SeasaveV7 on Windows 7 CTD Operator's Cookbook
Bottle Sample Salinity
Bottle sample salinities are calculated in both PSal (Portasal Data Acquisition program) and DECODR, software developed by SIO-CalCOFI from Fortran source code by Mantyla & Newton.
Visual Basic source code for the calculation of salinity from conductivity :
'two conductivity values, from two Portasal cell fills; averaging 5 cond readings = 10 cond ratio readings total that must agree within 0.0004
For j = 1 To 2
cr2 = cr!(j) * cr!(j)
sqcr = Sqr(cr!(j))
deltas = (BathT# - 15#) / (1# + 0.0162 * (BathT# - 15#)) * (0.0005 - 0.0056 * sqcr - 0.0066 * cr!(j) - 0.0375 * cr!(j) * sqcr + 0.0636 * cr2 - 0.0144 * cr2 * sqcr)
sal!(j) = 0.008 - 0.1692 * sqcr + 25.3851 * cr!(j) + 14.0941 * cr!(j) * sqcr - 7.0261 * cr2 + 2.7081 * cr2 * sqcr + deltas
With datalog
.Row = currrow% 'reccnt%
.Col = 7 + j
.Text = Format(sal!(j), "0.00000")
' .Text = Str(.Col)
End With
Next j
AveSal! = (sal!(1) + sal!(2)) / 2
'References: the practical salinity scale 1978 (the unesco equation of state of seawater) , for lab salinometers
'When IAPSO Standards or Sub Standard are run, any drift! between first value a last value must be removed
salin(1, 1) = sal(1, 1)
salin(1, 2) = sal(1, 2)
For J = 1 To 2
drift = (sal(1, J) - sal(nta%, J)) / (nta% - 1)
dri = 0#
For ic% = 2 To nta%
If (cr!(ic%, J) > check) Then GoTo 609
dri = dri + drift
salin(ic%, J) = sal(ic%, J) + dri + offst
Next ic%
Next J
We never see salinities over 44 and sample the same section of ocean so we do not apply different corrections or algorithms.
Origintal Fortran code converted to Visual Basic:
Original Fortran Code:
C CALCULATE SALINITY
C
CR2=CR(IB,K)*CR(IB,K)
SQCR=SQRT(CR(IB,K))
DELTAS = (T(IB) - 15.) / (1. + 0.0162 * (T(IB) - 15.))
* * (0.0005 - 0.0056 * SQCR - 0.0066 * CR(IB,K)
* - 0.0375 * CR(IB,K) * SQCR + 0.0636 * CR2
* - 0.0144 * CR2 * SQCR)
SAL(IB,K)= 0.0080 - 0.1692 * SQCR + 25.3851 * CR(IB,K)
* + 14.0941 * CR(IB,K) * SQCR - 7.0261 * CR2
* + 2.7081 * CR2 * SQCR
* + DELTAS
C
C REFERENCES: THE PRACTICAL SALINITY SCALE 1978 (THE UNESCO
C EQUATION OF STATE OF SEAWATER), FOR LAB SALINOMETERS
C WHEN COPENHAGEN SAMPLES ARE RUN, ANY DRIFT BETWEEN FIRST VALUE AND
C LAST VALUE MUST BE REMOVED
C
DO 610 K=1,2
DRIFT=(SAL(1,K)-SAL(NTA,K))/(NTA-1)
DRI=0.
DO 609 IC=2,NTA
IF(CR(IC,K) .GE. CHECK) GO TO 609
DRI=DRI+DRIFT
SALIN(IC,K)=SAL(IC,K)+DRI + OFFST
609 CONTINUE
610 CONTINUE
Seabird Salinity Algorithm (from Seasoft 7.23.1)
Practical Salinity = [PSU]
(Salinity is PSS-78, valid from 2 to 42 psu.)
