Bathymetry Post-Processing Guide

Revision Revision 1.0,11/28/2016

Chesapeake Technology, Inc.

eMail: [email protected]

Main Web site: http://www.chesapeaketech.com

Support Web site: http://www.chestech-support.com

1605 W. El Camino Real, Suite 100

Mountain View, CA 94040

Tel: 650-967-2045

Fax: 650-450-9300
Bathymetry Post-Processing Guide Chesapeake Technology, Inc. Copyright 2016

Contents

1 INTRODUCTION 5

1.1 SUPPORTED SENSORS 5

1.2 BATHYMETRY LICENSE 5
1.3 SYSTEM REQUIREMENTS 6
1.4 MANUAL LAYOUT 8
1.5 PROGRAM WORKFLOW 8
1.5.1 POST-PROCESSING BATHYMETRY WORK-FLOW 8

2 BATHYMETRY BASICS 8

2.1 THE HELP MENU 9

2.2 POST PROCESSING RIBBON 9
2.3 BATHYMETRY RIBBON 10
2.4 THE VIEW RIBBON 12
2.5 TOOLS RIBBON 14
2.6 BATHYMETRY FILE MANAGEMENT 15
2.6.1 BATHYMETRY FILES 17
2.6.2 GRIDS 20
2.6.3 TIDE FILES 23
2.6.4 SOUND VELOCITY FILES 24
2.6.5 EXTERNAL NAVIGATION FILES 26
2.7 DISPLAYING AND COLORING BATHYMETRIC DATA 26
2.7.1 SETTING THE BATHYMETRY DRAWING MODE 28
2.7.2 THE COLOR WINDOW 29
2.7.3 SHADED RELIEF EFFECT 31
2.8 BATHYMETRY SETTINGS 33
2.9 BATHYMETRY PROJECTS AND FILES 35
2.10 CREATING A PROJECT 36

3 TIME AND GEOREFERENCING 36

3.1 ASSUMPTIONS ABOUT TIME AND DATES 36

3.2 SPECIFYING A COORDINATE SYSTEM AND PROJECTION 36

4 POST-PROCESSING DATA 37

4.1 WORKFLOW 37
4.2 VESSEL CONFIGURATION AND MANAGEMENT 37
4.3 IMPORTING BATHYMETRY DATA 47
4.3.1 BATHYMETRY FILES 48
4.3.2 TIDE AND SOUND VELOCITY FILES 56

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4.3.3 EXTERNAL ATTITUDE AND NAVIGATION FILES 56

4.4 TIDE AND SOUND VELOCITY MANAGER 56
4.4.1 TIDE FILE SELECTION 57
4.4.2 SOUND VELOCITY SELECTIONS 57
4.4.3 GENERATE A TIDE AND SOUND VELOCITY REPORT 58
4.5 BATHYMETRY PROCESSING OPTIONS 59
4.5.1 POSITION GROUP 60
4.5.2 ATTITUDE 60
4.5.3 HEIGHT COMPUTATION 61
4.5.4 SOUND VELOCITY SOURCE 63
4.5.5 DEFAULT FILTERS 63
4.5.6 SAVING AND APPLYING SETTINGS 63
4.6 MERGE 65
4.6.1 MERGE FILE SELECTION 66
4.6.2 MERGE – AUXILIARY DATA SELECTION 68
4.6.3 MERGE – ERROR MODEL DATA 68
4.6.4 MERGE -- FILTER SETTINGS 70
4.6.5 MERGE RESOLUTION AND TROUBLESHOOTING 71
4.7 FILTER NAVIGATION AND ATTITUDE 73
4.8 FILTER BATHYMETRY 74
4.8.1 AUTOMATIC FILTERS 74
4.8.2 SWATH EDITOR 80
4.8.3 AREA EDITOR 80
4.9 PATCH TEST CALIBRATION 82
4.10 PROCESS AMPLITUDE 82
4.10.1 IMPORTING BACKSCATTER DATA 82
4.10.2 AMPLITUDE UNITS 83
4.10.3 RAW BACKSCATTER VISUALIZATION 83
4.10.4 BACKSCATTER PROCESSING 83
4.10.5 EMPIRICAL GAIN NORMALIZATION (EGN) 84
4.10.6 AUTOMATIC GAIN COMPENSATION (AGC) 84
4.10.7 NADIR FILTER 84
4.11 GRID BATHYMETRY DATA 85
4.12 GRID OPERATIONS 85

5 PATCH TEST CALIBRATION TOOL 85

5.1 SCOPE 85
5.2 INTRODUCTION 85
5.3 PREREQUISITES 86
5.4 THE PATCH TEST CALIBRATION (PTC) USER INTERFACE 87
5.5 PATCH TEST PROCEDURE 89
5.6 POSITION TIME DELAY 89
5.7 PITCH BIAS 95
5.8 ROLL BIAS 99
5.9 HEADING BIAS 108
5.10 CONCLUSION 117

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5.11 REFERENCES 118

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1 Introduction
The SonarWiz Bathymetry module is a powerful addition to SonarWiz that integrates
swath sonar data acquisition and processing into the SonarWiz mapping package.
SonarWiz Bathymetry handles most commercial swath mapping systems on the market
including multibeam echo-sounders and phase-measuring bathymetric sidescan
(PMBS). A collection of powerful editors and processing algorithms are available to
convert raw bathymetric soundings and their associated acoustic backscatter into
polished grids for export into GIS software.

The bathymetric and amplitude products can be used to enhance sidescan and
subbottom data in the same project through the use of map corrections, datum
alignment tools, and 2D and 3D visualizations.

1.1 Supported Sensors

SonarWiz Bathymetry supports a large number of swath bathymetry systems including

both conventional multibeam echosounders (MBES) and interferometric or phase
measuring bathymetric sidescan (PMBS) sonars. Best results are usually obtained from
the sonar system’s native binary format, but SonarWiz also supports a number of
proprietary formats generated by 3rd party acquisition software. Supported data formats
currently include:

 EdgeTech JSF (*JSF)

 GeoAcoustic GeoSwath RDF (*RDF)
 Hypack HSX (*.HSX)
 Imagenix DeltaT (*.83P)
 Kongsberg (*.ALL)
 Lowrance StructureScan 3D (*SL3)
 SEA SwathPlus (*SXI, *SXP)
 Klein (*.SDF)
 R2Sonic (*.R2S)
 Reson (*.S7K, *.7K)
 Triton eXtended Format (*.XTF)
 WASSP Multibeam (*.NWSF)

Additional Data formats can be added by contacting CTI Support.

1.2 Bathymetry License

The SonarWiz Bathymetry module is licensed separately from the main SonarWiz
Program and the feature must be activated on the Sentinel license key (dongle) to
enable the Bathymetry processing features.

To verify that Bathymetry Processing is enabled on your hardware license key, use
the CTI Dongle Manager (See the SonarWiz User Guide 1.4.6) and check for the
line Bathy post processing is enabled, as shown in Figure 1 below:

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Figure 1: CTI Dongle Manager showing bathy post processing enabled

Bathymetry processing can be added to SonarWiz by contacting the CTI Sales

department.

1.3 System Requirements

The SonarWiz Bathymetry module is licensed separately from the main SonarWiz
Program and the feature must be activated on the Sentinel license key (dongle) to
enable the Bathymetry processing features. Bathymetry processing can be added to
any SonarWiz processing license by contacting the CTI Sales department.

