Chesapeake Times
Technical Review, Issue 6
July 2021
Letter from the General Manager

Every 17 years, the East Coast is home to the cicadas, a type of cricket that emerges from their hibernation, having lived underground for all those years. For a few weeks this spring, these bugs are active all at once, making a tremendous sound that can drown out a conversation. I think they are excited about talking to one another, missing their friends for the last 17 years, and having a good time.

For us non-cicadas, we too seem to be emerging from our hideaway (though not necessarily sleeping for the last 2 decades). And although it may not all happen at once, we are slowly getting out to see everyone, do things that were put on hold for a while, and have our face-to-face conversations. We are starting to see a few conferences take place and here at Chesapeake, we have begun working on our Winter Training event to be held in Charleston.

More details to come, but for now, save the date: December 14 – 16. We plan to have lectures, boat demos and invited our partners to show off their products. After 2 years, it will be a nice to see everyone again. We probably will not be as loud as the cicadas, but then again, after a few weeks they head back underground for another 17 years.

In this edition of the Chesapeake Times, we highlight some of the work done last quarter and new features in the upcoming release of SonarWiz. 7.8.0. We touched on many parts of the program, adding features requested by our users. You will read about our new sidescan import, as we added a unique method to do the actual sample count for each file, up to 32k per channel. This works great for the high-resolution SAS systems. You will also read about the work we did on adding tides to our sub bottom processing and will see how these values are used in the data. For bathymetry, I looked at how we can edit data in the main display. A quick and easy way to remove bad data. Any time we do height corrections to the data, we throw around terms that may be confusing. We have an article going through Ellipsoid and Orthometric height and tidal datums in SonarWiz to show how the data gets corrected. And more. I hope you enjoy this edition of the Chesapeake Times.

Once SonarWiz 7.8.0 release goes out, the process starts over again, as we work on the next update. However, you will not need to wait 17 years, but around 2 months, as will be adding the Globalization and language update to the next release. This will be a nice benefit to all our international clients.

Summertime has been the time for vacations, spending time with friends and family and to relax a bit. But we are not all away on holidays as summertime is also the best time for survey work. If you run into any issues, as always, feel free to contact us, by phone or email. We will get you going.

Have a safe and healthy summer.

- Harold Orlinsky, General Manager
SonarWiz 7.7.8 New Features and Technical Notes

Expanded CSF Sample Count Options .......................... Jonathan Fleetwood, Engr
Adding Tides & Starting Elevation to Sub-Bottom Data . Christopher Favreau, CTO
Applying Antenna Elevations SonarWiz ......................... David Finlayson, Chf Scientist
A New Tool for Bathy Editing .......................................... Harold Orlinsky, General Mgr
New Far Field Tracking for Sidescan Data ..................... Patrick Zynda, Support Engr
Expanded CSF Sample Count Options
Recently we've seen a good amount of interest in higher-resolution sidescan. Recordings can be made at 10,000 or more samples per channel, to allow for centimeter-level resolutions over relatively wide swaths. Customers want to make the most of the systems they've invested in and offer high-resolution deliverables.
To accomodate these needs, the upcoming 7.8.0 release of SonarWiz will include some new sidescan import sample count options. Previously, sidescan files could be imported with 1024, 2048, or 4096 samples per channel. Now, a user-selectable or automatically-detected number of samples can be imported, with a significantly expanded overall range.

Here's a look at the advanced sidescan import options window ("Advanced Settings..." button from either the sidescan import Open window or Options/File Options/SSS Import Settings:
The "Manual" setting allows for a sample count per channel to be entered by hand. The allowable upper limit has been increased to 32,768 samples per channel (the lower limit has been lowered as well, due to some less-frequent use cases revolving around processing speed, disk space, or older recordings). For the frequent case in which a set of files with fixed, known sample count needs to be imported, but that sample count isn't one of the previously-offered powers of two, this is a good option. Raw samples are brought in as-is, with no resampling and no wasted disk space.