Note: Absolute Salinity (TEOS-10) is available in our seawater calculator, SeaCalc III. All other SBE Data Processing modules output only Practical Salinity, and all parameters derived from salinity in those modules (density, sound velocity, etc.) are based on Practical Salinity.
Salinity calculation:
Using the following constants
A1 = 2.070e-5, A2 = -6.370e-10, A3 = 3.989e-15, B1 = 3.426e-2, B2 = 4.464e-4, B3 = 4.215e-1, B4 = -3.107e-3, C0 = 6.766097e-1, C1 = 2.00564e-2, C2 = 1.104259e-4, C3 = -6.9698e-7, C4 = 1.0031e-9
C Computer Code –
static double a[6] = { /* constants for salinity calculation */
0.0080, -0.1692, 25.3851, 14.0941, -7.0261, 2.7081
};
static double b[6]={ /* constants for salinity calculation */
0.0005, -0.0056, -0.0066, -0.0375, 0.0636, -0.0144
};
double Salinity(double C, double T, double P) /* compute salinity */
// C = conductivity S/m, T = temperature deg C ITPS-68, P = pressure in decibars
{
double R, RT, RP, temp, sum1, sum2, result, val;
int i;
if (C <= 0.0)
result = 0.0;
else {
C *= 10.0; /* convert Siemens/meter to mmhos/cm */
R = C / 42.914;
val = 1 + B1 * T + B2 * T * T + B3 * R + B4 * R * T;
if (val) RP = 1 + (P * (A1 + P * (A2 + P * A3))) / val;
val = RP * (C0 + (T * (C1 + T * (C2 + T * (C3 + T * C4)))));
if (val) RT = R / val;
if (RT <= 0.0) RT = 0.000001;
sum1 = sum2 = 0.0;
for (i = 0;i < 6;i++) {
temp = pow(RT, (double)i/2.0);
sum1 += a[i] * temp;
sum2 += b[i] * temp;
}
val = 1.0 + 0.0162 * (T - 15.0);
if (val)
result = sum1 + sum2 * (T - 15.0) / val;
else
result = -99.;
}
return result;
}
CalCOFI uses a variety of analytical instruments to measure our oceanographic samples. Many, such as the Turner Designs 10AU fluorometer, have a RS232 serial interface that can output measurements electronically during sample analysis. This white paper will outline basic RS232 serial communication data logging techniques using a PC. This basic interface strategy should be platform-independent but all examples will be MS Windows based.
Basics terminology
Many instruments come with sophisticated software to control the analytical processes. Hopefully, the software is included with the instrument and is not an expensive add-on. Depending on the complexity of the analysis, there may be no alternative to the manufacturer's software. Especially if the instrument is software-driven or visualization tools are needed during the assay. But if the analytical instrument has a serial port, it may be possible to easily capture the output to a text file and import into a spreadsheet or programming language.
Hardware requirements
Once you see data and can save it to a text file, you are recording your instrument's output. Importing these data into Excel or writing a parsing routine in Matlab would be the next step.
You can test your serial data collection setup by attaching a serial device like a GPS to your PC. If you are successful at seeing and logging its data, the setup should work on any instrument that outputs data. Just be sure to configure the com settings properly.
CTDBackup is a SIO-CALCOFI developed CTD cast file auto-backup utility. The CTDBackup icon on the Windows desktop is mapped to the hot-key combination <Ctrl><Alt> B. This key combination is pressed immediately upon completion of a CTD cast, once Seasoft data acquisition is stopped. CTDBackup zips all the cast files (.hex, .hdr, .mrk, .xmlcon, .nav, .bl) into a single zip file which is copied to a flash drive, backup drive or dir, & data server, if available.
Additionally, a sample log base file is created using the CTDATDEPTH event file (Q:\CODES\YYYY\YYMM\Events\YYMMCTDATDEPTH.csv) which contains the GPS date, time, lat, lon, order occupied, CalCOFI line & sta data at the time the CTD reach terminal depth. This timestamp is historically the official cast time and position reported in all data products such as Data Report and hydrographic database. If the CTDATDEPTH event file is unavailable, the .nav file date, time, lat, & lon plus .hdr file information is substituted.
