CRUISE REPORT: ACT2010
(Updated SEP 2017)





Highlights











                          Cruise Summary Information

               Section Designation  ACT2010
Expedition designation (ExpoCodes)  316N20100404
                  Chief Scientists  Dr. Lisa Beal / RSMAS
                             Dates  2010 Apr 04 - 2010 Apr 23
                              Ship  R/V Knorr
                     Ports of call  Cape Town, South Africa 

                                                  33° 20' 45" S
             Geographic Boundaries  27° 28' 34" E               28° 54' 47" E
                                                  35° 43' 14" S

                          Stations  40
      Floats and drifters deployed  0
    Moorings deployed or recovered  7 moorings deployed


                             Contact Information:

                                Dr. Lisa Beal
  University of Miami • Rosenstiel School of Marine and Atmospheric Science.
                 4600 Rickenbacker Causeway • Miami, FL 33149
               Tel: 305-421-4093 • Email: lbeal@rsmas.miami.edu






















                                    ACT0410
                              R/V Knorr, KN197-6
                        4 April 2010 to 23 April 2010
              Cape Town, South Africa - Cape Town, South Africa
                       Chief Scientist: Dr. Lisa Beal
             Rosenstiel School of Marine and Atmospheric Science.





















                                 Cruise Report
                                 23 April 2010
                              Data Submitted by:
  Oceanographic Data Facility, Computing Resources and Research Technicians
       Shipboard Technical Support/Scripps Institution of Oceanography
                           La Jolla, CA 92093-0214
















Summary

A hydrographic survey consisting of Rosette/CTD/LADCP sections, underway 
shipboard ADCP and float deployments in the Agulhas was carried out early 
2010. The R/V Knorr departed Cape Town, South Africa on 4 April 2010.

40 Rosette/CTD/LADCP casts were made. Water samples (up to 12) and CTD data 
were collected on each Rosette/CTD/LADCP cast, usually made to within 5-70 
meters of the bottom. Salinity, dissolved oxygen samples were analyzed for up 
to 12 water samples from each cast of the principal Rosette/CTD/ LADCP 
program. Concurrent temperature, conductivity, dissolved oxygen measurements 
were made at the time samples were taken.

The cruise ended in Cape Town, South Africa 23 April 2010.


DESCRIPTION OF MEASUREMENT TECHNIQUES

1.  CTD/Hydrographic Measurements

ACT2010 Hydrographic measurements consisted of salinity, dissolved oxygen 
water samples taken from most of the 40 Rosette casts. Pressure, temperature, 
conductivity/salinity, dissolved oxygen, data were recorded from CTD 
profiles. The distribution of samples is shown in the following 2 figures.


Figure 1.0: ACT0410 Sample distribution, stations 1-20.

Figure 1.0: ACT0410 Sample distribution, stations 21-40.


1.1.  Water Sampling Package

Rosette/CTD/LADCP casts were performed with a package consisting of a 12-
bottle rosette frame (SIO/ STS), a 12-place carousel (SBE32) and 12 10.0L 
Niskin bottles (SIO/STS). Underwater electronic components consisted of a 
Sea-Bird Electronics SBE9plus CTD (SIO/STS #796) with dual pumps (SBE5), dual 
temperature (SBE3plus), dual conductivity (SBE4C), dissolved oxygen (SBE43), 
altimeter (Benthos 100m).

The CTD was mounted horizontally in an SBE CTD cage attached to the bottom of 
the rosette frame and located to one side of the carousel. The SBE4C 
conductivity, SBE3plus temperature and SBE43 dissolved oxygen sensors and 
their respective pumps and tubing were mounted in the CTD cage, as 
recommended by SBE. Pump exhausts were attached to the sensor bracket on the 
side opposite from the sensors. The altimeter was mounted on the inside of 
the bottom frame ring. The 300 KHz LADCP (RDI) was mounted vertically on one 
side of the frame between the bottles and the CTD as well as above the CTD. 
Its battery pack was located on the opposite side of the frame, mounted on 
the bottom of the frame. Table 1.1.0 shows height of the sensors referenced 
to the bottom of the frame.






Table 1.1.0 Heights referenced to bottom of rosette frame.

                Instrument                  Height in cm
                ——————————————————————————  ————————————
                Temperature sensors                   11
                SBE35                                 11
                Altimeter                              4
                Transmissometer                        8
                CDOM Fluorometer                      49
                Pressure sensor                       28
                Inner bottle midline                 112
                Outer bottle midline                 119
                BB LADCP XDCR Face midline            11
                Zero tape                            180


The rosette system was suspended from a UNOLS-standard three-conductor 0.322" 
electro-mechanical sea cable. The sea cable was terminated at the beginning 
of ACT. Reterminations were performed prior to station 30 when a kink was 
found in the winch wire 2 ft. above termination. Kink was from an unknown 
source. Technician also performed a total retermination after 14 kinks were 
found in about 50 meters of wire above termination. These kinks were 
determined to be from CTD touching bottom. The CTD package was found in good 
condition after recovery and the data was not at all affected. The R/V 
Knorrʼs DESH-6 winch was used for all casts.

The deck watch prepared the rosette 10-30 minutes prior to each cast. The 
bottles were cocked and all valves, vents and lanyards were checked for 
proper orientation. Once stopped on station, the rosette was moved out from 
the forward hanger to the deployment location under the squirt boom using an 
air-powered cart and tracks. The CTD was powered-up and the data acquisition 
system started from the computer lab. The rosette was unstrapped from the 
air-powered cart. Tag lines were threaded through the rosette frame and 
syringes were removed from CTD intake ports. The winch operator was directed 
by the deck watch leader to raise the package. The A-frame and rosette were 
extended outboard and the package was quickly lowered into the water. Tag 
lines were removed and the package was lowered to 10 meters, until the 
console operator determined that the sensor pumps had turned on and the 
sensors were stable. The winch operator was then directed to bring the 
package back to the surface, re-zero the wire-out reading, and begin the 
descent.

Most rosette casts were lowered to within 5-70 meters of the bottom, using 
the altimeter, winch wire-out, CTD depth and echosounder depth to determine 
the distance.

For each up cast, the winch operator was directed to stop the winch between 
3-12 standard sampling depths. These depths were staggered every station. To 
insure package shed wake had dissipated, the CTD console operator waited 30 
seconds prior to tripping sample bottles. An additional 10 seconds elapsed 
before moving to the next consecutive trip depth, to allow the SBE35RT time 
to take its readings.

Recovering the package at the end of the deployment was essentially the 
reverse of launching, with the additional use of poles and snap-hooks to 
attach tag lines. The rosette was secured on the cart and moved into the aft 
hanger for sampling. The bottles and rosette were examined before samples 
were taken, and anything unusual was noted on the sample log.

Each bottle on the rosette had a unique serial number, independent of the 
bottle position on the rosette. Sampling for specific programs was outlined 
on sample log sheets prior to cast recovery or at the time of collection.

Routine CTD maintenance included soaking the conductivity and oxygen sensors 
in fresh water between casts to maintain sensor stability.


1.2.  Navigation and Bathymetry Data Acquisition

Navigation data was acquired at 1-second intervals from the shipʼs GP90 GPS 
receiver by a Linux system beginning April 6 2010.

The bottom depths reported in the data transmittal files were recorded on the 
Console Logs during acquisition, and later input manually into the postgreSQL 
database. Knudsen depths were typically reported, unless depth data were not 
available.


1.3.  Underwater Electronics

An SBE35RT reference temperature sensor was connected to the SBE32 carousel 
and recorded a temperature for each bottle closure. These temperatures were 
used as additional CTD calibration checks.


Table 1.3.0:  ACT0410 Rosette Underwater Electronics.

                                                        Serial         A/D      Stations
Instrument/Sensor            Mfr./Model                 Number         Channel  Used
———————————————————————————  —————————————————————————  —————————————  ———————  ————————
Carousel Water Sampler       Sea-Bird SBE32 (12-Pl.)    3231807-0487   n/a      1-40
CTD                          Sea-Bird SBE9plus          381            n/a      1-40
Pressure                     Paroscientific Digiquartz  58952          n/a      1-40
Primary Temperature (T1)     Sea-Bird SBE3plus          03P-4924       n/a      1-40
Primary Conductivity (C1a)   Sea-Bird SBE4C             04-3399        n/a      1-40
Dissolved Oxygen             Sea-Bird SBE43             43-0275        Aux4/V6  1-40
Primary Pump                 Sea-Bird SBE5T             05-1799        n/a      1-40
Secondary Temperature (T2)   Sea-Bird SBE3plus          03P-4588       n/a      1-40
Secondary Conductivity (C2)  Sea-Bird SBE4C             04-2765        n/a      1-40
Secondary Pump               Sea-Bird SBE5T             05-3245        n/a      1-40
Altimeter                    Benthos, 100m              1182           Aux3/V4  1-40
Reference Temperature        Sea-Bird SBE35             35-0011        n/a      1-40
LADCP                        RDI WHM300-I-UG50          13330          n/a      1-40
Deck Unit (in lab)           Sea-Bird SBE11             11P21561-0518  n/a      1-40
     


The SBE9plus CTD was connected to the SBE32 12-place carousel providing for 
single-conductor sea cable operation. The sea cable armor was used for ground 
(return). Power to the SBE9plus CTD (and sensors), SBE32 carousel and Benthos 
100 altimeter was provided, but not operating correctly.


1.4.  CTD Data Acquisition and Rosette Operation

The CTD data acquisition system consisted of an SBE-11plus (V2) deck unit and 
three networked generic PC workstations running CentOS-5.4 Linux. Each PC 
workstation was configured with a color graphics display, keyboard, trackball 
and DVD+RW drive. One system had a Comtrol Rocketport PCI multiple port 
serial controller providing 8 additional RS-232 ports. The systems were 
interconnected through the shipʼs network. These systems were available for 
real-time operational and CTD data displays, and provided for CTD and 
hydrographic data management.

One of the workstations was designated the CTD console and was connected to 
the CTD deck unit via RS-232. The CTD console provided an interface and 
operational displays for controlling and monitoring a CTD deployment and 
closing bottles on the rosette. The website and database server and maintain 
the hydrographic database for ACT. Redundant backups were managed 
automatically.