See the SonarWiz User Guide Section 1.3.1 for the minimum system configuration
specifications for SonarWiz. Bathymetry processing requires workstation class
computers with abundant memory and fast read and write access to storage
devices. The following are recommended for best performance:

Minimum: Pentium 4, 8 GB RAM (8 GB R/T PC) 2-GB HD space

Operating Systems: Windows7, Windows 8, or Windows 10 (32 and 64-bit

versions)

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Multi-threading/32 Bit/64 Bit Support: SonarWiz currently supports multi-core

processors on 32 and 64 bit architecture however the 32-bit version of SonarWiz
currently only runs in 32 Bit mode. SonarWiz5 User Guide 6.01.0033 Chesapeake
Technology, Inc. copyright 2016-2017 Beginning in January, 2016, 64-bit SonarWiz
6.04 is available to customers in the SonarWiz download section of
www.chestechsupport.com.

LICENSING NOTEs: The Sentinel SuperPro license key (dongle) used to license
SonarWiz requires a physically available USB port to plug it in, whether this is on the PC
running SonarWiz, or on a networked PC supporting a network dongle license. You may
run SonarWiz on a PC while logged in directly on that PC, or when accessing the PC via
Remote Desktop, as long as that instance of SonarWiz on the PC is able to obtain
licensing from a local or network dongle. Only one instance of SonarWiz at a time may
run on a single PC.

3D Viewer / Editors

Starting with 6.04 series SonarWiz, full support for all display features requires
DirectX11, an optional item in Windows7, but a default feature of Windows8, and
Windows10. Both the graphics card, and OS, need to support DirectX11.

CTI3DViewer application is launched on a system that does not meet the minimum
hardware requirements, a diagnostic message with information on which exact
requirement was violated will be shown (Figure 2 below), and the application will exit.

Figure 2: Graphics Card Error

If your graphics card is supported and you get this diagnostic message, please, try
updating your graphics card drivers.

Supported graphics cards:

 GeForce GT 5200; GeForce 6800 GS and 6800 GT; GeForce 7600 and higher.
 Quadro FX 1500;
 ATI Radeon 9600; ATI Radeon 9800 series; ATI Radeon X700 XT and higher.
 Intel GMA 4500MHD; Intel GMA X3100 (G31/G33/GM45/GS45 chipsets).

Unsupported graphics cards:

 Intel GMA 900/950 (946GZ / Q965 / Q963 /940GML /945G /945GU / 945GT)
 GeForce4 MX 4000; GeForce4 7300 GT.

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Overall, most built-in cards that do not support pixel and vertex shaders, and on-board
graphics accelerators are a gamble.

1.4 Manual Layout

The Sections in the SonarWiz Bathymetry Processing Guide are organized by major
function groupings in the same sequence as the typical program work-flow. This layout
enables new users to bathymetry processing to read each section in sequence from
importing bathymetry files all the way to producing a final bathymetric products and
visualizations. Basic familiarity with swath bathymetry terminology and operation are
assumed.

This guide is a supplement to the SonarWiz Users Guide. For more information on the
basic operation and use of SonarWiz refer to the User Guide.

1.5 Program Workflow

The typical workflow from start to finish is listed in the following pages. Each step in the
work flow list has a corresponding section in this manual.

Section 1 (this section) is an introduction to the bathymetry processing module and this
processing guide. Section 2 is a guide to understanding the layout of the bathymetry
module windows and buttons. Section 3 describes important assumptions about time,
units of measure and coordinate systems. Section 4 describes the bathymetry
processing steps in detail. Sections Error! Reference source not found. through
Section Error! Reference source not found. are not part of the normal work-flow but
describe necessary tools that are called upon from time to time depending on the
project.

1.5.1 Post-Processing Bathymetry Work-flow

1. Set Program Preferences (Section 2.8)

2. Create new, or open existing SonarWiz Project (see Section 2.8 of the SonarWiz User Guide)
3. Configure Vessel (Section 4.2)
4. Import Bathymetry Data (Section 4.3)
5. Import Tides and Sound Velocity Profiles (Section 4.4)
6. Set Processing Options (Section 4.5)
7. Merge (Section 4.6)
8. Filter Navigation and Attitude (Section 4.7)
9. Filter Bathymetry (Section 4.8)
10. Patch Test Calibration (Section 4.9)
11. Re-merge to incorporate changes made in Steps 7—10
12. Process Amplitude (Section 4.10)
13. Grid Bathymetry Data (Section 4.11)
14. Perform Grid Operations (Section 4.12)
15. Export and Visualize Data (Section Error! Reference source not found.)

2 Bathymetry Basics

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The primary functions of SonarWiz bathymetry are:

1. Process raw bathymetry soundings into bathymetric and amplitude surfaces

2. Visualize and analyze bathymetry data
3. Integrate bathymetry information with sidescan and subbottom data

In addition, SonarWiz bathymetry contains many tools for manipulating and exporting
sonar data and for handling the import and export of various auxiliary sensors required
to properly process bathymetry and bathymetric amplitude data. This section provides a
brief overview of the additional user interface elements specific to bathymetric
processing through which these functions are provided. For more information about the
basic operation of SonarWiz, please see Section 2 of the SonarWiz User Guide.

2.1 The Help Menu

This small menu is the first stop for users experiencing difficulties or questions about the
program. It is shown in Figure 3.

Figure 3: Help Menu

The SonarWiz User Manual and the Bathymetry Processing Guide (this document) are
opened from this menu in the default PDF viewer.

2.2 Post Processing Ribbon

Several important features have been added to the Sonar File Tasks group of the Post
Processing Ribbon to support bathymetric processing.

Figure 4: Post Processing Ribbon Enhancements

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Table 1: Bathymetry Tools in the Post Processing Ribbon

Name Icon Description

Vessel Button Use to open the Vessel Editor and the

Vessel Configuration Manager (Section 4.2
on page 37)

Import Button Use to import binary bathymetry files

(Section 4.3 on page 47)

Export Button Use to access various bathymetry export

products such as reports, sounding export,
and GSF conversion. (Section Error!
Reference source not found. on page
Error! Bookmark not defined.)

2.3 Bathymetry Ribbon

The Bathymetry Ribbon is only visible with a valid bathymetry license. Most bathymetry
processing features are accessed through the Bathymetry Ribbon. The icon buttons are
organized left-to-right in the approximate order that the tools should be used during
bathymetry processing. Table 1 briefly describes the icon functions and provides links to
the appropriate sections in this Guide.

Figure 5: Bathymetry Ribbon Toolbar

Table 2: Bathymetry Ribbon Tools Description

Name Icon Description

Settings Default bathymetry processing settings (Section

4.5 on page 59)

Tide & SV Control the assignment of tide and sound velocity

Manager profiles to individual bathymetry track lines
(Section 4.4 on page 56)

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Merge Open the Merge dialog where raw bathymetry

data is converted into processed soundings
(Section 4.6 on page 65)

Filter Apply automatic filters to bathymetry data

(Section 4.8 on page 74)

Process Apply signal processing tools to raw sounding

Backscatter backscatter values (Section 4.10 on page 82)

Patch Test Launch the Patch Test Calibration (PTC) tool for
adjusting the orientation angle alignments of the
transducers. (Section 5 on page 85)

Swath Editor Launch the Swath Editor tool for manual editing
and inspection of bathymetry and backscatter of
a single track line. (Section Error! Reference
source not found. on page Error! Bookmark
not defined.)

Area Editor Launch the Area editor for manual editing and
inspection of all bathymetry and backscatter
found over a selected geographic area. (Section
Error! Reference source not found. on page
Error! Bookmark not defined.)

Navigation and Inspect, edit and filter navigation and attitude

Attitude Editor time series stored in individual track line files.
(Section Error! Reference source not found.
on page Error! Bookmark not defined.)