Lastly, the .hdr, .mrk, .nav files are merge into a single .prn file for printing & binding with the console ops & cast plots.
Setup & Operation
Description | CTDBackup Form |
CTDBackup.cfg - CTDBackup is typically installed at C:\CTDBackup and the ctdbackup.cfg file sets the next station to zip and the default data & file paths (see image). Once the cruise information is updated in the cfg, no further editing is required unless non-consecutive numbering occurs. CTDBackup is programmed to expect sequential cast numbering 001, 002, ...;normally the CTDBackup CFG form is not seen unless there are configuration issues. If it cannot find the right cast files, it is usually because stations numbers are not consecutive or the CTD header and files were mis-numbered. If misnumbered, Quit, rename the files, then press <CTRL><Alt> B once more. The Sample Deep 1st & Sample Shallow 1st toggle changes the bottle order. In the cfg file, the values is set to 24 - Sample Shallow 1st.
|
|
CTDBackup Success Form - when <CTRL><ALT> B are pressed in combination, the 7-zip windows will appear as Seabird cast files are zipped - do not close the dialog box before the 7-zip windows close. The CTDBackup Success form will display, listing all the backup files generated as well as the sample log base file. The first time CTDBackup is run, the user should verify the files are labeled properly and going to the right locations. This form reminds the CTD operator to turn off the deck unit and unplug the ISUS sensor battery. If the network & data server are unavailable, change the CESL Log Path from Q: to a 2nd flash drive letter. The log will not be available to the CESL tablet unless the 2nd flash drive is "sneaker-netted" to CESL. |
BtlVsCTD (Bottle vs CTD) is a Windows program developed by SIO-CalCOFI. It uses Seasoft-generated CTD asc files and bottle data files (CalCOFI's sta.csv or IEH format).
In Step 1: the program averages 4 seconds of CTD sensor data prior to bottle closure then merges it with corresponding bottle data into a single csv. After removing fliers & mistrips, regressions for O2, Chl-a, & NO3 are calculated from the remaining bottle data vs sensor measurements.
In Step 2: the regression coefficients are applied to Seasoft-processed 1m binavg CTD data generating additional columns of bottle-corrected data.
"Sta.csvs" are created from the CTD .mrk or .btl files by CTDBackup & CESL. When bottle samples are process using DECODR, salts, nutrients, chlorophylls, and oxygens, data populate the sta.csvs for each cast.
Step 1 - BtlVsCTD uses an un-averaged CTD asc file, processed by Seasoft and the .bl file to find the bottle-trip-scan starting point. It averages 4 (or more, user-entered) seconds of data prior to bottle closure then merges the CTD data with the bottle data from sta.csv or IEH so regressions can be derived such as seen here:
http://www.calcofi.com/cruises/2015-cruises/calcofi-1507oc/575-1507oc-ctd-processing-summary.html
Refer to the Data formats page for file formats required: http://www.calcofi.com/references/data-formats.html
Once the correction coefficients have been derived interactively in Excel. BltVsCTD Step 2 applies them to 1m binavg upcast & downcast CTD asc data, generating the "Cruise_Corr" data columns.
Individual station regressions, using only bottle samples from a particular station, are also derived dynamically by BtlVsCTD. This results in "Sta_Corr" data and is considered the best bottle-corrected CTD data we generate. But this requires at least 10 bottle samples per station to work well. Otherwise, the cruise-corrected CTD data are preferred. This process is repeated once final bottle data are available.
BtlVsCTD has several other module that edit & update the CTD.csvs generated by merging CTD with bottle data.
BtlVsCTD has been around a long time and is written in Visual Basic 6. It has evolved over the years, originally using IEH-formatted data and now our sta.csvs format. This program is pretty specific to CalCOFI's file structure so it may require quite a bit of work to adapt to other datasets.
