GPS Navigation Supplemented with Existing Bathymetry Data During Fathometer Lapses from USGS Cruise 07005 from May 15 to May 16, 2007, in the Corsica River Estuary, Maryland

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Frequently-anticipated questions:


What does this data set describe?

Title:
GPS Navigation Supplemented with Existing Bathymetry Data During Fathometer Lapses from USGS Cruise 07005 from May 15 to May 16, 2007, in the Corsica River Estuary, Maryland
Abstract:
Submarine groundwater discharge (SGD) into Maryland's Corsica River Estuary was investigated as part of a larger study to determine the importance of nutrient delivery to Chesapeake Bay via this pathway. Resource managers are concerned about nutrients that are entering the estuary via submarine groundwater discharge from this primarily agricultural watershed that may be contributing to eutrophication, harmful algal blooms, and fish kills. An interdisciplinary U.S. Geological Survey (USGS) science team conducted field operations in the estuary in April and May 2007. Techniques used included continuous resistivity profiling (CRP), piezometer sampling, seepage meter measurements, and collection of a radon tracer time series. Better understanding of the style, locations, and rates of groundwater discharge could lead to improved models and mitigation strategies for estuarine nutrient over-enrichment in the Corsica River Estuary, and other similar settings. More information on the field work can be accessed from the Woods Hole Coastal and Marine Science Center Field Activity webpage: <http://quashnet.er.usgs.gov/data/2007/07005/>
  1. How should this data set be cited?

    Cross, VeeAnn A. , 2011, GPS Navigation Supplemented with Existing Bathymetry Data During Fathometer Lapses from USGS Cruise 07005 from May 15 to May 16, 2007, in the Corsica River Estuary, Maryland: Open-File Report 2010-1094, U.S. Geological Survey, Coastal and Marine Geology Program, Woods Hole Coastal and Marine Science Center, Woods Hole, MA.

    Online Links:

    This is part of the following larger work.

    Cross, VeeAnn A. , Bratton, John F. , Worley, Charles R. , Crusius, John, and Kroeger, Kevin D. , 2011, Continuous resistivity profiling data from the Corsica River Estuary, Maryland: Open-File Report 2010-1094, U.S. Geological Survey, Coastal and Marine Geology Program, Woods Hole Coastal and Marine Science Center, Woods Hole, MA.

    Online Links:

  2. What geographic area does the data set cover?

    West_Bounding_Coordinate: -76.149864
    East_Bounding_Coordinate: -76.119082
    North_Bounding_Coordinate: 39.086800
    South_Bounding_Coordinate: 39.078067

  3. What does it look like?

  4. Does the data set describe conditions during a particular time period?

    Beginning_Date: 15-May-2007
    Ending_Date: 16-May-2007
    Currentness_Reference:
    Range of times refers to the CRP data collection, not the original times of the bathymetry datasets used.

  5. What is the general form of this data set?

  6. How does the data set represent geographic features?

    1. How are geographic features stored in the data set?

    2. What coordinate system is used to represent geographic features?

  7. How does the data set describe geographic features?


Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)

  2. Who also contributed to the data set?

  3. To whom should users address questions about the data?

    VeeAnn A. Cross
    U.S. Geological Survey
    Marine Geologist
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA 02543-1598

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)
    vatnipp@usgs.gov


Why was the data set created?

The purpose of these GPS files is to provide navigation with bathymetry to aid in the continuous resistivity profile (CRP) data processing. During original data acquisition, there were periods of time when no fathometer data was available. These files incorporate best available bathymetry data at the location of the navigation fix.


How was the data set created?

