Diamond NAgg Map

Calculates nitrogen concentration and aggregation state across FTIR maps of diamond plates. Each spectrum in the map gets a baseline correction, a thickness normalization and a least-squares fit to reference spectra, and the results are saved as maps.

How it works

1. Reads a Thermo Fisher Nicolet OMNIC .map file with FTIR_OMNIC_MAP_Reader into an xarray dataset.
2. Removes the baseline of each spectrum with asymmetric least squares (pybaselines).
3. Normalizes each spectrum for thickness by comparing it with a type IIa reference spectrum over 1800-2313 and 2390-2670 cm^-1.
4. Fits the nitrogen region (up to 1400 cm^-1) with a bounded least-squares combination of the C, A, X, B and D center reference spectra plus a constant and a linear term. The reference spectra come from the QUIDDIT program.
5. Converts the A and B fits to ppm (factors 16.5 and 79.4) and calculates total nitrogen and %B for every point.
6. Saves maps of A ppm, B ppm, %B, total N, C and D as PNG and TIFF, plus example plots of the baseline, type IIa and nitrogen fits on a grid of points across the map.

Install and run

Requires Python 3.13 or later.

uv tool install diamond-nagg-map
diamond-nagg-map path/to/sample.map --output Results

pip install diamond-nagg-map also works. Versions before 0.9.0 have a broken diamond-nagg-map command. To install the latest code from GitHub instead, use uv tool install git+https://github.com/whtowbin/Diamond_NAgg_Map.

Options:

• --output: folder for the maps and plots (default Results).
• --lam, --p: baseline parameters passed to pybaselines.whittaker.asls (defaults 2e7 and 1e-6).
• --n_examples: grid of points to plot example fits for, either N for an N x N grid or NX NY (default 5). Each point produces three plots.

From Python:

from diamond_nagg_map.DiamondNAggMap import process_map

process_map("sample.map", "Results", baseline_lam=1e7, baseline_p=1e-5, n_examples=(3, 3))

Limitations

• Reads only OMNIC .map files from Nicolet FTIR microscopes.
• Fits type IaA/B diamonds. Type Ib support is not finished.
• Single-spectrum processing lives in diamond-ftir-package.

License

MIT. See LICENSE.