Dataset: CTD - SAM Data Files
Deployment: KNOX22RR

CTD SAM Data Files

Principal Investigator:

Dr Stuart Painter (National Oceanography Centre, NOC)

Co-Principal Investigator:

Dr John T Allen (National Oceanography Centre, NOC)

Contact:

Dr Stuart Painter (National Oceanography Centre, NOC)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Coccolithophores of the Patagonian Shelf 2008 (COPAS08)

Current State:

Final no updates expected

Version:

29 June 2010

Deployment Synonyms:

COPAS08

Version Date:

2010-06-29

Data URL:

https://www.bco-dmo.org/dataset-deployment/453089/data

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Description

SAM data - CTD profile sampling files used to calibrate the various sensors

'sam' files are sampling files used to calibrate the various sensors for the CTD profile data
The files contain information from the moment each Niskin bottle was closed for each
measured parameter (salinity, temperature, oxygen, etc), as well as the salinometry
bottle data and the discrete Winkler oxygen titration data which have been pasted into
each sam file.

These data have been included in these files as it should allow the calibration coefficients
to be recalculated if necessary but more importantly also provides an accountable record
of how the data were calibrated. It is worth noting that the sam files are created for
the purpose of deriving calibration coefficients from uncalibrated datafiles. Once the
calibration is derived the sam files are not recreated. This means that the salinity and
oxygen values found in the sam files are based on the manufacturers calibration only.

Methods & Sampling

Dataset acquisition description

In total 168 CTD profiles were completed on cruise KNOX22RR. The maximum
depth of the profiles varied from less than 10 m for the collection of water for
separate carboy experiments performed by other cruise participants to a maximum
of 5204 m. Most casts, however, extended to ~1000 m offshore and were limited by
topography along the shelf break and inshore.

Profile casts down to 1000 m were interspersed with water collection casts to
increase the along-track resolution of the hydrographic data and to resolve the
deeper structure beyond the euphotic zone.

Data Processing Description

Dataset Processing Description

SeaBird CTD Processing
Data was acquired using SeaBird SeaSave for SBE 911 software (v7). Following each cast, data acquisition was stopped and saved to the deck unit PC. The logging software output four files per cast with the following forms: nnnnn.hex (raw data file), nnnnn.con (data configuration file), nnnnn.bl (contained record of bottle firing locations and nnnnn.hdr (header file), where 'nnnnn' was the 3-digit station number followed by the 2-digit cast number. Raw data files were processed using SeaBird SBE Data Processing software version 7.18b according to Scripps Oceanographic Institute protocols. Output files from the SeaBird processing were of the form nnnnn.cnv (binary up and down casts),
nnnnn.btl and nnnnn.ros (bottle firing information). Instrument manufacturer calibrations are used in these processing stages.

Additional data processing was continued within Mstar, a Matlab based data processing system developed at the National Oceanography Centre, Southampton. A brief summary of the processing steps and relevant scripts is provided below. Intermediate processing files have not been submitted to the BCO-DMO database. Only the final calibrated downcast data has been submitted (so called 2db files)

Basic CTD data processing
ctd0: This converts the SBE processed 24Hz SeaBird .cnv file into netCDF format, setting the required header information. Output: ctd22RRnnnnn_24Hz

ctd1: This carries out a de-spike on the .24Hz data and averages it into a 1Hz file, (ctd22RRnnnnn_1Hz).
Salinity, potential temperature and density are derived from the primary and secondary temperature and conductivity sensors using the international equation of state. Finally a 10 second averaged file is created, (ctd22RRnnnnn_10s).

ctd2: Requires the user to find the first in-water, deepest and last in-water data-cycle from the .1Hz file. This script then extracts data to correspond to the full up and down casts (ctd22RRnnnnn.ctu file) and purely the downcast (ctd22RRnnnnn.2db), averaged into 2db bins.

Advanced data processing for calibration purposes See dataset SAM Data Files
fir0: This converts the SBE processed .ros file into netCDF format. It then takes relevant data-cycles from the .10s averaged file and pastes them into a new file fir22RRnnnnn containing the mean values of all the variables at the bottle firing locations.

samfir: This creates a master file (samnnnnn) for the cast from a blank template file and pastes in selected variables from the fir22RRnnnnn file. Variable selection depends upon the variables listed in the template file.

sal0: Converts and reformats the salinity bottle data from salinometry measurements from Excel text files into NetCDF format. Output file: salnnnnn.bot

passal: Pastes salinity bottle file values from salnnnnn.bot into sam22RRnnnnn file.
Output file: sam22RRnnnnn.

botcond: Bottle salinities are twice converted to conductivity values using temperature from the primary and then secondary CTD sensors. This allows independent calibration of the two sensors.
Result added to sam22RRnnnnn files.

