ctdcast

Processing and reporting for shipboard CTD and LADCP data: from raw instrument files through QC'd, CF/CCHDO-aligned netCDF and a compiled profiles grid, to self-contained HTML. The reports are portable HTML files — all figures embedded as base64 PNGs, no external requests — in three types: per-cast station pages, transect section pages, and a cruise-wide time series page.

Designed for use at sea where internet connectivity is limited or absent. All output files are fully self-contained and work offline.

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Install

pip install ctdcast

For development (editable install from source):

git clone https://github.com/ocean-uhh/ctdcast
cd ctdcast
python -m venv venv
source venv/bin/activate        # macOS / Linux
# venv\Scripts\activate         # Windows
pip install -e ".[dev]"         # runtime + tests + docs + ruff

Dependencies: gsw, matplotlib, pillow, numpy, xarray, netcdf4, jinja2, pyyaml, ruamel.yaml, scipy

CTD conversion: seasenselib converts raw CNV files to the netCDF format expected by ctdcast (ctdcast draft or ctdcast run). Install with pip install seasenselib. Pre-converted netCDF files from other tools must match ctdcast's variable naming convention (see docs).

To verify the installation, run the bundled demo against the committed fixture casts:

ctdcast run config_demo.yaml   # writes demo_report/index.html

For a full walkthrough see the Quickstart guide.

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Quick start

Quick look (no config file needed)

Raw CNV files fresh off the instrument? One command gives you station pages + index + map:

ctdcast draft /path/to/cnv/           # generates ./ctd_draft/index.html
ctdcast draft /path/to/cnv/ out/ --cruise odb2026   # with cruise ID
ctdcast draft /path/to/cnv/ --dry-run               # preview what would happen

Requires seasenselib for CNV conversion (pip install seasenselib).

Full workflow (with config)

For sections, time series, and LADCP panels you need a config.yaml:

1. Write a config

ctdcast init                        # writes a template config.yaml
ctdcast init --interactive          # guided setup: prompts for paths and
                                      # auto-detects sections/timeseries from profiles.nc
ctdcast validate config.yaml        # check paths before the first run

2. Generate

ctdcast run config.yaml             # smart update — skips up-to-date pages
ctdcast run config.yaml --force     # rebuild everything
ctdcast run config.yaml --only 42   # rebuild one cast page

Open <output.dir>/index.html in any browser.

Diagnose the acquisition-clock error (System vs GPS clock) for a cruise with ctdcast clock config.yaml — it prints a verdict and a paste-ready processing.clock block without writing anything.

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Input data

File	Description
ctd_nc/stageN/*_stageN.nc	Per-cast netCDF files, one per CTD cast per stage
profiles.nc	Compiled profiles on a 1 dbar grid
ctd_sections.yaml	Section definitions — which casts belong to each transect

ctd_sections.yaml format

sections:
  KTout:
    description: "Kögur Transect outflow"
    color: "#e41a1c"
    cast_numbers: [[1, 12], 15]   # ranges and/or individual cast numbers
  FARDWO:
    description: "FARDWO mooring array"
    color: "#377eb8"
    cast_numbers: [[20, 35], "22b"]   # add "NNNb" to include a lettered sibling cast

Cast numbers are kept in the order written. An integer or range selects the plain casts; a lettered sibling event (from a NNNb / NNN_b file) is a distinct cast and must be named explicitly as a quoted "NNNb" string.

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Output structure

<output.dir>/
    index.html              front page — map + stats + navigation
    casts.html      table of all casts (latest first)
    sections.html           section cards with links
    timeseries.html         T, S, O₂ vs time × pressure
    sbe_sensors.html        sensor inventory + which sensor was used on which cast
    casts/
        cast_001.html
        cast_002.html
        ...
    sections/
        section_KTout.html
        ...

Each station page shows: CT profile, T/S/σ₀ triple-axis profile, T-S diagram coloured by O₂ saturation, auxiliary profiles (O₂, fluorescence, turbidity), N²/Turner-angle stability panels, and a cruise-track map with the cast highlighted.

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GEBCO bathymetry

Maps show GEBCO 2025 bathymetry when gebco_nc is set in config.yaml. The file (~8 GB) is not bundled. Maps render without bathymetry if the path is missing — not an error.

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Documentation

Full documentation: ocean-uhh.github.io/ctdcast

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Acknowledgements

Development of this package started during the Odón de Buen cruise of AEI-DFG DS-MIXSED. DS-MIXSED is funded by the Agencia Estatal de Investigación (AEI) through the PCI 2024 call — projects PCI2024-155022-2 and PCI2024-155084-2 — and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) — Projektnummer 541914507.

Development was assisted by Claude Code (Anthropic) and GitHub Copilot code review.