection or denoising.)

SIMULATED PATH ELEMENTS:

• Incident Spectra (Source spectra): Incident spectra is simulated through spekpy package. The oputput is a tuple of arrays, one having the energy values (X), and the other the fluence of the spectrum (Y). For the whole details visit spekpy documentation.

• Fluorescence Spectra Transmission: Elements are supposed to be in layers. Elemental composition of the probe must be given before, and it is formed by the position of each element and the relative abundance to the whole probe. Once the composition is set the fluorescence spectra produced by the source spectra is correctly transmitted through the different layers. (Air is used as the last layer of the material, but can be removed). (Air is the only material with thickness, the rest are used with fixed z = 1mm).

• Detector effects. Several detector effects are simulated. Mainly:

  • Escape peaks
  • Sum peaks
  • detector efficiency

• Approximations and Future improvements

The transmission of the source spectra has not been properly simulated. That is, the same source spectra arrives to all elements in the different layers. As well, once the different fluorescence spectra are being transmitted through different layers, only transmission is simualted but not the creation of new spectra with this fluorescence spectra as a source.

Another important approximation is that transmission (photon material absortion) is approximated by perfect composited materials. No impurities or noise is being introduced here but probably it will be a very good idea to do it.

Full 3D photon path with geometric and other constraints.

Spectra_gen is based into threee main libraries:

• Spekpy. Python package for Xray tube spectrum simulation (That is the incident spectrum producing the Xray fluorescence spectra)
• Xraylarch : Python package used to get the mass_atenuation coefficients of a mix of a certain compound as a function of energy.
• Scikit-beam : Python package used to get the energies and cross sections for all the Xray lines in an element.

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Installation

Setting the environment and related packages:

As the package makes use of skbeam, a install_skbeam.py (and install_spekpy.py) script is included with the package so run: " python install_skbeam.py" in order to isntall it (link to the skbeam documentation for all the different installation procedures, this one is the reccomended one). This files are typically lcoated: /opt/conda/lib/python3.10/site-packages/multiel_spectra when you download it.

1. set conda environment named 'base'
2. run: "python install_skbeam.py" in conda base environment
3. run: "python install spekpy.py"
4. install the rest of dependencies (torch, xraylarch, scipy..etc).

The order is important since usually the packages created outside the conda environment will not be linked into the environment.

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Support

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Roadmap

• 3d simulation

• proper transmission and excitation simulation

• Material mix and impurities simulation

• ANN element detection

• ANN denoising

Contributing

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