The LMG data acquisition systems continuously log data from a suite of instrumentation throughout the cruise. This document describes the format of that data and its location on the distribution CDs. It also contains important information which may affect how this data is processed such as instrument failures or other known problems with acquisition.

The data collected during this cruise is distributed on a CD-ROM written in ISO9660 level-1 format. This data format has very strict requirements on filenames and organization. However, it is readable by virtually every computing platform.

All of the data has been archive with the Unix "tar" command, then compressed using Unix "gzip" compression. Tar files have the ".tar" extension and Gzipped files have a ".gz" extension. Tools are available on all platforms for uncompressing and de-archiving these formats. On Macintosh, Stuffit Expander with DropStuff will open a tar archive and uncompress gzipped and Unix compressed files. For Windows9X, WinZip, a shareware utility included on this CD (remember, it is shareware) will open these files.

IMPORTANT: Read the last section in this document, Acquisition Problems and Events, for important information that may affect the processing of this data.

It is often useful to know exactly how an archive was produced when expanding its contents. Tar files were created using the following commands:

To create a list of the files in the archive:

To extract the files from the archive:

G-zipped files will have a ".gz" extension on the filename. These files can be decompressed after de-archiving, using:

Adcp/

The ADCP data set is broken up into files representing 24 hours of data collection. The files are named pingdata.xxx (xxx representing a day number). Note that these extensions do NOT represent Julian day numbers. Please refer to the file’s creation date.

Some ADCP data is also transmitted to RVDAS. East and North vectors for ship’s speed relative to the reference layer and ship’s heading are archived in the navigational data section of RVDAS.

AWS/

The Automated Weather Station data was emailed to us twice a day from University of Wisconsin-Madison. The are two different weather stations with the argos ids of 8930 and 8932. The AWS8930.gz and AWS8932.gz files are compressed archives which contain text files containing the data sent to the ship.

Cal/

Refer to the instrument.coeff file (in coeff.tar) for information on how the JGOFS dataset was processed.

The Graphs.gz file is a compressed archive that contains post-script graphs for each CTD cast. For each Cast there are three graph files Light.LMG0203.##.ps, TempSal.LMG0203.##.ps, and Oxy.LMG0203.##.ps, where ## represents the cast number. The Light.LMG0203.##.ps is a graph of the voltages of the following sensors: PAR, Transmissometer, CDOM Transmissometer, and Fluorometer. The TempSal.LMG0203.##.ps is a graph of Temperature and Salinity for both the primary and secondary sensors. The Oxy.LMG0203.##.ps is a graph of Oxygen Temp., Primary Temp., Oxygen Percent Sat., and Oxygen mL/L.

All CTD data acquired on the cruise can be found in the Raw.gz archive within the CTD/Raw/ directory. The data for each station consists of four files. The filename convention is as follows: G0203##.EEE, where G is for the Gould, 0203 is the Cruise # , ## is the cast number, and EEE is the extension. Which will be one of the four type listed below.

.dat Actual cast data in SeaBird format.

.bl Information pertaining to the water sampling bottles for each cast.

.hdr ASCII "header" containing user specific information for each cast.

.con Instrument configuration file used for the cast.

.cnv ‘Converted’ engineering unit data file

.ros Scans marked with the bottle fire confirmation bit

.btl A summary of the data in the .ros file

.con A copy of the original .con file used during the cast

.asc The data portion of the .cnv converted data file written in ascii

.hdr Header file

The cast was split into the down and up cast. The downcast are archived in the DownCast.gz file, and the upcast in the UpCast.gz file. The Bottle.gz archive contain the .btl files for each cast. The RosFiles.gz contains the .ros file for each cast. Finally the Cast.gz archive contains the .cnv and .con files for whole cast both up and down.

This directory contains the all the files used to collect and process the CTD data. It contains the following:

Seasoft Version 4.242 (SS4242d1.exe, SS4242d2.exe)

Process.bat the processing batch file use to post-process the data.

*.con Instrument configuration file used for the cast

*.dsp The display files used.

*.cfg The configuration file used by the post-processing software

Excel spreadsheet of chlorophyll data for each cast where water samples were taken.

The MOCNESS data resides in the MOC1.gz and MOC10.gz archive for the 1-meter and 10-meter respectively. The data set from each cast is made up of three files. The filenames consist of the station number and an extension: .pro .raw or .tab. The type of data in each file is listed below.

