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mi-ctd-data-processing

This reposisory contains the Ireland's Marine Institute's CTD Data Processing functionality.

The main aim of this work was to create a consistent set of data processing steps that could be used both at sea, with limited internet access, and back in the office/laboratory.

The Marine Institute uses 3 Jupyter Notebooks, written in python, to process CTD data from acqusition, conduct quality control checks and carry out calibration based on bottles collected concurrent to CTD measurements:

  1. CTD Profiles Processing: CTD_profiles_processing.ipynb
  2. Calibrations
  3. Quality Checks

CTD Data Processing Jupyter Notebook

The purpose of this notebook was to create a consistent set of data processing steps that could be used both at sea, with limited internet access, and back in the office/laboratory. Following on from this it was decided to make the notebook more accessible and usable to scientists other than physical oceanographers (eg. chemists and fisheries scientists). This allows them to provisionally process CTD data on their research cruises and generate indicative plots of the water masses they are moving through while at sea. The notebook has automated CTD Data Processing, reducing processing time and workload on physical oceanographers.

A data processing routine was designed based on a scientific consensus with contributions from international scientific groups to address the main challenges we faced within our organisation with processing CTD data. The routine uses Sea-Bird Data Processing software through a Jupyter Notebook written in Python. The use of Sea-Bird software requires running the notebook on a Windows machine. To find out more about Sea-Bird software and how to download it click here

The notebook was developed using Python 3.12 and requires the following python packages and versions. A set of commands to install these through Anaconda can be found here

  • chevron=0.14.0
  • numpy=1.26.4
  • pandas=2.2.2
  • pyodbc=5.0.1
  • seawater=3.3.5
  • bokeh=3.5.1
  • xlrd=2.0.1
  • widgetsnbextension=3.6.1
  • jupyterlab_widgets

A set of supporting scripts can be found in the scripts folder and PSA templates needed to files to configure the SBE processing steps can be found in the psa_templates folder.

Quality Checks Jupyter Notebook

To be completed

Calibrations Notebook

To be completed

To cite this work please reference:

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