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Python tools for quality control of real-time and delayed-mode glider data.

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rugliderqc

A collection of python tools to quality control real-time and delayed-mode profile-based glider NetCDF files. It uses a modified version of the ioos_qc package to add quality flag variables to the datasets that are outlined in the Required and Strongly Recommended tests in the IOOS QC Manual of Glider Data. We have also developed additional tests to further quality control glider data, such as a test that flags CTD profile pairs that are severely lagged, which can be an indication of CTD pump issues.

This code is designed to run on profile-based glider NetCDF files with a specific file and directory structure. The files are processed to NetCDF using the gncutils package.

Full documentation of this repo can be found in the wiki.

Note: this repository is under development

Installation

git clone https://github.com/rucool/rugliderqc.git

cd rugliderqc

conda env create -f environment.yml

conda activate rugliderqc

pip install .

Requires replacing scripts in the ioos_qc package (.../envs/rugliderqc/lib/python3.9/site-packages/ioos_qc) with all files of the same name in ./ioos_qc_mods (as of 12/8/2021, only qartod.py) after the environment is created.

Usage

python run_glider_qc.py glider-YYYYmmddTHHMM

This wrapper script runs:

  1. check_science_variables.py
  2. check_duplicate_timestamps.py
  3. glider_qartod_qc.py
  4. interpolate_depth.py
  5. ctd_hysteresis_test.py
  6. summarize_qartod_flags.py
  7. time_shift.py
  8. add_derived_variables.py
  9. move_nc_files.py

Acknowledgements

Development was supported in part by the Mid-Atlantic Regional Association Coastal Ocean Observing System.

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