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Oceanographic Observations, Hudson Shelf Valley, U.S. Geological Survey Open-File Report 02-217

Data Processing

Data processing was conducted using the WHOI-USGS Oceanographic Data Processing system that runs in Matlab (, and keeps data in EPIC standard NetCDF files ( 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 data is stored internally. After recovery, SEASOFT programs (Sea-Bird Electronics, Inc. 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 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 records.

The fully processed data files meet the EPIC NetCDF standard developed by the NOAA Pacific Marine Environmental Laboratory ( 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.

BASS tripods

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 care.

Wind stress

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.

CTD Data

The Conductivity/Temperature/Depth (CTD) casts were processed with Seasoft software available from Sea-Bird Electronics, Inc ( 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 variables.

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 expansion.

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 parameters.

9) Asciiout: Outputs a data file to ascii format.

Percentage light transmission over 0.25 m is computed by the Seasoft software as:

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.

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Title Page / Contents / Tables / Figures / Abbreviations / Introduction / Field Program / Observations / Instrumentation / Data Processing / Fouling / Mooring/Data File ID / Results / Digital Data / Acknowledgements / References / Matlab / Supplementary / Metadata
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