glidertest: diagnostics and HTML reports for OG1 glider data

glidertest reads a glider mission in OG1 format and tells you what is in it and what looks wrong: sensor drift, dive–climb bias, quenching, flight-model performance, sampling gaps, and the QC flags the file already carries. It is a diagnostic tool only — it never modifies your data and never fills in a value it could not determine.

As a library. Every diagnostic is a function: plots.plot_quench_assess(ds, 'CHLA') draws the chlorophyll quenching check, tools.compute_daynight_avg(ds) returns the numbers behind it. Call the ones you want from a notebook, on your own xarray.Dataset, and look at the figure — see API reference and the example notebook.

As a report. glidertest report mission.nc --report-dir reports/ runs every diagnostic that applies to the file and writes a self-contained HTML report: a landing page about the mission, one page per sensor present (CTD, oxygen, optics), a flight page for gliders that report a flight-model velocity, and an inventory page about the file itself. Every figure is embedded, so the pages work offline and can be mailed or dropped on a share. Many missions in one directory get a fleet page with a map and a table. The same from Python is reports.report(ds, "reports/").

The report is the library run in a fixed order; nothing in it is unavailable as a function.

Live demo

Open the example report — two missions, a SeaExplorer in the Baltic and a Seaglider in the Labrador Sea, built from the sample data by this site’s own documentation build.

Getting started

• Quickstart
  • Input: an OG1 mission file
  • Install
  • Run it
  • Open it
  • From Python or a notebook
  • What to look at first
  • Where next

Examples

• Glidertest demo
• 1. Load dataset
• 2. General mission overview
• 3. Sensors data overview
• CTD
• Example HTML report

Reference

• CLI reference
  • glidertest report
  • glidertest navigator
• The HTML report
  • Live example
  • Output layout
  • What the diagnostics tell you
  • Report pages
  • The QC section
  • Colour and status conventions
  • What the report does not do
  • Many missions
• API reference
  • Entry points
  • Modules
  • Legacy

Links

• GitHub repository
• Report a problem
• OG1 format manual

Background

We recommend the OceanGliders best-practice guides, starting with the Oxygen SOP, and the GliderTools package for processing and for addressing some of the issues glidertest points out.

The diagnostics build on:

• Bennett, J., Stahr, F., and Eriksen, C. (2019). Determining Seaglider Velocities Automatically. http://hdl.handle.net/1773/44948

• Frajka-Williams, E., Eriksen, C. C., Rhines, P. B., and Harcourt, R. R. (2011). Determining vertical water velocities from Seaglider. Journal of Atmospheric and Oceanic Technology, 28(12), 1641–1656. https://doi.org/10.1175/2011JTECHO830.1

• Thomalla, S. J., Moutier, W., Ryan-Keogh, T. J., Gregor, L., and Schütt, J. (2018). An optimized method for correcting fluorescence quenching using optical backscattering on autonomous platforms. Limnology and Oceanography: Methods, 16, 132–144. https://doi.org/10.1002/lom3.10234

Indices and tables

• Index

• Module Index

• Search Page