Once the deck watch had deployed the rosette, the winch operator lowered it 
to 10 meters. The CTD sensor pumps were configured with a 5-second startup 
delay after detecting seawater conductivities. The console operator checked 
the CTD data for proper sensor operation and waited for sensors to stabilize, 
then instructed the winch operator to bring the package to the surface and 
descend to a specified target depth (wire-out). The profiling rate was no 
more than 60m/min depending on sea cable tension and sea state.

The progress of the deployment and CTD data quality were monitored through 
interactive graphics and operational displays. Bottle trip locations were 
transcribed onto the console and sample logs. The sample log was used later 
as an inventor y of samples drawn from the bottles. The altimeter channel, 
CTD depth, winch wireout and bathymetric depth were all monitored to 
determine the distance of the package from the bottom, allowing a safe 
approach at depth.

Bottles were closed on the up cast by operating an on-screen control. The 
winch operator was given a target wire-out for the bottle stop, proceeded to 
that depth and stopped.

After the last bottle was closed, the console operator directed the deck 
watch to bring the rosette on deck. Once the rosette was on deck, the console 
operator terminated the data acquisition, turned off the deck unit and 
assisted with rosette sampling.


1.5.  CTD Data Processing

Shipboard CTD data processing was performed automatically during each 
Rosette/CTD/LADCP deployment, and at the end of each Trace Metals rosette 
deployment using SIO/ODF CTD processing software. The Trace Metals rosette 
contained its own CTD and carousel. These data were acquired using SBE 
SeaSave software, then copied to a Linux workstation for further processing.

Processing was performed during data acquisition for Rosette/CTD/LADCP 
deployments. The raw CTD data were converted to engineering units, filtered, 
response-corrected, calibrated and decimated to a more manageable 0.5- second 
time series. The laboratory calibrations for pressure, temperature and 
conductivity were applied at this time. The 0.5-second time series data were 
used for real-time graphics during deployments, and were the source for CTD 
pressure and temperature associated with each rosette bottle. Both the raw 24 
Hz data and the 0.5-second time series were stored for subsequent processing. 
During the deployment, the data were backed up to another Linux workstation.

At the completion of a deployment a sequence of processing steps was 
performed automatically. The 0.5-second time series data were checked for 
consistency, clean sensor response and calibration shifts. A 2-decibar 
pressure series was then generated from the down cast. Both the 2-decibar 
pressure series and 0.5-second time series data were made available for 
downloading, plotting and reporting on the shipboard cruise website.

Rosette/CTD/LADCP data were routinely examined for sensor problems, 
calibration shifts and deployment or operational problems. The primary and 
secondary temperature sensors (SBE3plus) were compared to each other and to 
the SBE35 temperature sensor. CTD conductivity sensors (SBE4C) were compared 
to each other, then calibrated by examining differences between CTD and check 
sample conductivity values. The CTD dissolved oxygen sensor data were 
calibrated to check sample data. Additional Salinity and O2 comparisons were 
made with respect to isopycnal surfaces between down and up casts as well as 
with adjacent deployments. Vertical sections were made of the various proper 
ties derived from sensor data and check for consistency.

The primary temperature and conductivity sensors were used for reported CTD 
temperatures and conductivities.


1.6.  CTD Acquisition and Data Processing Problems

ODF acquisition software was not functioning properly for the first cast. The 
frame length and modulo count had changed between the test cast and the first 
cast. This led to the appearance of a 20 db pressure offset. Acquisition was 
performed with SBE software for station 1-3, then reverted back to ODF 
acquisition prior to station 4.

Salinity for stations 1-3 were erratic. It was found the deck unit settings 
were not set to SBE specifications and were corrected prior to station 4. 
Timing offsets were applied in processing to 1-3 and corrected for salinity.

Station 30, the CTD package was laid on its side on the sea floor. The ship 
was repositioned on shift change at the same time as CTD approached the 
bottom of the cast. The relative surface current was 4 knots. The current 
structure indicated bi-directional flow split at mid-depth. There was about 
700 m of winch-wire in excess of the relative depth. Some moments after ship 
was repositioned, the CTD package reached the bottom and was laid on its 
side. The sensors were facing the opposite direction of the seafloor. The 
sensors did not register any sea floor sediment or material interference in 
the signal, thus the incident was not reported until the CTD was brought back 
to surface. The data appeared intact. Subsequent data checks have shown data 
to be good. Approximately 50 m of winch-wire was kinked in 14 places, 
indicating the package was still falling in the water column for the first 
several bottle stops.





1.7.  CTD Sensor Laboratory Calibrations

Laboratory calibrations of the CTD pressure, temperature, conductivity and 
dissolved oxygen sensors were performed prior to ACT0410. The calibration 
dates are listed in table 1.7.0.


Table 1.7.0:  ACT0410 CTD sensor laboratory calibrations.

Sensor                                S/N       Calibration  Calibration 
                                                Date         Facility
————————————————————————————————————  ————————  ———————————  ———————————
Paroscientific Digiquartz Pressure    58952     16 Dec 2009  SIO/STS
Sea-Bird SBE3plus T1 Temperature      03P-4924  11 Dec 2009  SIO/STS
Sea-Bird SBE3plus T2 Temperature      03P-4588  11 Dec 2009  SIO/STS
Sea-Bird SBE4C C1 Conductivity        04-3399   10 Feb 2010  SBE
Sea-Bird SBE4C C2 Conductivity        04-2765   10 Feb 2010  SBE
Sea-Bird SBE43 Dissolved Oxygen       43-0275   1 July 2009  SBE
Sea-Bird SBE35 Reference Temperature  35-0011   07 Feb 2010  SBE


ODF typically calibrates sensors about two months before an expedition.


1.8.  CTD Shipboard Calibration Procedures

CTD 381 was used for all Rosette/CTD/LADCP casts during ACT. The primary 
temperature sensor (T1/03P-4924) and conductivity sensors (C1/04-3399) were 
used for all reported CTD data for stations 1-40. The SBE35RT Digital 
Reversing Thermometer (S/N 3528706-0011) served as an independent calibration 
check for T1 and T2. In-situ salinity and dissolved O2 check samples 
collected during each cast were used to calibrate the conductivity and 
dissolved O2 sensors.


1.8.1.  CTD Pressure

The Paroscientific Digiquartz pressure transducer (S/N 58952) was calibrated 
in Dec 2009 at the STS/ODF Calibration Facility. The calibration coefficients 
provided on the report were used to convert frequencies to pressure; then the 
calibration correction slope and offset were applied to the converted 
pressures during each cast. Pre- and post-cast on-deck/out-of-water pressure 
offsets varied from -0.1 to+0.5db before and after the aborted test cast. An 
additional -0.2db correction was applied during data acquisition/block-
averaging starting with station 1.

1.8.2.  CTD Temperature

The same primary (T1/03P-4924) and secondary (T2/03P-4588) temperature 
sensors were used for all 40 stations. Calibration coefficients derived from 
the pre-cruise calibrations, plus shipboard temperature corrections 
determined during the cruise, were applied to raw primary and secondary 
sensor data during each cast.

A single SBE35RT was used as a tertiary temperature check. It was located 
equidistant between T1 and T2 with the sensing element aligned in a plane 
with the T1 and T2 sensing elements. The SBE35RT Digital Reversing 
Thermometer is an internally-recording temperature sensor that operates 
independently of the CTD. It is triggered by the SBE32 carousel in response 
to a bottle closure. According to the manufacturerʼs specifications, the 
typical stability is 0.001°C/yr. The SBE35RT on ACT was set to internally 
average over an 8 second period.

Tw o independent metrics of calibration accuracy were examined. At each 
bottle closure, the primary and secondary temperature were compared with each 
other and with the SBE35RT temperatures.

The primary temperature sensor exhibited a second-order pressure response, 
and the secondary sensor did as well when compared to the SBE35RT.

All corrections made to CTD temperatures had the form: 


                                         2
                          T    = T + tp P + tp P + t
                           cor         2      1     0


Residual temperature differences after correction are shown in figures 
1.8.2.0 through 1.8.2.1.


Figure 1.8.2.0: T1-T2 by station (-0.01°C ≤T 1 -T 2≤0.01°C).

Figure 1.8.2.1: SBE35RT-T1 by station (-0.01°C ≤T 1 -T 2≤0.01°C).


1.8.3.  CTD Conductivity

Primary conductivity sensor SBE4C-3399 and secondary conductivity sensor 
SBE4C-2765 were used for all 40 stations. Calibration coefficients derived 
from the pre-cruise calibrations were applied to convert raw frequencies to 
conductivity. Shipboard conductivity corrections, determined during the 
cruise, were applied to primary and secondary conductivity data for each 
cast.

Corrections for both CTD temperature sensors were finalized before analyzing 
conductivity differences. Two independent metrics of calibration accuracy 
were examined. At each bottle closure, the primary and secondary conductivity 
were compared with each other. Each sensor was also compared to conductivity 
calculated from check sample salinities using CTD pressure and temperature.

The differences between primary and secondary temperature sensors were used 
as filtering criteria to reduce the contamination of conductivity comparisons 
by package wake. The coherence of this relationship is shown in figure 
1.8.3.0.


Figure 1.8.3.0:  Coherence of conductivity differences as a function of 
                 temperature differences.


Uncorrected conductivity comparisons are shown in figures 1.8.3.1 through 
1.8.3.3.


Figure 1.8.3.1:  Uncorrected C1 -C2 by station (-0.01°C ≤T 1 -T 2≤0.01°C).

Figure 1.8.3.2:  Uncorrected C(Bottle) -C1 by station (-0.01°C ≤T 1 -T 2≤0.01°C).

Figure 1.8.3.3:  Uncorrected C(Bottle) -C 2 by station (-0.01°C ≤T1-T2≤0.01°C).


First-order time-dependent drift corrections (changing conductivity offset 
with time) were determined for each sensor. After applying the drift 
corrections, second-order pressure responses were evident for each 
conductivity sensor.