  1. From what previous works were the data drawn?

    (source 1 of 1)
    Source_Contribution:
    The continuous resistivity profile (CRP) system used on this cruise was an AGI SuperSting marine system described at the website: www.agiusa.com/marinesystem.shtml. The particular system used for this acquisition was a 50-m streamer with an 11 electrode array with electrodes spaced 5 meters apart. The source electrodes are graphite, while the receiver electrodes are stainless steel. A dipole-dipole configuration was used for the data collection in which two fixed current electrodes are assigned with the measurement of voltage potential between electrode pairs in the remaining electrodes. The maximum depth below the water surface the streamer can reach is approximately the streamer length. So for the 50-m streamer, maximum depth is about 12.5 meters. Each line of data acquisition records several files. The two files necessary for processing are the *.stg and the *.gps file. The STG file contains the resistivity data, while the GPS file contains the navigation information. The navigation system used in concert with the CRP system is a Lowrance LMS-480M with an LGC-2000 GPS antenna and a 200 kHz fathometer transducer. The transducer also contains a temperature sensor. Lowrance indicates the speed of sound used by the system is 4800 feet/second. Both the temperature and depth information are recorded in the logged GPS file. There are instances where no depth or temperature information is recorded due to an equipment problem. The CRP system images the subsurface electrical properties of an estuarine, riverine or lacustrine environment. Resistivity differences can be attributed to subsurface geology (conductive vs less conductive layers) and hydrogeologic conditions with fresh water exhibiting high resistivity and saline conditions showing low resistivity.

  2. How were the data generated, processed, and modified?

    Date: Jan-2010 (process 1 of 18)
    Using ArcCatalog 9.2 copied the point shapefile day1gpsclean.shp to day1gpsclean_moredepth.shp. The shapefile day1gpsclean.shp is equivalent to resgpspnts_jd135.shp prior to the addition of more attributes. This process step, as well as all subsequent process steps were performed by VeeAnn A. Cross. To see the processes that were used to generate the day1gpsclean.shp file, see the metadata for resgpspnts_jd135.shp. The metadata is available at: <https://pubs.usgs.gov/of/2010/1094/html/catalog.html> under the navigation section.

    Person who carried out this activity:

    VeeAnn A. Cross
    U.S. Geological Survey
    Marine Geologist
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA 02543-1598

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)
    vatnipp@usgs.gov

    Data sources used in this process:
    • day1gpsclean.shp

    Data sources produced in this process:

    • day1gpsclean_moredepth.shp

    Date: Jan-2010 (process 2 of 18)
    Within ArcMap 9.2, used a USGS Wood Hole toolbar called VACExtras v2.1 to extract the depths from a grid at point locations in a point shapefile. The tool used was VACExtras - Raster - Extract Depth. The input grid was combelev with the results going to day1gpsclean_moredepth.shp and placed in a new attribute "grdinfo".

    Data sources used in this process:

    • day1gpsclean_moredepth.shp
    • combelev

    Data sources produced in this process:

    • day1gpsclean_moredepth.shp

    Date: Jan-2010 (process 3 of 18)
    The bathymetry grid is a combined elevation dataset in which the bathymetric values take into account tides. The fathometer associated with the CPR system does not make tidal corrections. For processing the CRP data, it's the "uncorrected" depths that are needed. The most accurate way to do this would be to take out the tide component from the bathymetry grid. However, tide stations in the immediate area of the survey location and time were not available. So a less accurate, but simpler approach was tried. In the shapefile day1gpsclean_moredepth.shp, a new attribute was added called "diff" as a floating point attribute. In the original shapefile, the attribute containing fathometer data is "depth_m". Because "depth_m" is positive and the information in grdinfo is negative (from the bathymetry grid), I use field calculator with the following equation: diff = DEPTH_M + grdinfo My idea is that over the time frame of a single line of data collection, the difference between the measured depth (DEPTH_M) and the tide corrected depth (from the grid in grdinfo) should be a fairly straightforward offset. The lines that are missing depth values usually have at least one point with a depth value. That value can be used as the baseline and verify that information with the previous (or next) line acquired closest in time.

