Data processing was conducted using the WHOI-USGS
Oceanographic Data Processing system that runs in Matlab (www.mathworks.com/),
and keeps data in EPIC standard NetCDF files (www.pmel.noaa.gov/epic/).
The ABS data were processed using Matlab.
After data were decoded and calibrated, they were carefully checked
for instrument malfunctions and then edited. The beginning and end
of each data series were truncated and wild points deleted. Short
data gaps (less than about 8 data values, which is half an hour
for Seacats and tripods) were filled by linear interpolation. The
data were carefully checked at each stage of processing. After editing,
the basic version of the data file includes all variables recorded
at the basic sampling interval. An hour-averaged data file and a
low-pass filtered data file were created from the basic version.
The low-pass filter essentially removes all fluctuations having
periods shorter than 33 hours (Flagg et al., 1976). Low-pass filtered
data was subsampled every 6 hours.
SEACAT and MicroCAT
SEACAT and MicroCAT data is stored internally. After recovery,
SEASOFT programs (Sea-Bird
Electronics, Inc. www.seabird.com) were used to read the data into a file on
a personal computer, convert to calibrated oceanographic units,
calculate salinity and density, and write the data to ASCII
flat files. ASCII files were translated to NetCDF,
and the data was edited, truncated, averaged, and filtered using
the WHOI-USGS system.
The ADCP observations were processed using USGS
software (available at woodshole.er.usgs.gov/operations/stg/pubs/ADCPtools/)
and elements of the WHOI-USGS Oceanographic Data Processing
system. The ADCP's were configured to record data in
beam coordinates (rather than earth coordinates). Upon recovery,
the ADCP data was transferred to a personal computer
using a PCMCIA Flash Memory card. These data were converted
to NetCDF format using software available for the ADCP
Toolbox (above). Matlab routines were used to check for data quality,
flag bad values, convert to earth coordinates using a 4-beam or
3-beam solution, truncate the data at the beginning and end of the
deployment, and discard bins that were always beyond the water surface.
Some near-surface bins were not discarded although, at times of
low tide, the side-beam reflection renders this data invalid, so
near-surface ADCP data must be interpreted with care.
On occasion, the ADCP skips an ensemble record because
the data is poor. Data have blank placeholders for the missing ensemble
The fully processed data files meet the EPIC NetCDF
standard developed by the NOAA Pacific Marine Environmental
These EPIC standards provide a universal vernacular allowing researchers
from different organizations to share oceanographic data without
needing translation. The final data file is our Best Basic Version
(BBV) indicating that it is clean of erroneous values,
converted into earth coordinates, and compliant with the outlined
standards. Data from the bins closest to the sea surface are included
in the BBV, although many are erroneous. The depth
of the first good bin changes with changes in the water elevation
primarily due to tides. Until more sophisticated methods of cleaning
the near- surface data are instituted, judgment will be needed in
interpreting the layers.
MIDAS data was recorded on a Tattletale hard disk,
and then copied to a personal computer's hard disk after recovery.
The WHOI-USGS system was used to decode and calibrate
the data, compute secondary variables, and perform all further processing.
Processing of BASS current meter data assumes a constant
sound speed of 1500 m/s.
In order to sample wave frequencies as well as the tidal and low-frequency
fluctuations the AQUATEC acoustic backscatter sensor (ABS)
sampled a 10 minute burst at 1 Hz every half hour.
The older ABS sampled a 12 minute burst once per hour
at 1 Hz. These bursts were averaged to produce a time
series of profiles with 0.5 hour sampling included in this report.
The acoustic intensity from AQUATEC ABS was calibrated
to sediment concentration in tank test along with the OBS
sensors using a combination of sediment from a sediment trap on
the tripod and bottom samples taken near tripod A. Other processing
on the ABS data included removing the system range
dependence by an empirical derived function that was developed from
scattering by a uniform suspension of fine particles. Attenuation
due to suspended sediment particles was not accounted for in this
processing as the sediment concentration were not high enough to
reduce the amplitude of the bed echo.
Transmissometer data was processed along with the other data from
Seacat and tripod systems. Beam attenuation coefficients (units
of l/m) were computed from the light transmission observations
as -4(ln(T/100)), where T is percent light transmission
over a beam length of 0.25 m. The beam attenuation coefficient is
linearly proportional to the concentration of suspended material
in the water if the particles are of uniform size and composition
(Moody and others, 1987). However, the size of the particles in
the water changes with time, especially during resuspension events,
and thus the beam attenuation measurements must be interpreted with
Wind stress was calculated from wind speed and direction using
the formulas of Large and Pond (1981). Currents and wind stress
were low-pass filtered using the PL33 filter (Flagg
et al., 1976), which removes fluctuations having periods shorter
than 33 hours. Low-passed data were subsampled every 6 hours.
The Conductivity/Temperature/Depth (CTD) casts were
processed with Seasoft software available from Sea-Bird
Electronics, Inc (www.seabird.com). Data were processed using Seasoft programs
in the following order:
1) Datcnv: This program converts raw data from the
CTD into temperature, conductivity, pressure, and other
2) AlignCTD: Advances oxygen data 1 to 5 seconds relative
to pressure. No oxygen data was collected on the Oceanus cruise.
3) Wildedit: Deletes any "wild" data points.
4) Celltm: Corrects the conductivity for thermal mass
5) Filter: Low pass filters pressure with a time constant of 0.15
seconds to increase the pressure resolution.
6) Loopedit: Marks and removes those scans where the CTD
was moving too slowly or traveling backwards due to ship roll.
7) Binavg: Averages the data into pressure bins.
8) Derive: Computes sigma t, depth, and other derived oceanographic
9) Asciiout: Outputs a data file to ascii
Percentage light transmission over 0.25 m is computed by the Seasoft
Trans(%) = mV + b,
where V is the transmissometer voltage and m and b are calibration
constants. Beam attenuation is computed as:
Beam attenuation = - 4ln(Trans(%))
No calibration constants were available for the profiling
transmissometer used on the RV Oceanus cruise;
m=20 and b=0 were used (assumes transmissometer reads 5 volts in
clear water). For the RV Endeavour cruise, m
= 20.292 and b = - 101 were used.
Suspended sediment samples
At sea, water samples were filtered through pre-weighed 0.4
micron Millipore filters. In the laboratory, the filters were air
dried and weighed. Weights were corrected using a paired filter.