Tide Editor Launch the Tide Editor to inspect, import and edit
tide records (Section Error! Reference source
not found. on page Error! Bookmark not
defined.)

Sound Velocity Launch the Sound Velocity Editor to inspect,

Editor import and edit sound velocity profile records.
(Section Error! Reference source not found.
on page Error! Bookmark not defined.)

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Cross-section Launch the bathymetry cross-section viewer over

a profile drawn by the user. (Section Error!
Reference source not found. on page Error!
Bookmark not defined.)

3D Viewer Open the 3D visualization tool. (Section Error!

Reference source not found. on page Error!
Bookmark not defined.)

Import External Open a dialog to import external navigation and

Sensor Data attitude data such as POS M/V SBET files.
(Section 4.3.3 on page 56)

Shaded Relief The shaded relief group is used to control the

Group shading effect on bathymetry grids visualized in
the main display window. (Section 2.6 on page
15)

2.4 The View Ribbon

The View Ribbon functions have been enhanced to work with bathymetric data. For the
most part, the View Ribbon buttons function the same as with sidescan and subbottom
data (See Section 2.4 of the SonarWiz User Guide). For example, the file Opacity slider
now also applies to bathymetry files and can make bathymetry data transparent or
opaque as required and the Drawing Mode selector now has options for selecting
bathymetry drawing options (see Figure 6).

Figure 6: The View Ribbon

New for bathymetry is the Bathymetry Views Button . This button reveals a
sub-menu that allows the user to turn on and off several windows unique to bathymetry
processing. These menu items are described in Table 3.

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Table 3: Bathymetry Views Menu Options

Menu Item Description

Bathymetry Settings… Opens the project level bathymetry

settings menu (Section 4.5 on page 59 for
details)

Cross Track Profile (Real-Time Only)

Real-time Bathy Swath View… (Real-Time Only)

Real-time Helm Display… (Real-Time Only)

Color Window Opens the color control window. (Section

2.6 on page 15)

Post-Processing Toolbar Opens the bathymetry post-processing

toolbar with quick access to helpful tools

Show Bathy Area Selections Turn on or off the display of previous line
and area selections. See below for
details.

Shaded Relief Settings Open the shaded relief dialog for

controlling shade effects on bathymetry
grids. (Section 2.6 on page 15)

The Opacity Slider sets the transparency of raw bathymetry

soundings. When the slider is all the way to the left, the bathymetry is completely
transparent, when all the way to the right, the bathymetry is completely opaque.

The Drawing Mode button has a new section Bathymetry Drawing Modes (Figure 7)
dedicated to display of bathymetry soundings. Table 4 describes the available options.
See Section 2.7 on page 26 for a more detailed description of how bathymetry is
visualized in SonarWiz.

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Figure 7: Bathymetry Drawing Modes Options

Table 4: Bathymetry Display Modes Menu Options

Menu Item Description

Draw Raw Bathymetry Draw sounding data colored by depth

Draw Backscatter Draw sounding data colored by amplitude

Navigation Plot Mode Draw the track centerline only

Navigation Plot Thickness Set the thickness of the track centerline

(Slider)

Show Only Accepted Show unflagged soundings only.

Bathymetry Points (only applies to the main window)

Show Accepted and Show flagged and unflagged soundings

Rejected Bathymetry Points (only applies to the main window)

Show Only Rejected Show flagged soundings only.

Soundings (only applies to the main window)

2.5 Tools Ribbon

The Tools Ribbon contains a number of useful utilities for examining binary bathymetric
files (Figure 8).

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Figure 8: Tools Ribbon

Most of the binary file types supported by SonarWiz have an associated button in the
File Utilities group labeled by the file type’s 3-letter windows extension. For example, the
Kongsberg binary file extension is ALL and SonarWiz has a set of four utilities shown

beneath the button in Figure 9 which can:

 Extract navigation data from an ALL file.

 Create a report of the packet types found in an ALL file.
 Extract a detailed report on the packet contents.
 Create a report showing the sonar installation parameters recorded in the ALL file.

Figure 9: Kongsberg ALL File Utilities

These utilities are useful for setting up the import properties when bringing data into
SonarWiz and can be very handy for troubleshooting when things go wrong.

2.6 Bathymetry File Management

The SonarWiz bathymetry module adds support for several new data types including
bathymetry track line files, grids, tide files, sound velocity profile files, and external
navigation files. As these data are imported or created, they are placed into the
appropriate branch of the Project Explorer (See Section 2.4.1.14 in the SonarWiz User
Guide).

As shown in Figure 10, each branch or section of the Project Explorer is dedicated to
one file type (e.g., Maps, Bathymetry Files, Grids, etc.). Each branch can be further sub-
divided into sub-groups to help organize and manipulate large collections of files.

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Figure 10: Project Explorer window

Various operations in SonarWiz are performed on selected files. You can select one file
at a time by LEFT CLICK or select multiple files by CTRL+LEFT CLICK with the mouse.

At each level in the Project Explorer hierarchy, there is a white check-box icon to the left
of the name. When this box is checked, the file is visible in the main display window and
active for operations. When the box is unchecked (blank), the file is hidden from display
in the main window and will not participate in file operations. A third, partially-selected
state is available for branch and sub-group levels. A filled box indicates some of the files
beneath this level are checked and some are unchecked. Figure 11 shows the
bathymetry branch of the file explorer with various selection states.

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Figure 11: Bathymetry branch showing various selection states

Changing the selection state at the sub-group or branch level will apply to all files
beneath that level. You can quickly activate or hide a group of files by grouping the files
into a Sub-Group and then manipulating the sub-group check box.

You can collapse all of the files in a group or branch by clicking the small + and - sign to
the far left of the row.

The Context Menu (right-click menu) inside the Project Explorer provides access to
almost all of the major operations that can be performed in SonarWiz. When you open
the context menu (right click) at the branch or group level, only operations that are
available to groups of files of that type will be shown. When you open the context menu
at the file level, only operations available to a single file are shown.

The following sections describe the operations available for the various data types
introduced to support bathymetry processing. There are up to 3 context menus available
for each data types:

1. Branch context menu (opened by Right+Click on the branch label)

2. Sub-group context menu (opened by Right+Click on the sub-group label)
3. File context menu (opened by Right+Click on the individual files)

The SubGroup context menu is the same for all data types and simply allows the
deletion of the context group. All files that had been placed in the SubGroup are moved
to the next higher level.

2.6.1 Bathymetry Files

When you successfully import a bathymetry file, the original data file is not moved or
changed in any way. Instead a CDF file is created in the bathy folder your SonarWiz
Project. All manipulations of the data from this point forward are applied to the CDF file
only.

Each successfully imported bathymetry file in a SonarWiz project has an entry in the
Bathymetry Files branch of the Project Explorer.

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The Merge Status of a bathymetry file indicates whether or not bathymetry has been
computed for this file. There are three Merge States a bathymetry file can be in:

1. (Red) File cannot be merged

2. (Yellow) File requires merging.
3. (Green) File is merged.

Initially, bathymetry files are imported in the Yellow merge state (requires merging).
Performing a successful merge operation (Section 4.6 on page 65) will turn the status to
Green. Some actions such as changes to the Vessel Configuration or editing navigation
or attitude files will change the Merge status of the bathymetry files from Green (Merged)
to Yellow (Needs merging). This indicates that the bathymetry calculated for these files
is out-of-date and needs to be recomputed to reflect the changes to the vessel and
navigation. Figure 12 shows a group of bathymetry files where one group is green
(merged) and the other is yellow (needs merging).

