Preparing to Calibrate a New Cruise
Cruise Data Directory Structure
Before calibrating a cruise, the CTDO2 data files must be placed in a cruise calibration directory which has a predefined layout. There are Matlab© functions within CTDCAL Toolbox which will help in creating the correct directory structure. The root of the cruise directory CRUISEDIR from now on, can be anywhere. For this example, let CRUISEDIR be /data/cruises/stc02/, since the examples in this document are taken from the Subtropical Cells cruise in 2002.
 | Warning: |
|---|---|
We strongly discourage using the CTDCALDIR as the CRUISEDIR. If they are chosen to be the same location, then each subsequent cruise will require a new installation of CTDCAL Toolbox and there is an increased risk of path conflicts with multiple versions of the same software. |
From within the Matlab©. interpreter, follow the steps outlined in example Example 2 to create the cruise calibration directory tree described above.
Example 2. Creating the cruise calibration data directory tree using Matlab© CTDCAL Toolbox functions.
cd /data/cruises/
cruise_dir = make_cruise_dir('.','stc02')
ls stc02
ans =
bottle/
calibrated/
mfiles/
figures/
log/
oxy/
proc_data/
raw_data/
salts/
tmp/
register_cruise.m
ctdcalpath.m
This directory tree is a duplicate of the standard cruise directory set up on the PhOD ctd_proc and ctd_acq computers.
Cruise Metadata Management
There is a large amount of metadata associated with acquiring and calibrating CTDO2 data on a research cruise. In the CTDCAL Toolbox the metadata of interest describes the locations on the disk of the various data files described in Appendix A as well as the information describing the space-time domain of the research cruise. The function register_cruise.m is the means by which this metadata is made available to the CTDCAL Toolbox.
Once a new cruise calibration directory tree has been created as described in the Section called Cruise Data Directory Structure a new register_cruise.m will be created in CRUISEDIR/mfiles. This file should be edited by the user to contain the metadata relevant to the current cruise calibration project. The important elements of this file are described below.
% The cruiseid is the case sensitive character mneumonic which
% will be used to reference the current cruise calibration project.
cruiseid = 'stc02';
% How are the Seabird ctd files named? This is also case sensitive on linux computers.
% We recommend that you use lower case for everything to minimize the chance for conflicts.
% e.g. stc2001.cnv, stc2001.hdr, stc2001.btl etc. Notice that the filestub variable
% below doesn't have to be the same as the cruiseid above.
file_name_prefix = 'stc2';
% The number of digits used in creating the file names from the file_name_prefix and
% a variable station number.
% TODO: This does not allow for multiple casts at the same station as per WOCE specs.
nDigits = 3;
% Are the extensions to the Seabird Data files written in upper case or lower case?
% e.g. stc2001.CNV or stc2001.cnv. This must be true for all or none of the relevant
% file types. (cnv, bl, btl)
sbe_is_upper_case_extensions = false;
% Where is the main cruise calibration working directory?
% This directory is the top level root directory
% which contains a copy of the cruise data, the calibration reports, figures, and all the
% user editable m-files copied from the ctdcal/demos directory. See the User's Guide
% for more explanation.
calibration_dir = fullfile('doris','snowden','CTD','test','stc02');
% NOTE: pseudo platform independent representation of directories. On Windows you must add
% 'C:' or '\\computername' as the first argument to fullfile. (fullfile('C:','doris',etc...))
% Where are the working calibration data directories?
% These should be the same as the cruise_dir above but
% you have the option of changing the data directory tree root if you don't want to copy
% the data files to a local directory after every station.
% The directory structure suggested below is the one created by create_cruise_dir.m It is
% recommended but not required that you stick with this structure.
cal_data_dir = calibration_dir;
cal_autosal_dir = fullfile(cal_data_dir,'salts');
cal_oxy_dir = fullfile(cal_data_dir,'oxy');
cal_btl_dir = fullfile(cal_data_dir,'bottle');
cal_cnv_dir = fullfile(cal_data_dir,'raw_data');
cal_hdr_dir = fullfile(cal_data_dir,'raw_data');
cal_bl_dir = fullfile(cal_data_dir,'raw_data');
% Where are the source data directories?
% These are the directories containing the original data stored immediately
% after collection. e.g. they might be on the ctd acquisition computer or on
% a network mounted mapped disk. The directories listed below are only referenced
% if you choose to use the update_calibration_data.m function. If you sync the data directories
% by hand or using sneaker net then the preferences below are not referenced by
% any other ctdcal toolbox function.