Properties of some sample Klein data with exactly 2,400 samples per channel in the original recording:
The "Actual" setting allows for automatically increasing the sample count a file can hold as it's imported. The allowable sample count for a file starts off low in this mode, at the minimum, and is increased to hold additional samples each time a larger sample count is detected in the raw sonar file. Importing multiple files at once with this mode might result in differing sample counts among the resulting CSF files; each import is treated individually. For situations in which you want to bring in files at full resolution without having to figure out the sample count ahead of time, this is a good choice.

An additional benefit of the "Actual" mode is that, like the manual mode above with a known fixed sample count, the data isn't resampled to fit into a fixed-sized array. Before, it could happen that a sample count change in the middle of an import file would result in subsequent pings being of higher average intensity than prior ones due to the resampling method used. This mode could be sub-optimal in terms of disk space; though rare, some variable-length recordings could switch from a low sample count to a much higher one just near the end of the file, resulting in much of the space occupied by the earlier records being wasted.
We're excited about the new sample count offerings for CSF sidescan files. There are a good number of additional improvements that could fall naturally out of these changes, so expect future versions of SonarWiz to expand on these capabilities.
- Jonathan Fleetwood, Engineer
Applying Antenna Elevations
When Processing Bathymetry in SonarWiz
When real-time kinematic (RTK) corrections are available in the survey area, it is possible to achieve sub-decimeter vertical positioning of the sonar system without the need to apply tides or vessel squat measurements. Bathymetry collected in this way is referenced to the satellite ellipsoid rather than to the more conventional orthometric or tidal datum, so it is usually required to apply a vertical transformation to move the bathymetry into the desired output datum. SonarWiz has all the tools needed to perform these calculations in a straightforward workflow.
 
Navigation and Attitude Editor
 
The first step is to examine the navigation in the SonarWiz Navigation and Attitude Editor. Change the displayed charts to show both the RawAttitude.Heave and the RawPosition.Altitude as shown in Figure 1.
Figure 1: Display of a few seconds of heave from the motion sensor and antenna altitude from the positioning system.
If your data has been processed through a high-quality Kalman filter that integrates the inertial motion into the antenna positions, you will see the vertical motion of the position altitude is highly correlated with the inertial heave. This is the case in Figure 1. In this case, when you merge the data, you will want to turn OFF the heave sensor and rely on the antenna heights alone to correct for heave motion (more on this below).
Figure 2: Setting the merge dialog to ignore heave and apply antenna altitude (heights)
If for some reason your antenna altitude is not reliably measuring the wave motion seen in your heave sensor, you can still use the antenna altitude information as a “GPS tide”. What you do is apply a low-pass filter to the Altitude data to remove as much of the wave motion as possible while maintaining the longer period elevation of the vessel as shown in Figure 3. During the merge process, we will use the heave sensor to correct for wave motion and the antenna altitude to set the vertical datum (“tide”) as shown in Figure 4.
Figure 3: Display of a few seconds of heave from the motion sensor and antenna altitude from the positioning system after applying a 60-second low-pass filter to the altitude
Figure 4: Setting the merge dialog to combine heave and antenna altitude (heights)
Converting from Ellipsoid Heights to Orthometric Heights
 
GNSS measure elevations relative to an idealized ellipsoid model of the earth’s surface. If you examine the y-axis values of the Altitude graph in Figure 2, you will notice that the antenna height is about -20.315 m. That is, the antenna is about 20.315 m below the GNSS reference ellipsoid in this location. It is more common to reference bathymetry to orthometric heights (approximately, mean sea level) or to a chart datum based on tide measurements. So, we need to apply a vertical offset between our output vertical datum and the ellipsoid.
 
