mat-xrd-digitizer

XRD Digitizer

Goal

To convert an image or screenshot of an X-Ray Diffraction (XRD) pattern into a digitized, numeric .xy data file, which can then be used by downstream analysis tools like mat-xrd-phase-analysis.

This skill leverages the AI Agent's built-in Vision/Language Model (VLM) capabilities. The Agent will visually parse the provided image to extract key peak positions (2-theta) and approximate relative intensities, and then use a provided script to mathematically generate a representative pseudo-Voigt profile.

Instructions

1. Extract Peaks Visually

Provide the agent with an image (e.g., screenshot) of the XRD plot. The agent will visually inspect the plot and identify the coordinates of the major peaks.

Handling Multiple Curves/Colors: If the image contains multiple XRD patterns, the user should specify which curve to digitize by its color, label, or position (e.g., "digitize the red curve" or "digitize the curve labeled 'sample A'"). The agent will then selectively extract peaks from only that specific curve.

Agent Action: The agent should:

1. Create a JSON file (e.g., peaks.json) containing the extracted peaks as an array of objects for the target curve. CRITICAL: You must ensure every single visible peak, including the tiny minor peaks, is reported and digitized to ensure accurate full-profile refinement downstream.
2. Save a copy of the original image (e.g., original_plot.png) in the same directory as the JSON file for future reference.

Example peaks.json format:

[
  {"2theta": 8.8, "intensity": 0.05, "fwhm": 0.3},
  {"2theta": 15.8, "intensity": 0.08, "fwhm": 0.3},
  {"2theta": 33.1, "intensity": 1.00, "fwhm": 0.3}
]

Note: intensity should be normalized between 0 and 1.0 (where the highest peak is 1.0). fwhm defaults to 0.3.

2. Generate the Digitized .xy File

Use the provided script to generate the experimental .xy file based on the extracted peaks.

# Env: base-agent
python .agents/skills/mat-xrd-digitizer/scripts/digitize_plot.py peaks.json --output digitized_plot.xy --min-x 5.0 --max-x 80.0

Parameters:

• input: The JSON file containing the extracted peak parameters.
• --output: Path to save the resulting .xy file.
• --min-x: Minimum 2-theta value to generate (default: 5.0).
• --max-x: Maximum 2-theta value to generate (default: 90.0).
• --points: Number of data points in the .xy file (default: 4000).
• --noise: Amplitude of experimental noise to add (default: 0.01).
• --background: Amplitude of exponential background baseline (default: 0.05).

Examples

For a full working example of extracting and digitizing a YBCO plot: See examples/digitize-ybco/README.md.

# Env: base-agent
python .agents/skills/mat-xrd-digitizer/scripts/digitize_plot.py .agents/skills/mat-xrd-digitizer/examples/digitize-ybco/peaks.json --output test_ybco.xy

Constraints

• Approximation: The digitized plot is a mathematical approximation using pseudo-Voigt profiles. It does not perfectly recreate the exact pixel-by-pixel raw data of the original scan, but it is highly effective for downstream phase matching tools.
• Vision Accuracy: The accuracy of the 2-theta positions entirely depends on the clarity of the provided image axes.
• Environments: Scripts require the base-agent Conda environment. Each code block MUST specify the environment.

References

• Pseudo-Voigt profile generation is standard practice in XRD peak fitting (e.g., Rietveld refinement tools).

Related Skills

• mat-xrd-phase-analysis: Use the generated .xy file to identify the material phases.

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Author: Bowen Deng Contact: GitHub @learningmatter-mit