pysotope 1.6.0

Pysotope is an open-source package meant to processes raw data measured from the OSIBL GC-IRMS. Corrections are automatically calculated but the user must verify and confirm their application.

pysotope (v.1.6.0).

Pysotope is an open-source package meant to processes raw data measured from the OSIBL GC-IRMS. Corrections are automatically calculated but the user must verify and confirm their application.

Note: pysotope was tested using jupyter lab and jupyter notebook. Compatibility with alternative python IDEs may require custom configuration.

Data Corrections

• Drift (weighted means least squares)
• Linearity (log, exponential, or linear fit)
• Methanol derivitization - user is asked for methanol values
• PAME - calculates the isotopic composition of PAME, if run in the sequence (set argument pame=True)
• VSMOW - calculated using C18, C20, and C28 standards, tested on C24 standard.

Features

• Uncertainty/error associted with each correction is automatically calculated and included in each data output.
• Compatible with hydrogen and carbon isotope measurements
• Modifiable standard isotopic values
• Due to non-linear linearity expression, a exponential or logarithmic curve is automatically fit to the linearity standards.
• Assign chain lengths using interactive plot (requires Jupyter Lab or Jupyter Notebook)

Installation

pip install pysotope

Arguments

• pame (default False) - if True, the package will automatically identify and correct PAME values in the sequence.
• user_linearity_conditions (default False) - if True, during linearity correction, user will be asked for a cutoff value under which samples with peak areas lower than the cutoff will be excluded from the analysis.
• alt_stds (default False) - if True, the user can modify the default standard values. These changes will be saved for the user, but will reset upon package update.

e.g.,

import pysotope

# Edit standard data
pysotope.standard_editor()

# Process IRMS data
pysotope.iso_process(pame=True, user_linearity_conditions = False)

# Assign chain lengths
%matplotlib widget
pysotope.assign_chain_lengths()

Use

• Run pysotope and provide the file path to the IRMS output data
• Answer questions
• Data output is split into mean of samples, individual samples, and standards in three .csv files
• Output log contains all user decisions, equations used for corrections, descriptive statistics, and time codes for user actions
• Figures are saved locally

Contributing

Contributions to pysotope are welcome! If you encounter any issues or have suggestions for improvements, please open an issue or submit a pull request on the GitHub repository.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contact

For questions or inquiries, please contact:

• Author: Dr. Gerard Otiniano & Dr. Elizabeth Thomas
• Email: [e-mail]