Example Step 2 Instructions - see CTD Data Processing Protocol
BTLvsCTD: Run Step 2:Correct CTD ASC data then merge w/Btl Data, DB csv out. Preliminary sta.csvs in the CSV dir or IEH (bigieh or arch.ieh) in the same dir as the CTD ASC files are required. YYMMEvents.CSV (corrected if available) also needs to be in CTD ASC dir. It is important that the Event file, if available, is cleaned up and complete. Order occupied, CTD at Depth event number, line and station numbers need to be in order & correct. Every CTD station requires a "CTD at Depth" event. If an event was not logged one needs to be added, in doing so the new event number will have an added decimal increment of 0.1 per event.
Step 2: File Selection - Navigate to the ASC folder and select all u*.ASC files. The d*.ASC files will be automatically processed concurrently. The leading d or u and trailing box are used to correctly parse the ASC file name to retrieve cruise and station numbers.
Step 2: Sensor Configuration - Using SBE CON or XMLCON files as a guide fill the Voltage Settings boxes. If different stations had different configurations (i.e., sensors were moved to different voltage positions on the CTD) process files individually with the correct fields. If a sensor was only removed from the CTD no changes are necessary as the data will be processed as 0. Fluorescence multiplier and V0 Setting have no effect.
Step 2: IEH and Headers - Check the appropriate box for IEH comparison if IEH was selected on the Main Page. If Sta.csvs are used, ignore any ieh setting. Make sure you check Add Line Sta from hdr. The other two have no effect (legacy remnants).
Step 2: Correction Coefficients - Replace the YYMM with the correct cruise designation by highlighting the YYMM in the Coefficients Set dialog. Check the appropriate boxes and enter the necessary coefficients for the required corrections. If a correction is not being made do not include and enter 0 in the necessary fields. Also "Include btl data..." and use the -9.990e-29 Bad Flag value to match SBE bad flags. Save the coefficient CFG to the cruise's CTD directory.
Step 2 will output station CSV files and various combined tabulations of CTD and Bottle data:
DECODR 2014: Data Processing Notes, sta.csv version
DECODR 2014 is SIO-CalCOFI's data processing suite which processes and merges the bottle & CTD data collected on each CalCOFI station. DECODR combines CTD sensor measurements with the corresponding depth bottle data into station data files (75+ sta.csvs). Station and cast information, such as weather, are stored in a single casts file (casts.csv). The casts & sta.csv formats, adopted in 2011, replaces the legacy data processing file formats based on 128-col computer punch cards: 00, 20, 22, W3, stacst, wea & IEH. The SIO-CalCOFI hydrographic database, Cruise Data Reports, and IEH archive data files are products generated by DECODR from casts.csv and sta.csvs.
CTD Data
CTD data processing is done using Seasoft, Seabird's data processing software (please refer to the CTD Data Processing Manual for specifics). DECODR 2014 will import 1m (or 4-second) binavg matching-depth CTD data into the sta.csvs. Early in data processing, the importing of CTD data is very useful for bottle vs CTD data quality control. The early cross-checking of bottle and CTD data expedites data quality assessment for both data types, discreet seawater samples and electronic sensor measurements. When compared on the cruise, early detection of bottle mistrip issues or sensor failure is possible.
Once bottle data are final, these data are used to bottle-correct the CTD sensor data. The preliminary CTD data in the sta.csvs, used during point-checking, are replaced by final, bottle-corrected CTD sensor data and hybrid (bottle and CTD) data products are published. Standard depth data, which may be interpolated when necessary, are often replaced with bottle-corrected CTD sensor measurements (temperature, salinity, and oxygen).
Seawater Sample Processing
Each sample assay generates a data file for each station - some assays may combine multiple stations in a run into one file. These data files reside in specific directories for each data type. Each data processing module will parse the runs in their respective subdirectories and build a station list to process.
