Data Acquisition (Download in proprietary formats)

This document describes the initial steps required to bring raw instrument data into a standardized processing pipeline. These steps correspond to Stage 0 of the RAPID data processing and management.

1. Overview

Most mooring instruments output data in proprietary formats (e.g., SeaBird .cnv, ASCII logs, or binary files). The acquisition stage covers:

  • Locating and organizing raw instrument files

  • Extracting metadata from deployment records

  • Converting proprietary formats into a structured and inspectable format

This stage includes no scientific processing, and is typically done at sea as soon as a mooring is recovered and instruments are available.

2. Download

Raw instrument data are downloaded e.g. from MicroCATs using SeaBird’s SeaTerm software and saved as ASCII files.

For the newer 6000 series of MicroCATs it was discovered that the older version of the SeaTerm software misses a line of data every time it completes a block of 220 lines. The newer SeaTermV2 software downloads the data in .xml format, which is then converted to .cnv format using the ‘tools’ menu (see section 18.6).

Expected inputs:

  • One file per instrument (e.g., .cnv, .hex, .txt, .dat)

  • Deployment metadata (e.g., info.yaml)

Reference: Cunningham, S.A. (2010) RRS Discovery Cruise D344, 21 Oct-18 Nov 2009. RAPID Mooring Cruise Report. Southampton, UK, National Oceanography Centre Southampton, 225pp. (National Oceanography Centre Southampton Cruise Report 51) https://nora.nerc.ac.uk/id/eprint/263915/1/nocscr051.pdf

Instrument Data Acquisition

This section outlines the procedures for downloading data from Seabird SBE37 SMP instruments, depending on firmware version.

Legacy Firmware (pre-3.0d)

For most instruments with serial numbers below 6000, use SeaTerm:

  1. Connect the instrument and launch SeaTerm.

  2. Under Configure, select SBE37.

  3. Choose the correct COM port and set baud rate to 9600.

  4. On the Upload Settings tab, check Upload all data into a single file.

  5. On the Header Information tab, ensure Prompt for Header Information is checked.

  6. Open a capture file (e.g., 5768_recovery.log).

  7. Press Return or click Connect—you should see:

    SBE 37-M
S>

    (Press return repeatedly if needed.)

  8. Type Stop to halt logging. Record the time (UTC).

  9. Type DS and note the clock drift from UTC.

  10. Record the “Sample Number” (number of samples taken).

  11. Stop the capture file.

  12. Click Upload.

  13. When prompted, enter ship, cruise, and mooring details.

  14. Add additional comments (e.g., instrument fouling, damage).

  15. Save the file (e.g., 5768_data.asc or 5768_cal_dip_data.asc).

  16. Confirm upload completion and check contents of .asc file.

Modern Firmware (3.0d and above)

For instruments with serial numbers >6000 or upgraded units, use SeaTermV2:

  1. Connect instrument and launch SeaTermV2 (not regular SeaTerm).

  2. Under Configure, choose SBE37 → SBE 37 RS232.

  3. If auto-connect fails, manually configure baud rate (usually 9600 or 38400).

  4. Once connected, open a capture file (e.g., 6338_recovery.log).

  5. Send DS to check clock drift relative to UTC.

  6. Send Stop to halt logging and note the UTC timestamp.

  7. (Optional) To increase transfer speed, type baudrate=38400.

  8. Switch baud rate in software and re-send the command to confirm.

  9. Turn off the capture file once response is complete.

  10. Click Upload, enter filename (e.g., 6338_data.xml).

  11. In the upload dialog: - Check Text Upload - For mooring data, choose upload as a single file - For cal dips, select by scan number range

  12. Click Start to upload data.

  13. After upload, go to Tools → Convert .XML Data File.

  14. Select the XML file and confirm output directory.

  15. Under Output Optional Variables, check Date and Time.

  16. Select Seconds since Jan 1, 2000.

  17. Click OK. This produces a .CNV file ready for use in the Stage 1 conversion routines.