Quick Start Guide to Bathymetry Processing

Owned by David Finlayson
Last updated: 2024-04-26 by Patrick Zynda (Unlicensed)
12 min read

This guide will show you how to import and process swath bathymetry data in SonarWiz.

For more information about the individual commands, please refer to the User Guide found in the Help Menu of SonarWiz. You can download a PDF version of this guide here.

By following this procedure, you’ll learn how to:

  • Configure a vessel file with navigation, motion and bathymetric sensors

  • Import bathymetric data

  • Load and apply sound velocity profiles and tide records

  • Edit and clean navigation and bad soundings

  • Process swath bathymetry backscatter

  • Create bathymetry and amplitude grids

Download Demonstration Data
You can download a copy of the data set used here and follow along on your own computer.
Dataset to Download

Instructions

  1. Click the New Project Icon to open the Create New Project Dialog

     

  2. Enter a Project name and Project Folder, then set the approximate position of the data. This can be done either by entering in a known location or Get from File – navigate to a single file from the project (note: at this point, only one file is needed to set the geodesy, regardless of the number to be processed). Click the Automatically Select CRS button and SonarWiz will select a UTM coordinate system appropriate for your project location.

     

     

    Note: the Coordinate Source section does not apply to bathymetry projects.

  3. In the program, go to the second tab -- Post Processing -- and select Import | Bathymetry Files…

     

  4. Set the Import Geodesy of the raw files. The JSF files in the demonstration data were recorded using WGS 84 geodetic (latitude and longitude) positions. So the appropriate spatial reference ID is EPSG:4326:



  5. In the file Open dialog, click the File Type Specific Options button to specify the bathymetry packets to import. Most file types, such as S7K and ALL, have an Auto option that will attempt to pick the best navigation, bathymetry and imagery packets available in the file.

     

  6. Select one or more bathymetry files to import and click Open.

     

  7. The selected files will begin to import into SonarWiz immediately.

     

  8. When the import is completed, you should see the files listed in the Project Explorer and the bathymetry data will draw in the main display window:

     

  9. To control the colors of the bathymetry in the main display, Open the Color Window from the Mapping toolbar and set the Datatype to Bathymetry:


    You can adjust the color palette and the color scale mode.

  10. SonarWiz will automatically configure a Vessel for the project from information stored in the bathymetry files you import. However, the configuration information may be wrong or incomplete. It is a good idea to open up the Vessel Editor and make any necessary adjustments. Select Vessel | Open Vessel Editor… from the Post Processing ribbon menu.

     

  11. In the Vessel Editor, you can configure the Vessel Shape and Size, Vessel Properties and Sensor Offsets. Any changes you make are saved immediately. When you are done, simply close the Vessel Editor.

     

  12. If you made any changes to the vessel, notice that the colored icon next to each bathymetry data set in the Project Explorer will turn yellow. This is to indicate that the bathymetry is out of date and needs to be recomputed, or re-Merged.

     

  13. Right-click the Tide Files branch of the Project Explorer and Select Edit/Import Tide Files…

    For more information on how to use the CTI Tide Editor see https://sonarwiz.atlassian.net/l/c/0BFaeS9a.

     

  14. Right-click the Sound Velocity Files branch of the Project Explorer and Select Edit/Import Sound Velocity Files…

    For more information on how to use the CTI Sound Velocity Editor see .

  15. Click the Bathymetry | Tide + SV Manager… button to open the Tide and Sound Velocity Manager.

     

  16. In the Tide and Sound Velocity Manager, select a tide file and sound velocity profile for each bathymetry data set. Use the Auto Tides… and Auto SV… buttons to let SonarWiz assign the files based on time and distance. You should also set the source for the surface sound velocity (default: Sensor Value) and the ray tracing method: (Profile is recommended if SVP are available, Sensor Value otherwise).

    Click OK to close the Tide and Sound Velocity Manager.

  17. Right-click the External Navigation Files branch in the Project Explorer and select Add/Import External Navigation Files… if these will be used. Otherwise, SonarWiz will extract the navigation from the internal navigation stored in the bathymetry files.