Processed filename *.pro

This file contains the processed data for each tow, written in ASCII to disk in a simple configuration, which consists of:

Rows 1-5 header information about sensors and the tow

Succeeding rows data for each column heading with each value separated by 2 spaces.

time Julian day, hours and minutes expressed as decimal

pres depth (m)

temp temperature degrees C

theta potential temperature, formulae from Fofonoff and Millard 1983

sal salinity ppt

sigma potential density, formulae from Fofonoff and Millard 1983

angle angle 0-90

flow flow counts 0000-9999

hzvel horizontal velocity (knots)

vtvel vertical velocity (m/min)

vol seawater volume filtered (m3)

net net number

fluor fluorescence (0-5 volts)

ptran extinction coefficient (0-5 volts)

oxycurrent 0-5 volts

oxytemp 0-5 volts internal to the probe

oxygen dissolved oxygen (ml/l)

lat latitude decimal degrees

lon longitude decimal degrees

Raw filename *.raw

This file contains the raw data from the underwater unit. These "*.raw" files can be used in the playback mode to re-process the data (see page 33 MOCNESS instructions), and also serve as the backup in case there are problems with the processed data file.

For each tow, data is written (as it appears in the acquisition window) in ASCII to disk in a simple configuration, which consists of:

Rows 1-5 header information about sensors and the tow

The fields are as follows and are discussed individually below.

N1 net count, counts of left response switch, 00-99

N2 net count, counts of right response switch, 00-99

AA net angle in degrees, 00-99

PPPPP pressure value, converted to decibars by the deck computer

BBB battery voltage (divide value by 10)

$GPGLL latitude and longitude in decimal degrees

Tab filename *.tab

The statistical summary for a given *.pro file. For each net, the following parameters are included:

pmin,pmax,pavg minimum, maximum and average depth of net

tmin,tmax,tavg minimum, maximum and average temperature of net

smin,smax,savg minimum, maximum and average salinity of net

amin,amax,aavg minimum, maximum and average angle of net

spmin,spmax,spavg minimum, maximum and average horizontal velocity (kt) of net

armin,armax,aravg minimum, maximum and average vertical velocity (m/sec) of net

#obs total number of observations while net was open

vol total seawater volume filtered for net

Captured screens, filenames *.bmp

The OPC was tow along with eh 1-meter MOCNESS. The data collected from these tows are in the OPC.gz archive. Connected to the OPC during these tows was the CDOM Fluorometer, and a flow meter. The CDOM Fluorometer was connected to the Underway System for the southbound Drake crossing, and the OPC was to collect that data, this data is archived the DrakeOPC.gz file.

Map/

PostScript and JPG cruise track plots have been produced for this cruise.

All data is organized in folders under the main file. Four folders are contained within the main directory: processed data (Profile Data), the raw data files for each of the analyses (Oxygen and Nutrient) and a file containing all salinity data.

A test cast of the CTD rosette was conducted on April 13, 2002 just south of Anvers Island (65’ 11.22, 64’ 15.56) in 280 meters of water depth. All bottles were closed near the surface and the rosette was lowered to 100 meters where it stayed for approximately five minutes. Results of nutrient and oxygen analysis for all bottles are located in the rosette test file in the profile data. Bottles 1, 2 and 22 were suspected initially from oxygen analysis but only bottle 22 was confirmed to be leaking from the nutrient data. This bottle was not used for water column acquisition intended for sample analysis.

Nutrients and oxygen (Winkler titrations) determinations from water samples taken from casts during the GLOBEC III cruise (LMG0203) are organized into folders under the profile data directory and are labeled by event numbers and cast numbers. Each folder contains:

The bottle sensor files given above were matched with casts where water samples were taken from the rosette. Water samples were not taken on all casts, so CTD sensor data for some casts is not contained in these folders. Bottle data for all casts is located in the folder labeled "CTDbottlesensor".