Processing all of one sample type is performed in batch, in similar fashion, for each datatype: salts, oxygens, chlorophylls, nutrients, and primary productivity samples. Stations may be processed in smaller groups or individually by checking or unchecking the station(s) to process. Each data processing module generates an output file of calculated measurements for examination and assessment of data issues & quality.
Each processing module ingests data files generated during the analysis of each seawater sample. As needed, the data files are manually 'cleaned-up' - edited and corrected - using a text editor such as Ultraedit then reprocessed. The output from edited files are once again checked for data quality and the process repeated until the data files are consider 'point-check ready'. Then the data from each assay are merged into station files (sta.csvs) by rerunning each DECODR modules with the 'Update CSVs' option checked. This populates the casts.csv with cast information and sta.csvs with bottle data.
Datacodes are used to annotate the best data for publication. By default, bottle data are data coded for use to generate Data Reports, database csvs & IEH generation.
Casts.csv and sta.csvs are located in the CSV subdirectory. Each module run with generate backup files archived in the CSV\BAK subdir. Each backup is timestamped & flagged with the data update type.
DECODR Basics
General Notes:
DECODR uses C:\DECODR\decodr.cfg to configure the program. It is mandatory for it to be in that specific dir. The executable may be run from any location but the cfg file has to be local. The default datapath is the root data dir YYMM. The SUMMARY dir datapath is set by changing the '0' to '1' in cfg line 9. Or by selecting the SUMMARY box in DECODR's main window (upper right).
decodr.cfg explained
Settings | Description |
1411 1407 1404 1402 1311 | Current Cruises being processed |
1407 | Last cruise picked |
C:\CODES\2014\1407\ | Default datapath; SUMMARY directory is retired* |
C:\CODES\2014\1407\ | Datapath of last run |
C:\Decodr\ | Decodr default exe path |
100 | Max salinity samples per data file |
JRW DMW JLW DNF MGS | Initials of Primary Processors |
22.5 1.80 45.0 0.75 3.00 | Nutrient Standard Concentrations - format is important! xx.x x.xx xx.x x.xx #.## |
0* | Summary dir? 0=No, 1=Yes (Retired in 2011) |
There are two version of CELogGPS - the newest version of CELogGPS uses a touch-screen PC or tablet with very little (virtual) keyboard interaction and a plainer version which also requires little key-entry once configured. But the user-interface is not as graphical or touch-friendly.
This web page describes the configuration and operation of the original version of CELogGPS that is configured by a variety of text files (.txt). This version can also be used on a touch-screen tablet but is not optimized for that style of input.
CELogGPS (CELogGPS1806.exe; download link) is a SIO-CalCOFI Windows program that records cruise events and activities timestamped with GPS date-time-lat-lon. Other notable events such as marine mammal-avifauna sightings, CUFES, or any data-generating activity may also be recorded. The GPS position is either logged directly into the PC running the program or is available on a shared network directory:
Setup & Configuration
The events list & form options are configured by text files defined in the CELogGPS.cfg, which may be edited from the Config/Edit CELog.cfg menu (see figure):
Event Number Scheme - to create unique event number IDs or indexes for a cruise, chronological or Julian numbering can be used.
NUMERIC (default) will set the event number as numeric and chronological ie 001, 002, 003...
JULIAN is used for standalone loggers on the same cruise that are not networked, not using a shared eventnumber.txt file. If JULIAN is selected, the next field Julian format's LONG or SHORT affects the length of Julian time recorded as the event number.
SHORT result in DOY.HHMM, which is Julian Day of the year, with Jan 1st = 1; Dec 31st = 365; HHMM current time in hour & minutes.
LONG
adds seconds to Julian Time so the event format becomes DOY.HHMMSS. LONG is used if cruise events may occur at the same time on a minute-scale so need to be resolved by seconds.Julian format | Events Select - this option contains two separate feature options (which should be separate - next version perhaps). Julian format is described in the last entry JULIAN. LONG or SHORT affects the timestamp length. Completely separate (and almost forgotten) is the MULTI or SINGLE option added quickly for the Marine Mammal users.