Figure 12: Bathymetry in various Merge states

Sometimes a bathymetry file will be encountered that is missing information necessary

to compute bathymetry. The merge status will be set to Red (cannot be merged).

Many of the most important bathymetry operations can be performed from the
bathymetry branch context menus. Table 5 describes the branch-level context menu and
Table 6 describes the file-level context menu.

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Table 5: Bathymetry branch context menu

Label Description

Merge… Start a Merge operation (Section 4.6)

Filter… Start a Filter operation (Section 4.8)

Process Backscatter… Signal processing on backscatter

(Section 4.10)

Tide and Sound Velocity Manager… Manage tide and sound velocity profiles
(Section 4.4)

Properties… Summary report on the selected files

New SubGroup Create a new SubGroup

Table 6: Bathymetry files context menu

Label Description

Zoom To Zoom the main window display to the

selected file

Navigation and Attitude Editor… Edit navigation and attitude for the selected
file (Section Error! Reference source not
found.)

Swath Editor… Edit bathymetry on the selected file (Section

Error! Reference source not found.)

Settings… Edit the bathymetry settings for the selected

file (Section 4.5)

Merge… Merge the selected file (Section 4.6)

Filter… Filter the selected file (Section 4.8)

Process Backscatter… Start backscatter processing operation

(Section 4.10)

Tide and Sound Velcity Manage tide and sound velocity files
Manager… (Section 4.4)

Hide Hide the selected file (uncheck)

Isolate Show only this file (uncheck everything else)

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Replace Aux Data… Replace the auxiliary data in this file with
external navigation and attitude data
(Section 4.3.3)

Status… Run a status report on this file (useful for

troubleshooting)

Properties… Run a properties report on this file

Delete Selected Bathymetry Delete the selected CDF files

Files… (Only the SonarWiz data is deleted, does not
touch original data files)

View in Waterfall (beta) Open a bathymetry file in a waterfall display

(similar to sidescan). This is experimental

View Point Cloud in 3D Viewer Open the 3D viewer and display the
soundings as a point cloud (Section Error!
Reference source not found.)

2.6.2 Grids

Grid files are located in the Grid branch of the Project Explorer.

Figure 13: Grid branch of the Project Explorer

When a grid is created in SonarWiz or imported to a SonarWiz project from a third-party

source, the grid file is copied into the Grids folder of the SonarWiz project. The original
file is not used. The check boxes to the left of the grid name indicate whether the grid is

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displayed in the main window or not. Grids can be grouped into SubGroups and
controlled together similar to Bathymetry Files (see Section 2.6).

Each grid in SonarWiz is assigned a grid type from those listed in Table 7. Imported
grids are always assumed to be depth grids. Grids are assigned a color pallet based on
the Grid Type and some operations may be restricted to certain grid types. The grid type
is indicated by the color of the grid icon to the left of the grid filename. Grey is
Backscatter, Blue is Depth and Red is Standard Deviation and Density grid types. You
can also find the grid type by opening the Grid Properties from the File context menu.

Table 7: SonarWiz grid types

Grid Type Color Pallet Shaded Relief Z-Value

Backscatter Backscatter No Sidescan and Swath bathymetry

backscatter

Bathymetry Bathymetry Yes Depths, positive down

Standard Standard No Statistical measures of

Deviation Deviation accuracy, units are the same as
associated depth

Density Density No Statistical measures of counts.

When a grid is removed from the SonarWiz project it is NOT deleted, the grid files
remain in the Grid folder of the project until they are deleted manually by the user.

Grid operations are performed using the grid Context Menus. The branch-level context
menu, described in Table 8, allows for the creation and addition of grids to the project.
The file-level context menu, described in Table 9, performs operations on the selected
grids.

Table 8: Grid branch-level context menu

Label Description

Add/Import Grid Files… Add an existing grid to the project

Create New Grid… Create a new grid for the project

Reload All Grids… Reload grids. Useful when a grid has been updated by a
process outside of SonarWiz.

New SubGroup Create a new SubGroup

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Table 9: Grid file-level context menu

Label Description

Grid Editor… Edit the grid and the underlying bathymetry data in the
Area Editor (Section Error! Reference source not
found.)

Reload Grid… Reload a grid from disk. Useful if a process outside of

SonarWiz has changed the grid values

Interpolate Grid… Interpolate small data gaps in a grid using the existing
grid values as the source data (Section 4.12)

Update Grid… Re-create the grid using the same input files and
settings used originally. Use this when the underlying
bathymetry has been remerged or edited and you want
the grid to reflect the changes. (Section 4.12)

Copy Grid… Make a copy of the grid

Export Grid As… Export the grid data into another format (Section 4.12)

Contour Grid… Create a vector contour map of the gridded values.

Merge Grids… Merge selected grids into a single unified grid.

Offset/Scale Grid… Apply a scalar and multiplier to the grid values.

Reproject Grid… Reproject the grid into another coordinate system.

Volume Calculator… Compute the volume and difference between two grids
in the same project. (Section 4.12)

Shaded Relief Image… Create a GeoTiff image of the grid with shaded relief
effect

Open in 3D Viewer… Open the grid in the 3D Viewer. The Z value of the grid
becomes the z dimension. (Section Error! Reference
source not found.)

Properties… Open the grid properties report on the selected grid

Remove Selected Grid Remove the selected grid from the project. The grid is
NOT deleted from the project folder and can be added
again at a later time.

TIP: Use the Properties report (Figure 14) to determine the grid type for setting the
correct color pallet and for looking at the dimensions of the grid. Only workstation-class

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computers can handle grids that much exceed about 25 million cells (about 5000 rows x
5000 columns).

Figure 14: Grid properties report

For more information on grids and gridding bathymetric data types. See Section 4.12 on
page 85.

2.6.3 Tide Files

Tide water lever records that have been successfully imported into a SonarWiz project
are displayed in the Tide Files branch of the Project Explorer (Figure 15). SonarWiz
tide files are XML files that are stored in the Tides branch of the project folder.

Only tide files that are checked are available for assignment in the Tide and Sound
Velocity Manager (Section 4.3.2) and during the Merge process (Section 4.6). If you do
not want a tide file to be available, uncheck it in the Project Manager.

The Branch level context menu described in Table 10, allows the user to Add existing
tide tables or to import new tide tables, the File-level context menu described in Table
11, allows the user to edit or delete the selected tide file.

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Figure 15: Tide Files branch of the Project Explorer

Table 10: Tide File branch-level context menu

Label Description

Add Existing File(s)… Add existing SonarWiz tide files to the project

Edit/Import Tide Files… Open the Tide Editor to create a new SonarWiz tide file

Table 11: Tide File file-level context menu

Label Description

Edit Edit the selected tide file in the Tide Editor

Properties Create a report on the selected Tide file

Remove Remove the selected tide file from the project. The tide
file is NOT deleted and remains in the Tides folder.

For more information about using tides in bathymetry processing see Section 4.3.2 on
page 56.

2.6.4 Sound Velocity Files

Sound velocity profile (SVP) records that have been successfully imported into a
SonarWiz project are displayed in the Sound Velocity Files branch of the Project
Explorer (Error! Reference source not found.). SonarWiz sound velocity files are XML
files that are stored in the SVP branch of the project folder.

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Figure 16: Sound Velocity Files branch of the Project Explorer

Only SVP files that are checked are available for assignment in the Tide and Sound
Velocity Manager (Section 4.3.2) and during the Merge process (Section 4.6). If you do
not want an SVP file to be available, uncheck it in the Project Manager.

When an SVP is checked, a small icon will appear at the specified location on the
main map window (Figure 17).

