rexafs for Rust

Rust-powered X-ray absorption analysis, developed under the codename xraytsubaki. The core includes normalization, AUTOBK, Fourier transforms, group processing, EXAFS fitting, structure handling, LCF/PCA and spectrum tools.

Publication on crates.io is pending. In this checkout, run cargo test -p rexafs. After publication, add the library with cargo add rexafs.

Start with a spectrum

use rexafs::{io, Spectrum};
let mut spectrum = io::read_qas_transmission("scan.dat")?;
spectrum.fft()?;
assert_eq!(spectrum.k().unwrap().len(), spectrum.chi().unwrap().len());
// For your own data: Spectrum::from_arrays(&energy, &mu)?;
# Ok::<(), Box<dyn std::error::Error>>(())

fft() calculates missing normalization and background results using the selected methods and defaults. normalize(), calc_background(), fft() and ifft() also support explicit chaining. The same stage names are used in Python and TypeScript. The standalone process() facade has been removed.

Configure methods with NormalizationMethod, BackgroundMethod, PrePostEdge, AUTOBK and XrayFFTF. Setters invalidate dependent results. Alternative methods remain selectable; unimplemented methods return explicit errors. Inputs to from_arrays must be finite, equal-length arrays with strictly increasing energy in eV. Result getters expose the spectrum's intermediate and final arrays.

See the API guide for examples, units and ownership. Spectrum and Group remain aliases for XASSpectrum and XASGroup.

Features and scope

• Default trust-region: optional fitting solver support.
• refeff-runner: ReFEFF's Rust EXAFS engine, with path outputs for fitting.
• feff10-runner: the FEFF10 backend through the feff10 dependency.
• plotting: core plot builders through ruviz.
• amcsd, materials-project, cod: optional structure sources.
• ndarray-compat: legacy ndarray calculation path; the default is nalgebra.

Existing FEFF path files can be fitted without compiling a calculation backend. FeffFit and the fitting module support single and joint datasets, independent batches and k/R/q fit spaces. FeffFlavor::Feff10 parsing is still separate from FEFF10 execution; see the historical compatibility notes in the repository. The native core has broader APIs than the Python and JavaScript bindings.

Licensed under MIT OR Apache-2.0; dependency and fixture notices remain applicable.

Plotting (Feature-Gated)

Core plotting is available behind the plotting feature using ruviz.

cargo run -p rexafs --features plotting --example plot_demo

On Apple Silicon, if your linker resolution requires an explicit target linker:

CARGO_TARGET_AARCH64_APPLE_DARWIN_LINKER=clang cargo run -p rexafs --features plotting --example plot_demo

plot_demo writes outputs to:

• crates/rexafs/target/plot_demo

plot_demo coverage:

• FEFF85L module runs from full feff.inp: Co, FeO_withPb, MnO2, ZnSe
• Real fitting via FeffFit::fit(): Cu, ZnSe
• Fit plots per material: k, k + window, r, r + window range

To regenerate Cu/ZnSe fit references directly from XrayLarch:

uv run --with xraylarch python crates/rexafs/scripts/generate_larch_fit_references.py

Strict FEFF fit parity is regression-tested against these regenerated Cu/ZnSe fixtures:

• compared fields: amp, de0, sig2, dr values and stderr
• compared stats: chi_square, reduced_chi_square, n_idp, r_factor
• tolerance policy: relative tolerance 20% with absolute fallback 1e-8 (de0 value uses 0.2 eV absolute fallback near zero)

Important behavior

• Plotting APIs are available through PlotXAS with a mutable entrypoint: plot(&mut self).
• Plot text rendering uses typst(true) by default for scientific notation-friendly labels/ticks.
• Plotting auto-computes missing intermediates when required:
  • mu() may call normalize() and renders flattened mu(E) by default
  • norm() may call normalize()
  • k() may call calc_background()
  • r() may call calc_background() and fft()
• k() panels use symmetric y-limits (-y_lim..y_lim) and y-axis units derived from kweight.
• FeffFitResult::plot().k() defaults to fit/dataset kweight unless .kweight(...) overrides it.
• r() panels default to xlim(0.0, 6.0).
• r() defaults to magnitude traces. Calling .real() and/or .imag() switches to those components unless .mag() is also included (e.g. .r().mag().real().imag()).
• FeffFitResult::plot().r() includes path |chi(R)| traces when magnitude is active.
• Window overlays are disabled by default.
• .window(true) is an alias that enables both .window_fn(true) and .window_box(true) for k() panels.
• .window_fn(...) is supported only on k() panels.
• .window_box(...) is supported on k() panels, and on r() panels for FeffFitResult plots; it renders two range markers (min/max), not a rectangle.
• FeffFitResult now includes varying_names, covariance, and correlation (matrix order follows varying_names).
• Multi-panel output is PNG-only in this phase.

XASSpectrum examples

use rexafs::prelude::*;
use rexafs::xafs::io::load_spectrum_QAS_trans;

let path = format!("{}/tests/testfiles/Ru_QAS.dat", env!("CARGO_MANIFEST_DIR"));
let mut spectrum = load_spectrum_QAS_trans(path)?;

spectrum.plot().mu().save_png("flat_mu.png")?;
spectrum.plot().norm().edges(true).save_png("norm_edges.png")?;
spectrum.plot().k().kweight(2.0).window(true).save_png("chi_k.png")?;
spectrum.plot().r().save_png("chi_r_mag.png")?;
spectrum.plot().r().real().save_png("chi_r_real.png")?;
spectrum.plot().r().mag().real().imag().save_png("chi_r_all.png")?;

spectrum
    .plot()
    .mu()
    .norm()
    .k()
    .r()
    .title("overview")
    .save_png("overview.png")?;
# Ok::<(), Box<dyn std::error::Error>>(())

XASGroup examples

use rexafs::prelude::*;

let mut group = XASGroup::new();
// populate group.spectra ...

group.plot().mu().save_png("group_overlay.png")?;
group.plot().mu().select(&[0, 2]).save_png("group_selected.png")?;
group.plot().mu().stacked(0.25).save_png("group_stacked.png")?;
# Ok::<(), Box<dyn std::error::Error>>(())

FeffFitResult examples

use rexafs::prelude::*;

let mut fit = FeffFitResult::default();
// populate fit result vectors or datasets ...

fit.plot().k().save_png("fit_k.png")?; // uses fit kweight by default
fit.plot().k().window(true).save_png("fit_k_window.png")?; // with window
fit.plot().r().save_png("fit_r.png")?; // includes path |chi(R)| traces
fit.plot().r().window_box(true).save_png("fit_r_window.png")?; // with range markers
fit.plot().r().real().save_png("fit_r_real.png")?;
fit.plot().r().mag().real().imag().save_png("fit_r_all.png")?;
fit.plot().k().dataset(0).save_png("fit_dataset0_k.png")?;
# Ok::<(), Box<dyn std::error::Error>>(())