If your survey area is relatively small, the easiest way to offset the elevation is to enter the difference between the ellipsoid and your desired datum. In my example, I was able to use NOAA’s VDatum utility (Figure 5) to find that the offset from ITRF2014 to NAVD88 is 23.172 m +/- 0.06 m
Figure 5: VDatum indicates that the offset from ITRF2014 to NAVD88 is 23.172 m
We can enter this offset in the merge dialog of SonarWiz as a User Entered Height Offset:
Figure 6: Setting a static datum offset as a User Entered Height offset
If the offset between the ellipsoid and your output vertical datum change throughout your survey area, a single value offset may not be accurate enough to meet specifications. Instead, you will need to load a grid of offsets into the program and have SonarWiz interpolate the offset value for each ping. SonarWiz supports a large number of grid formats, including the GTX format used by VDatum. For example, Geoid18 tile g2018u1 covers the survey area of our example. You can load this grid directly into SonarWiz to examine it:
Figure 7: Geoid18 tile g2018u1 from the VDatum distribution loaded into SonarWiz.
If we want to use this grid to convert our ellipsoid heights to orthometic heights we will need to change the sign of the grid so the conversion goes in the correct direction. Right-click the grid and select the Invert Grid command. This changes the sign of the grid we have imported into our project. We can then use this new grid in our merge dialog.
 
In the merge dialog, set Apply vertical datum offset to: YES and in the Vertical Datum Grid File box below, click the “...” button to open the file picker. Navigate to the copy of the grid in the Grids folder of your project and select it as shown in Figure 8.
Figure 8: A vertical datum offset grid loaded into the merge dialog. Each ping in the project will interpolate the grid for a position-specific offset value
When you merge the data, SonarWiz will use the platform position to interpolate the vertical offset from the datum grid.
 
Using accurate antenna heights in surveying eliminates a lot of problems that typically occur when using tide tables leading to ugly busts in the bathymetry. Directly and accurately measuring the elevation of the platform is much better than trying to estimate it from tide tables and squat calculations. SonarWiz gives you the tools you need to apply antenna heights and transform the resulting bathymetry into the output datum your clients require.
- David Finlayson, Chief Scientist
Adding Tides and Starting Elevation to Sub-Bottom Data
New for SonarWiz 7.8.0: we are adding the ability to utilize Tide data to correct Sub-Bottom sonar data.  In addition to Tide data we are also adding a Starting Elevation value for each Sub-Bottom file. This will allow the user to specify the elevation for the survey. 

SonarWiz Sub-Bottom data has several sources of Elevation data and Depth data:
These data add together to describe where the sonar is located vertically. In other words a Vertical Offset of the Sub-Bottom sonar data. This information together with the travel time will allow a more accurate location for geological features and other items of interest. In order to better illustrate this here are 2 pictures utilizing Starting Elevation and Sensor Depth.
In the above illustration a mountain lake with a starting elevation (the highest level of the water) is shown at 1000m above sea level. The sonar is at 10m depth. The total vertical offset for the sonar is 950m elevation. Since SonarWiz uses Depth (positive down) to denote the vertical offset SonarWiz will show -950m as the start of the sonar data.
Another illustration shows a desert lake with a starting elevation of -1000m below sea level. The sonar is again at 10m depth. The total Vertical Offset for the sonar is now -1010m elevation. Since SonarWiz uses Depth (positive down) to denote the Vertical Offset, SonarWiz will show 1010m as the start of the sonar data.

So what’s the difference between Elevation and Depth values? In the above 2 examples I have stated the total Vertical Offset initially as an Elevation. Elevations are positive in the up direction (towards space). SonarWiz uses Depth which is positive in the down direction (towards the earth’s core).  Here is an illustration showing the difference:
Using Tide and Starting Elevation In SonarWiz

Tide data and starting elevation are applied to the Sub-Bottom data by using the SBP Tides and Vertical Offsets tool located on the SonarWiz Post Processing ribbon bar. 