MULTI - will convert the events selection list on the right to checkboxes. This allows more than one selection to be recorded - events will combine/append in the order of selection. Marime mammal observers created a sightings event list so events could be a combination of selected options.
SINGLE - default - only one event is selected at a time.
PC Time PST/PDT/UTC - CalCOFI logs all data collected & events on Pacific Standard Time (PST). Computers that run CELogGPS may be set to PDT or UTC so this setting applies a time offset automatically without changing the computer's clock. All CalCOFI data acquisition computers are set to PST all year long but we often run CELogGPS on the shipboard CTD data acquistion computers. On RV Sally Ride, all the data acquistion computers are set to UTC; on other ships, depending on time of the year, computers may be set to PDT. This option will apply an offset to the event time based on the setting - if NO correction is desired, set this to PST.
Notes - these options are easily changed using the Config menu in the upper left.
Three files are required by CELogGPS and usually reside in the shared, mapped network Events dir: currpos.csv, eventnumber.txt, orderocc.txt. OrderOcc.txt increments automatically when the Station Arrival event is recorded. OrderOcc's numbering can be off if Station Arrival is not recorded or recorded too many times.
Operation
Once configured, CELogGPS requires very little keyboard interaction. Event selection may be done from the list by stylus, mouse, or trackball. Once an event is recorded, the cursor automatically moves down to the next event on the list and is selected ie after CTD DEPLOYED is recorded, CTD AT DEPTH is auto-selected as the next event. Compose your events list to use this feature to simplify the event selection process and be aware the cursor will move automatically. Our events list is composed with a typical CalCOFI station sequence in mind: STATION ARRIVAL, CTD, secchi, vertical nets, towed nets, and misc other data-generating activities.
General Notes
At the bottom of the CELogGPS form are several fields (from left to right): comments-status, F1 for Help (needs work), GPS Status, Date PST, Time PST, Order Occ.
Please record all events possible even if they are well after the actual event time. It is useful to annotate "late-entry" into the comments field to identify late events so date-time & lat-lon can be corrected from log sheets or other sources when available. The main purpose of the event number is to assign a unique identifier to data generating activities on a cruise. It also functions as a cruise journal, highlighting sequences of activities, recording unique or rare events, and to record time & position of general cruise events.
CELogGPS saves the events in a couple ways - locally in the C:\CELogGPS dir - it saves an event-specific csv such as YYMMStationEvents.csv. It also contributes to the shipboard data network master events file YYMMEvents.csv. CELogGPS also saves a html version of the events file since opening the events csv in Excel will lock the file, making new entries impossible and the program crash. So if you must open the events.csv, copy it locally and open it on your own workstation. Do not open the shared network version.
The CELogGPS screen should display all events recorded by any networked event logger - this is useful in situations like if Aft Control forgets to do a CTD AT DEPTH event, the CTD operator can see the event is missing & record one.
Other features -
Latest Changes
v1711 - added a PC Time PST/PDT/UTC offset option
v1407 - added MET TSG Temperature & Salinity display to the activities form. These were added for the CUFES personnel to key-enter those values when their MET feed was not working. When checked, the 'autofill to Comments' will add these two values to the eventlog event comments field.
Corrected Conversion Algorithm for CalCOFI Station Grid And Their Implementation in Several Computer Languages by Edward Weber & Thomas Moorem, NOAA Fisheries, 2013 CalCOFI Report v 54.
Matlab scripts by Robert Thombley, SIO-CalCOFI with Sep2014 error correction by Augusto Valencia, UABC; based on Weber & Moor 2013.