Figure 17: SVP locations indicated in the map window

The Branch level context menu described in Table 12, allows the user to Add existing
tide tables or to import new tide tables, the File-level context menu described in Table
13, allows the user to edit or delete the selected tide file.

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Automatic Sound Velocity Import

Some bathymetry file types contain embedded sound velocity profiles. If SonarWiz
recognizes these packets it will automatically import the Sound Velocity file and add it to
the project. SonarWiz will select the time and location of the beginning of the track line to
place the SVP profile.

Table 12: Sound Velocity Files branch-level context menu

Label Description

Add Existing File(s)… Add existing SonarWiz tide files to the project

Edit/Import Tide Files… Open the Tide Editor to create a new SonarWiz tide file

Table 13: Sound Velocity Files file-level context menu

Label Description

Edit Edit the selected tide file in the Tide Editor

Properties Create a report on the selected Tide file

Remove Remove the selected tide file from the project. The tide
file is NOT deleted and remains in the Tides folder.

For more information about using sound velocity profiles in bathymetry processing see
Section 4.3.2 on page 56.

2.6.5 External Navigation Files

External navigation records that have been successfully imported into a SonarWiz
project are displayed in the External Navigation Files branch of the Project Explorer.
External navigation records include post-processed trajectories in binary format such as
Applanix SBET files or corrected navigation from AUV surveys stored in CSV format in
pre-defined formats.

The branch-level context menu for External Navigation Files uses a stream-lined
interface to NavInjectorPro with pre-defined navigation file templates (See Section 6.1.3,
page 700 of the SonarWiz User Guide) for more information.

2.7 Displaying and Coloring Bathymetric Data

Before SonarWiz can display bathymetry or backscatter from bathymetry files, the files
must first be merged (see Section 2.6.1 on page 17). If the file is in an unmerged state,
the only display option available will be a simple track line indicator in the map view as
shown in Figure 18.

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Figure 18: Freshly imported bathymetry files before merge

After a successful merge operation (bathymetry files have a Green merge indicator). The
soundings can be displayed in the map window as shown in Figure 19.

Figure 19: Bathymetry soundings displayed after merge

Only checked bathymetry files will be displayed in the map window. Unchecked files
are hidden.

The View > Opacity slider controls the transparency of the sounding data. It is
sometimes useful to make all the bathymetry transparent to see what is located beneath.

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2.7.1 Setting the Bathymetry Drawing Mode

The bathymetry drawing mode determines how bathymetry files will be displayed in the
Map Window. The bathymetry drawing mode can be changed in two places:

1. From the View > Drawing Mode > Bathymetry Drawing Modes menu
2. By changing the Color Window DataType drop down selection.

The drawing modes available are:

1. Draw Raw Bathymetry. This draws the individual soundings computed during the merge
operation colored by depth. The Bathymetry color pallet is used. If you zoom closely into
the data you will see the individual sounding points on the map as shown in Figure 20.

Figure 20: Individual soundings visible in map view colored by depth

2. Draw Backscatter. This draws the individual soundings computed during the merge
operation colored by backscatter intensity. The Backscatter color pallet is used. The same
area shown in Figure 20 is colored by backscatter intensity in Figure 21.

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Figure 21: Individual soundings visible in map view colored by backscatter intensity

3. Navigation Plot Mode. Turns off the display of individual soundings and displays only a plot
of the center track line as shown in Figure 22. As described in Section 2.4, there are some
controls over the thickness and color of the navigation plot mode display.

Figure 22: Bathymetry data displayed in Navigation Plot Mode

2.7.2 The Color Window

The Color window controls how colors will be assigned to bathymetry data types in the
SonarWiz map window.

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The Color Window is opened from the Map Toolbar (View > Post-Processing Views >
Map Toolbar) by clicking on the color pallet icon.

The Color Window is a dockable window frame that can be placed anywhere in the
SonarWiz program window. It can be made to auto-hide on small screens to make more
room for the main display.

The Color window has four sections (see Figure 23):

1. The DataType section. Selects the active data type. Backscatter, Bathymetry, Density and
Standard Deviation are the data types associated with bathymetry processing. If data type
Backscatter or Bathymetry is selected from the drop down, the bathymetry drawing mode
will switch to Raw Bathymetry or Backscatter as appropriate automatically.
2. The Mapping section. On the left there is a histogram of all the values in the selected
datatype. On the right is a color pallet legend showing how the colors will be mapped to the
histogram of data. You can manually adjust the range of the color pallet by using the mouse
and sliding the upper and lower sliders on the histogram display. Any changes are
immediately visible in the mapping window.
3. The Pallet Options. Here you can select from among the built-in color pallets. Check the
smooth box to smooth the color transitions in the pallet, check the invert box to apply the
color pallet in the reverse sense. Finally, you can click the Edit Pallet button to edit the pallet
and/or create a new pallet for the data.
4. The Mapping Range. In this section you can manually set the minimum and maximum
mapping range of the color pallet. You can also hit the Scale to Data button to automatically
rescale the minimum and maximum values to where the data is.

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Figure 23: Color window

When you make an adjustment to a color pallet, all data types loaded into SonarWiz that
use the assigned color pallet will automatically reflect the change. Note that some data
types share color pallets. For example, the Bathymetry and Backscatter sounding data
types share a color pallet with the Bathymetry and Backscatter Grid data types. In this
way all bathymetry---whether displayed as raw sounding or gridded format---is colored
using the same color scheme.

2.7.3 Shaded Relief Effect

Depth grids take their colors from the Bathymetry color pallet (see above). A useful
shaded relief effect can be applied to bathymetry grids to give a pseudo 3-dimensional
appearance. A comparison of the same grid colored by depth only is shown in Figure 24
and the same grid shown with the shaded relief setting turn on is shown in Figure 25.

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Figure 24: Example of a grid colored by depth only

Figure 25: Example of grid colored by depth with shaded relief

To turn on the Shaded relief effect, you must have a depth grid displayed in the map
window (See Section 2.6.2). Shading cannot be applied to raw sounding data.

Use the Bathymetry > Shaded Relief tools to control the shade effect.

Figure 26: Shaded relief section of the Bathymetry toolbar

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Table 14: Shaded relief toolbar settings

Label Description

On (checkbox) Activate or deactivate the shaded relief effect on depth

grids

Vertical Exag. Change the vertical exaggeration of the relief from 0 to

10x

Light Azimuth Set the bearing of the illumination source.

Light Elevation Set the altitude above the horizon of the illumination
source

Type Set the shade algorithm to use

Apply Slope Correction Color by shade and slope.

The sliders in the Shaded Relief toolbar are interactive, but you may want to specify the
shading parameters directly. This option is available from the View > Bathymetry Views
> Shaded Relief Settings dialog as shown in Figure 27.

Figure 27: Shaded relief settings dialog

For more information on creating bathymetry grids see Section 4.11 on page 85.

2.8 Bathymetry Settings

SonarWiz contains a number of Preferences and Settings options specific to Bathymetry

projects. These settings are found in the Bathymetry Settings page of the Preferences

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and Settings dialog which is accessed by clicking the green dot icon in the upper left
corner of the SonarWiz screen.

Figure 28: Bathymetry project settings

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Table 15: Bathymetry Settings and Preferences

Label Description

Immediately execute the Uses the default settings to merge a bathymetry file on
Merge process after import.
importing a raw
bathymetry file

Broadcast processed Not used in Post-Processing

bathymetry samples
during real-time
acquisition

Transmit progress and Several of the Editors and Viewers in SonarWiz are
status messages on separate processes from the main program. This is the
UDP Port port they communicate on and can be changed if there is
interference for some reason.