    Data sources used in this process:

    • day1gpsclean_moredepth.shp

    Data sources produced in this process:

    • day1gpsclean_moredepth.shp

    Date: Jan-2010 (process 4 of 18)
    Within ArcMap 9.2, used a USGS Wood Hole toolbar called VACExtras v2.1 to extract the depths from a grid at point locations in a point shapefile. The tool used was VACExtras - Raster - Extract Depth. The input grid was big3_nad83 with the results going to day1gpsclean_moredepth.shp and placed in a new attribute "estdepth". The grid used in this case is from the NOAAEstuarine Bathymetry dataset from Chesapeake Bay. This gridded dataset is part of the combined elevation dataset. In the combined dataset, interpolation and smoothing modified the values somewhat. By extracting data from both grids, I'll be able to choose the most viable source.

    Data sources used in this process:

    • big3_nad83
    • day1gpsclean_moredepth.shp

    Data sources produced in this process:

    • day1gpsclean_moredepth.shp

    Date: Jan-2010 (process 5 of 18)
    In ArcMap 9.2 added an attribute to day1gpsclean_moredepth.shp called "diff2" as a floating point attribute. Because "depth_m" is positive and the information in estdepth is negative (from the estuarine bathymetry grid), I use field calculator with the following equation: diff2 = DEPTH_M + estdepth I added another attribute to the shapefile called "pos_est" and defined the value as a float. Used field calculator on this field to perform the following calculation: pos_est = estdepth * -1. This has the effect of converting the depth value extracted from the estuarine bathymetry to a positive number.

    Data sources used in this process:

    • day1gpsclean_moredepth.shp

    Data sources produced in this process:

    • day1gpsclean_moredepth.shp

    Date: Jan-2010 (process 6 of 18)
    In ArcMap 9.2 added a float attribute to day1gpsclean_moredepth.shp called "pred_val". This attribute wil be used to hold the "predicted" depth values at each point. These predicted values will be based on applying an offset to the actual extracted depth values to hopefully fill in where fathometer data is absent from the original files.

    Data sources used in this process:

    • day1gpsclean_moredepth.shp

    Data sources produced in this process:

    • day1gpsclean_moredepth.shp

    Date: Jan-2010 (process 7 of 18)
    In looking at day one of data collection, I tookk the pos_est attribute and added 0.5 to calculate the predicted value. This was done in ArcMap 9.2 with the pred_val attribute selected in day1gpsclean_moredepth.shp and the following calculation used by the field calculator: pred_val = pos_est + 0.5. The value of 0.5 was derived by looking aththe last couple of depth values in L11F1 and seeing the offset between the measured fathometer values and the extracted estuaryine bathymetry values.

    Data sources used in this process:

    • day1gpsclean_moredepth.shp

    Data sources produced in this process:

    • day1gpsclean_moredepth.shp

    Date: Jan-2010 (process 8 of 18)
    These values seem reasonable for L12F1. Within ArcMap 9.2, in the attribute table of day1gpsclean_moredepth.shp I selected all the records for L12F1. Then used XTools Pro (v 5.2) - Table Operations - Export Table to Text. I used day1gpsclean_moredepth.shp as the input feature layer, chose the option to use selected features, and only selected the pred_val attribute for export, and exported to the output file L12F1_bathy.txt. For the encoding method, I used ANSI (Windows charset). This selection is important because I'm going to use AWK scripts for reformatting, and AWK prefers the ANSI text format.

    Data sources used in this process:

    • day1gpsclean_moredepth.shp

    Data sources produced in this process:

    • L12F1_bathy.txt

    Date: Jan-2010 (process 9 of 18)
    I then ran an AWK script under CYGWIN to reformat these exported depth values into the SDDPT format consistent with the fathometer format used in the original GPS files. This is the format that the processing software will expect. The awk script used was awkfmtdepth:
    {
    printf("$SDDPT,%0.1f,0.0*56\n",$1)
    }
    
    The program is run with the following command line:
    awk -f awkfmtdepth L12F1_bathy.txt > L12F1.sddpt
    

    Data sources used in this process:

    • L12F1_bathy.txt

    Data sources produced in this process:

    • L12F1.sddpt

    Date: Jan-2010 (process 10 of 18)
    Two additional AWK scripts (under CYGWIN) were run on the original GPS files to extract the individual portions of the navigation records: the GPRMC string which contains the navigation and the SDMTW string which contains the temperature information. The awk script used to extract the GPRMC data was awk_justgprmc2:
    BEGIN {
    FS = ","
    }
    {
    FS = ","
    if ($1=="$GPRMC")
    	{
    	print $0
    	}
    }
    
    This script was run with the command line:
    awk -f awk_justgprmc2 L12F1.gps > L12F1.gprmc
    
    The awk script used to extract the SDMTW data was awk_justsdmtw:
    BEGIN {
    FS = ","
    }
    {
    FS = ","
    if ($1=="$SDMTW")
    	{
    	print $0
    	}
    }
    
    This script was run with the command line:
    awk -f awk_justsdmtw L12F1.gps > L12F1.sdmtw
    

    Data sources used in this process:

    • L12F1.gps

    Data sources produced in this process:

    • L12F1.gprmc
    • L12F1.sdmtw

    Date: Jan-2010 (process 11 of 18)
    Under CYGWIN I can use the "paste" command to put the 3 individual files (*gprmc, *sddpt, and *sdmtw) together into a single file. This method works because each file contains the same number of rows. Essentially, it's a triplet of information on separate lines. The command line is in the format: paste -d '\n' file1 file2 file3 > output where file1 = L12F1.gprmc file2 = L12F1.sddpt file3 = L12F1.sdmtw output = L12F1_fixbathy.gps

    Data sources used in this process:

    • L12F1.gprmc
    • L12F1.sddpt
    • L12F1.sdmtw

    Data sources produced in this process:

    • L12F1_fixbathy.gps

    Date: Jan-2010 (process 12 of 18)
    Many files from the second day of data collection (May 16, 2007) were also missing bathymetry information. These files were handled in a similar manner to L12F1 from the first day of data collection. Using ArcCatalog 9.2 copied the point shapefile day2gps.shp to day2gps_moredepth.shp. The shapefile day2gps.shp is equivalent to resgpspnts_jd136.shp.

    Data sources used in this process:

    • day2gps.shp

    Data sources produced in this process:

    • day2gps_moredepth.shp

    Date: Jan-2010 (process 13 of 18)
    Based on the results from the work with L12F1, I made the decision to only work with the estuarine bathymetry data to fill the gaps in the GPS files. Within ArcMap 9.2, used a USGS Wood Hole toolbar called VACExtras v2.1 to extract the depths from a grid at point locations in a point shapefile. The tool used was VACExtras - Raster - Extract Depth. The input grid was big3_nad83 with the results going to day2gps_moredepth.shp and placed in a new attribute "estdepth". The grid used in this case is from the NOAAEstuarine Bathymetry dataset from Chesapeake Bay.

    Data sources used in this process:

    • day2gps_moredepth.shp
    • big3_nad83

    Data sources produced in this process:

    • day2gps_moredepth.shp

    Date: Jan-2010 (process 14 of 18)
    As with the first day of processing, I added several values to the attribute table within ArcMap 9.2. The following attributes were added as floating point attributes: diff2, pos_est, and pred_val. The field calculator was used on each field with the following equations:
    diff2 = depth_m + estdepth
    pos_est = estdepth * -1
    
    The equation for the pred_val attribute varied depending on the line of data.
    for L24 the equation was pred_val = estdepth + 0.2
    L25, pred_val = estdepth + 0.3
    L26, pred_val = estdepth + 0.4
    L27, pred_val = estdepth + 0.5
    L28, pred_val - estdepth + 0.6
    
    Based on the other information in the file, the assumption was that the tide was rising.

