1. Getting Started Guide

Introduction to the Interface

When you first open XRD Analyzer, the WebAssembly engine starts loading Pyodide in the background. Because it downloads a full Python compilation alongside scientific libraries like NumPy and SciPy, this first launch takes about 8 to 12 seconds depending on your connection. Once loaded, the engine is cached by your service worker, enabling instant loads on subsequent visits.

Step 1: Loading Experimental Data

To begin, you can drag and drop your raw scan file onto the dashed loading zone or click the prompt to select a local file. If you don't have a dataset ready, click the **"Or load example data"** button. This imports a pre-loaded pattern of alpha-Quartz (SiO₂), along with its reference Crystallographic Information File (CIF), giving you an immediate preview of the tool's capabilities.

Step 2: Configuring Pre-processing Filters

Use the sidebar controls to adjust pre-processing filters. The background removal toggle uses the SNIP algorithm to filter out baseline noise caused by thermal diffuse scattering or fluorescence. You can adjust the Savitzky-Golay smoothing window slider to reduce measurement noise, or toggle $K\alpha_2$ stripping to remove secondary reflections.

The background removal process uses Python's pybaselines.whittaker.snip function:

# Typical background clipping iteration
background, params = snip(intensity, max_half_window=40, decreasing=True)

Step 3: Running Peak Detection and Fitting

Navigate to the peak detection tab in the sidebar. Adjust the height and prominence thresholds to isolate experimental peaks relative to the background level. Click **"Auto-detect Peaks"** to identify peaks, calculate matching d-spacings via Bragg's Law, and fit them using a Pseudo-Voigt model. Fitting results, including FWHM and area, will display in the peak table.

Step 4: Database Search & Phase Matching

If you want to identify phases, go to the CIF Matcher tab. You can upload custom `.cif` files or search the Crystallography Open Database (COD) by typing formulas (like Fe2O3 or SiO2) into the search bar. When you import a phase, it overlays theoretical reflection sticks on the plot, calculating a Figure-of-Merit (FOM) match coefficient.