C(Bottle) − CCTD differences were then evaluated for response to temperature 
and/or conductivity, which typically shifts between pre- and post-cruise SBE 
laboratory calibrations. Temperature and conductivity responses essentially 
showed the same picture, so each sensor was fit to conductivity response. 
Both C1 and C2 required a second-order correction.

After conductivity responses were corrected, the pressure-dependent 
correction for C1 required a minor adjustment to flatten out the deep end.

The residual differences after correction are shown in figures 1.8.3.4 
through 1.8.3.12.


Figure 1.8.3.4:  Corrected C1 -C2 by station (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.5:  Corrected C(Bottle) -C1 by station (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.6:  Corrected C(Bottle) -C2 by station (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.7:  Corrected C1 -C2 by pressure (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.8:  Corrected C(Bottle) -C1 by pressure (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.9:  Corrected C(Bottle) -C2 by pressure (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.10:  Corrected C1 -C2 by conductivity (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.11:  Corrected C(Bottle) -C1 by conductivity (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.12:  Corrected C(Bottle) -C2 by conductivity (-0.01°C ≤T1-T2≤0.01°C).


Corrections made to all conductivity sensors had the form:


                               2             2     2
                C    = C + cp P + cp P + cp C + c C + c + c
                 cor         2      1      0     2     1   0


Only CTD and bottle salinity data with "acceptable" quality codes are 
included in the differences.


Figure 1.8.3.13:  Salinity residuals by station (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.14:  Salinity residuals by pressure (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.3.15:  Salinity residuals by station (Pressure>2000db)


Figures 1.8.3.14 and 1.8.3.15 represent estimates of the deep salinity 
accuracy of ACT0410. The 95% confidence limits are ±0.000904 PSU relative to 
bottle salinities for deep salinities, and ±0.00307 PSU relative to bottle 
salinities for all salinities where T1-T2 is within ±0.01°C.


1.8.4.  CTD Dissolved Oxygen

A single SBE43 dissolved O2 sensor (DO/43-0275) was used during this leg. The 
sensor was plumbed into the primary T1/C1 pump circuit after C1.

The DO sensor was calibrated to dissolved O2 check samples taken at bottle 
stops by matching the down cast CTD data to the upcast trip locations on 
isopycnal surfaces, then calculating CTD dissolved O2 using a DO sensor 
response model and minimizing the residual differences from the check 
samples. A non-linear least-squares fitting procedure was used to minimize 
the residuals and to determine sensor model coefficients, and was 
accomplished in three stages.

The time constants for the lagged terms in the model were first determined 
for the sensor. These time constants are sensor-specific but applicable to an 
entire cruise. Next, casts were fit individually to check sample data. 
Consecutive casts were checked on plots of Theta vs O2 to check for 
consistency.

Standard and blank values for check sample oxygen titration data were 
smoothed, and the oxygen values recalculated, prior to the final fitting of 
CTD oxygen.


Figure 1.8.4.0:  O2 residuals by station (-0.01°C ≤T1-T2≤0.01°C).

Figure 1.8.4.1:  O2 residuals by pressure (-0.01°C ≤T1-T2≤0.01°C).


The standard deviations of 3.04 μmol/kg for all oxygens and 0.76 μmol/kg for 
deep oxygens are only presented as general indicators of goodness of fit. ODF 
makes no claims regarding the precision or accuracy of CTD dissolved O2 data.

The general form of the ODF DO sensor response model equation for Clark cells 
follows Brown and Morrison [Brow78], and Millard [Mill82], [Owen85]. ODF 
models DO sensor secondary responses with lagged CTD data. In situ pressure 
and temperature are filtered to match the sensor responses. Time constants 
for the pressure response τp, a slow (τTf) and fast (τTs) thermal response, 
package velocity (τdP), thermal diffusion (τdT) and pressure hysteresis (τh) 
are fitting parameters. Once determined for a given sensor, these time 
constants typically remain constant for a cruise. The thermal diffusion term 
is derived by low-pass filtering the difference between the fast response 
(Ts) and slow response (Tl) temperatures. This term is intended to correct 
non-linearities in sensor response introduced by inappropriate analog thermal 
compensation. Package velocity is approximated by low-pass filtering 1st-
order pressure differences, and is intended to correct flow-dependent 
response. Dissolved O2 concentration is then calculated:


                      Ph                                              dOc      dP
                 (C  ————)                    (C T  + C T  + C P + C  ——— + C  —— + C dT)
                   2 5000                       4 l    5 S    7 l   6 dt     8 dt    9
O ml/l = [C V   e         + C  • f   (T/P) • e
 2         1 DO              3    sat     


where:

O2ml/l     Dissolved O2 concentration in ml/l
VDO        Raw sensor output
C1         Sensor slope
C2         Hysteresis response coefficient
C3         Sensor offset
fsat(T,P)  O2 saturation at T,P (ml/l)
T          in situ temperature (°C)
P          in situ pressure (decibars)
Ph         Low-pass filtered hysteresis pressure (decibars)
Tl         Long-response low-pass filtered temperature (°C)
Ts         Short-response low-pass filtered temperature (°C)
Pl         Low-pass filtered pressure (decibars)

dOc
———        Sensor current gradient (µamps/sec)
dt

dP
——         Filtered package velocity (db/sec)
dt

dT         low-pass filtered thermal diffusion estimate (Ts - Tl)
C4 - C8    Response coefficients



1.9.  Bottle Sampling

At the end of each rosette deployment water samples were drawn from the 
bottles in the following order:

    • O2
    • Salinity

The correspondence between individual sample containers and the rosette 
bottle position (1-12) from which the sample was drawn was recorded on the 
sample log for the cast. This log also included any comments or anomalous 
conditions noted about the rosette and bottles. One member of the sampling 
team was designated the sample cop, whose sole responsibility was to maintain 
this log and ensure that sampling progressed in the proper drawing order. Nor 
mal sampling practice included opening the drain valve and then the air vent 
on the bottle, indicating an air leak if water escaped. This observation 
together with other diagnostic comments (e.g., "lanyard caught in lid", 
"valve left open") that might later prove useful in determining sample 
integrity were routinely noted on the sample log. Drawing oxygen samples also 
involved taking the sample draw temperature from the bottle. The temperature 
was noted on the sample log and was sometimes useful in determining leaking 
or miss-tripped bottles. Once individual samples had been drawn and properly 
prepared, they were distributed for analysis. Oxygen and salinity analyses 
were performed on computer-assisted (PC) analytical equipment networked to 
the data processing computer for centralized data management. 1.10. Bottle 
Data Processing Water samples collected and properties analyzed shipboard 
were centrally managed in a relational database (PostgreSQL 8.1.11) running 
on a Linux system. A web service (OpenACS 5.3.2 and AOLServer 4.5.0) front-
end provided ship-wide access to CTD and water sample data. Web-based 
facilities included on demand arbitrary proper ty-proper ty plots and 
vertical sections as well as data uploads and downloads.

The sample log (and any diagnostic comments) was entered into the database 
once sampling was completed. Quality flags associated with sampled properties 
were set to indicate that the property had been sampled, and sample container 
identifications were noted where applicable (e.g., oxygen flask number).

Analytical results were provided on a regular basis by the various analytical 
groups and incorporated into the database. These results included a quality 
code associated with each measured value and followed the coding scheme 
developed for the World Ocean Circulation Experiment Hydrographic Programme 
(WHP) [Joyc94]. Table 1.10.0 shows the number of samples drawn and the number 
of times each WHP sample quality flag was assigned for each basic 
hydrographic property: 


Table 1.10.0:  Frequency of WHP quality flag assignments.

                              Rosette Samples Stations - 57
      —————————————————————————————————————————————————————————————
               Reported              WHP Quality Codes
                levels   1      2       3     4     5     7      9
      —————————————————  —     ———     ——     —     —     —     ———
      Bottle      436    0     432      0     0     0     0       4
      CTD Salt    436    0     435      1     0     0     0       0
      CTD Oxy     425    0     425      0     0     0     0      11
      Salinity    300   15     287     13     0    12     0     109
      Oxygen      429    3     409     20     0     0     0       4


Various consistency checks and detailed examination of the data continued 
throughout the cruise.


Science Party

Chief Scientist  Lisa Beal            RSMAS, University of Miami
Mooring Team     Mark Graham
                 Robert Jones
Moorings/LADCP   Adam Houk
SADCP/LADCP      Clement Rousset
CTD              Courtney Schatzman   Scripps Institution of Oceanography
                 Robert Thombley
South African    Tinus Sonnekus       Nelson Mandela Metropolitan University
  students       Brett Kuyper         University of Cape Town (bromoform trace gas) 
                 Megan van der Bank   University of the Western Cape
                 Nausheena Parker     University of the Western Cape
                 Media Dallas Murphy
SSSG             Amy Simoneau         Woods Hole Oceanographic Institution 
                 Anton Zafereo



GENERAL CRUISE PLAN

The plan was to deploy all moorings beginning inshore at P1 and ending 
offshore at P5, with CTDO2/LADCP casts on and between mooring sites conducted 
at night. Then transit back inshore for a continuous underway shipboard ADCP 
section of the Current. Finally, conduct synoptic CTD line back offshore. 
Seven full-depth current meter moorings were successfully deployed, moorings 
A to G. One tide gauge and four C-PIES were also successfully deployed, P1 to 
P5. 40 CTDO2/LADCP stations were occupied. Only one weather day was used.

After a 48-hour steam from Cape Town, where the ship left port at about 17:00 
GMT on 4th April 2010, a test CTD station and bathymetric survey for P1 were 
conducted on 6 April beginning at 18:00 GMT. Mooring deployment operations 
began 08:00 GMT on 7th April (first light and o6:00 local time) with P1 and 
A. Mooring deployments continued with one long mooring deployed per day, 
except 10th April when operations were suspended because of weather, through 
mooring F on 13th April. During this time CTDO2/LADCP casts were occupied at 
night on and between mooring positions. On the evening of the 13th April the 
first C-PIES (P2) mooring was deployed. The final long mooring G, was 
deployed on 14th April, followed by the three remaining C-PIES, to wrap up 
mooring operations on 15th April. Following the remaining CTDO2/LADCP cast, 
an underway transit across the Current was made during 16th April to obtain a 
synoptic section of velocities with as little contamination from time 
variability as possible. Once back inshore, mooring A was recovered (17th 
April) to amend a design flaw on the top float: a weight was added to the 
bottom of the frame to counterweight the ADCP and help the float stay upright 
(see next section). P1 and A were then redeployed successfully. To finish the 
cruise, we occupied another CTDO2/LADCP section across the Current from 
onshore to off shore (20 stations) out to P5, to capture as synoptic a 
dataset as possible. This line was begun on 17th April and finished on 20th, 
when we headed back towards Cape Town.