    Data sources used in this process:

    • day2gps_moredepth.shp

    Data sources produced in this process:

    • day2gps_moredepth.shp

    Date: Jan-2010 (process 15 of 18)
    Within ArcMap 9.2, in the attribute table of day2gps_moredepth.shp I selected all the records for L24F1. Then used XTools Pro (v 5.2) - Table Operations - Export Table to Text. I used day2gps_moredepth.shp as the input feature layer, chose the option to use selected features, and only selected the pred_val attribute for export, and exported to the output file L24F1_bathy.txt. For the encoding method, I used ANSI (Windows charset). This selection is important because I'm going to use AWK scripts for reformatting, and AWK prefers the ANSI text format. This procedure was repeated for each of the following lines:
    L24F2 output to L24F2_bathy.txt
    L25F1 output to L25F1_bathy.txt
    L26F1 output to L26F1_bathy.txt
    L27F1_part1 output to L27F1_part1_bathy.txt
    L27F1_part2 output to L27F1_part2_bathy.txt
    L28F1 output to L28F1_bathy.txt
    

    Data sources used in this process:

    • day2gps_moredepth.shp

    Data sources produced in this process:

    • L24F1_bathy.txt
    • L24F2_bathy.txt
    • L25F1_bathy.txt
    • L26F1_bathy.txt
    • L27F1_part1_bathy.txt
    • L27F1_part2_bathy.txt
    • L28F1_bathy.txt

    Date: Jan-2010 (process 16 of 18)
    I then ran an AWK script under CYGWIN to reformat these exported depth values into the SDDPT format consistent with the fathometer format used in the original GPS files. This is the format that the processing software will expect. The awk script used was awkfmtdepth:
    {
    printf("$SDDPT,%0.1f,0.0*56\n",$1)
    }
    
    The program is run with the following command line: awk -f awkfmtdepth inputfile > outputfile
    Where the input files and corresponding output files are: L24F1_bathy.txt - L24F1.sddpt L25F1_bathy.txt - L25F1.sddpt L26F1_bathy.txt - L26F1.sddpt L27F1_part1_bathy.txt - L27F1_part1.sddpt L27F1_part2_bathy.txt - L27F1_part2.sddpt L28F1_bathy.txt - L28F1.sddpt

    Data sources used in this process:

    • L24F1_bathy.txt
    • L25F1_bathy.txt
    • L26F1_bathy.txt
    • L27F1_part1_bathy.txt
    • L27F1_part2_bathy.txt
    • L28F1_bathy.txt

    Data sources produced in this process:

    • L24F1.sddpt
    • L25F1.sddpt
    • L26F1.sddpt
    • L27F1_part1.sddpt
    • L27F1_part2.sddpt
    • L28F1.sddpt

    Date: Jan-2010 (process 17 of 18)
    One additional AWK script (under CYGWIN) was run on the original GPS files to extract the GPRMC string data which contains the navigation. Unlike the first day of data collection, these original GPS files don't contain temperature data so that extraction wasn't possible. The awk script used to extract the GPRMC data was awk_justgprmc2:
    BEGIN {
    FS = ","
    }
    {
    FS = ","
    if ($1=="$GPRMC")
    	{
    	print $0
    	}
    }
    
    This script was run with the command line: awk -f awk_justgprmc2 inputfile > outputfile
    Where the input files and corresponding output files are: L24F1.gps - L24F1.gprmc L25F1.gps - L25F1.gprmc L26F1.gps - L26F1.gprmc L27F1_part1.gps - L27F1_part1.gprmc L27F1_part2.gps - L27F1_part2.gprmc L28F1.gps - L28F1.gprmc

    Data sources used in this process:

    • L24F1.gps
    • L25F1.gps
    • L26F1.gps
    • L27F1_part1.gps
    • L27F1_part2.gps
    • L28F1.gps

    Data sources produced in this process:

    • L24F1.gprmc
    • L25F1.gprmc
    • L26F1.gprmc
    • L27F1_part1.gprmc
    • L27F1_part2.gprmc
    • L28F1.gprmc