CTD calibration
Conductivity calibration
Calibration of the CTD conductivity (salinity) and oxygen sensors was performed on the data.
The calibration of the two Seabird conductivity channels to the salinometry results revealed a generally good agreement in both cases but also highlighted the presence of a drift on the primary conductivity channel, as shown by plots of conductivity difference against station number (i.e. time). This suggests that conductivity 2 and temperature 2 (from the secondary CTD sensor) provide more reliable estimates of salinity although the overall impact of the drift on the primary channel remained small.

SeaBird claims that the correct in-situ calibration for their conductivity sensors is a linear function of conductivity with no offset. Plots of conductivity difference against conductivity added support to this and therefore the calibration coefficients A and B were calculated as

conductivity = A* ( primary conductivity)

conductivity = B* (secondary conductivity)

where

and

and cond2_bot is the sample bottle conductivity determined with the secondary temperature variable.
Coefficient A was determined to be 1.000186 and coefficient B was determined to be 1.000098.
Corrected Seabird conductivities were calculated through the application of coefficient A to primary conductivity and coefficient B to the secondary conductivity channel.

Residual conductivity differences calculated as bottle conductivity minus corrected Seabird conductivity (btc-uc) were typically ±0.003 mS/cm for both channels but considerable scatter was present within the data.

The mean (±stdev) conductivity residuals were -0.000051±0.0027 mS/cm and 0.00000051±0.0019 mS/cm for conductivity channels 1 and 2 respectively.

Oxygen calibration
The linear regression between Seabird 43 oxygen concentrations (in ml/l) and manual Winkler titrations produced a regression equation of
y = 1.048204 * SBEoxy + 0.058575
where y = corrected oxygen concentration.

The typical range of residual values (i.e. corrected Seabird oxygen concentration - bottle titration estimate) was ±0.06 ml/l.

The mean (±stdev) residual estimate however was 0.0036±0.0395 ml/l.

BCO-DMO Edits
- Original data contributed as NetCDF files
- ARM Tools NetCDF Windows routine cdf2ascii.exe used to convert the data to ASCII format
- ARM Tools NetCDF Windows routine ncdump.exe used to extract header information (parameters and sensors)
- CTD Station id, date, time, lat, lon imported from file: COPAS08_ctd_positions_updated.xls

Station Notes
- Station ctd22RRb2401: Odd name due to unusual sampling positions (between stations)
- Station ctd22RRb2501: Odd name due to unusual sampling positions (between stations)
- Station ctd22RRb2601: Odd name due to unusual sampling positions (between stations)
- Station ctd22RRb4701: Odd name due to unusual sampling positions (between stations)
- Station ctd22RRb6001: Odd name due to unusual sampling positions (between stations)
- Station ctd22RR08901: During the upcast communications with the CTD package failed and the data files were considered corrupt and subsequently not processed. There is no data for this station
- Station ctd22RR14601: This station was scheduled but in the end not sampled due to time constraints. There is no data for this station
- Station ctd22RR14701: This station was scheduled but in the end not sampled due to time constraints. There is no data for this station

More information about this dataset deployment

Funding

Award Number	Funding Source
JGS 1166	Defence Science and Technology Laboratory
NNX08AJ88A	National Aeronautics & Space Administration
OCE-0728582	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird 911

Supplied Description:

Data was acquired using SeaBird SeaSave for SBE 911 software (v7)

Sample Header File

* Sea-Bird SBE 9 Data File:

