xdart

X-ray diffraction processing and analysis, from live acquisition to notebooks.

xdart combines detector-image integration, multi-angle stitching, reciprocal-space mapping (RSM), and fitting in one desktop application. It uses pyFAI for azimuthal and grazing-incidence integration and xrayutilities for stitching and reciprocal-space mapping. The same processing tools are available in Python through xrd_tools, the headless core included with xdart.

This README describes xdart 1.2.1. Release notes · Upgrading from 1.1.5 · Limitations and workarounds

Install · GUI workflow · Stitch · RSM · Python and notebooks · Development

Quick start

1. Install Pixi and open a new terminal. Python and conda do not need to be installed separately.

2. Install the published release:

   pixi global install -c https://prefix.dev/xrd-tools -c conda-forge xdart
   

3. Launch the xdart app/shortcut, or run xdart in a terminal.

To update a global installation, close xdart and run pixi global update xdart. To work from source, follow the source-checkout setup. Global installation and source-checkout installation are separate environments.

Pixi and conda/mamba supply the compiled dependencies needed by the GUI. Pip-only GUI installation is best-effort. See the installation guide for alternative installers, headless Python environments, and troubleshooting.

The GUI (xdart)

The Scattering Workspace combines processing controls, a data browser, plots, and analysis tools. Select a processing mode beside Run:

Standard and grazing-incidence integration support masks, intensity thresholds, background subtraction, normalization, and parallel processing. Analysis tools include overlays, peak/phase fitting, reference phases, and notebook export.

GUI quick start

1. Set the Project folder and Save Path. The default output folder is <Project>/xdart_processed_data.
2. Under Experiment, choose a matching PONI calibration and an optional mask. Calibrate and Make Mask open the corresponding tools.
3. Choose the source format and input files or directory. Check image paths, scan selection, and metadata as appropriate for your source.
4. Select Int 1D, Int 2D, or Int 1D (XYE). Set axes, point counts, ranges, and conditioning. Advanced contains the detailed corrections.
5. Choose Cores, then Run. Batch suppresses intermediate plot updates and displays the saved result at completion.
6. Select saved results and frames in the Data Browser. Use Raw image, Metadata, and the fitting tools to inspect them.

For Q/2θ conversion, xdart uses the acquisition/calibration wavelength. For a fixed scattering angle, Q changes with wavelength; 2θ is an angle.

For grazing incidence, choose Experiment → Configuration → Grazing and set the incidence-angle motor or manual angle. GI offers Qip/Qoop profiles and maps, Q–χ, and exit-angle modes. Choose Q–χ + Qip–Qoop when both directly integrated maps are needed; the derived Q–χ display is only an approximation.

Stitch 1D and Stitch 2D

Stitch combines raw detector frames with scan-angle metadata. Select Stitch 1D or Stitch 2D beside Run.

1. Set the Project folder, output location, and source: SPEC + Image Series, SPEC + Eiger, or metadata-bearing NeXus. Choose Files or a Folder; folder discovery supports Subdirs and Filter. For SPEC, check Image Path and Image Stem. A blank stem uses <SPEC name>_scan<N>_. An Eiger master alone does not supply scan angles.
2. Select scans. All produces one output per scan; Select accepts groups, such as 1,2,[3-5,8] for two separate outputs plus one combined output. Groups apply to each selected SPEC file. Files + NeXus combines the selected containers/entries; use Entry to restrict entries.
3. Select a calibration or create one with Calibrate. Choose pyFAI MultiGeometry or xrayutilities histogram as the backend. The shared calibration workflow saves a pyFAI goniometer calibration and its xrayutilities .xu.json partner. XU requires its own calibration or that partner; an arbitrary PONI is insufficient. pyFAI's advanced PONI + offsets route requires matching angle mappings and reference angles.
4. Choose Standard or Grazing, then configure ranges, point counts, Normalize, Threshold, and Mask File. GI incidence/tilt may come from metadata motors or manual angles.
5. Optionally use Preview to check membership and warnings, then Run. Run validates the inputs even without Preview.
6. Open the saved _stitch1d.nexus or _stitch2d.nexus result. Full shows the combined result; contributor rows inspect its source frames. Append skips compatible completed outputs; Replace/Overwrite recomputes them.