 
CURRENT METER MOORING DEPLOYMENTS

Deployment Operations:

Each mooring deployment consisted of the following operations.

1. Bathymetric survey of proposed site using SeaBeam: 

Looked for a flat area 1/4 to 1/2 nautical mile square at the desired depth 
and near the mooring line. The SeaBeam swath width used was typically 60 
degrees (1.7 x water depth). An averaged sound speed profile from the AUCE 
East London section was used to calibrate the SeaBeam for corrected depths. 
This worked well except over the shelf or in deep waters to the east of the 
Agulhas. For the latter, just-collected CTD data was used. You can tell the 
calibration is off when the bottom has a ridge along the mid-axis of the 
swath and the surveyed area looks “scalloped”. Previously planned survey 
grids didn’t necessarily work too well, since the depth required for mooring 
de- sign was not always found at the preliminary position (errors in ETOPO1). 
Therefore, coming up to the preliminary site along the mooring line and 
continuing until and past the desired depth was best, before doubling back 
for a swath either side if necessary. Waypoints for the survey were 
communicated to the bridge via telephone.

2. Adjust mooring design for new target depth: 

Once a new target was found, the new depth was communicated to Mark so that 
the mooring design can be modified with more or less shots of wire, if 
necessary. The time required for the mooring deployment was estimated as 
approximately 1 hour per 1000 m.

3. Ship set up for Mooring Deployment:

For each set-up I asked the Mate to steer into the wind at 1.5 knots through 
the water for 15 minutes or so at the target site. By maintaining a heading 
into the wind, we eliminate windage from the ship - because there is almost 
no windage on the mooring as it is streamed out, windage on the ship causes 
wire angle.

During that time, the course and speed over ground was noted. Then, together 
with the expected duration of mooring deployment (approximately 1000 m per 
hour), we could ascertain how far off and in which direction the ship should 
set-up from the target site. When the wind was blowing opposite to the 
current, we needed 4 or 5 knots over ground to get 1-2 through the water with 
the current - hence some set-ups were over 10 nm from our target! On 
occasions when we headed into both wind and current, 1.5 knts through the 
water would have us approaching the target backwards, drifting 1-2 knts with 
the current! In those cases fall back was TOWARDS the target, hence our 
anchor drop was before we reached the target. For the most part, anchor drop 
was calculated as a vector product of fall back and current advection. For 
the moorings over 2000 m long, advection was equal or greater in distance 
than fall back.

4. Deployment: 

Each mooring was deployed top buoy first, starting at the set-up site and 
ending at the target with anchor deployment. Serial numbers of instruments, 
notable changes, and times for each stage of the mooring were recorded on a 
mooring deployment sheet (from Mark). At anchor drop, position, time, and 
depth were noted.

5. Ranging:

Immediately after the anchor drop, send someone up to the Bridge to watch the 
top float go under (if it remains on the surface the mooring has parted). Ask 
the Bridge to stop engines. Ask SSSG to switch off Knudsen and SeaBeam 
(anything around 12 kHz should be off). Listen for “last gasp” from the 
radio. The transducer is put over the starboard side to range off the 
releases. When the mooring reaches the bottom, the time is noted.



6. Triangulation:

Once the mooring is on the bottom, Adam conducts a triangulation to get an 
accurate position for the final anchor site, after fall back and drift from 
the anchor drop position. (Only necessary for tall moorings that can be 
dragged for as last resort.) The triangulation requires ranging from three 
points 1/2 - 2/3 water depth from anchor drop position. Note - need to know 
average sound speed to the depth of the releases, not to the bottom. Finally, 
the releases should be DISABLED.

7. CTD/LADCP cast at mooring site.

P1: First day of mooring deployments (7/4/2010) were hampered by strong winds 
and sea state, plus currents of 3 or 4 knots. P1, the bottom-lander with 
pressure gauge, is designed so that the release on the package lets go two 
small buoys on a 150 m line and the package is then recovered by hauling on 
the line. A second release, the ‘deployment release” is used to deploy the 
package by lowering on a wire (via winch) to the sea bed, then releasing and 
winding back in the wire together with the deployment release. For 
deployment, the ship maintained target position, hence the wire angle was 
large (next time better to make 1 - 1.5 kts through water, as for long 
mooring deployments).

P1 touched the bottom (slack on the wire) before it was released quickly. 
But, subsequent interrogation with the pack- age release told us it was not 
upright (later realised that since release was mounted upside down on the 
package it would always tell us it was not upright). For this reason we 
thought the mooring was on its side and popped it to recover it and redeploy 
upright. The floats were seen on the surface, but after a few minutes the 
strong current pulled the floats under once the rope was unwound. Captain 
Kent Sheasley devised a way to recover the mooring even though we could no 
longer see the top float: the ship was positioned parallel to southwestward 
cur- rent, with mooring site 50 m from port side. The mooring line would be 
streaming SW with the current. A piece of weighted line, with chain and two 
grappling hooks attached was lowered over the fantail. The ship then 
manouevred sideways until the mooring site was left 50 m to starboard - i.e. 
passing the grappling line across the streaming line. The grappling line was 
then slowly pulled back aboard - and success! The mooring line was hooked 
first time and P1 was retrieved. Due to the design flaw, the mooring was not 
redeployed until 17/4/2010. An extra buoy was added to help float the line on 
the surface for recovery. Final position of P1: 33° 20.608’ S, 27° 28.889’ E 
at 59.5 m depth.

A: 

During deployment of mooring A (7/4/2010) the ADCP was pushed out of the top 
buoy and jammed against the frame by towing through a hefty sea state. We 
brought it back onboard and cut a piece of PVC piping to wedge between the 
frame and the ADCP to keep it in place. The mooring was subsequently deployed 
successfully. However, Mark Graham later reported a design flaw of the top 
floats on all moorings - he noticed that they were floating upside down and 
should be weighted on the bottom so that upon recovery they would float 
upright. Otherwise there is no strobe, no radio, and no ARGOS beacon to aid 
recovery. We returned to mooring A on 17/4/2010 and recovered it successfully 
on a calm day with small northwestward current (meander). A small length of 
chain with 20 lb weight was added to the top float and the mooring 
redeployed. Final position of A: 33° 33.384’ S, 27° 35.916’ E at 329 m depth.

B through G: 

The rest of the moorings were deployed without incident, except that G was 
towed for several hours because the mooring set-up was estimated while in 3-4 
knots of current (Agulhas meandered offshore), but the current was actually 1 
-2 knots for most of the deployment. All top buoys, with the exception of 
mooring B, were ballasted to float upright. For configuration of the ADCPs 
and Aquadopps, see Appendix A. Fall rates averaged 125 m per minute.


Final positions of moorings:

B: 33° 39.216’ S, 27° 39.474’ E at 1275 m depth.
C: 33° 46.938’ S, 27° 43.188’ E at 2210 m.
D: 34° 01.242’ S, 27° 51.798’ E at 3620 m.
E: 34° 17.190’ S, 28° 01.554’ E at 3730 m.
F: 34° 32.322’ S, 28° 09.732’ E at 4010 m.
G: 34° 49.314’ S, 28° 20.502’ E at 4270 m.


Detailed mooring diagrams A through G can be found in Appendix C.

Four current-meter and pressure-sensor equipped inverted echo sounders (C-
PIES) were deployed at the off shore end of the mooring line; P2 - P5. 
Configuration of the C-PIES was for a 3.6 year deployment (with 20% safety 
margin): Travel time 24 times per hour (4 times every 10 minutes), Pressure 
and temperature 3 times per hour, speed and direction 3 times per hour (burst 
sampling). Deployments were simple and quick, made with the ship making 1 - 
1.5 knts through the water. The toggle line, float, and current meter were 
lowered aft by hand, and 50 m of wire streamed. Then the PIES was lifted by 
it’s bottom-mount frame using the outboard winch on the A-frame and a quick-
release line. We released the PIES on target, not accounting for advection 
down- stream. Ranging on the C-PIES was successful, with the time to bottom 
well predicted by a 72 m per minute fall-rate. Telemetering on the C-PIES was 
much less successful. A DS-7000 deckset was borrowed from Sabrina Speich’s 
group in Brest specifically for burst telemetering. However, using an over-
the-side transducer, the results were inconsistent. Only on P4 were we able 
to obtain data that made sense (i.e. travel times in the 5-6 s range for 
~4000 m depths). Setting a gain of any more than 5 produced garbage data 
(easy to tell because numbers come in continuously rather than in bursts 
after measurement intervals).

The single biggest problem for signal-to-noise seemed to be the depth of the 
transducer. When the current was strong the transducer streamed and did not 
sink very well - this made for noisy data. For successful telemetry of data 
on the turnaround cruise we will need to utilise the shipboard 
transducer.  Telemetering during CTD operations also poses challenges from 
thruster noise, however parallel operations will be necessary to cut down on 
the long time frame needed for file telemetry during the turn- around cruise. 

Launch positions and nominal depths of the C-PIES are as follows:

P2: 34° 40.368’ S,  28° 15.4270’ E at 4157 m depth.
P3: 34° 57.4852’ S, 28° 25.6620’ E at 4327 m.
P4: 35° 20.7544’ S, 28° 39.7290’ E at 4360 m.
P5: 35° 44.03’ S,   28° 54.00’ E   at 4480 m.


