An Application Program Interface for Automating and Parallelizing EddyPro®

Dr. June Skeeter

Natural Resources Canada

About EddyPro®

“EddyPro® Software” (2021) is one of the most popular applications for processing Eddy Covariance (EC) data.

  • It designed to provide easy, accurate EC flux computations LI-COR (2021).
  • Open source software with a graphic user interface (GUI)
    • Interfaces with a processing pipeline is executed in FORTRAN
    • Based on the “ECO2S” (2011) package

Who Uses EddyPro?

26 of the 35 respondents who answered the question, indicated that they use EddyPro®.

Advantages of EddyPro®

The GUI makes flux processing accessible.

  • Point and click processing without need for coding
  • Users can see the wide range of methods options available
    • Links to comprehensive documentation
  • Works great for processing a single season of EC data

Disadvantages of EddyPro®

Point and click processing becomes a bottle.

  • New runs must be initiated each time more data comes in
    • Ample room for error when conducted by inexperienced users (e.g., research assistants)
    • Leads to delays in processing
  • Long records take a long time to process, users may avoid:
    • Testing alternate methods
    • Flux recalculation

How the API Can Help?

The Application Program Interface (API) can be used to automate and parallelize flux processing.

  • Call the API from command line, a python script, or run in a Jupyter Notebook
    • Schedule runs at regular intervals as new data come in
    • Setup multiple runs to compare processing methods
  • API will process longer in parallel to expedite processing
    • Can reduce processing time by a quarter or more

How the API Can Help?

The Application Program Interface (API) can be help standardize flux processing.

  • Template .eddypro files serve as the basis for a project
    • View/modify options using the GUI or a text editor
  • Works with LICOR (GHG) or Cambpbell (TOA5) files

Allows for quick differentiation

How does it work?

There are two main routines in the API which will be run in sequence when calling the script.

cd Path\To\eddyProAPI
.\.venv\Scripts\activate
python .\eddyProAPI.py --siteID ID --fileType ghg --dateRange 2024-06-01 2024-08-31

Pre-processing

  • Inspect for changes in metadata
    • Identify groups of common configuration
  • Parses the high frequency data to generate descriptive statistics
    • Optional pre-filtering to exclude bad data
  • Generate biomet and dynamic metadata files on-the-fly
    • Reads Biomet.Net database files

Processing

  • Runs EddyPro® over the desired time period
    • Use a template .eddypro file to ensure standardized processing
    • Appended run-specific information (inputs, directories, etc.)
  • Executes raw Data processing in parallel
  • Flux processing and correction applied on a per-group basis
  • Dump outputs to Biomet.Net database files

What’s next?

This project is still under development.

  • Comprehensive documentation page will be available in the coming weeks
    • Basic usage instructions can be found on the repo page
  • I am looking for interested users to help with Beta testing!
    • Please reach out if you would like to try it out: june.skeeter@nrcan-rncan.gc.ca

References

“ECO2S.” 2011. Infrastructure for Measurements of the European Carbon Cycle consortium. http://gaia.agraria.unitus.it/eco2s.
“EddyPro® Software.” 2021. LI-COR; Infrastructure for Measurements of the European Carbon Cycle consortium. https://www.licor.com/env/support/EddyPro/software.html.
LI-COR, Inc. 2021. “EddyPro® Version 7.0 Help and User’s Guide.” LI-COR, Inc. Lincoln, NE. https://www.licor.com/env/support/EddyPro/topics/introduction.html#top.

See the repo here