For fitting, return to Full and select Intensity. Phase fitting needs an appropriate radial Q/2θ profile and wavelength; GI cuts support peak fits. Keep calibration, camera orientation, and recorded motor conventions consistent.

Reciprocal-space mapping (RSM)

RSM grids raw frames and their recorded motor positions into a volume. It is a finite workflow with Preview, Run, and Stop.

1. Choose the source and scan groups as for Stitch. 42,43 produces separate maps; [42-44] combines those scans.
2. Select or create a calibration. RSM currently requires six-circle PSIC geometry and the calibration's .xu.json partner within the Project. Single-2θ, four-circle, and two-circle partners are not supported.
3. Leave Use the calibration's refinement enabled to apply detector-angle zero offsets, mount refinement, and the fitted energy correction: scan energy + (fitted calibration energy − recorded calibration energy). Distance and beam centre are used even when this option is disabled. The calibrant's fitted sample displacement is not transferred to the sample.
4. Choose HKL or Q Cartesian (Qx, Qy, Qz; Å⁻¹). HKL also needs a UB matrix from the source, typed values, or a SPEC scan. Advanced → Angle mapping maps metadata to mu, eta, chi, phi, nu, del.
5. Set the grid counts, initially 40 × 40 × 40, plus normalization, thresholds, masks, and corrections. Bounds come from the selected data; each count must be at least two, with at most 8,000,000 voxels in total.
6. Preview, then Run. Outputs normally end in _rsm.nexus. Append skips unchanged completed results; Replace/Overwrite recomputes them. Stop cancels the current calculation and remaining queue.
7. Inspect the saved map's three planes and profiles, 3D Viewer, or Custom Slice. Tools provide lineout, 2D, and 3D peak fits. Display Log and background controls do not rewrite the scientific fit inputs.

Opening a saved result does not rerun the calculation or restore a complete processing setup. Preserve raw data and calibration for processing replay.

Calibration and masking

For Int modes, Calibrate opens pyFAI calibration to produce a PONI file. For Stitch/RSM, the shared calibration dialog supports direct-beam distance fitting, calibrant frames, and Quick calibration with a resumable session. The calibrant scan's energy field represents acquisition energy; the fitted energy correction is retained separately. Imported beam coordinates remain geometry values unless explicitly edited as a direct-beam scan locator.

Use a calibration appropriate to the detector, image dimensions, and camera orientation. A mismatched calibration or mask can prevent integration; failed runs display the reason.

Mask File accepts .edf or .npy. Make Mask saves beside the source as <source-stem>-mask.edf and selects it automatically; an existing mask at that path is replaced. Closing without saving keeps the previous selection. Threshold applies per-frame intensity limits independently of the mask; turning it off does not disable the mask or make nonfinite pixels valid.

For headless direct-beam fitting, see the API guide and distance-calibration notebook.

Live acquisition and output handling

For supported Int 1D/2D sources, enable Live to process new arrivals. Run becomes Pause / Resume; Stop ends the run and closes its output.

• Append continues a compatible processed NeXus scan, skipping frames already present. Replace/Overwrite reprocesses it. Int 1D (XYE) does not support Append. Stitch/RSM Append skips complete results, as described above.
• Single follows the current selection; Overlay keeps patterns for comparison. Pin a slice cut with Cmd+P (Ctrl+P on Windows/Linux).
• Processed NeXus results retain integrated data, metadata, and thumbnails. Keep the referenced raw images for full-resolution inspection and set the Project folder after moving a project.
• The browser can also open files in NeXpy or silx view, included with the GUI installation.

Data export and saving

Int and Stitch save processed NeXus results; Int 1D (XYE) writes text patterns. Stitch also saves an XYE profile companion. GI Stitch's saved Qip/Qoop cuts have XYE companions whose third column is sqrt(abs(I)), an estimate rather than propagated uncertainty, as their headers state.