WEATHER AND SEA SURFACE TEMPERATURE (Brett Kuyper)

The weather data fell into three main categories; synoptic charts, daily 
predicted wind fields, and sea state. In addition, we downloaded sea surface 
temperature images which proved very useful to track the Agulhas meander that 
passed the ACT line during our experiment. Synoptic charts were gathered from 
the South Africa Weather Service (SAWS) website. The charts were updated 
approximately every 6 hours, based on UTC time and can be obtained from 
either:

http://metzone.weathersa.co.za/images/articles/ma_sy.gif?1271298099935 or 

http://www.weathersa.- 
co.za/Weather.asp?Dte=Today&Vw=Over&Zoom=Ctry&Ref=01&Ad=0&Skin=Default&ProdTy
pe=1&Menu=1&VI=True&M=0&Menu=3&ProdType=3&Zoom=Ctry&Ref=01&Vw=Over&Dte=Today&
frameURL=http://metzone.weathersa.co.za/viewforum.php?f=1 

This is simply a chart showing the weather as it is, there is no analysis 
that has been applied to the charts.

Wind forecasts were obtained from WindFinder 
(http://www.windfinder.com/forecasts/wind_- globe_akt.htm), which provides 
forecast projections of the wind for different times of the day at different 
scales. Charts of South Africa turned out to be the most useful, however more 
localised information can be obtained if needed. One chart every morning was 
gathered for the wind at about noon every day. This data complimented the 
synoptic charts in better understanding the weather on any given day.

The Oceanweather website (http://www.oceanweather.com/data/) provided 
information on sea state twice daily. We downloaded one chart each morning. 
The data are a composite of observational data through VOS and model data. 
There is probably a fair degree of skill in the chart, how- ever the spatial 
scale was too large to be of much help in predicting wave heights along the 
mooring line.

Finally, sea surface temperature images were obtained from The Marine Remote 
Sensing Unit (MRSU) in South Africa. Images were usually available from their 
website (http://www.afro- sea.org.za /) at approximately 11:30 am local time 
each day for the previous day. The images can be emailed to your account 
either by subscribing on the website or by emailing Christo Whittle 
(christo.whittle@uct.ac.za ). The images were produced reliably each day (not 
at the weekend), however cloud cover often limited coverage.

The SST images showed a solitary meander passing over the ACT line, beginning 
8th April. The meander propagated downstream with a speed of roughly 12 km 
per day and measured about 150 km in off shore extent and 200 km in 
alongshore extent. The Agulhas found off shore did not appear to be 
diminished in speed or transport. Strong northwestward flow was found at the 
leading edge of the shear-edge cyclone.


SHIPBOARD ADCP PROGRAM (Clement Rousset)

Knorr is equipped with two hull-mounted ADCPs: a 300 kHz instrument profiling 
down to 100 m with 4 m bins and a 75 kHz collecting interleaved broadband and 
narrowband pings each with 16- m bin length and ranges of 600 m and 800 m, 
respectively. The 300 kHz was switched on from the beginning of the cruise, 
collecting bottom-track and water-track pings for the two-day transit over 
the shelf. On 6th April at 14:12 the 300 kHz was reconfigured with water-
track pings only, and the OS75 was switched on in interleaved mode. This set-
up remained for the rest of the cruise.

The data acquisition system aboard is UHDAS, maintained by Jules Hummon and 
Eric Firing at the University of Hawaii. Data are processed in real time and 
provided as 15-minute average ocean velocity profiles in matlab format. Live 
figures of ocean velocity, updated every 5 minutes, are available on the 
shipboard website: http://www.knorr.whoi.edu/n_index.shtml . Heading 
correction was supplied by posmv (primary) and phins (back up).

wh300_cont_uv.mat, os75bb_cont_uv.mat and os75n- b_cont_uv.mat contain ocean 
velocities stored in variable uv. Eastward velocities were stored in 
uv(:,1:2:end) and northward velocities were stored in uv(:,2:2:end). Bad data 
are represented by NaN.

wh300_cont_xy.mat, os75bb_cont_xy.mat and os75n- b_cont_xy.mat contain three 
variables: z which is the depth bins, zc which is the center of depth bins, 
and xyt, in which the first column is longitude, the second is latitude, and 
the third is time.

Time is zero-based decimal days, counting from January 1st 2010 at 00:00, so 
that January 1st 2010 at 12:00 is 0.5. Therefore, OS75 started at decimal day 
95.5920, while WH300 started at decimal day 93.5808. Three transects of the 
Agulhas Current were extracted during the cruise, named SE, NW, and SE2 (see 
figures in this section and front page). SE is from data collected onshore to 
off shore (in SouthEast direction at 154°T) during mooring deployments. 
Because the transect took 10 days to complete and an Agulhas meander moved 
over the mooring line during this period, these data are badly aliased by 
unresolved temporal variability. 

The NW transect was completed underway in 15 hours and represents the best 
snapshot. The final transect, SE2 was a synoptic CTD/LADCP section collected 
over 3.5 days. The Agulhas Current transport between the surface and 800 m is 
about 50 Sv (from NW section).

 
LOWERED ADCP PROGRAM (Adam Houk)

LADCP Setup:

Full water column velocity profiles were collected using a dual-300kHz 
Workhorse Monitor configuration. All equipment, including a back-up 
instrument, cables, and two battery packs were supplied by Dan Torres of 
Woods Hole Oceanographic Institution. The serial numbers of the WH300’s were 
4896, 4897, and 10417. The batteries were “SeaBattery” 48-Volt power modules, 
looking like square plastic boxes with an oil filled bladder inside. Mounting 
brackets for the ADCP’s and battery on the CTD frame were provided by Scripps 
Institution of Oceanography.

The upward-looking ADCP was mounted near the outer edge of the rosette, above 
the upper rim of the frame. The downward-looking ADCP was mounted in the 
center of the frame with the transducer face about 20cm above the deck. The 
sea-battery was secured adjacent to the downward-looking ADCP using ratchet 
straps. Both ADCP’s ran off a single battery pack using a star-cable. The 
ADCPs were configured for 20 8-meter bins, zero blanking distance, and an 
ambiguity velocity of 250 cm/s. The units were configured for staggered 
single-ping ensembles every 0.8/1.2 seconds. Measurements were saved in beam 
coordinates, with 3-beam solutions and bin-mapping disabled (see Appendix B 
for command files). Both upward-looking ADCPs were running firmware version 
51.36, while the downward-looking ADCP was running version 50.36.

Data Acquisition Setup:

Inside the main lab of the Knorr, a dedicated computer running Windows 2000 
with two built-in serial ports was set up as the primary data acquisition 
platform. An American Reliance Inc. LPS-305 programmable power supply was 
used as the primary battery charger. The supply was programmed to output 58 
Volts (+29/-29). Initially, the charger was plugged directly into the battery 
for recharging between stations using a third cable. About half- way through 
the first series of casts, the charger was plugged into one of the two long 
power/ communication cables that ran from the acquisition computer to the 
ADCPs while the rosette was inside its bay. This was done on Dan Torres’ 
recommendation that the battery be charged through the star cable.

Deployment and Recovery: Lowered ADCP operations began on April 6th, 2010 
with a “test” cast near the beginning of the main transect line. No 
operational problems were found with the dual-300kHz setup. Station 01 was on 
April 7th, around 20:48 UTC. Initial operations proceeded more slowly than 
anticipated, as the two LADCP shift operators needed to familiarize 
themselves with the equipment and procedures. After the first four or five 
casts, as they became more comfortable with the equipment, the typical 
deployment procedure was as follows:

• About 10 minutes prior to arrival on station, the LADCP operator wakes up 
  the two ADCPs using RDI’s BBTalk terminal program.

• After verifying the current drawn by the battery has reached minimal level 
  (0.2 to 0.4 Amps), the battery charger is powered off.

• Internal clock, memory and instrument voltage check are made. Clocks are 
  synchronized to the ship’s GPS. The operator would NOT erase the ADCP's 
  recorder unless the unit was over two-thirds of its capacity, and then only 
  with my permission.

• The appropriate command file would then be sent to the instrument to 
  initiate sampling. The output from this operation is captured to a log-
  file.

• Once the ‘cs’ command was sent, the operator would listen for audible 
  ‘pings’ from both ADCPs to verify operation.

• Replace the vent plug on the battery, disconnect the two serial cables, and 
  insert the dummy plugs.

The operator noted the time and position for the beginning of the cast, the 
maximum CTD depth in the middle of the cast, and the end of the cast on the 
log sheet. Upon the safe recovery of the rosette, the operator would begin 
the recovery procedure:

• After verifying the battery charger is off, the operator would plug both 
  serial cables into the appropriate connectors and open the battery purge 
  port.

• The battery charger is powered on as soon as possible to maximize the time 
  available for charging.

• The operator uses BBTalk to send a ‘break’ signal to both ADCPs, halting 
  data collection and closing the data file.

• The instrument baud rate is changed to 115,200 bps to minimize the download 
  time.

• The most recent good data file is transferred to a temporary cruise 
  directory on the acquisition computer.

• The operator copies the downloaded data files to a separate folder, labeled 
  by station number. The files are renamed here using the cruise convention: 
  ‘ACT0410_DN_nnn.000’ or ‘AC- T0410_UP_nnn.000’ where ‘nnn’ is the station 
  number.

• The baud rates are changed back to 9600 and the ADCPs are powered down.

The main transect line was 20 CTD stations, starting with ‘CTD-01’ at mooring 
‘P1’ and ending with station CTD-20, at mooring ‘P5’. CTD/LADCP casts were 
made at each of these stations during the mooring deployment period, April 
7th through the 15th. A second series of consecutive casts along the same 
transect line began at station CTD-22, between moorings P1 and A (CTD-21 was 
only 60 m deep, so the LADCP was not deployed), on April 17th at 08:15 UTC, 
ending at station CTD-40, near station P5 on April 20th at 07:05 UTC.

Of the total 40 LADCP casts performed, only one station was a loss for data. 
The instruments did not ping on CTD-14 due to an error in the 
‘wh300_master.cmd’ file. The command file had been temporarily altered to 
comment out the ‘cs’ or start pinging command. This was a result of 
troubleshooting steps taken in an attempt to resolve a perceived problem with 
the upward-looking (slave) ADCP not producing an audible ‘ping’ upon reaching 
station 12. Initially, it was thought to be a problem with the instrument 
itself, and s/n 4896 was swapped out for the spare, s/n 10417. When this unit 
also did not produce an audible ping, the battery was swapped out with its 
spare as well. This action, at first, appeared to solve the problem, and we 
proceeded with the cast at station 12.

