CTD_adjusted

[lauryntalbot]

added CTD_adjusted.py, tests and documentation

[lauryntalbot]

Summary

This PR adds a new CTD post-processing workflow for generating adjusted timeseries and gridded products, including thermal lag and CT lag corrections.

The workflow produces _adjusted NetCDF outputs following standard pyglider processing.

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Code Changes

pyglider/ncprocess.py

• Updated make_gridfiles to support:
  • maskfunction
  • max_gap

pyglider/utils.py

• Added functions required for CTD adjustment workflow:
  • flag_conductivity_in_depth_space
  • interpolate_over_salinity_NANs
  • apply_thermal_lag
  • flag_CTD_data
  • adjust_CTD
  • maskQC4
• Removed deprecated gappy_fill_vertical

pyglider/process_adjusted.py

• Added new processing script to:
  • flag CTD data
  • apply CT lag (dTdC) and thermal lag (alpha, tau)
  • generate adjusted timeseries and gridded outputs

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Documentation Updates

docs/adjust_CTD.md

• Added detailed documentation for:
  • CTD adjustment workflow
  • thermal lag correction
  • user-configurable parameters

docs/index.md

• Added reference to adjust_CTD.md

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Tests

Added tests validating the workflow for multiple glider platforms:

• tests/test_process_adjusted_slocum.py
• tests/test_process_adjusted_seaexplorer.py

These tests:

• run the full process_adjusted workflow
• validate output variables, values, and metadata

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Test Data

YAML inputs

• tests/example-data/example-slocum/adjusted.yml
• tests/example-data/example-seaexplorer/adjusted.yml

Expected outputs

• Slocum:
  • tests/expected/example-slocum/L0-timeseries/dfo-rosie713-20190615_adjusted.nc
  • tests/expected/example-slocum/L0-gridfiles/dfo-rosie713-20190615_grid_adjusted.nc
• SeaExplorer:
  • tests/expected/example-seaexplorer/L0-timeseries/dfo-eva035-20190718_adjusted.nc
  • tests/expected/example-seaexplorer/L0-gridfiles/dfo-eva035-20190718_grid_adjusted.nc

---

Notes

• Thermal lag correction is applied when alpha and tau are provided
• CT lag correction is applied when dTdC is non-zero
• Workflow supports YAML-defined constants or function arguments
• Tests confirm consistent behaviour across both Slocum and SeaExplorer datasets

[jklymak]

@lauryntalbot what is the status here? I should be able to review tomorrow

[jklymak]

Why is this all in the docs? I'm confused.

[jklymak]

Similarly, this should not be in the docs?

[jklymak]

Same