SusMat-SWAXS 2.1.5

A collection of python scripts for uploading analytical data to iRODS

SWAXS tools

Description

This is a collection of scripts to perform data conversion and integration on X-ray scattering data, specifically for data collected on the Xenocs Xeuss SWAXS instrument.

Available tools:

• sm-datconv - Converts Xenocs format 1D data (.dat) to TOPAS compatible .xye format
• sm-edfh5 - Convert EDF files to HDF5 format with metadata preservation
• sm-saxsint - Integrate 2D SAXS data from Xenocs Xeuss instruments with background subtraction
• sm-waxsint - Integrate 2D WAXS data from Xenocs Xeuss instruments with absorption correction
• sm-spharm - Visualize spherical harmonics functions from TOPAS coefficients

Installation

Install in a virtual environment to avoid dependency conflicts:

pip install SusMat-SWAXS

Usage

All scripts are available as command-line tools after installation. Use the --help flag with any command to see detailed usage information.

sm-datconv

Converts Xenocs format 1D data (.dat) to TOPAS compatible .xye format.

Input: .dat file with tab-separated columns for q, I(q) (and optionally sigma).

Usage:

sm-datconv <filename_without_extension>

Output: .xye file with tab-separated columns for 2θ, I, and error (if present in input).

Batch processing example (PowerShell):

Get-ChildItem -Filter *.dat | ForEach-Object -Process {sm-datconv $_.BaseName}

sm-xrdmlconv

Converts Malvern PANalytical format 1D data (.xrdml) to TOPAS compatible .xy format.

Input: .xrdml file .

Usage:

sm-xrdmlconv <filename_without_extension>

Output: .xy file with tab-separated columns for 2θ and I and a .json file containing metadata.

sm-edfh5

Convert multiple EDF files to a single HDF5 file with metadata preservation.

Usage:

sm-edfh5 <path to directory containing edf files>

sm-saxsint

Integrate 2D SAXS data from Xenocs Xeuss instruments with background subtraction and absorption correction.

Usage:

sm-saxsint <sample.edf> <mask.edf> [OPTIONS]

Key options:

• --poni <file.poni> - PONI calibration file
• --background <bkg.edf> - Background file for subtraction
• --bkg_factor <float> - Background scaling factor (default: 1.0)
• --unit <q|2th> - Radial unit for integration (default: q)
• --xmin <float> - Minimum q value (default: 0.004)
• --xmax <float> - Maximum q value (default: 0.7)
• --opencl - Use OpenCL acceleration (requires pyopencl)
• --raw2D - Display 2D image in lab frame

Output:

• *_1D.dat - Integrated 1D data
• *_subtracted.dat - Background-subtracted data
• *.svg - Visualization plot

sm-waxsint

Integrate 2D WAXS data from Xenocs Xeuss instruments with absorption correction.

Usage:

sm-waxsint <sample.edf> <mask.edf> [OPTIONS]

Key options:

• --poni <file.poni> - PONI calibration file
• --background <bkg.edf> - Background file for subtraction
• --bkg_factor <float> - Background scaling factor (default: 1.0)
• --unit <q|2th> - Radial unit for integration (default: q)
• --xmin <float> - Minimum q value (default: 0.36)
• --xmax <float> - Maximum q value (default: 3.8)
• --lac <float> - Linear absorption coefficient in cm⁻¹ for thickness correction
• --thickness <float> - Sample thickness in cm for transmission correction
• --noabs - Disable absorption correction
• --opencl - Use OpenCL acceleration (requires pyopencl)
• --raw2D - Display 2D image in lab frame

Output:

• *_1D.dat - Integrated 1D data
• *_subtracted.dat - Background-subtracted, absorption-corrected data
• *.svg - Visualization plot

sm-spharm

Visualize spherical harmonics functions using coefficients from TOPAS academic output files.

Usage:

sm-spharm C00 C20 C22P C22M C40 C42P C42M C44P C44M C60 C62P C62M C64P C64M C66P C66M C80 C82P C82M C84P C84M C86P C86M C88P C88M [OPTIONS]

Arguments: 25 spherical harmonics coefficients (c00 through c88m) from TOPAS output file

Options:

• --output <filename> / -o <filename> - Output filename for the plot (default: sph_harm.svg)
• --resolution <int> / -r <int> - Angular resolution for the plot (default: 200)

Example:

sm-spharm 1 -0.54889 0.48504 0.74711 0.79916 -0.33178 0.16323 0.45369 \
          -0.29782 -0.29214 -0.43949 0.01524 0.09042 0.85340 0.40316 \
          -0.01881 1.47673 -0.55751 -0.68970 0.02621 -0.06565 -0.56472 \
          1.00981 -0.12339 -0.25831 --output my_spherical_harmonics.svg

Output: 3D visualization plot showing the spherical harmonics function in real space

Support

Submit an issue on github: https://github.com/Sustainable-Materials-Lab/SusMat-SWAXS

Contributing

Contact Samuel Eyley if you are interested in contributing.

Authors and acknowledgment

Originally authored by Samuel Eyley.

Significant portions of code were developed with the help of Github Copilot (2025).

License

MIT License