Link to MatLab downloadable code authored by Robert Thombley, SIO-CalCOFI
(Abstract from pdf) "Converting between geographic coordinates in latitude and longitude and the line and station sampling pattern of the California Cooperative Fisheries Investigations (CalCOFI) program is a commonly required task for conducting research on the California Current ecosystem. This note presents several corrections and clarifications to the previously published algorithms for performing these conversions. We include computer code to implement the algorithms in Java™1, Perl, Python, and R. We note that freely available code to conduct the conversions in Fortran, Matlab®2, JavaScript™, and Visual Basic®6 has previously been published, and an online conversion tool is also available. A future version of the PROJ.4 cartographic projections library will also include support for CalCOFI conversions, thereby allowing for convenient conversions using the GRASS GIS, PostGIS, Python, Perl, R, and many other programs and programming languages."
For individual language - Java, Perl, Python, or R - implementations & downloads, see the algorithms page
CESL (pronounced Cecil, after the sea-sick sea serpent cartoon character ) is CalCOFI's Electronic Sample Log, which replaces the traditional clipboard and sample log form.
BASICS
CESL auto-loads the bottle depth information from a base file created by the CTDBackup program from the CTD cast files. CTDBackup uses the .mrk & .hdr files plus CTDATDEPTH event (.csv created by CELogGPS) to build the CTD cast's seawater sampling scheme that fills the form. This is a live, dynamic document that the watchleader should check, edit, comment, annotate, & revise to accurately log all seawater samples taken plus any sampling notes or issues.
Important note: the .mrk file must accurately report the bottle closures - if any extra markers were generated or markers missed then the .mrk file should be edited before CTDBackup is run. Refer to CTDBackup for additional info.
CESL expects station numbering to be consecutive (001, 002, 003...) and requires a base file generated by the CTDBackup (<Ctrl><Alt>B) program. If a base file is unavailable, the station cast info may be entered manually (line.sta, order occ, total # of bottles closed) then the sample log completed & saved normally.
O2 case, salt case, and nutrient rack color are selected from the drop-down boxes by the watchleader or sampling team.
Bottle options, such as LTER Salt Only or MISTRIP, may be selected for a bottle by double-clicking the niskin or sample number at a particular depth then selecting from the pop-up list (see the alternate bottle section below). Once all seawater samples are drawn, sample drawers initials added, and all fields checked for correctness, click [Save] (or menu File/Save Everything or <Ctrl>S). This will save & print the log for station bookkeeping, generate the individual sample assay files (Salt, O2, Chl) , & generate data processing csvs.
[Save] does the following:
YYYY = year; YYMM = year month cruise designation; ### = order occupied
Note: any step of the log or file saving sequence may be performed separately by using the menu File options - see image.
Oxygen samples draw temperatures may be entered surface to deep by first double-clicking the surface bottle O2 draw temp cell. CESL will ask if you want to enter temperatures in reverse order - click YES. (This method is preferred over having CTDBackup fill the form in reverse order, surface bottle at row 1). When entering the O2 draw temperatures, the decimal is not required if <Enter> is hit instead of mouse-clicking. Also when <Enter> is hit, the draw temp plus other depth info is saved into an insurance file which can be reloaded if the program crashes by pressing <F3>.
If the salt or nutrient samples are continuing a case or rack, enter the starting sample bottle number in row 1 (of the salt or nut field) then hit <Enter>. You will be prompted to renumber the rest of the column automatically.
Double-clicking a comments field will bring up the comments editor. Please use a semi-colon as text separator since the saved form is comma-delimited. This rule applies to any cell where entries are delimited (e.g. initials, DIC bottles).
The CalCOFI Handbook is a compilation of information for cruise participants. It explains many aspects of the science performed at sea, particularly the sample drawing methods for each sample type.
CalCOFI Data File Formats
CalCOFI standard practices for sample analysis, data processing, metadata & general methodology.
SIO-CalCOFI software used at-sea and ashore, developed by the SIO CalCOFI Technical Group. Plus other software: auto-titrator oxygen analysis software developed by SIO's Ocean Data Facility; Seabird Seasoft & Data Processing software; Microsoft Office, Ultraedit, Ztree, hxD hex editor, Matlab, Surfer, Ocean Data View.