In the SBP Tides and Vertical Offsets window simply click the Tide Height check box and choose a Tide file to apply. Then select the sonar data files to apply it to. Click the OK button to apply the new data to the selected Sub-Bottom sonar data files.
Once the data has been applied, the window will close and the Tide Height and other Vertical Offset values can be seen in the file's properties or by using the Info At Cursor tool in the SonarWiz SBP Digitizer window.
file propertise showing the vertical offsets
info at curser tool available in SBP Digitizer window
Data can be included or excluded from the Vertical Offset calculation used to correct the sub-bottom sonar data using the application's SBP annotation/display options.
The Vertical Offsets, including Tide Height and Starting Elevation, will be used in the various Sub-Bottom sonar related data exports. These include SEGY export, batch image export, contact export, and digitized features.
-Christopher Favreau, Chief Technology Officer
A New Tool for Bathy Editing
In the latest version of SonarWiz, processing bathymetry just got a little easier. (In my opinion, of course). Editing data is relatively straightforward, finding those soundings that are “flyers” or “anomalies”, which as hydrographers, we determined are invalid and need to be removed. But sometimes we miss finding the sounding and it remains in the dataset, requiring us to go back into the editor for further editing. It could be just one or two points from hundreds of thousands of good ones.

SonarWiz 7.8.0 has a new editing tool to work directly on the bathy data in the main display – without the need to go into the swath or grid editor. When sonar data is imported, all sounding points are drawn. Shown as an overview, the data has the filled in appearance; zooming in, you can see each sounding point displayed as a unique point.
The typical route for data processing would be to use the Swath editor or Area editor, to display the line (or lines) for removing invalid data points. The program has different filters and displays, and folks tend to find one they like and use it. But here is frustrating part. After spending time on cleaning the data and then show it back in the main display, we notice data points that have been missed for removal. We then need to start the process again, opening the editor to find the few points missed. Large outliers are easy to detect, but in the example below, these data points were missed in the editor.
Swath Editor, cleaning invalid data points. Sounding shown around the barge are
removed in the plan, cross section view and 3D view
After editing, notice the few sounds missed on the south side of the barge. In the swath editor, these points were missed.
In the latest release, we added a tool that will edit the data, without the need to go back into the editor. In the Bathymetry tab, a new icon “Plan View Editor” will allow you to reject or accept soundings. And even added the auto merge, updating the data set to reflect the changes made.
I like to use the polygon feature, which allows me to get to the exact areas with the bad soundings. The rectangle works just as well.
After editing, the few soundings at the south end of the barge that were missed earlier, have been removed.

This new editor is the perfect tool to help with the editing of bathymetry data. The ability of importing data, enabling to display individual files, and showing all soundings has been in SonarWiz for a while. Last year, we updated the drawing to take advantage of the Octree method for working with larger data sets. And now, in this latest release, the ability to edit data right in the main display will speed things up for getting to a final product. This tool is just one more way to allow our users to work with multibeam, single beam and Lidar data.
-Harold Orlinsky, General Manger
New Far Field Tracking for Sidescan Data
In version 7.07.05 of SonarWiz, we added the ability for sidescan users to track the far-field of their data in post processing in order to remove erroneous data that was captured during the survey. Often times when recording sidescan data in a narrow river or canal, you will often see the edges of your swath range display washed out like the image below.
In prior versions of SonarWiz, you could use the Far Field Threshold tool in the Advanced Settings dialog to attempt to remove this data, but it offered almost no control over how much was removed and where. Since SonarWiz already contained the dialog and automatic algorithms to track data with the Bottom Tracker, we decided to add support for far field tracking here.

To access the new tools, import some sidescan data into your project and open the Bottom Tracker which should now have a new tab for the Far Field.
All of the controls for tracking the altitude are the same as the far field, you can either use the Threshold Detection algorithm to attempt to automatically track out the erroneous data or use the manual tools to insert points.
Once you have tracked the far field and applied the new track, you will need to use the Adjusted Displayed Range tool to trim the data from the plan view.
In our first development wave for this feature, we simply added the ability to track and trim the erroneous data and have the changes appear in the Sonar Coverage report. Our goal for future development is to have this implemented into the Batch Bottom tracker, have the erroneous data removed from signal processing algorithms, and much more.
-Patrick Zynda, Support Engineer
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