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Joint-Photon-Sciences-Institute

xraylarch-mcp

by Joint-Photon-Sciences-Institute
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xraylarch-mcp

MCP (Model Context Protocol) server that wraps xraylarch for X-ray spectroscopy analysis. Load, process, analyze, and plot XAS/XAFS spectra through Claude Desktop or Claude Code with natural language tool calls. Supports XANES normalization, EXAFS extraction, Fourier transforms, linear combination fitting, PCA, FEFFIT shell fitting, and publication-quality plotting.

Installation

pip install xraylarch-mcp

Related MCP server: fdmnes-mcp

Configuration

Claude Desktop

Add to your Claude Desktop configuration (claude_desktop_config.json):

{
  "mcpServers": {
    "xraylarch": {
      "command": "python",
      "args": ["-m", "xraylarch_mcp"]
    }
  }
}

Claude Code

claude mcp add xraylarch -- python -m xraylarch_mcp

Quick Start

Ask Claude:

"Load the spectrum at ~/data/fe_foil.xdi and show me the normalized XANES"

Claude will:

  1. Call larch_load_spectrum to read your data

  2. Call larch_normalize to perform pre-edge subtraction and normalization

  3. Call larch_plot with plot_type="norm" to generate a publication-quality plot

Tool Reference

I/O Tools

Tool

Description

larch_load_spectrum

Load a spectrum from file (.xdi, .dat, .csv, .prj, etc.)

larch_read_athena_project

Read/inspect Athena project files

larch_list_groups

List all loaded spectrum groups

larch_inspect_group

Detailed view of a group's arrays and scalars

larch_remove_group

Remove a group to free memory

XAFS Analysis Tools

Tool

Description

larch_normalize

Pre-edge subtraction and normalization (wraps pre_edge)

larch_autobk

EXAFS background removal (AUTOBK algorithm)

larch_xftf

Forward Fourier transform: chi(k) -> chi(R)

larch_xftr

Back Fourier transform: chi(R) -> chi(q)

larch_fluo_corr

Fluorescence self-absorption correction

larch_mback_norm

MBACK normalization (alternative for problematic data)

larch_estimate_noise

Noise estimation in chi(k) and chi(R)

larch_cauchy_wavelet

Cauchy wavelet transform for simultaneous k- and R-resolution

larch_rebin

Rebin to standard 3-region XAFS energy grid

Plot Tools

Tool

Description

larch_plot

Publication-quality plots (mu, norm, flat, dmude, chi_k, chi_r, chi_q, cauchy_wavelet)

Math Tools

Tool

Description

larch_smooth

Smooth arrays with Lorentzian/Gaussian/Voigt kernel

larch_deriv

Numerical derivative

larch_interpolate

Interpolate onto new energy grid

larch_merge_groups

Merge/average multiple spectra

larch_deglitch

Remove glitch points

Fitting Tools

Tool

Description

larch_lcf

Linear combination fitting against standards

larch_pca

Principal Component Analysis

larch_feffit

FEFFIT EXAFS shell fitting

larch_peak_fit

Peak fitting (Gaussian, Voigt, etc.)

Interactive Tools

Tool

Description

larch_interactive_norm

Open an interactive HTML page to tune normalization parameters

larch_apply_norm_params

Apply normalization parameters from a saved JSON file

Interactive normalization workflow

  1. Ask Claude to interactively normalize your spectrum

  2. An HTML page opens in your browser with Plotly.js plots and sliders

  3. Adjust E0, pre-edge range, post-edge range, and polynomial degree — plots update in real time

  4. Click Save Parameters to download a JSON file, or Copy to Clipboard

  5. Tell Claude to apply the saved parameters

"Load Pdfoil.prj and let me interactively choose the normalization parameters"

Advanced

Tool

Description

larch_run_code

Execute arbitrary Python code in the larch session

Resources

The server exposes documentation resources that Claude can read on demand:

  • larch://docs/xafs — XAFS analysis reference

  • larch://docs/io — I/O functions reference

  • larch://docs/fitting — Fitting reference

  • larch://docs/feff — FEFF interface reference

  • larch://docs/interactive — Interactive tools reference

  • larch://docs/examples/xanes — XANES workflow example

  • larch://docs/examples/exafs — EXAFS workflow example

Links

License

BSD-3-Clause (matching xraylarch)

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