SCD2025266

[jeff-jackson-dfo]

Processing Steps

Background

A new CTD data set now requires processing. Use the following workflow to properly process the CTD data set. Normally the data set is associated with a mission. The data set might only be a single profile but could be hundreds of profiles; which will impact the length of time required and the possible steps required.

Normally the CTD data is acquired using Sea-Bird Scientific instruments but might also be acquired using RBR instruments or instruments from another manufacturer.

Prep Work

• Secured a copy of the cruise report from ARC or chief scientist (if available)
• Copied raw CTD data from SRC
• Copied available Autosal salinity data from SRC
• Copied available Winkler dissolved oxygen data from SRC
• Obtained copy of electronic event log and/or CTD log sheets
• Obtained copies of Dry and/or Wet log sheets (if available)
• Latest version of CTDDAP software installed; along with supported version of Sea-Bird data processing software
• Latest versions of MATLAB®, R, RStudio, and Python available on Software Center installed

Warning
When processing a Ecosystem Trawl Survey (a.ka.a Groundfish mission); remember that the file name must use set number in place of event number.

Processing Steps

• Step 1 - Compute Calibrations

  • Obtained R script templates used for calibrations
  • Computed new linear correction for CTD conductivity sensor(s)
  • Computed new Soc correction for CTD dissolved oxygen sensor(s)

• Step 2 - Apply Calibrations

  • Copied old CTD configuration files (CON or XMLCON) and updated with revised sensor calibrations
  • Reprocessed CTD data using CTDDAP and new CON files
  • Run Calibration scripts again using corrected QAT data to validate calibration(s) worked

• Step 3 - Update Metadata

  • Ran the MATLAB® script output_ctd_header_info on calibrated ODF files
  • Opened header.txt in Microsoft Excel
  • Inspected metadata for required updates
  • Copied, edited, and ran MATLAB® template for updating metadata

• Step 4 - Add Quality Flag Fields and Run Automated Checks

  • Executed the MATLAB® script add_qfs_to_odf to add quality flag fields to the ODF files and run automated quality control checks
  • Copied RMarkdown template and updated it for current mission
  • Knitted RMarkdown file to produce HTML file
  • Opened HTML file containing profile plots to do a quick visual inspection

• Step 5 - Apply pH Calibration

  • (if required) Applied pH linear correction if provided by tracer group

• Step 6 - Consult with Physical Scientist

  • Physical scientist given copy of calibrated ODF files
  • Physical scientist evaluated data quality (e.g. using Temperature-Salinity plots)
  • Physical scientist provided feedback on data quality

• Step 7 - Visually Inspect Data

  • Ran the MATLAB® script odf_qc to visual inspect CTD profiles one at a time and assign flags to suspect data points
    Note: Operator should refer to physical scientist feedback and report produced from automated checking to help make judgements on suspect data points

• Step 8 - Make Final Metadata Updates

  • (if required) Executed a MATLAB® script to do some final updates (e.g. documenting that the secondary sensor data should be used instead of the primary sensor data) to the ODF file metadata

• Step 9 - Archive Data and Email Notification

  • Copied files to SRC
  • Loaded files into ODF_ARCHIVE database
  • Notified data archivist and respective data manager