     

  18. Click Merge… on the Bathymetry Ribbon bar to recompute the bathymetry any time you have made a change to the project that would affect the bathymetry.

     

  19. Merge Wizard - File Selection. Select the files you want to recompute. Click Next.

     

  20. Merge Wizard - Auxiliary Data Selection. Control how SonarWiz will compute the position, attitude and height of the survey. There are various options for applying tides, pressure sensors and antenna elevations. Click Next.

     

  21. Merge Wizard - Error Model Data. If you want to use the C.U.B.E. gridding algorithm, you will need to define the uncertainty on each bathymetric sounding. SonarWiz offers several options from a simple IHO model to a full error model computation. Click Next.

     

  22. Merge Wizard - Filter Settings. The final step in the merge process is to apply automatic filters to the data. There are 10 filter algorithms available including angle/range limiters, density filters and more. These filters can be run outside of the Merge process by clicking the Filter button in the Bathymetry ribbon menu. Click Finish to run the merge process.


    SonarWiz will remember the merge settings you have specified. If you need to re-merge the data in the future, you can click Finish at any time in the Merge Wizard to use the previous settings.

  23. After the Merge process is completed, the indicator next to each bathymetry data set in the Project Explorer should turn green again.

     

  24. To edit the Navigation or Attitude data for bathymetric data sets, Select the dataset with the mouse and click the Navigation and Attitude Editor icon in the Bathymetry ribbon menu.


    The Navigation and Attitude Editor has commands for removing spikes from bad navigation, applying low-pass filters to antenna heights and other useful features.

     

  25. To manually edit bathymetric soundings, SonarWiz provides two different editors. The first, is the Swath Editor. The Swath Editor allows you to edit a single bathymetry data set at a time. This is a good editor to use to remove bad soundings that repeat on each ping such as surface reflections or cavitation interference rolling down the hull over the transducers.

    To open the Swath Editor, select a trackline in the Project Explorer or in the main display and click the Swath Editor icon in the Bathymetry ribbon menu.

     

    The second editor is the Area Editor. This editor allows you to clean up all the overlapping soundings in a selected polygon. This is a good editor to use to clean up complicated topography or submerged debris.
    To open the Area Editor, click the Area Editor icon in the Bathymetry Ribbon menu and then draw a box around the area you wish to edit:


    The Area Editor will open all of the bathymetric data in the selection where you can edit the soundings in a 3D point cloud display.

     

  26. To correct roll, pitch and heading bias, use the Patch Test Utility. Select the Patch Test icon in the Bathymery ribbon menu, and then select the type of calibration you want to correct.


    Draw a profile across your patch lines to open the calibration utility. For roll calibration, draw a line across two or more overlapping lines. For heading and pitch, draw your line parallel to two or more overlapping lines.


    Adjust the port and starboard channels until the overlapping profiles are aligned. The example shows a roll test over a flat section of seabed. This is before calibration:


    This is after:


    Click Save to save the results to the vessel. The merge icons next to your bathymetry lines should turn yellow, indicating that the data needs to be merged again with the new offset values.

  27. To create a grid of your bathymetric data, zoom the main display to the area you wish to grid. Right-click the Grids branch of the Project Explorer and select the Create New Grid… command.

    NOTE: Only the bathymetry files you have enabled (checked) in the Project Explorer will be added to the grid. You must have at least 1 bathymetry file checked.

     

  28. In the Gridding Setup window:


    Data Source: Internal
    Grid Extents: defaults to the size of the screen
    Grid Cell Size: Pick something appropriate for your data.
    Output Grid File Root Name: pick a base name for the grids that will be created
    Primary Grid Surface Type: Depth
    Grid Algorithm: Mean
    Optional Grids: as desired

    Click OK to start the gridding process.