Log diagnostics file Creates a file used by CTI Staff to diagnose problems in
during bathy the Bathymetry Merge process
processing.

Enable Pyramid drawing Experimental pyramid drawing (instead of raw

bathymetry)

Select Bathymetry By default, SonarWiz will use the gridding engine that
Gridding Engine matches your computer processor. You can override that
choice here. The 64-bit gridder will not work on 32-bit
architectures.

For more information about other Program settings see the SonarWiz User Guide
Section 2.7.1.

2.9 Bathymetry Projects and Files

Section 2.8 of the SonarWiz User Guide describes the standard project folder structure
for Sidescan and Sub-bottom projects. SonarWiz Bathymetry are designed to fit neatly
into this existing structure.

Bathymetry will add a few new folders and data types to the structure as shown in Table
16.

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Table 16: Folders and Files specific to bathymetry projects

Folder Description

bathy Stores the imported bathymetry files in CDF format

grids Stores imported and newly created grid files in GRD

format, along with supporting projection (PRJ) and
metadata (XML) files.

SVP Stores imported sound velocity profiles in SonarWiz XML

format

Tide Stores imported tide files in SonarWiz XML format

Vessels Stores vessel configuration files in SonarWiz XML format

2.10 Creating a Project

Creating a bathymetry project follows the same procedure as a normal SonarWiz project
and is described in detail in Section 2.9 of the SonarWiz User Guide. However, creating
a project automatically by dragging a bathymetry file onto the SonarWiz program is not
fully supported.

3 Time and Georeferencing

SonarWiz makes a number of assumptions about the coordinate system and time
system in use while processing bathymetry data. Minimizing timing and coordinate
system transformations is one way to keep the complexity of swath mapping under
control.

3.1 Assumptions about Time and Dates

Precise timing is critical for synchronizing swath sonar data to auxiliary support
information such as navigation and attitude records, tides and sound velocity data. It is
important that all time corrections be applied during the import process so that the
internal unit of time is consistent within the project.

It is highly recommended that users collect and process all data using a standard time
zone. Having some instruments on local time while others are on world time can be a
source of problems for bathymetry processing.

3.2 Specifying a Coordinate System and Projection

Unless otherwise indicated, all bathymetry computations in SonarWiz use the Cartesian
coordinate system defined by the Project coordinate system. Geographic coordinates
are first converted to the project coordinate system before calculations are performed. It

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is therefore critical that the user select an appropriate coordinate system for the
geographic area of interest to minimize map distortion.

The units of length, velocity and volume are assumed to match the project coordinate
system definition. Users in the United States using the US Standard measurements
should pay attention that input data is consistent. Not all sonar systems and ancillary
equipment such as sound velocity probes and motion sensors indicate the unit of
measure (feet or meters). If SonarWiz cannot determine the unit of measure, it will be
assumed to match the project defaults.

4 Post-Processing Data

4.1 Workflow

1. Create a new Project

2. Create/Import a new Vessel
3. Load Data Files
a. Sonar Data
b. Sound Velocity Casts
c. Tides
d. Auxiliary Navigation
4. Merge Bathymetry
5. Inspect and Filter Navigation
6. Filter the Bathymetry Repeat as Necessary
7. Grid the Bathymetry
8. (Optionally) Perform Sensor Calibration (Patch Test)
9. Manually Edit Bathymetry (Swath and Area Editors)
10. Visualize Data
11. Export Data

4.2 Vessel Configuration and Management

You must configure a vessel with information about your sonar system installation before
bathymetric processing can proceed. The Vessel Editor is used to identify to SonarWiz
the types of navigation, motion measurement and sonar equipment deployed on the
vessel and their respective positions and orientations on the vessel. Collectively, these
measurements are known as Lever Arms. All lever arms are measured relative to an
arbitrary point on the vessel known as the Vessel Reference Point (VRP).

The first task on configuring a new vessel is to open the Vessel Editor and create a New
Vessel:

Click the Post Processing > Vessel > Open Vessel Editor…

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Figure 29: Open the vessel editor tool

This will open the Vessel Editor with a Default Vessel:

Figure 30: Vessel Editor with a default vessel

Type a new name and a description for the vessel in the Vessel Name and Vessel
Description text boxes. You should see that the name of the vessel changes from
Default to your selected vessel name as shown in Figure 4.

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Figure 31: Vessel name and description boxes

Next, define the dimensions of your vessel: its width, length and draft. These settings do
not affect the survey data, they are used for the 3D window display. At the same time,
specify the location of the VRP on the boat. Again, this does not affect the survey results
so the location can be approximate if not known precisely.

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Figure 32: Specify vessel dimensions and draft

Finally, specify the position of the Waterline. Note that it is important that the vertical
distance from the VRP to the waterline be accurate as this value is used in both tide
computations and sonar ray tracing to determine the depth of the transducer below the
water level.

At this point you should have completely defined the coordinate system of your vessel.
Look at the 3D view and note that the position of the VRP is approximately correct and
that the waterline is located accurately relative to the VRP.

Figure 33: 3D view of the vessel coordinate system

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The 3D panel shows the vessel axis relative the VRP. All of the measurements that
follow are relative to the VRP with the X, Y and Z axis positive in the direction shown by
the green arrows. See also Table 17.

Table 17: SonarWiz lever arm axes and orientation conventions

Axis Name Description Sign

Convention

X - axis Athwart ships Positive to Starboard

Y - axis Fore and Aft Positive forward

Z - axis Up and Down Positive down

Roll Rotation about the Y – axis Positive starboard

down

Pitch Rotation about the X - axis Positive bow up

Heading (Yaw) Rotation about the Z - axis Positive bow to

starboard

To configure a vessel for Bathymetry processing, we will need to add 3 instruments to

the vessel: (1) a Swath Bathy sonar, (2) a position sensor, and (3) a motion sensor.

Many bathymetry files contain this information embedded in a configuration packet. If

SonarWiz can recognize the packet, this is the easiest way to configure the vessel.

To import the sensor configuration, go to File > Import Sensors… and select a
bathymetry file with a configuration packet.

Figure 34: Import sensor configurations into the vessel

If importing the sensor configuration fails or the configuration packet was not present.
You will need to manually configure the sensors.

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To add a sensor click the button labelled Add new sensor… in the lower-left corner of
the vessel editor.

Figure 35: Manually add a new sensor to the vessel configuration

This opens the add sensor dialog:

Figure 36: Adding a new sensor to the vessel

Figure 9 shows adding an Applanix POS MV position sensor to the vessel. Its sensor
class is (1) Motion Sensor and its Sensor model is Applanix POS MV. You can give this
sensor any Name you like to help you remember the device and you can change the
color of its location marker on the 3D display. Finally, you specify the sensor location
relative to the VRP on the boat. X, Y, and Z coordinates specify the translation of the
sensor from the VRP. Roll, Pitch and Heading specify an orientation to apply to the
sensor data (if any).

In the example (Figure 36), the position sensor is located at the VRP and there are no
orientation angles to apply, so, all of the lever arms are set to zero. Click OK when you
are satisfied.

You should now see the location of the Position sensor labeled on the 3D diagram with a
colored dot corresponding to your selection:

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Figure 37: Position sensor located on the 3D display

If you have made an error, you can select the sensor in the table and then click the Edit
sensor or Delete sensor buttons to change the sensor.

The position sensor is important because it is the tracking point of the vessel. The X and
Y coordinates of the boat will be relative to this point, as well as the z- value if position
height is used for vertical datum.

