Ship CTD data processing pipeline

Step-by-sep CTD processing recipe using NPI tools

Overview

Post- processing of ship CTD profile data consists of automated processing from raw files to .cnv using SeaBird software, and subsequent post-processing starting with .cnv and culminating with a netCDF file (.nc).

Overly complicated schematic of ship CTD post-processing (to be developed..).

Two methods of post-processing are documented here. One uses Matlab and the NetCDF-Creator app, the other uses the kval Python library. While not entirely equivalent, he two methods can both be used to produce high-quality checked and formatted CTD data in netCDF format.

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• 1) Automated batch processing using SeaBird software
• 2a) Post-processing in Matlab and NetCDF-Creator

- or -

• 2b) Post-processing in Python

See also:

• Salinometer guidelines

• Using the NetCDF-Creator

Quick summary of the procedure

1. Automated batch processing using SeaBird software

• Apply processing steps in Seabird’s SBEDataProcessing software (Windows only). Can be set up to run for all profiles in batch.

  • Data conversion - Converting raw files aquired by the CTD (.hex, .XMLCON, .bl, .hdr) to readable files. (.cnv, .btl).

  • Temporal filter - Light smoothing of time series.

  • Cell thermal mass correction - Adjust for lag in temperature response in T and C measurents.

  • Loop editing - Edit out data when the CTD rosette was not moving at a steady rate.

  The following steps may be applied in the SBE software or in the following post-processing step:

  • Derive - Calculate (preliminary) salinity and density.

  • Bin average - Bin data to 1 dbar bins.

  • Filter - Additional filtering of CDOM.

2. Manually guided post-processing in Matlab or Python.

• Option 1: Post-processing in Matlab and NetCDF-Creator

• Option 2: Post-processing in Python using the kval library.

• Post-processing steps:

  • Parse .cnv files.

  • Manual inspection / QC of the data.

  • Semi-manual outlier editing.

  • Joining profiles together (after binning, if necessary).

  • Calibration of salinity (and chlorophyll if available) based on laboratory measurements.

  • Automatic and manual addition of metadata.

  • Export to netCDF format (but may also be exported to .mat or .csv for analysis).

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Temporary: CTD workshop resources

Setup instructions and other resources for the CTD workshop on 12.12 can be found here: