PyIRoGlass

PyIRoGlass is a Bayesian MCMC-founded Python algorithm, written in the open-source language Python3, for determining ${\mathrm{H}}_2\mathrm{O}$ and ${\mathrm{CO}}_2$ species concentrations in the transmission FTIR spectra of basaltic to andesitic glasses. We leverage a database of naturally degassed melt inclusions and back-arc basin basalts to delineate the fundamental shape and variability of the baseline underlying the ${\mathrm{CO}}_3^{2-}$ and ${\mathrm{H}}_2{\mathrm{O}}_{\mathrm{m},1635}$ peaks, in the mid-infrared region. PyIRoGlass employs Bayesian inference and Markov Chain Monte Carlo sampling to fit all probable baselines and peaks, solving for best-fit parameters and capturing covariance to offer robust uncertainty estimates.

Manuscript

Find the PyIRoGlass manuscript published at Volcanica on for a more detailed description of the development and validation of the method. If you use this package in your work, please cite:

Shi, S., Towbin, W. H., Plank, T., Barth, A., Rasmussen, D., Moussallam, Y., Lee, H. J. and Menke, W. (2024) “PyIRoGlass: An open-source, Bayesian MCMC algorithm for fitting baselines to FTIR spectra of basaltic-andesitic glasses”, Volcanica, 7(2), pp. 471–501. doi: 10.30909/vol.07.02.471501.

@article{Shietal2024,
    doi       = {10.30909/vol.07.02.471501},
    url       = {https://doi.org/10.30909/vol.07.02.471501},
    year      = {2024},
    volume    = {7},
    number    = {2},
    pages     = {471-501},
    author    = {Shi, Sarah C. and Towbin, W. Henry and Plank, Terry and Barth, Anna and Rasmussen, Daniel and Moussallam, Yves and Lee, Hyun Joo and Menke, William},
    title     = {PyIRoGlass: An open-source, Bayesian MCMC algorithm for fitting baselines to FTIR spectra of basaltic-andesitic glasses},
    journal   = {Volcanica}
}

Documentation

Read the documentation for a run-through of the PyIRoGlass code.

Run on the Cloud

If you do not have Python installed locally, run PyIRoGlass on Google Colab.

Run and Install Locally

Obtain a version of Python between 3.8 and 3.12 if you do not already have it installed. PyIRoGlass can be installed with one line. Open terminal and type the following:

pip install PyIRoGlass

Make sure that you keep up with the latest version of PyIRoGlass. To upgrade to the latest version of PyIRoGlass, open terminal and type the following:

pip install PyIRoGlass --upgrade