At station 13, the audible ping again was absent. The chief scientist decided 
to proceed with the full cast in lieu of a short test cast to examine the 
echo intensity from the ADCPs. Upon recovery, we discovered that the data 
from both units appeared to be fine, and it was then apparent that there was 
never any problem with the upward-looking transmitted power. Only the audible 
ping produced by the ADCP’s DSP board was missing, or at least intermittent. 
The LADCP operator on duty for station 14 was not aware of the change to the 
command file, and ran the script as instructed. Since the master ADCP was 
never told to start pinging, no data were collected from either unit during 
this cast. The master script was corrected for subsequent casts. A table 
summary of station times and locations can be found in Appendix B.




Data Processing: 

The two raw ADCP data files were copied to a dedicated laptop for processing. 
Using RDI’s WinADCP, the files were examined to determine the approximate in-
situ and out-situ ensemble numbers. The raw data files were then trimmed, 
discarding any out-of-water ensembles, using RDI’s ‘BBSub’ utility. A trimmed 
version of the raw file was saved to a separate directory for processing. 
Navigation data were extracted from the uncorrected half-second time-series 
CTD data provided by the CTD operator, downloaded over the ship’s network. 
Once the files were in the proper directories, the “first-pass” processing 
could be executed.

The initial processing of the raw ADCP data was done using version 10.8 of 
the M. Visbeck (& A. Thurnherr) MATLAB toolbox, modified by G. Krahmann. The 
‘process_cast(nnn)’ script was run, with ‘nnn’ representing the station 
number, which called subroutines to copy, load, scan in, and run the shear 
and least-squares inverse methods. About a dozen graphics are generated with 
useful diagnostic information and the final water column profile. The 
processing scripts required significant modifications that were not 
anticipated, primarily to ensure the ADCP and GPS data were properly loaded. 
Two small m-files were added: ‘load_ctd_for_nav.m’ and ‘load_ctd_- 
for_prof.m’ to the local /m directory that were called by the 
‘prepctdprof.m’, ‘prefctdtime.m’ and ‘prepnav.m’ scripts to generate mat-
files for processing. Manual changes to the ‘cruise_params.m’ and 
‘prepare_cast.m’ code were also necessary to ensure that only the navigation 
data would be used in the first-pass processing. When the first-pass was 
finished, the operator would note in the log sheet the calculated depth based 
on the integrated vertical velocity and compare it to the max- imum depth 
reported by the CTD.

During processing the following warning messages were encountered:

• 16 casts returned the warning message: “Large up-down compass difference”, 
  with a value ranging from 15 to 20 degrees.

• Two casts, stations 2 and 24 returned the warning “Different Lag Results!!! 
  Check New Rou- tine”.

• 30 out of 40 casts returned the warning: “Increased error because of shear-
  inverse difference”.

Cast 6 had an unusually large calculated time lag between CTD and LADCP, -103 
seconds. Casts 23 and 24 were -6 and - 7 seconds respectively. All other 
casts were between 0 to 3 seconds. Cast 30 showed evidence of being dragged 
along the bottom for a brief period, however no damage was done to the 
downward-looking ADCP.

Towards the end of the cruise, all casts were re-processed to include CTD 
data and 15-minute averaged ADCP profile data from the hull-mounted 75 kHz 
Ocean Surveyor. The SADCP data were downloaded from UHDAS as two mat-files: 
‘contour_xy.mat’ and ‘contour_uv.mat’. Stations 1 and 22 had no SADCP data 
available, and stations 2, 4, 5 and 6 had no ‘good’ data available, likely 
due to rough sea conditions during the cast. The two figures show, 
respectively, final-processed cross- sections from stations 1 through 20, and 
stations 21 through 40.


Summary: 

Overall, the two 300kHz ADCPs performed well, with no major communication or 
power issues. The practice of listening for an audible ping to confirm the 
instruments are sampling may not necessarily be a reliable test, since it 
became clear that both upward-looking AD- CPs used during this cruise, have a 
sporadic problem with their audible output. Both units experienced 
significant drops in profile range at depths below 2000 meters, down to 
around 50 meters at the 3000 to 4000 meter range. Calculated depths based on 
the integrated w-velocity tended to over-estimate the maximum depth of the 
cast, possibly due to the large lateral movement of the CTD package and high 
pitch and roll values? Many stations appeared to have a small negative bias 
in the u-velocity error plot of the upward-looking ADCP during the downcast, 
possibly related to turbulence in the wake of the rosette.

 
CTD PROGRAM (Courtney Schatzmann and Robert Thombley)

A full report of the ODF CTDO2 program is available separately. Included here 
is a summary of the most pertinent information. A total of 40 stations were 
occupied and 40 Rosette/CTD/LADCP casts made. Water samples (up to 12) and 
CTD data (pressure, temperature, conductivity, dissolved oxygen) were 
collected on each cast, usually to within 5-70 meters of the bottom (distance 
off bottom increased after package grounded during station 31).


Instrumentation: 

The package consisted of a 12-bottle rosette frame (SIO/STS), a 12-place 
carousel (SBE32) and 12 10.0L Bullister bottles (SIO/STS). Underwater 
electronic components consisted of a Sea-Bird Electronics SBE9plus CTD 
(SIO/STS #796) with dual pumps (SBE5), dual temperature (SBE3plus), dual 
conductivity (SBE4C), dissolved oxygen (SBE43), and an altimeter (Benthos 
100m). The CTD was mounted horizontally in an SBE CTD cage attached to the 
bottom of the rosette frame and located to one side of the carousel. Pump 
exhausts were attached to the sensor bracket on the side opposite from the 
sensors. The altimeter was mounted on the in- side of the bottom frame ring. 
The downward-looking 300 KHz LADCP (RDI) was mounted vertically on one side 
of the frame between the bottles and the CTD. The LADCP battery pack was also 
mounted on the bottom of the frame. The upward-looking 300 kHz LADCP was 
mounted above the rosette on the top of the frame.

The rosette system was suspended from a UNOLS-standard three-conductor 0.322" 
electro-mechanical sea cable. The sea cable was terminated at the beginning 
of ACT. Re-terminations were performed prior to station 30 and 31, after a 
kink was found in the winch wire.


Operations: 

The deck watch prepared the rosette 10-30 minutes prior to each cast. The 
bottles were cocked and all valves, vents and lanyards were checked for 
proper orientation. Once stopped on station, the rosette was moved out from 
the forward hanger to the deployment location under the squirt boom using an 
air-powered cart and tracks. The CTD was powered-up and the data acquisition 
system started from the computer lab. The rosette was unstrapped from the 
air-powered cart. Tag lines were threaded through the rosette frame and 
syringes were removed from CTD intake ports. The winch operator was directed 
by the deck watch leader to raise the package. The A-frame and rosette were 
extended outboard and the package was quickly lowered into the water.

Tag lines were removed and the package was lowered to 10 meters, until the 
console operator determined that the sensor pumps had turned on and the 
sensors were stable. The winch operator was then directed to bring the 
package back to the surface, re-zero the wireout reading, and begin the 
descent.

For bottom approaches, the altimeter, wire out, Knudsen depth, and CTD depth 
were all used to help determine distance off bottom. For each up cast, the 
winch operator was directed to stop the winch at between 3 and 12 sampling 
depths, which were staggered every station. To insure package shed wake had 
dissipated, the CTD console operator waited 30 seconds prior to tripping 
sample bottles. An additional 10 seconds elapsed before moving to the next 
consecutive trip depth, to allow the SBE35RT time to take its readings.

Recovering the package at the end of the deployment was essentially the 
reverse of launching, with the additional use of poles and snap-hooks to 
attach tag lines. The rosette was secured on the cart and moved into the aft 
hanger for sampling. The bottles and rosette were examined before samples 
were taken, and anything unusual was noted on the sample log. Each bottle on 
the rosette had a unique serial number, independent of the bottle position on 
the rosette. Routine CTD maintenance included soaking the conductivity and 
oxygen sensors in fresh water between casts to maintain sensor stability.


Data Acquisition and Processing: 

The data acquisition system consisted of three PCs running linux. One was 
designated as console and connected to the CTD deck unit. The console 
provided an interface and graphic display for monitoring incoming data and 
closing bottles. CTD sensor pumps were configured with a 5-second delay after 
detecting sea water conductivities. The target lowering rate was 60 m/min, 
but this was not achieved for the first few stations because the package was 
flying too much in the strong currents. Weight was added to the bottom of the 
frame, which solved the problem. After the last bottle was closed, the 
console operator directed the deckwatch to bring the rosette on deck. Once 
the rosette was on deck, the console operator terminated the data 
acquisition, turned off the deck unit and assisted with rosette sampling.

Shipboard CTD data processing (and data back-up) was performed automatically 
during each cast, when the laboratory calibrations for pressure, temperature, 
and conductivity were applied. At the completion of a deployment a sequence 
of processing steps were performed automatically. The 0.5-second time series 
data were checked for consistency (primary and secondary sensors com- pared), 
clean sensor response, and calibration shifts. A 2-decibar pressure series 
was then generated from the down cast. Additional Salinity and O2 comparisons 
were made with respect to isopycnal surfaces between down and up casts as 
well as with adjacent deployments. Vertical sections were made of the various 
properties derived from sensor data and checked for consistency. Both the 2-
decibar pressure series and 0.5-second time series data were made available 
for downloading, plotting and reporting on the shipboard cruise website.

The ODF acquisition software was not functioning properly for the first cast. 
The frame length and modulo count had changed between the test cast and the 
first cast and this led to the appearance of a 20 db pressure off set. 
Acquisition was performed with SBE software for station 1-3, then reverted 
back to ODF acquisition prior to station 4.

Salinity for stations 1-3 were erratic. It was found the deck unit settings 
were not set to SBE specifications and was corrected prior to station 4. 
Timing off sets were applied in processing to 1-3 and corrected for salinity.


