EddyPro API

Written and maintained by Dr. June Skeeter under an open copyright license©.

About

EddyPro® is a popular software application for processing high frequency Eddy Covariance (EC) data via a graphic user interface (GUI). This application program interface (API) can be used to automate and parallelize processing with Eddy Pro® to minimize computation times.

Installation & Setup

For now, the API will only work on windows. There are plans to expand to mac/linux ... eventually.

1. Install EddyPro. Make not of where the root installation of EddyPro ends up (e.g., C:/Program Files/LI-COR/EddyPro-7.0.9/) as you will need this later

2. Clone the repository

git clone --recurse-submodules https://github.com/CANFLUX/EddyPro_API

3. Run the installation routine

cd Path\To\eddyProAPI
python pyDbTools\setupPyVenv\install.py

• This routine will walk you through a series of prompts to define important path variables. You must define:
  • The base path to your EddyPro Installation
  • A path to your database folder (if desired for dynamically reading biomet data)
  • A path to the root folder containing your raw high frequency data
• The script will then create a python virtual environment (.venv) and install all required packages.
  • A .venv allows you to install packages while keeping them isolated from your base Python installation to avoid potential dependency issues that could arise from conflicting version of packages.

Running the API

The API can be called via command line; instructions are given below. You can also run it vai API_Run.ipynb if you prefer.

1. Before running EddyPro, you should decide which settings you want to use. You can select an appropriate .eddypro file from the Templates folder or use an existing .eddypro file form previous work.

• The template files can be used to define the processing parameters and ensure they remain standardized between runs. They can be inspected using the EddyPro GUI or a text editor. It is suggested to use 'ClosedPathStandard.eddypro' for systems with an closed path analyzers (e.g., LI-7200) and 'OpenPathStandard.eddypro' for systems without any close path analyzers. You can also define your own template file by modifying a template in the GUI or with a text editor and saving with a new filename name.
  • How will these files be used? The API will read the settings from these files and then dynamically update settings in EddyPro (paths, dates, etc.) to automate runs. Settings that will be overwritten can be found in config_files/eddyProDynamicConfig.ini

2. Call the API

   a. Activate the virtual environment. Note if you are on a system which restricts the execution of scripts, first you need to temporarily set your execution policy in order to activate the environment: Set-ExecutionPolicy Unrestricted -Scope Process

   .\.venv\Scripts\activate

   b. Call the program. In this example, the program will execute for the current year, on the "BB" site, using Templates/ClosedPathStandard.eddypro to define the processing procedures.

   py eddyProAPI.py --siteID BB --eddyProStaticConfig Templates/ClosedPathStandard.eddypro