XraySA

X-ray Scattering Analysis Tools — a Dash web app for reducing and analyzing fixed-energy and resonant X-ray scattering (SAXS/WAXS/GI-SWAXS) data from synchrotron beamlines.

Tabs

Tab	Description
PTable	Periodic table element lookup
XAS Calculations	Sample-stack transmission/attenuation calculations across an energy range, via XrayDB
Scattering 2D & 1D	The core scattering tool: upload a detector image (and optionally a .poni calibration file), set up pyFAI geometry, and run azimuthal integration. Live 2-D views in both pixel space and remapped qx/qy space, plus 1-D I(q) and cake (q vs. χ) plots Hot-pixel masking (square/circular regions by center + size), independent of intensity thresholding An accumulating azimuthal wedge region list (add/remove/clear), each drawn on the q-space image and producing its own I(q) curve Q-range filtering, multiple output units, and CSV export
Grazing Incidence (GI-SWAXS)	Promotes the shared pyFAI integrator to a FiberIntegrator for grazing-incidence geometry (incident/tilt angle, sample orientation). qxy/qz detector image with an adjustable display range, azimuthal wedges, and accumulating vertical/horizontal line-cut regions (each mirrorable about qxy=0/qz=0) Combined 1-D plot overlaying every azimuthal/vertical/horizontal curve, with its own Q-range trim
Resonant Scattering	Load a folder of detector images spanning an energy series (energy parsed from each filename); per-file 2-D/1-D preview with the wavelength overridden from that file's own energy, an ROI accumulator on the pixel-space image, a background NEXAFS job (ROI intensity vs. energy), and a background energy-colored 1-D overlay across the whole series
Batch SWAXS	Run 1-D and/or 2-D q-space processing over a whole folder of detector images in the background (with a live progress bar); choose either the Scattering 2D & 1D (azimuthal) or Grazing Incidence (fiber) integrator, reusing that tab's geometry/regions
SWAXS Merging	Average multiple integrated profiles and merge/splice two averaged profiles together

Setup

Requires Python 3.

macOS / Linux:

git clone https://github.com/josecdiazm/XraySA.git
cd XraySA
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Windows (PowerShell):

git clone https://github.com/josecdiazm/XraySA.git
cd XraySA
python -m venv venv
.\venv\Scripts\Activate.ps1
pip install -r requirements.txt

Notes for Windows:

• If Activate.ps1 fails because script execution is disabled, run Set-ExecutionPolicy -Scope Process -ExecutionPolicy Bypass once, then retry the activation line.
• If python isn't recognized, or points to an unexpected install (e.g. MSYS2/Git Bash's Python instead of a normal Windows one), check Get-Command python -All to see every python.exe on your PATH, and either reorder PATH or invoke the correct one directly by its full path, e.g. & "C:\Users\<you>\AppData\Local\Programs\Python\Python3xx\python.exe" -m venv venv.
• The clone URL above uses HTTPS, not SSH — it works with no GitHub login or SSH key needed, since this repo is public. If you get a Permission denied (publickey) error, you're likely using an git@github.com:...-style SSH URL instead; switch to the HTTPS one shown here.

Running

python app.py

The app runs at http://127.0.0.1:8050.

Updating

If you cloned this repo with git, pull the latest changes and reinstall dependencies (in case new ones were added):

cd XraySA
git pull
pip install -r requirements.txt

If you instead downloaded a ZIP of the repo rather than using git clone, there's no update command — download a fresh ZIP from the repo's main branch and replace the old folder. If you expect to update regularly, it's worth switching to git clone once so future updates are just git pull.

Notes

• Built on pyFAI for detector calibration/azimuthal integration and fabio for reading detector image formats (edf, cbf, tif, etc.), in addition to .npy/.npz.
• Batch SWAXS uses Dash's background callbacks (dash[diskcache]) for progress bars on long-running batch jobs.
• Folder inputs (Batch SWAXS, SWAXS Merging) can be filled via a native folder-picker dialog, cross-platform through tkinter, run in a subprocess to avoid freezing the app.
• File inputs (Resonant Scattering, SWAXS Merging, Batch SWAXS) also support drag-and-drop as an alternative to browsing.
• This is a local-only tool (server and browser on the same machine) — it is not hardened for exposure on a network.