Calibration: 

For shipboard calibration procedures, including salinity and oxygen analysis, 
see the full CTD report. For salinity, the 95% confidence limits are ±0.00120 
PSU relative to bottle salinities for deep salinities, and ±0.00335 PSU 
relative to bottle salinities for all salinities where T1-T2 is within 
±0.01°C. The standard deviations of 2.05 μmol/kg for all oxygens and 0.49 
μmol/kg for deep oxygens are only presented as general indicators of goodness 
of fit. ODF makes no claims regarding the precision or accuracy of CTD 
dissolved O2 data.


PHYTOPLANKTON AND NUTRIENTS (Tinus Sonnekus)

Samples for phytoplankton and nutrients were collected at 30 of the 40 ACT 
CTD stations. Normally, the Deep Chlorophyll Maximum (DCM) or Fluorescence 
Maximum (F-Max) are identified on the downcast and Niskin bottles triggered 
in them on the upcast. In this instance, with no fluorescence measurements 
the maximum was assumed to be near the thermocline.

Sampling:

Water was collected from the surface, seasonal thermocline, and below (0, 5-
113 m, and 150 m). Samples were collected for size fractionated chl-a, 
phytoplankton identification, and nutrients.

Chlorophyll-A analysis:

Half a litre (500 ml) of water from each sample depth was filtered through a 
Sartorius filter tower cascade set-up with the following filter paper: Top - 
20 μ m Nylon Net Millipore filter to collect microphytoplankton; Middle - 2 μ 
m Macherey-Nagel filter to collect nanophytoplankton; Bottom - 0.7 μ m GF/F 
Whatman filter to collect picophytoplankton.

The filter papers were sealed in tin foil, labeled and placed in a -20°C 
freezer for later analysis.

Chl-a will be extracted and read on a Turner Designs 10AU Fluorometer in the 
phytoplankton laboratory of the South African Institute for Aquatic 
Biodiversity, South Africa.

Phytoplankton identification:

One litre of water was collected from each sample depth, pre- served with 
either 2% Lugols (20 ml) (Karayanni et al. 2004), 10 % buffered formalin, or 
gluterhaldehyde and stored for later analyses. The samples were always added 
to the fixative so that the preserved cells experienced the minimum target 
fixative concentration at all times.

 
Phytoplankton cast: 

At CTD stations 9,10,11, and 12 an 80 μm ring net was deployed vertically to 
100 m and winched up to the surface at 0.5 m/s. The contents of the cod-end 
were washed into a 250 ml honey jar containing 2% Lugols solution and stored 
for later analyses. Identification of all taxa to the lowest taxonomic level 
will be done at the Nelson Mandela Metropolitan University (NMMU) and SAIAB 
using Light and Scanning Electron Microscopy.


Nutrients: 

Acid washed 50 ml “urine jars” were rinsed twice with water directly from 
each sample depth and filled full (5 – 10 ml space were left to allow 
expansion during freezing). Bottles were labelled and placed in a -20°C 
freezer for later analysis. The nutrients will be analysed in Dr. Howard 
Waldron’s laboratory in the Department of Oceanography at the University of 
Cape Town.

To access the data please contact Dr. Tom Bornman at t.bornman@saiab.ac.za.











Appendix A - Configuration of Moored ADCPs and Aquadopps

WorkHorse Monitor, 150 kHz
CR1
WM1
CF11111
EA0
EB0
EC1500
ED3000
ES35
EX11111
EZ0111101
WA50
WB1
WD111100000
WF352
WN50
WP45
WS800
WV175
TE01:00:00.00
TP01:20.00
CK
CS
;
;Instrument = Workhorse Monitor
;Frequency = 153600
;Water Profile = YES
;Bottom Track = NO
;High Res. Modes = NO
;High Rate Pinging = NO
;Shallow Bottom Mode= NO
;Wave Gauge = NO
;Lowered ADCP = NO
;Ice Track = NO
;Surface Track = NO
;Beam angle = 20
;Temperature = 10.00
;Deployment hours = 14400.00
;Battery packs = 2
;Automatic TP = YES
;Saved Screen = 3
;
;Consequences generated by PlanADCP version 2.05:
;First cell range = 12.21 m
;Last cell range = 404.21 m
;Max range = 234.57 m
;Standard deviation = 1.06 cm/s
;Ensemble size = 1154 bytes
;Storage required = 16.90 MB (16617600 bytes)
;Power usage = 741.58 Wh
;Battery usage = 1.6
Aquadopp
------------------------------------------------------------
Measurement interval (s) : 1200
Average interval (s) : 120
Blanking distance (m) : 0.35
Diagnostics interval(min) : 720
Diagnostics samples : 20
Measurement load (%) : 4
Power level : HIGH
Compass upd. rate (s) : 2
Coordinate System : ENU
Speed of sound (m/s) : 1500
Salinity (ppt) : N/A
File wrapping : OFF
------------------------------------------------------------
Assumed duration (days) : 640.0
Battery utilization (%) : 450.0
Battery level (V) : 11.4
Recorder size (MB) : 5
Recorder free space (MB) : 5.000
Memory required (MB) : 2.9
Vertical vel. prec (cm/s) : 1.0
Horizon. vel. prec (cm/s) : 0.7
------------------------------------------------------------
Aquadopp Version 1.23
Copyright (C) 1997-2002 Nortek AS
============================================================









Appendix B - LADCP Station Summary and Command Files

                                             Int.  ctd 
                        In-    End            w    max 
       Date      Start  situ   cast   Stop  depth depth depth
Stn (yyyy/um/dd) time   time   time   time   (m)   (m)   (m)     Latitude    Longitude
——— ———————————— —————— —————— —————— —————— ———— ————— ————— —————————————— ——————————
  1  2010704107  20:31  20:42  20:56  21:04    59    60    59  -33  20.7508  27 28.854
  2  2010/04/07  22:05  22:21  22:27  22:45    74    74    93  -33  27.9732  27 32.3864
  3  2010/04/07  23:36  23:44  00:09  00:17   236   236   248  -33  33.6756  27 33.9405
  4  2010/04/09  11:33  11:52  12:45  12:55   660   662   672  -33  35.6379  27 37.8186
  5  2010/04/09  13:32  13:50  15:21  15:25  1203  1206  1217  -33  38.7961  27 39.2926
  6  2010/04/09  17:17  17:33  19:22  19:25  1708  1713  1720  -33  41.2994  27 41.7789
  7  2010/04/10  22:07  22:16  00:01  00:06  2135  2093  2110  -33  45.9951  27 40.9008
  0  2010/04/11  01:05  01:22  03:46  03:51  2874  2844  2914  -33  52.3487  27 47.6027
  9  2010/04/11  11:53  12:26  15:15  15:22  3583  3544  3559  -33  59.29    27 51.2047
 10  2010/04/11  17:46  10:09  20:49  20:59  3638  3615  3627  -34  6.8261   27 55.506
 11  2010/04/12  09:47  10:00  12:39  12:47  3725  3692  3700  -34  16.2511  27 59.4323
 12  2010/04/12  17:20  17:31  20:25  20:30  3870  3807  3822  -34  23.79    28 1.919
 13  2010/04/13  14:34  14:37  17:47  17:53  4049  3989  3999  -34  32.7666  28 4.7396
 14
 15  2010/04/14  16:56  17:07  20:12  20:16  4313  4259  4274  -34  50.2774  28 16.8616
 16  2010/04/15  23:30  23:43  02:40  02:47  4355  4320  4331  -34  57.741   28 23.6439
 17  2010/04/15  04:11  04:30  07:30  07:30  4375  4366  4380  -35  9.4014   28 31.4052
 10  2010/04/15  10:42  10:51  14:02  14:07  4394  4372  4387  -35  20.706   28 39.5077
 19  2010/04/15  15:27  15:41  10:45  10:52  4556  4510  4522  -35  31.4728  28 47.2116
 20  2010/04/15  22:20  22:25  01:32  01:31  4625  4600  4612  -35  43.2417  28 54.945
 21
 22  2010/04/17  00:04  00:15  00:32  00:30    90    87    95  -33  27.8219  27 32.6014
 23  2010/04/17  11:33  11:40  12:13  12:25   310   300   309  -33  33.4452  27 35.3443
 24  2010/04/17  12:40  12:50  13:56  14:00   625   602   615  -33  35.6743  27 37.3345
 25  2010/04/17  14:20  14:32  15:57  16:09  1271  1239  1252  -33  39.2773  27 39.4926
 26  2010/04/17  16:24  16:33  10:16  18:20  1832  1800  1813  -33  42.4899  27 41.7325
 27  2010/04/17  10:46  19:01  20:55  21:00  2253  2206  2215  -33  47.4201  27 44.0349
 20  2010/04/17  21:30  21:41  23:55  00:04  3180  3127  3178  -33  54.205   27 47.9048
 29  2010/04/18  00:50  00:53  03:36  03:44  3629  3585  3604  -34  3.0619   27 49.9382
 30  2010/04/18  04:17  04:25  07:40  07:53  3622  3622  3622  -34  11.6624  27 55.0878
 31  2010/04/18  10:52  10:59  14:00  14:04  3770  3712  3742  -34  21.6532  27 59.7579
 32  2010/04/18  14:42  15:00  18:02  18:07  3770  3823  3881  -34  26.0943  28 4.059
 33  2010/04/18  18:48  19:13  22:15  22:21  4042  4004  4054  -34  35.027   28 9.7359
 34  2010/04/18  23:04  23:07  02:00  02:07  4145  4095  4166  -34  40.9026  28 14.1271
 35  2010/04/19  03:06  03:30  06:30  06:34  4248  4222  4282  -34  51.3657  28 20.281
 36  2010/04/19  07:49  07:53  10:56  10:59  4305  4293  4333  -34  57.6936  28 24.3573
 37  2010/04/19  12:09  12:19  15:25  15:31  4370  4346  4386  -35  9.3159   28 31.9035
 30  2010/04/19  16:52  17:02  20:11  20:17  4360  4316  4366  -35  20.5161  28 38.7652
 39  2010/04/19  21:43  21:54  00:55  00:57  4470  4446  4498  -35  31.3463  28 46.5924
 40  2010/04/20  03:08  03:17  07:05  07:11  4512  4529  4612  -35  43.2062  28 53.4102