    Date: Jan-2010 (process 18 of 18)
    Under CYGWIN I can use the "paste" command to put the 2 individual files (*gprmc and *sddpt) together into a single file. The command line is in the format: paste -d '\n' file1 file2 file3 > output. The input and output files are as follows: input L24F1.gprmc L24F1.sddpt output L24F1_fixbathy.gps input L25F1.gprmc L25F1.sddpt output L25F1_fixbathy.gps input L26F1.gprmc L26F1.sddpt output L26F1_fixbathy.gps input L27F1_part1.gprmc L27F1_part1.sddpt output L27F1_part1_fixbathy.gps input L27F1_part2.gprmc L27F1_part2.sddpt output L27F1_part1_fixbathy.gps input L28F1.gprmc L28F1.sddpt output L28F1_fixbathy.gps

    Data sources used in this process:

    • L24F1.gprmc
    • L24F1.sddpt
    • L25F1.gprmc
    • L25F1.sddpt
    • L26F1.gprmc
    • L26F1.sddpt
    • L27F1_part1.gprmc
    • L27F1_part1.sddpt
    • L27F1_part2.gprmc
    • L27F1_part2.sddpt
    • L28F1.gprmc
    • L28F1.sddpt

    Data sources produced in this process:

    • L24F1_fixbathy.gps
    • L25F1_fixbathy.gps
    • L26F1_fixbathy.gps
    • L27F1_part1_fixbathy.gps
    • L27F1_part1_fixbathy.gps
    • L28F1_fixbathy.gps

  3. What similar or related data should the user be aware of?


How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?

  2. How accurate are the geographic locations?

    The navigation system used was a Lowrance 480M with an LGC-2000 Global Positioning System (GPS) antenna. The antenna was located at the anchor point for the resistivity streamer, which is also directly above the fathometer transducer mount point. The GPS system is published to be accurate to within 10 meters.

  3. How accurate are the heights or depths?

    The vertical accuracy of these files is a function of several factors. First of all is the accuracy of the original bathymetry dataset from which the depth values were extracted. And second is the offset applied to this bathymetry value to essentially add in the tidal component. Specific tide values were not acquired, but rather the grid bathymetry values were compared to actual valid fathometer reading to estimate and offset. These factors combine to detract from the vertical accuracy, making it probably more than 1 meter.

  4. Where are the gaps in the data? What is missing?

    These files represent the attempt to fill in all bathymetry gaps in the original GPP/fathometer data acquisition. The lines needing the supplmental data are L12F1, L24F1, L24F2, L25F1, L26F1, L27F1, and L28F1.

  5. How consistent are the relationships among the observations, including topology?

    Each file went through the same process steps in the attempt to supplment the missing fathometer data. Some of the files had sparse bathymetry data, while others had no fathometer data at all.


How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?

Access_Constraints: None.
Use_Constraints:
The public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. Please recognize the U.S. Geological Survey as the originator of the dataset.

  1. Who distributes the data set? (Distributor 1 of 1)

    VeeAnn A. Cross
    U.S. Geological Survey
    Marine Geologist
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA 02543-1598

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)
    vatnipp@usgs.gov

  2. What's the catalog number I need to order this data set?

    Downloadable Data

  3. What legal disclaimers am I supposed to read?

    Neither the U.S. government, the Department of the Interior, nor the USGS, nor any of their employees, contractors, or subcontractors, make any warranty, express or implied, nor assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, nor represent that its use would not infringe on privately owned rights. The act of distribution shall not constitute any such warranty, and no responsibility is assumed by the USGS in the use of these data or related materials. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

  4. How can I download or order the data?

  5. What hardware or software do I need in order to use the data set?

    The data are provided in a WinZip compressed file. The user must have software capable of uncompressing the archive. The navigation are presented in their NMEA string format.


Who wrote the metadata?

Dates:
Last modified: 14-Dec-2010
Metadata author:
VeeAnn A. Cross
U.S. Geological Survey
Marine Geologist
Woods Hole Coastal and Marine Science Center
Woods Hole, MA 02543-1598

(508) 548-8700 x2251 (voice)
(508) 457-2310 (FAX)
vatnipp@usgs.gov

Metadata standard:
FGDC Content Standards for Digital Geospatial Metadata (FGDC-STD-001-1998)
Metadata extensions used:


Generated by mp version 2.9.6 on Tue Dec 14 10:55:50 2010