     

  29. The new grids will be added to the Project Explorer and they will appear underneath your bathymetric soundings in the main display. At this point, you may want to change the bathymetry View Settings to show only navigation lines so the grid can be seen. Select the View ribbon menu and then Drawing Mode | Bathymetry Drawing Modes | Navigation Plot Mode


    This will change the main display to show only the navigation lines for your bathymetry and allow the grid to shine through:


  30. Enable a Shaded Relief effect on the surface in the view menu:

    Use the sliders to adjust the Vertical Exaggeration, Light Azimuth and Light Elevation. The grid will respond immediately:



  31. To change the color palette of the grids you create, Select the grid in the Project Explorer and then click the Display tab in the grid Properties window. You can change the color palette in the Color Scale drop down directly or you can click the “…” button to open the Color Scale Properties dialog with full control of the color mapping.

     

  32. To Export a grid out of SonarWiz, Right-Click the grid in the Project Explorer and select the Export Grid As… command.


    SonarWiz supports more than 20 export formats for grids.


    Click OK to export the grid.

  33. To Process the Amplitude Data in bathymetric files, Switch the display to show backscatter. On the View Ribbon menu, select Drawing Mode | Bathymetry Drawing Modes | Draw Backscatter.

     

    This will switch the display to show you the raw intensity data from your bathymetry files

     

  34. To control the color of your backscatter data, open the Color window and change the Datatype to Backscatter. You can then select a new color palette for the backscatter.

     

  35. To normalize the bathymetry backscatter, enable (check) all of the bathymetry lines in your project and click the Process Backscatter… button in the Bathymetry Ribbon menu. This will open the Process Backscatter Wizard.


    Select the Check All button and click Finish to accept the default settings. SonarWiz will process the backscatter data you selected.



    When finished, the main display will show normalized backscatter:


     

  36. To Create a Grid of the backscatter data, Right-click the Grids branch of the Project Explorer and select Create New Grid…


    NOTE: only the enabled (checked) bathymetry files will be added to the grid

  37. In the Gridding Setup dialog…

    Data Source: Internal
    Grid Extents: defaults to the size of the screen
    Grid Cell Size: Pick something appropriate for your data.
    Output Grid File Root Name: pick a base name for the grids that will be created
    Primary Grid Surface Type: Amplitude
    Grid Algorithm: Blend
    Optional Grids: as desired (blend has no optional grids)

    Click OK to start the gridding process.

  38. The new Backscatter grid is added to the Project Explorer. The backscatter grid will appear underneath your bathymetry soundings, so as before, you may want to switch the Bathymetry Display mode to Navigation so that you can see the results (or turn off the Bathymetry lines in the Project Explorer)


    The backscatter Grid can be exported exactly like a bathymetry grid. Right-Click the grid in the Project Explorer and select the Export Grid As… command.

  39. The processed backscatter grid can also be exported as a GeoTiff. Set up the main display to show only the backscatter grid (temporarily turn off the bathymetry lines and any other features and map decorations that you do not want to show in the exported image). In the Post Processing Menu, select Export | Export Project As GeoImage.


    TIP: If you want to make your background transparent, make sure your background color does not occur in your color palette or some of your data may turn invisible when you export the image! For example, if you have a gray-scale color palette, do not choose white or black as your background color, try blue or red. Then, SonarWiz can safely remove all the red pixels from the image during the export without accidentally removing real data.

  40. To pick a target on a bathymetry file, Right-Click the bathymetry data set in the Project Explorer or in the Main window and select Digitize New Bathymetric Features… or Digitize New Backscatter Features…

     

    This will open the file in the Digitizing waterfall display where you can digitize new targets. You can open the same file in both Bathymetry and Backscatter digitizers at the same time!



    For more information about Contact Picking, see the

  41. To view your bathymetry data in 3D, enable 3D view in the View Ribbon Menu

     

  42. Select the bathmetry file or bathymetry grid you want to display (it must have z values to work) and check the Display in 3D View in the Properties window.


    The dataset will immediately render in the 3D Viewer where you can manipulate it with the mouse:

     

Copyright 2022, Chesapeake Technology, Inc.