GEddySoft_main

GEddySoft: A Python Package for Eddy Covariance Processing

This module contains the main processing function for the GEddySoft eddy covariance software package. It handles the complete workflow of processing raw high-frequency data from sonic anemometers and trace gas analyzers (e.g., PTR-TOF-MS) to calculate fluxes and quality control metrics.

Key Features

  • Flexible input handling for sonic and trace gas data

  • Comprehensive quality control including:

    • Spike detection (Vickers & Mahrt 1997)

    • Stationarity tests (Foken & Wichura 1996)

    • Integral turbulence characteristics (Thomas & Foken 2002)

    • Instrument diagnostics

  • Advanced processing options:

    • Multiple coordinate rotation methods

    • Time lag optimization

    • Spectral corrections

    • Flux uncertainty estimation

  • Parallel processing support for large datasets

  • HDF5-based data storage with rich metadata

Author

Bernard Heinesch University of Liège, Gembloux Agro-Bio Tech

License

GEddySoft is available under the terms of the MIT License.

Functions

GEddySoft_main

Process eddy covariance data for a single day (when used in multithread mode) or for the time period given in the ini file.
GEddySoft_main.GEddySoft_main(str_day, ini, log_filename)[source]

Process eddy covariance data for a single day (when used in multithread mode) or for the time period given in the ini file.

This function handles the complete processing chain for eddy covariance data, from raw high-frequency measurements to quality-controlled fluxes. It supports both single-threaded and parallel processing modes.

Parameters:

  • str_day (str) – Date string in format ‘YYYYMMDD’ for the day to process. Use ‘no_multithread’ for single-threaded mode.

  • ini (dict) –

    Configuration dictionary containing all processing parameters:

    • files: Input/output paths and file patterns

    • param: Processing parameters (QC thresholds, methods, etc.)

    • run_param: Runtime parameters

    • sonic: Sonic anemometer configuration

    • irga: Gas analyzer configuration

  • log_filename (str) – Path to the log file where processing messages will be written

Returns:

unique_days – List of successfully processed days

Return type:

list

Notes

The processing workflow includes:

  1. Data loading and synchronization

    • Sonic anemometer data

    • Trace gas measurements

    • Auxiliary meteorological data

  2. Quality control

    • Spike detection and removal

    • Diagnostic value checking

    • Missing data handling

  3. Coordinate rotations

    • Double rotation or

    • Planar fit method

  4. Time lag optimization

    • Covariance maximization

    • RH-dependent correction

  5. Flux calculations

    • Detrending options

    • Webb-Pearman-Leuning terms

  6. Quality assessment

    • Stationarity tests

    • Integral turbulence characteristics

    • Spectral analysis

  7. Uncertainty estimation

    • Random error (Finkelstein & Sims)

    • Detection limits

The function creates two types of output files:

  1. Results file (HDF5)

    • Fluxes and means

    • Quality flags

    • Processing parameters

  2. Covariance file (HDF5, optional)

    • Raw covariance functions

    • Time lag information

Examples

>>> # Process a single day
>>> ini = read_main_inputs('config.txt')
>>> log_file = 'processing.log'
>>> processed = GEddySoft_main('20240101', ini, log_file)