SeaBird processing#

Setup of batch processing of ship CTD data.

Processing setup#

  • Requires Windows OS.

  • Requires Seabird’s SBEDataProcessing software.

  • Requires a local copy of the CTD-Classic repository.

    • This contains the folders and files described in the recipe below.

    • Clone from Github here: CTD-classic[1]

A) Directory structure#

Duplicate the template folder template and rename to desired cruiseTag name (e.g. fs_YYYY). Keep in same directory as default_psa and default_scripts. This is because batch files will load processing scripts from those folders using relative pathing. If starting in a new work directory make sure to take a copy of those two directories as well.

B) Init structure#

  • copy all CTD files besides .cnv and .btl to the raw folder (.bl|.hdr|.hex|.XMLCON)

  • copy one .XMLCON file per CTD setting to the setup folder, meaning that if the setup of the CTD never changed then one .XMLCON file (e.g. of the first station) would be enough for the whole cruise

  • (if relevant) modify that .XMLCON file for CDOM using

    • Dark output=0

    • Scale factor=1

C) Initial setup for SBE batch processing#

Manually run SBE processing once in order to update the .psa files located in cruiseTag\setup\psa_general\. For the example files on the repo here a duplicate was used (cruiseTag\setup\psa_test\) to keep the default .psa files untouched.

1 Data Conversion#

  • Program setup file: cruiseTag\setup\psa_general\DatCnv.psa

  • Instrument setup file: \cruiseTag\setup\Sta0001.XMLCON

  • Input directory: cruiseTag\raw

  • Input files (first station is enough): Sta0001.hex

  • Output directory: \cruiseTag\proc

2 Filter#

  • Program setup file: cruiseTag\setup\psa_general\Filter.psa

  • Input directory: cruiseTag\proc

  • Input files (first station is enough): Sta0001.cnv

  • Output directory: \cruiseTag\proc

4 Cell Thermal Mass#

  • Program setup file: cruiseTag\setup\psa_general\CellTM.psa

  • Input directory: cruiseTag\proc

  • Input files (first station is enough): Sta0001.cnv

  • Output directory: \cruiseTag\proc

5 Loop Edit#

  • Program setup file: cruiseTag\setup\psa_general\LoopEdit.psa

  • Input directory: cruiseTag\proc

  • Input files (first station is enough): Sta0001.cnv

  • Output directory: \cruiseTag\proc

6 Derive#

  • Program setup file: cruiseTag\setup\psa_general\Derive.psa

  • Instrument setup file: cruiseTag\setup\Sta0001.XMLCON

  • Input directory: cruiseTag\proc

  • Input files (first station is enough): Sta0001.cnv

  • Output directory: \cruiseTag\proc

8 Bin Average#

  • Program setup file: cruiseTag\setup\psa_general\BinAvg.psa

  • Input directory: cruiseTag\proc

  • Input files (first station is enough): Sta0001.cnv

  • Output directory: \cruiseTag\proc

  • Name append: _bin

9 Bottle Summary#

  • Program setup file: cruiseTag\setup\psa_general\BottleSum.psa

  • Instrument setup file (modified version): cruiseTag\setup\Sta0001.XMLCON

  • Input directory: cruiseTag\proc

  • Input files (first station is enough): Sta0001.ros

  • Output directory: \cruiseTag\proc

13 Window Filter#

Run all three filter .psa once with one station to update them.

  • cruiseTag\setup\psa_general\W_Filter_short.psa (on .cnv file)

  • cruiseTag\setup\psa_general\W_Filter_long.psa (on _bin.cnv file)

  • cruiseTag\setup\psa_general\W_Filter_final_smooth.psa (on _bin.cnv file) This will for this manual run only overwrite files but the automatic processing later will produce an extra version at this point ending on _bin_cdom.cnv

D) Setup automated SBE batch processing#

We have now hopefully set up the .psa files for your dataset. We can now run the batch processing script which will process all the data in the cruiseTag\raw folder, adding new files to the cruiseTag\proc.

The template batch processing file is found in:

cruiseTag\script\stnA-stnB_call_processing.bat.

Start with making a copy of this file, e.g. cruiseTag\script\cruiseTag_batch_proc_all.bat.

The file can now be executed from a terminal, or by double clicking the file in Windows Explorer.

There are many configuration options in this file. You can toggle these options by editing the .bat file itself.

Example of options you can edit:

  • Process only profiles 30 to 35 (not all CTDs)

  • Don’t use window filtering for CDOM

  • Use a different .XMLCON file

  • etc..

When you run the .bat file, a terminal window will open up, and you will be prompter to press a key.

When you do, you should see the SBEDataProcessing software running through the processing for all the files you have specified.

Check the contents of cruiseTag\proc to confirm that the processing did actually produce new files.

E) Additional steps#

Different instrument setups#

In case the CTD setup changes multiple times during the cruise - i.e. sensors get swapped, added or removed. Then the whole process above (section C and D) has to be done again for each specific range of same stations (same CTD setup).

  • duplicate the psa_general folder and for instance name it after the station range

  • get one .XMLCON file for that station range and again modify CDOM if necessary

  • run all the steps one time manually with SBE processing to adjust the .psa files in the duplicated folder

  • duplicate the .bat file and adjust it to that station range. This will lead to multiple .bat files e.g. the first for stations 1-10, second 11-20 and last for 20-99999.

After setting this up once, all .bat files can be double clicked to run over the specific station ranges again for reprocessing or if data was updated for instance.

Different CTDs#

In case different CTDs are used on one cruise, for instance one 12 and one 24 rosette version. Create a second raw folder so there is one each (e.g. raw and raw_12) and treat both as separate sensor setups. Follow the procedure like above (section C and D) for each setup separately. Move the raw files into the specific folders and adjust the batch scripts of each setting to refer to the right raw folder. The output folder can still be the same proc directory.