Repeat the procedure to add the motion sensor:

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Figure 38: Add motion sensor to the vessel

In this example, the motion sensor is the Applanix POS MV which, as before, is located
at the VRP. So, there are zero lever arms. Click OK to add the sensor. You should see
the motion sensor added to the table below the 3D display:

Figure 39: Motion sensor added to the vessel

Now add the Swath Bathy sensor:

For this example, we will use an EdgeTech 6205 interferometer:

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Figure 40: Configuration of EdgeTech 6205 interferometer

There are a couple of things to note when configuring this sonar system. First, note that
this is a two-transducer system, so SonarWiz configures 2 channels of data, channel 0
corresponds to the port-facing transducer, and channel 1 corresponds to the starboard-
facing transducer. Second, the lever arms from the VRP to the transducer assembly are
the same for each channel, however, channel 0 must be rotated 180-degrees to face off
to the port.

The roll, pitch and heading orientation angles entered here (at this point) are usually the
nominal manufacturers values (converted to SonarWiz conventions). If a patch test
calibration has been completed, then adjust the nominal values accordingly. Otherwise,
the calibration procedure can be done in SonarWiz. The nominal installation orientation
angles for all supported sonar systems are available from CTI.

Once you click OK and return to the vessel editor, you should see the sonar marker
added to the 3D display as well as a row added for each channel in the sensor table:

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Figure 41: Vessel configuration after adding Swath Sonar

Take a moment to ensure that the Sonar is properly configured. The sonar should be
properly positioned on the boat, the sonar should be below the waterline, and the
individual sonar fans should be directed appropriately.

At this point, the vessel is properly configured for processing bathymetry. Close the
vessel editor. Your changes are saved automatically.

Verify that the new vessel has been selected for the current project by selecting the Data
Acquisition Tab > Select Vessel for Project

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Figure 42: Selecting a vessel for a project

The Select Vessel dialog opens and you should see the survey vessel shown in the drop
down:

Figure 43: Select vessel dialog

TIP: Note the options to export and import vessels here. It is easy to import a vessel
from a previous project. Save time in the future by selecting a previously used vessel
from the drop down or importing a vessel from another project.

NOTE: The Export Vessel dialog saves the vessel in the Vessel folder of your project.

4.3 Importing Bathymetry Data

Before bathymetric processing can begin, the following data must be imported into
SonarWiz:

1. Bathymetry files
2. Sound Velocity Profiles
3. Tide files (if surveying on a tidal datum)
4. External navigation files (if replacing the on-board navigation or attitude)

The following sections describe the import process in more detail for each file type.

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4.3.1 Bathymetry Files

Bathymetry files contain the raw sonar beam information and usually also contain
navigation and vessel attitude information.

When SonarWiz imports these data, the file is parsed and the beam geometry
information, positioning information and attitude information are extracted into a CDF
database. Beyond this step, the original file is not used.

NOTE: To import bathymetry files you must first have a vessel configured.

To import bathymetry, use Post Processing > Bathymetry Files…

Figure 44: Import bathymetry files

This opens the File Open dialog as shown in Figure 45.

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Figure 45: File import dialog

Select the files to import using the mouse.

If the import bathymetry format stores position data in a projected coordinate system
(e.g., Hypack HSX format), select the Navigation data in XY or grid format check box
and specify the coordinate system in use by the files using the Browse Coordinate
Systems button.

Several bathymetry file formats are provide with specific options to control how the file
will be imported. Those options are described below. Open the File Specific Options
Button and then select the appropriate tab to see the available options.

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4.3.1.1 EdgeTech JSF

There are no bathymetry-specific options for JSF files at this time. All of the options
shown are for Sidescan and Subbottom systems.

4.3.1.2 GeoAcoustic GCF

An amplitude scalar can be applied to imported amplitude data.

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4.3.1.3 Hypack (HSX files)

Hypack HSX files may contain multiple sources of position and heading. The user has
the option of setting the position source.

Hypack backscatter for bathymetry can be obtained either from the beam packet (RMB)
or from the sidescan packet (RSS). The latter is often used by Hypack to record high-
resolution Snippet and TruePix, sidescan data; sometime to the exclusion of RMB
packets which will be all blank

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4.3.1.4 Kongsberg ALL

Kongsberg ALL files have several options for storing bathymetry, position and attitude
packets. The user can select the packets they wish to process as well as indicate the
source for backscatter.

4.3.1.5 Klein SDF

The bathy processing section of the Klein SDF options provides the ability to switch the
source of depth, attitude and heading values. The Quality Threshold slider provides a

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way to filter out low quality data during the import process. Klein recommends starting
with the quality minimum of 65 to start.

4.3.1.6 R2Sonic

R2Sonic R2S files are not complete bathymetry records. They do not contain position
information. Usually these data have to be paired with either a Hypack HSX file or an
XTF file which contains the missing information. The Time Offsets box allows the user to
align the time between these two data sources.

R2Sonic systems can record 3 different backscatter types beam averaged, Snippets and
TruePix. The Backscatter source option allows the user to select between the different
options. Note that not all packets may be present in the file. Use the Tools > R2S packet
information utility to see what backscatter options are avialble.

The TruePix and Snippet backscatter are higher resolution that the bathymetry. The
backscatter interpolation method determines how these data are to be plotted. Either
SonarWiz will compute a beam amplitude value for each sounding, or it will attempt to
interpolate the position of each backscatter pixel based on the bathymetry profile. The
latter option is only recommended for small areas as it greatly increases the files size
and processing time.

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4.3.1.7 Reson S7K

Files in S7K format often contain bathymetry, backscatter, navigation and attitude data in
redundant packets. Use the Tools > S7K > Extract Packet information tool to see what
packets are included in any particular S7K file.

The options for bathymetry source select the packet to use for soundings

The options for Backscatter Interpolation select which packet will be used as the
backscatter source and the type of interpolation that will be performed. All of the
backscatter packets except the 7006 packet record backscatter at a higher resolution
than the bathymetry. Users have the option to plot the bathymetry at the beam detection
point (recommended) or SonarWiz will attempt to interpolate the backscatter pixels onto
the bathymetry profile.

The options for Navigation Source, Heading Source, and Heave Pitch Roll Source are all
similar. Select the packet you want to use. If more than 1 packet type is present, we
recommend picking the packet with the larger number, these are usually newer packet
definitions and contain more processing information.

S7K Units. The S7K file does not indicate the measurement unit of sonar soundings or
speed of sound velocity. For surveyors in the United States that configured the system to
survey in Feet and Feet per second, you must indicate the units here to tell SonarWiz
how to convert these data.

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4.3.1.8 SEA SwathPlus

The only SwathPlus options that affect bathymetry are the backscatter source. Users
can select from importing the Raw backscatter (recommended) or the processed
backscatter generated by SEA Swath Processor program during acquisition and
playback.

4.3.1.9 XTF Bathymetry

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XTF options allow the user to add time offsets to the data packets. There are also
options to select the source packets for attitude and position data.

4.3.2 Tide and Sound Velocity Files

Tide files are usually text files stored in a variety of formats specified by the local
hydrographic agency or various tide software formats. Use the CTI Tide editor to convert
these formats into a SonarWiz compatible XML file and add them to the project as
described in Section 2.6.3.

Sound Velocity Files are generated from a wide range of sound velocity probes and CTD
profilers. Use the CTI Sound Velocity Editor to convert these data into a SonarWiz
compatible XML file and add them to the project as described in Section 2.6.4.

4.3.3 External Attitude and Navigation Files

External navigation records that have been successfully imported into a SonarWiz
project are displayed in the External Navigation Files branch of the Project Explorer.
External navigation records include post-processed trajectories in binary format such as
Applanix SBET files or corrected navigation from AUV surveys stored in CSV format in
pre-defined formats.