* FileName = C:/CTD/balch-12-2008/06101.hex

* Software Version Seasave V 7.18b

* Temperature SN = 4307

* Conductivity SN = 2593

* Number of Bytes Per Scan = 44

* Number of Voltage Words = 5

* Number of Scans Averaged by the Deck Unit = 1

* Append System Time to Every Scan

* System UpLoad Time = Dec 17 2008 12:46:09

* NMEA Latitude = 48 45.00 S

* NMEA Longitude = 059 47.47 W

* NMEA UTC (Time) = Dec 17 2008 12:46:10

* Store Lat/Lon Data = Append to Every Scan

** Station/Cast: 06101

** LAT: 48 45.000S

** LON: 59 47.475W

** Bottom Depth: 466

** Cast Type: DN

** Event No: 200812171246

# units = specified

# bad_flag = -9.990e-29

# sensor 0 = Frequency 0 temperature, primary, 4307, 11-Sep-08

# sensor 1 = Frequency 1 conductivity, primary, 2593, 03-Sep-08 , cpcor = -9.5700e-08

# sensor 2 = Frequency 2 pressure, 0831, 17-Sep-08

# sensor 3 = Frequency 3 temperature, secondary, 2495, 11-Sep-08

# sensor 4 = Frequency 4 conductivity, secondary, 2766, 09-Sep-08 , cpcor = -9.5700e-08

# sensor 5 = Extrnl Volt 0 Fluorometer, Seapoint, primary

# sensor 6 = Extrnl Volt 1 irradiance (PAR), primary, 4644, 11 Feb. 2004

# sensor 7 = Extrnl Volt 2 transmissometer, primary, CST-1115-DR, 01 May 2008

# sensor 8 = Extrnl Volt 4 altimeter

# sensor 9 = Extrnl Volt 6 Oxygen, SBE, primary, 1129, 30-May-08p

# sensor 10 = Extrnl Volt 9 surface irradiance (SPAR), degrees = 0.0

# datcnv_date = Dec 17 2008 23:17:36, 7.18b

# datcnv_in = w:/06101.hex w:/06101.CON

# datcnv_skipover = 4800

# datcnv_ox_hysteresis_correction = yes

# datcnv_ox_tau_correction = yes

# wildedit_date = Dec 17 2008 23:17:41, 7.18b

# wildedit_in = w:/06101.cnv

# wildedit_pass1_nstd = 2.0

# wildedit_pass2_nstd = 10.0

# wildedit_pass2_mindelta = 0.000e+000

# wildedit_npoint = 500

# wildedit_vars = prDM t090C c0mS/cm t190C c1mS/cm sbeox0ML/L sbeox0Mm/Kg sbeox0PS flSP xmiss bat par spar cpar altM

# wildedit_excl_bad_scans = yes

# filter_date = Dec 17 2008 23:17:46, 7.18b

# filter_in = w:/06101.cnv

# filter_low_pass_tc_A = 0.030

# filter_low_pass_tc_B = 0.150

# filter_low_pass_A_vars =

# filter_low_pass_B_vars = prDM

# alignctd_date = Dec 17 2008 23:17:54, 7.18b

# alignctd_in = w:/06101.cnv

# alignctd_adv = sbeox0ML/L 7.000, sbeox0Mm/Kg 7.000, sbeox0PS 7.000

# celltm_date = Dec 17 2008 23:17:59, 7.18b

# celltm_in = w:/06101.cnv

# celltm_alpha = 0.0300, 0.0300

# celltm_tau = 7.0000, 7.0000

# celltm_temp_sensor_use_for_cond = primary, secondary

# loopedit_date = Dec 17 2008 23:18:03, 7.18b

# loopedit_in = w:/06101.cnv

# loopedit_minVelocity = 0.050

# loopedit_surfaceSoak: do not remove

# loopedit_excl_bad_scans = yes

# Derive_date = Dec 17 2008 23:18:10, 7.18b

# Derive_in = w:/06101.cnv w:/06101.CON# file_type = ascii

*END*

This mstar file created from sbe file 06101.cnv at 2008-12-18 11:22:36

condcal = 1.000186 * cond

cond2cal = 1.000098 * cond2

oxygen calibration = 0.058575 + 1.048204 * sbeoxy

Instrument Type

Generic Name: CTD Sea-Bird 911

Acronym: CTD SBE 911

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0035/

Generic Description:

The Sea-Bird SBE 911 is a type of CTD instrument package. The SBE 911 includes the SBE 9 Underwater Unit and the SBE 11 Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). More information from Sea-Bird Electronics.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
station	COPAS'08 station Id	text	station
date	date (GMT)	YYYYMMDD	date
time_at_bottom	time (GMT) at bottom of cast	HHMMSS	time
lon	Station longitude (West is negative)	decimal degrees	lon
lat	Station latitude (South is negative)	decimal degrees	lat
depth	Sample depth	meters	depth
filename	dataset filename	text	dataset_id
sampnum	sampnum	dimensionless	sample
statnum	statnum	number	station
botlnum	botlnum	number	bottle
botlflag	botlflag	dimensionless	flag
position	position on rosette	dimensionless	bottle
botsala	botsala	pss-78	sal_bot
botsalb	botsalb	pss-78	sal_bot
botsal	botsal	pss-78	sal_bot
botoxy	botoxy	ml/l	no_bcodmo_term
tfix	tfix	degC	temp
pH	pH	total	pH_sw
TA	TA	umol/kg	no_bcodmo_term
wireout	wireout	meters	wire_out
no2_plus_3	no2_plus_3	umol/l	no_bcodmo_term
sio3	sio3	umol/l	no_bcodmo_term
po4	po4	umol/l	PO4
no2	no2	umol/l	NO2
nh4	nh4	umol/l	NH4
cfc113	cfc113	pmol/kg	no_bcodmo_term
ccl4	ccl4	pmol/kg	no_bcodmo_term
press	press	dbar	press
temp	temp	degC	temp
cond	cond	S/m	cond
temp2	temp2	degC	temp2
cond2	cond2	S/m	cond2
sbeoxy	sbeoxy	ml/l	O2
sbeoxysat	sbeoxysat	percentage	O2sat
oxygen	oxygen	umol/kg	O2
oxysat	oxysat	ml/l	O2sat
fluor	fluor	ug/l	fluor
salin	salin	psu	sal
salin2	salin2	psu	sal
potemp	potemp	degC	potemp
potemp2	potemp2	degC	potemp

Database

Contribute Data

Dataset: CTD - SAM Data Files
Deployment: KNOX22RR

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: CTD - SAM Data FilesDeployment: KNOX22RR

Dataset acquisition description

Dataset Processing Description

Dataset: CTD - SAM Data Files
Deployment: KNOX22RR