Raw data files for the calculations generating the above presented data are located in the folders labeled "Nutrients", "Oxygen" and "Salinity". All oxygen calculations, standards and peripheral information (i.e. Bottle volumes) are contained in an excel workbook labeled "O2calculationsLMG0203.xls" under the oxygen folder. The manual for analysis and standardization of the system is also contained in the "Oxygen analysis" file. Prior to each series of analysis the titrator was standardized with a solution of KIO₃ (standard solution concentrations are listed in the calculation workbook). Standards were titrated until agreement reached + 2 L. A reagent blank determination was conducted at the start of the cruise and used throughout. Titrations performed on the Langford Amperometric system were logged during operation and the titration data is located in the raw data file under the folder "Oxygen analysis" and labeled according to the date the samples were run. Nutrient determinations were conducted on an Alpkem Flow Solutions segmented flow autoanalyzer. Operation and standardization of the system is described in detail in the Flow Solutions manual under the file "Alpkem manuals". Linearity checks were conducted at the beginning of the cruise for each of the ions and conducted at the start and completion of each sample sequence. Analysis integrity was also checked by sampling surface and bottom water bottles in duplicate. This process was repeated on most casts. The nutrient folder contains the raw data output by the Alpkem Flow Solutions system in a folder labeled Alpkem output. These files were exported to spreadsheet format and saved as excel files under the folder "Nutrient Spreadsheets". Corresponding ion concentrations for each depth were transferred to the profile data sheets. Salinity determinations were conducted on a Guildline model 8410 Portable Salinometer (PortaSal). Standardization was conducted using Copenhagen water prior to each series of determination and relevant information is entered in the spreadsheets.

The nutrient and oxygen determinations were checked superficially by plotting the results against the CTD sensor parameters Sigma Theta, Potential Temperature and Oxygen. The results of these comparisons can be accessed and viewed under the file "Property plots". In addition the Winkler oxygen titrations were compared to the CTD oxygen sensor and a least squared regression resulted in the relationship:

Y = 0.9298*X + 0.6162.

Where the Winkler titrations are located on the independent axis and CTD sensor output is on the dependent. Scatter is observed in the relationship and a concentration of determinations appears at the lower and upper range of the data. Variation could be due to equivalence time associated with the temperature sensor on the oxygen sensor. Significant scatter was also observed in the nutrient determinations when compared to each of the CTD sensor parameters. The scatter appears to be specifically associated with surface waters and more tightly aggregated data is observed in the deeper waters associated with lower oxygen concentrations and warmer temperatures

Postscript files of data stored each day on RVDAS for quality control analysis during the cruise. The are 3 types; metXXX.ps, navXXX.ps, and oceanXXX.ps where XXX is the julian date. Met files are a summary of the meteorological instruments, Nav files are a summary of navigational data, and Ocean files are a summary of underway seawater and bathymetry data.

rvdas/

RVDAS (Research Vessel Data Acquisition System) was developed at Lamont-Doherty Earth Observatory of Columbia University and has been used on the R/V Maurice Ewing for several years. It was adapted for use on the Nathaniel B. Palmer and her sister ship, the R/V Laurence M. Gould.

Below you will find detailed information on the data included. Be sure to read the "Significant Acquisition Events" section below for important information about data acquisition during this cruise.

RVDAS data is divided into two broad categories, Underway and Navigation. The groups are abbreviated "uw" and "nav". Thus, these two tar files, lmguw.tar and lmgnav.tar exist under the top-level rvdas directory. The instruments are broken down as shown. Each data file is g-zipped to save space on the distribution. Not all data types are collected everyday or on every cruise.

RVDAS data files are named following the convention: LMG[FileID].dDDD.

• The FileID is a 4-character code representing the system being logged, for example: lmet (for meteorology)
• DDD is the Julian day of the data collection

Data is received by the RVDAS system via RS-232 serial connections. The data files that comprise the rvdas data set are described below. A time tag is added to each line of data received and the data is written to disk.

Where, YY: two-digit year, DDD: Julian Day, HH: 2 digit hours, MM: 2 digit minutes SS.SSS: seconds. All times are UTC.

The delimiters used to separate fields in the raw data files are usually spaces and commas, but other delimiters are used (::, =, @) and occasionally there is no delimiter. Care should be taken when reprocessing the data that the fields separations are clearly understood. An example data

99+099:00:18:19.775 hf,305.2,lf,304.3

00+040:00:00:00.928 16-10-97 00:01:19 005.53 005.53 005.69 145 141 005.15 005.12 005.15

146 148 004.4 004.4 004.4 94.07 94.06 94.07 0981.40 -0.023 00.292 00.315

00+348:01:59:52.128 1539.40

00+040:00:00:06.153 6926 15.8827 0.2010 2.9218 3.239 4.334e-01

00+019:23:59:59.099 $PUHAW,UVH,-1.48,-0.51,250.6