% NOTE: The sync/update functionality has not been tested on mapped driveson a Windows computer
source_data_dir = fullfile(filesep,'doris','snowden','CTD','Data','stc02');
source_autosal_dir = fullfile(source_data_dir,'salts');
source_oxy_dir = fullfile(source_data_dir,'oxy');
source_btl_dir = fullfile(source_data_dir,'bottle');
source_cnv_dir = fullfile(source_data_dir,'raw_data');
source_hdr_dir = fullfile(source_data_dir,'raw_data');
source_bl_dir = fullfile(source_data_dir,'raw_data');
% Geographic region of the cruise. (For making maps)
% Defaults to 10 percent extension of the max/min
% of the station coordinates.
region = [-60 -30 -13 8]; %[west east south north]
% Temporal extent of the cruise.
begYr = 2002; begMnth = 2; begDay = 1;
endYr = 2002; endMnth = 2; endDay = 28;
cruise_dates = [datenum(begYr,begMnth,begDay) datenum(endYr,endMnth,endDay)] ;
% Assign some general options which will dictate the behavior of the ctdcal
% functions throughout the calibration procedure
% NOTE: These have not been implemented consistently throughout the toolbox and are experimental.
% Verbose operation to print messages to the screen.
options.verbose = true;
% Keep a running log of all operations performed.
options.logfile = ''; %if isempty then no log is kept.
Once the register_cruise.m file is current, execute it at the Matlab© prompt.
register_cruise
 | Alternative methods to manage the Matlab© search path |
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In addition to editing the global startup.m file to include the CTDCAL Toolbox path, the user has another option to include the necessary functions in the Matlab© path. The file CRUISEDIR/ctdcalpath.m should have been created at the same time as the CRUISEDIR by the make_cruise_dir.m function. This function, when executed from the command line, should place the relevant toolbox and cruise specific functions into the Matlab© search path. The user must issue the ctdcalpath command at the beginning of each new Matlab© session. |
Loading the Calibration Database
Once the cruise directory is created and the cruise has been registered by typing the register_cruise command, the relevant Sea-Bird© files must be manually copied in the correct locations in the directory tree.
Provided the set up has been down correctly and all files have been copied into the cruise directory tree, loading the cruise database with the information in the Sea-Bird© data files and the analyses performed by the salinity and oxygen analysts is a simple procedure. The following commands will load the Sea-Bird© data files and the oxygen titration results into the cruise database.
Example 3. Using load_bl
bl = load_bl('stc02')
btl = load_btl('stc02')
cnv = load_cnv('stc02')
oxy = load_oxy('stc02')
Editing and Loading the Autosal Analysis Results
The autosal system on the Ron Brown is equipped with an automatic data logging system to record the results of the analysis. Each analysis session should begin and end with a standard water analysis so that instrument drift can be detected and removed. At the end of each session the logging system creates three files, a *.hdr file, a *.dat and a *.raw file. The hydrographic technician on the Ron Brown typically converts the *.dat into a Microsoft Excel *.xls file format prior to submitting the results to the scientific party. Examples of all four file formats are in the CTDCAL/demos directory (See ww2_014sal.*).
The CTDCAL Toolbox toolbox reads the *.dat and *.raw formats for loading the cruise database. However, the *.dat files must be hand edited to augment the information automatically logged by the autosal and to adhere to a more uniform format. The chief scientist or CTDO2 technician should be responsible for editing and maintaining these files.
To edit the *.dat files first copy the originals to another directory (e.g. CRUISEDIR/salts/originals for archiving as the current copies will be changed. Next open the *.dat file in Excel. In the first column, the autosal logs the Sample ID. Typically, the Sample ID cell will contain the batch number of the standard water if the data represents a standard analysis and will either be empty, or contain the station number for acutal seawater samples. Edit this column by fensuring that no blank cells exist and all seawater samples are identified by a station number.
Next, add a new empty column AFTER the time column and before the remarks column. The column heading for this new column should be Rosette Position. Each cell should contain the position on the rosette carousel of the Niskin bottle which collected the current sample. This information is available on the sample log sheets filled out by the water samplers. This information is crucial for matching the water samples with the corresponding CTDO2 information.
Finally, save the file with the same name and extension as a tab separated ascii file. An example of a correctly edited *.dat file is in the CTDCAL/demos directory (See ww2_014saledited.dat).
Loading the results from the autosal analysis is more complicated due to constantly changing file formats etc. The file load_salts provides a template for the procedures to load the autosal results. It must be edited however, due to the specific nature of each cruise. Copy the load_salts.m from the CTDCALDIR CRUISEDIR/mfiles directory and rename it to something unique, e.g. load_salts_cruiseid.m. Repeat the same procedure for CTDCALDIR/read_autosal_dat.m. Edit the two files according to the instructions in the comments within the code.
Once the editing is completed, the following commands should load the autosal analysis into the cruise database.