U.S. Geological Survey Open-File Report 2005–1026

Hydratools Manual Version 1.0, Documentation for a MATLAB®-Based Post-processing Package for the Sontek Hydra

By Marinna Martini1, Chris Sherwood1, Rachel Horwitz1, Andree Ramsey1, Fran Lightsom1, Jessie Lacy2 and Jingping Xu2

1 USGS Woods Hole Science Center
2 USGS Pacific Science Center

U.S. Geological Survey Open-File Report 2005–1026

Click here to view OFR 2005-1026 in PDF format (901 KB).

Click here to download hydratools20apr06.zip, the Wave Data Processing Toolbox m-files (3,325-KB ZIP file). (A link to this toolbox also is available in the PDF file.)

Use of this program is described in: Wave Data Processing Toolbox Manual, by Charlene Sullivan, John Warner, Marinna Martini, Frances Lightsom, George Voulgaris, Paul Work, US Geological Survey Open-File 2005–1211. Check for later versions of this Open-File Report, because it is a living document. Program written in Matlab v7.1.0 SP3, and updated in Matlab (R2006a). The program ran on PC with Windows XP Professional OS.


Although this program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the United States Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.


Any use of trade, product, or fimrnames in this publication is for descriptive purposes only and does not imply endorsement by the U.S. Government.


The Sediment Transport Instrumentation Group (STG) at the U.S. Geological Survey (USGS) Woods Hole Science Center has a long-standing comitment to providing scientists with high quality oceanographic data. To meet this commitment, STG personnel are vigilant in checking data as well as hardware for signs of instrument malfunction. STG data sets are accompanied by processing histories to detail data processing procedures that may have modified the natural data signal while removing noise from the data.

The history also allows the data to be reprocessed in the ligth of new insight into instrument function and moored conditions. This toolbox was compiled to meet these data quality commitments for data generated by Sontek Hydra systems using both ADV and PCADP probes.

In the mid 1900's, the USGS Coastal and Marine Program began frequent deployments of Sontek Hydra systems in support of projects in estuaries, coastal, and continental shelf regions nationwide. Hydra data sets are large and complex in structure, and existing processing and editing tools consisted of fragments of MATLAB code written by USGS scientists to satisfy personal research needs.

This code did not meet STG quality control criteria. This toolbox permits engineers and scientists to monitor data quality by:

1. processing data with interactive critical review;

2. preserving data quality indicators;

3. preserving minimally processed and partially processed versions of data sets.

STG usually deploys ADV and PCADP probes configured as downward looking, mounted on bottom tripods, with the objective of measuring high-resolution near-bed currents. The velocity profiles are recorded with minimal internal data processing. Also recorded are parameters such as temperature, conductivity, optical backscatter, light transmission, and high frequency pressure. Sampling consists of high-frequency bursts(1–10 Hz) bursts of long duration (5–30 minutes) at regular and recurring intervals for a duration of 1 to 6 months. The result is very large data files, often 500 MB per Hydra, per deployment, in Sontek's compressed binary format.

This section introduces the Hydratools toolbox and provides information about the history of the system's development. The USGS philosophy regarding data quality is discussed to provide an understating of the motivation for creating the system. General information about the following topics will also be discussed: hardware and software required for the system, basic processing steps, limitations of program usage, and features that are unique to the programs

Table of Contents


Required Software



Quick Start

General Procedure for Processing a set of ADV and PCADP data

Organizing the data files

Gather the Metadata

Convert from Sontek raw binary to raw netCDF

Assess the data and quality information and use automated tools to remove noise

Interactive flagging, masking and bad data removal

Apply rotations and write the processed data in scientific units

Burst data vs Statistics data

Quality Files

Missing Sensors

Cleaning Up the Data

PCADP Ambiguity Correction

Orientation Issues

Depth, height and all that

Processing Transmissometers and Optical Backscatter Sensors





Help The Metadata Structure

The Settings, Inputs and Outputs for the Major Toolbox Functions







How to use Flagbadadv

Figure 1: Screen shot of flagbadadv.m GUI window

Figure 2: Detail of examples A, B & C for flagbadadv.m

How to use Browsehydraburst

Figure 3: Screen capture of browsehydraburst GUI

Quality File (*q.cdf) Variables

ADV Raw Burst File (*b.cdf) Variables

ADV Raw Statistics File (*s.cdf) Variables

PCADP Raw Burst File (*b.cdf) Variables

PCADP Raw Statistics File (*s.cdf) Variables

ADV & PCADP Best Basic Version Statistics File (*vp-cal.nc) Variables

ADV & PCADP Best Basic Version Burst File (*b-cal.nc) Variables

Attributes common to all Hydra files

Attributes specific to ADV data

Attributes specific to PCADP data

If you have Adobe® Acrobat® or Adobe® Acrobat®Reader® installed on your computer, you may view and print the PDF version of this report. Acrobat Reader, is a free download from Adobe Systems, Inc. Users with disabilities can view information concerning accessibility at access.Adobe.com .

Scientific contact: Marinna Martini

Coastal and Marine Geology Program > Woods Hole Science Center

U.S. Department of the Interior, U.S. Geological Survey
Persistent URL: http://pubs.usgs.gov/of/2005/1026/
Page Contact Information: USGS Publishing Network
Last modified: Wednesday, April 25 2007, 01:56:24 PM
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