;=================================================
; W H M A S T E R _ P R O T O . C M D
; LMB: Tue Apr 1 15:38:43 EDT 2008
;
; WH300kHz master/downlooker deployment script
; for new firmware v16.30
;==================================================
; Changes from previous deployment scripts:
; (1) "wm15" command for LADCP mode and no longer need "L" commands
; (2) only commands that change defaults are included (EA,ES etc removed)
; (3) data collected in beam coordinates (allows better inspection of
; raw data and 3-beam solutions if necessary)
; (4) staggered single-ping ensembles every 0.8/1.2 s (Andreas has seen
; bottom-interference in WH300 data in Antarctic - seems unlikely for
; Abaco, but does not lose us pings).
; (5) 20 8 m bins - for a range of 200 m (try less for deep casts)
; Changes made after email discussions with Eric and Andreas, April 2008
;
; Ask for log file
$L
; display ADCP system parameters
PS0
; Pause
$D2
; return to factory default settings
CR1
; activates LADCP mode (BT from WT pings)
WM15
; Flow control:
; - automatic ensemble cycling (next ens when ready)
; - automatic ping cycling (ping when ready)
; - binary data output
; - disable serial output
; - enable data recorder
CF11101
$D2
; coordinate transformation:
; - radial beam coordinates (2 bits)
; - use pitch/roll (not used for beam coords?)
; - no 3-beam solutions
; - no bin mapping
EX00100
; Sensor source:
; - manual speed of sound (EC)
; - manual depth of transducer (ED = 0 [dm])
; - measured heading (EH)
; - measured pitch (EP)
; - measured roll (ER)
; - manual salinity (ES = 35 [psu])
; - measured temperature (ET)
EZ0011101
;
$D2
; - configure staggered ping-cycle
; ensembles per burst
TC2
; pings per ensemble
WP1
; time per burst
TB 00:00:01.20
; time per ensemble
TE 00:00:00.80
; time between pings
TP 00:00.00
$D2
; - configure no. of bins, length, blank
; number of bins
WN020
; bin length [cm]
WS0800
; blank after transmit [cm]
WF0000
$D2
; ambiguity velocity [cm]
WV250
; amplitude and correlation thresholds for bottom detection
LZ30,220
$D2
; master
SM1
; send pulse before each ensemble
SA011
; wait .5500 s after sending sync pulse
SW05500
; # of ensembles to wait before sending sync pulse
SI0
$D2
; keep params as user defaults (across power failures)
CK
; echo configuration
T?
W?
$D5
; start Pinging
CS
; End Logfile
$L
;==============================================
; W H S L A V E _ P R O T O . C M D
; LMB: Sat Apr 5 15:03:52 EDT 2008
;
; WH300kHz slave/uplooker deployment script
; for new firmware v16.30
;==============================================
; Changes from previous deployment scripts:
; (1) "wm15" command for LADCP mode and no longer need "L" commands
; (2) only commands that change defaults are included (EA,ES etc removed)
; (3) data collected in beam coordinates (allows better inspection of
; raw data and 3-beam solutions if necessary)
; (4) staggered single-ping ensembles every 0.8/1.2 s (Andreas has seen
; bottom-interference in WH300 data in Antarctic - seems unlikely for
; Abaco, but does not lose us pings).
; (5) 20 8 m bins - for a range of 160 m.
;
; These changes made after email discussions with Eric and Andreas, April 
2008.
;
; Ask for log file
$L
; display ADCP system parameters
PS0
; Pause
$D2
; return to factory default settings
CR1
; activates LADCP mode (BT from WT pings)
WM15
; Flow control:
; - automatic ensemble cycling (next ens when ready)
; - automatic ping cycling (ping when ready)
; - binary data output
; - disable serial output
; - enable data recorder
CF11101
$D2
; coordinate transformation:
; - radial beam coordinates (2 bits)
; - use pitch/roll (not used for beam coords?)
; - no 3-beam solutions
; - no bin mapping
EX00100
; Sensor source:
; - manual speed of sound (EC)
; - manual depth of transducer (ED = 0 [dm])
; - measured heading (EH)
; - measured pitch (EP)
; - measured roll (ER)
; - manual salinity (ES = 35 [psu])
; - measured temperature (ET)
EZ0011101
$D2
; - configure for slave
; pings per ensemble
WP1
; time per ensemble
TE 00:00:00
; time between pings
TP 00:00.00
; slave
SM2
; listen for sync pulse before each ensemble
SA011
$D2
; - configure no. of bins, length, blank
; number of bins
WN020
; bin length [cm]
WS0800
; blank after transmit [cm]
WF0000
$D2
; ambiguity velocity [cm]
WV250
; amplitude and correlation thresholds for bottom detection
LZ30,220
$D2
; keep params as user defaults (across power failures)
CK
; echo configuration
T?
W?
$D5
; start Pinging
CS
; End Logfile
$L











CCHDO DATA PROCESSING NOTES

• File Online CCHDO Staff
316N20100404.exc.csv (download) #66e2c
Date: 2015-10-09
Current Status: unprocessed


• Available under 'Files as received' CCHDO
Date: 2015-10-09
Data Type: submission
Action: Website Update
Note:
316N20100404.exc.csv available as received, submitted 2015-07-07 by Robert
Key
notes: I started with the original bottle file you had posted, created a
header with minimal metadata, reset a few CTDOXY flags and values (from 0.0
and 2 to -999 and 9), and reprinted


• File Submission Robert Key
316N20100404.exc.csv (download) #66e2c
Date: 2015-07-07
Current Status: unprocessed
Notes
I started with the original bottle file you had posted, created a header with
minimal metadata, reset a few CTDOXY flags and values (from 0.0 and 2 to -999
and 9), and reprinted
System Message: Submitter requests file be attached to cruise 653


• Text version online J Kappa
Date: 2014-12-05
Data Type: CrsRpt
Action: Website Update
Note:
I've placed a new Text version of the cruise report on the website.
It includes all the reports provided by the cruise PIs, summary pages and
CCHDO data processing notes.


• PDF version online J Kappa
Date: 2014-11-21
Data Type: CrsRpt
Action: Website Update
Note:
I've placed a new PDF version of the cruise report: 316N20100404_do.pdf
online.
It includes all the reports provided by the cruise PIs, summary pages and
CCHDO data processing notes, as well as a linked Table of Contents and links
to figures, tables and appendices.

• 2014-10-15 BTL Submitted data update, to go online
Courtney
Schatzman
Changes:
1) Updated BTLNBR from bottle serial numbers to positional numbers.
2) Removed depth field
3) Corrected missing salinity and oxygen samples.
4) Fixed uncalibrated flags "1" in file.

• 2014-10-14 BTL Submitted Bottle data file fixed
Courtney
Schatzman
2014-10-14 BTL Website Update Available under 'Files as received'
CCHDO Staff  The following files are now available online under 'Files as 
received', unprocessed by the
CCHDO. act_hy1.csv

• 2014-08-13 Map Website Update Maps online
Rox Lee 316N20100404 processing - Maps
2014-08-13
R Lee
Contents
• Process
  o Changes
• Directories
• Updated Files Manifest
Process
Changes
• Map created from 316N20100404_hy1.csv
Directories
working directory:
/data/co2clivar/indian/act/316N20100404/original/2014.08.13_Map_RJL
cruise directory:
/data/co2clivar/indian/act/316N20100404
Updated Files Manifest
file stamp
316N20100404_trk.gif
316N20100404_trk.jpg

• 2014-08-12 BTL Website Update Exchange and netCDF files online
Roxanne Lee ACT2010 2010 316N20100404 processing - BTL/CTD
2014-08-12
R Lee
Contents
• Submission
  o Parameters
• Process
  o Changes
  o Conversion
• Directories
• Updated Files Manifest
Submission
filename submitted by date data type id
act2010.tar.gz Frank Delahoyde 2014-04-21 CrsRpt/BTL/CTD 1160
Parameters
act_hy1.csv
• CTDPRS
• CTDTMP
• CTDSAL [1]
• SALNTY [1]
• CTDOXY [1]
• OXYGEN [1]
• SILCAT [1] [2]
• NITRAT [1] [2]
• NITRIT [1] [2]
• PHSPHT [1] [2]
• BTL_LAT [3]
• BTL_LON [3]
• REFTMP [1] [3]
316N20100404_ct1.zip
• CTDPRS [1]
• CTDTMP [1]
• CTDSAL [1]
• CTDOXY [1]
• CTDNOBS [3]
• CTDETIME [3]
[1] (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13) parameter has quality flag 
column
[2] (1, 2, 3, 4) parameter only has fill values/no reported measured data
[3] (1, 2, 3, 4, 5) not in WOCE bottle file
[4] merged
Process
Changes
act_hy1.csv
• Change CTDPRS unit from DBARS to DBAR
• Change REFTEMP to REFTMP
316N20100404_ct1.zip
• Rename CTD files
Conversion
file converted from software
316N20100404_nc_hyd.zip 316N20100404_hy1.csv hydro 0.8.2-11-g372a577
316N20100404_nc_ctd.zip 316N20100404_ct1.zip hydro 0.8.2-26-g20de094
All converted files opened in JOA with no apparent problems.
Directories
working directory:
/data/co2clivar/indian/act/316N20100404/original/2014.08.12_BTL_CBG
cruise directory:
/data/co2clivar/indian/act/316N20100404
Updated Files Manifest
file stamp
316N20100404_nc_hyd.zip 20140724SIOCCHRJL
316N20100404_hy1.csv 20140724SIOCCHRJL
316N20100404_ct1.zip 20110803ODF
316N20100404_nc_ctd.zip 20110803ODF


• 2014-04-22 CrsRpt/BTL/CTD Website Update Available under 'Files as 
received'
CCHDO Staff The following files are now available online under 'Files as 
received', unprocessed by the
CCHDO. act2010.tar.gz

• 2014-10-29 CrsRpt  Website Update PDF version online
Kappa, Jerry I've placed a new PDF version of the cruise report: 
316N20100404_do.pdf
into the directory: http://cchdo.ucsd.edu/data/b/c36647/
It includes all the reports provided by the cruise PIs, summary pages and 
CCHDO data processing notes, as well as a linked Table of Contents and links 
to figures, tables and appendices.

