ctdcal: Process and calibrate CTD data in Python¶

This package is under development by the Oceanographic Data Facility (ODF) group at Scripps Institution of Oceanography (SIO). ODF uses data processing software and techniques that were developed internally and provide exceptional fitting of CTD and hydrographic data. The software is regularly updated to take full advantage of the latest coding standards and improvements.

The software is all-encompassing with the ability to process raw data, perform quality control with automated data flagging, easily visualize the finalized data, and export to netCDF using standardized conventions. Users have the ability to get the highest quality data out of their measurements.

Installation¶

ctdcal can be installed using pip:

$ pip install ctdcal

CLI usage¶

Initialize data folders¶

Initialize default /data/ folders by running:

$ ctdcal init

(Future versions of ctdcal are planned have more robust init options/flags/etc.)

Import and process data¶

To process data, copy over raw .hex and .xmlcon files into /data/raw/ and reference data to their appropriate folder (oxygen, reft, salt).

Users can process their data with individual ctdcal functions or try:

$ ctdcal process [--group ODF]

to process using ODF procedures.

Package usage¶

Explore user settings¶

Most ctdcal functions get settings from user_settings.yaml and subsequently config.py. Call the configuration loader to explore default settings:

from ctdcal import get_ctdcal_config
cfg = get_ctdcal_config()

# directories for I/O purposes
print(cfg.dirs)
print(cfg.fig_dirs)

# experiment-specific settings (e.g., expocode, CTD serial number) from user_settings.yaml
print(cfg.settings)

# dictionary mapping of short/long column names
print(cfg.columns)

As ctdcal continues to be developed, more robust tutorials will be added to our documentation.