Use a plot's export menu for additional cuts or PNG/SVG figures. Fitting tools provide CSV, Export Jupyter…, and Export marimo…. Help → Export Run notebook… exports current processing inputs for replay; Help → Export Analyze Results Notebook… exports a notebook that reads saved results without rerunning integration. These notebooks reference data files; exporting does not copy those files.

Headless quick start (xrd_tools)

xrd_tools provides integration, stitching, RSM, NeXus I/O, peak/phase fitting, and strain analysis without the desktop GUI. For example, integrate an image with an existing PONI calibration:

from xrd_tools.io import read_image
from xrd_tools.integrate import load_poni, poni_to_integrator, integrate_1d

ai = poni_to_integrator(load_poni("calibration.poni"))
image = read_image("detector.tif")
result = integrate_1d(image, ai, npt=1000, unit="q_A^-1")
q, intensity, sigma = result.radial, result.intensity, result.sigma

To write complete processed scans, use ReductionPlan, Scan, NexusSink, and run_reduction, as shown in the headless reduction notebook. The processed-data notebook covers reading saved results, thumbnails, and original raw frames.

Notebooks

The GUI installation includes JupyterLab, marimo, and notebook widgets:

xdart-notebook                         # JupyterLab in the installed environment
xdart-notebook --register-kernel       # Register "Python (xdart)" for VS Code
xdart-notebook --marimo results.py     # Open an exported marimo notebook

In an editable Pixi checkout, use pixi run --locked xdart-notebook instead. Select the corresponding Python kernel and Run All. See notebook setup for kernel registration, widgets, and missing-kernel troubleshooting.

The notebook gallery covers batch integration, GI, stitching, RSM, peak/phase fitting, strain, and time-resolved analysis. Examples default to deterministic demonstration data and need no private data.

Development

Use the shared Pixi workspace for an editable source installation:

git clone https://github.com/v-thampy/xdart.git
cd xdart
pixi install --locked
pixi run --locked xdart

The default main branch contains the current source. To use the exact 1.2.1 release, run git switch --detach v1.2.1 before installing. The lockfile covers Apple Silicon macOS, Linux x86-64, and Windows x86-64. Each machine installs its own environment; keep the shared lockfile unchanged when testing on another machine.

To update an existing checkout after saving or committing local work:

git pull --ff-only
pixi install --locked
pixi run --locked xdart

Source edits take effect after restarting xdart. See the editable setup guide, Windows instructions, and test and packaging commands.

Limitations and troubleshooting

Read limitations and workarounds before upgrading or reusing older output. In particular, older Standard seam-window results need full regeneration with Replace/Overwrite, and full-turn I(χ)/cake ranges should use Auto. Derived GI Q–χ displays are approximate and do not replace directly integrated maps for quantitative analysis.

If a run fails, check its displayed reason and terminal log. Check calibration, image/mask dimensions, source metadata, and output access before retrying. For high memory use, reduce Cores; the memory planning target is advisory. Avoid modifying or synchronizing output files while xdart is writing them. Installation and notebook troubleshooting are in the installation guide. Native Windows/SMB and GUI behavior still require release qualification; a passing offscreen test does not establish native behavior.

Contributing

Bug reports and contributions are welcome through GitHub issues and pull requests. Include the xdart version, operating system, steps to reproduce, and error message when reporting a problem.

License and citation

First-party code is MIT licensed; portions of the headless core retain their BSD-3-Clause license. SPDX: MIT AND BSD-3-Clause.

If you use xdart in research, cite the project and the underlying scientific packages used in your analysis:

xdart: SSRL X-ray diffraction toolkit. https://github.com/v-thampy/xdart

Acknowledgments and contact

Developed at the Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, by Vivek Thampy — vthampy@stanford.edu.

Thanks to the authors and contributors of pyFAI (including its FiberIntegrator), xrayutilities, NeXpy, silx, NumPy, SciPy, lmfit, and pymatgen, and to the users who provide feedback and improvements.