The branch-level context menu for External Navigation Files uses a stream-lined
interface to NavInjectorPro with pre-defined navigation file templates (See Section 6.1.3,
page 700 of the SonarWiz User Guide) for more information

4.4 Tide and Sound Velocity Manager

Use the Tide and Sound Velocity Manager in the Bathymetry tool bar to
assign the appropriate tide and sound velocity profile to each bathymetry track line in the
project.

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Figure 46: Tide and Sound Velocity Manager

Each active (checked) bathymetry track line is shown in the Dataset column of the
manager. After that, columns indicate the selected tide file and the sound velocity
processing options.

4.4.1 Tide File Selection

You can manually select the tide file for each track line individually, or you can select
multiple rows in the table and assign the same tide file to all of the selected rows at
once.

The list of available tide files is built from the active (checked) tide files that have been
loaded into the Tide Files branch of the Project Explorer (Section 2.6.3).

The Auto Tides… button will assign the best available tide file to each track line based
on the selection of the Nearest in Time or Nearest in Distance radio buttons below.
Note that tide files must have valid times and positions for this option to work.

4.4.2 Sound Velocity Selections

There are several columns that specify how sound velocity information will be used for
bathymetry processing.

The Surface SV column specifies where the surface sound velocity at the transducer will
be derived. Surface sound velocity is used to adjust the beam takeoff angles when the
surface sound velocity differs from the sound velocity used to do the beam forming.
SonarWiz will automatically adjust the takeoff angles if the surface sound velocity differs
from the sound velocity used during beam forming. The options are:

1. Off – do not attempt to modify takeoff angles

2. Sensor Value – Use the sound velocity recorded by a surface sound velocity sensor
3. Profile—Lookup the surface sound velocity of the transducer from the Sound Velocity
Profile. Note this option is only available if a sound velocity profile has been assigned to this
file in the SV column.
4. Fixed Value – use the fixed value column for surface sound velocity.

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The Ray Trace method describe show SonarWiz will project the beam to the seafloor.
The options are:

1. Profile—Raytrace the beams through the sound velocity profile to the seafloor. This option
is only available if a sound velocity profile has been assigned to this file in the SV Column.
2. Sensor Value---Assume the sound velocity is uniform and equal to the SV sensor
3. Mean Value---Assume the sound velocity is uniform and equal to the depth-weighted mean
of the sound velocity profile. This option is only available if a sound velocity profile has been
assigned to this file in the SV column.
4. Fixed Value---Assume the sound velocity is uniform and equal to the fixed value column

The sound velocity in the Fixed value column is used as the speed of sound Fixed
Value is selected in either the Surface Value or the Ray Trace method.

The Use SV Profile is used to assign a particular sound velocity profile to each track
line. You can select any profile in the drop down list. The list is populated with all the
checked sound velocity profiles loaded into the Sound Velocity Files branch of the
Project Explorer (See Section 2.6.4).

You can use the Auto SV… button to quickly assign the best available sound velocity
profile to each track line based on the selection of the radio buttons nearest in time or
nearest in distance.

4.4.3 Generate a Tide and Sound Velocity Report

Click the Report button to generate a report with the current settings:

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4.5 Bathymetry Processing Options

Project-level settings are applied to all new bathymetry files. They contain settings on
how position and attitude information will be applied, how the vertical datum will be
determined, and set up automatic filters if you wish to run them on every track line.

It is a good idea to set these up before importing and processing bathymetry data. You
can review and override these settings on a file-by-file basis during the Merge operation
(see Section 4.6).

To open the Settings dialog go to click the Settings… icon in the Bathymetry
Toolbar.

Figure 47: The bathymetry settings option

The settings are divided into groups of related options which will be discussed below.

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4.5.1 Position Group

The Position Group settings contain options for determining the positioning of
bathymetry data.

Figure 48: Position Group Settings

The most common option to modify is the Vessel Configuration. The default vessel
configuration is called “Default” and will be shown initially. If you configure more than
one vessel in the project, you will need to use the drop down to select the vessel
configuration to use.

The positon source sets whether SonarWiz will use the position packets read from the
sonar file itself (internal) or if it will use positioning from an (external) file source.

Finally, there is a read-only property which shows the conversion from meters to the
survey units of measure. For surveys in US Foot you will see a ratio of about 3.2808.

Table 18: Position Settings Properties

Property Description

Vessel Set the Vessel Configuration to use

Meters to Units (Read-Only) conversion factor from meters to the survey

units of measure

Positon Source Sets the source of the position data (internal or external)

4.5.2 Attitude

The orientation of the transducers is a critical component of the bathymetry calculations.

The Attitude section of the bathymetry settings determines how the attitude values will
be determined and used.

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Figure 49: Attitude settings

The attitude source drop down allows the user to select to use the attitude packets
stored in the bathymetry file or to use attitude values from an external navigation file.

In some cases it may not be desirable to apply roll, pitch or heading to bathymetry, you
can optionally turn them off here. Also, there are cases where the attitude angles are
reversed due to peculiar vessel configurations. You can easily reverse the sign of the
angles here as a trouble-shooting feature.

Table 19: Attitude settings options

Property Description

Attitude Source Set the attitude source to internal or external file

Apply roll Apply roll during bathymetry computations

Apply pitch Apply pitch during bathymetry computations

Apply heading Apply heading during bathymetry computations

Reverse Roll Reverse the sign of the roll angle

Angle Sign

Reverse Pitch Revese the sign of the pitch angle

Angle Sign

Reverse Reverse the sign of the heading angle

Heading Angle
Sign

4.5.3 Height Computation

The elevation of a sounding is always reported relative to the survey datum. The survey
datum is computed according to the settings in the Height Computation section.

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Figure 50: Height computation options

There are four standard survey datum:

1. Tides Only: Soundings are relative to the tidal datum. Be sure to define the waterline offset.
2. Pressure Only: (AUV & ROV) Soundings are relative to the water surface.
3. Tides + Pressure: (AUV & ROV) Soundings are relative to the tidal datum.
4. Antenna Heights: Soundings are relative to the GNSS datum. Position lever arm is computed,
waterline and tides are ignored.

After the sounding depths are computed above, SonarWiz can optionally add two
additional vertical offsets to the depth values:

Vertical Datum Grid: The datum grid value will be looked up based on the position of the
vessel on each ping.

User-entered Height: A static offset added to the soundings.

Property Description

Attitude Heave Apply heave during bathymetry computations

Heave Source Use internal of external heave source?

Reverse Heave Reverse the sign of heave

Sign

Apply vertical If yes, SonarWiz will look up the value from a datum grid for
datum offset each ping based on the vessel position and add this value to
the bathymetry soundings

Vertical Datum The filename of the datum grid (many grid formats are
Grid File supported).

Apply user Apply a static offset to the data?

entered height
offset

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Set user entered Enter a value to be added to all soundings during merge
height offset

Apply antenna Normally only the X and Y coordinate of the position are
heights used, but if this option is set, then bathymetry will be relative
to the elevation of the position Z value. (Tides will be ignored)

Apply tide Soundings will be computed relative to the tide value. Vessel
corrections waterline offset is used

Apply pressure Soundings will be relative to the fish depth as defined by the
depth pressure sensor and (optionally )the tide level.

4.5.4 Sound Velocity Source

This panel sets the default sound velocity source for angle corrections and ray-tracing.

Chose the default source for the surface sound velocity calculations. This value is used
to calculate the launch angle of sound rays from the sonar. The best option is to use a
real-time sound velocity record from a sensor mounted near the head (SV Sensor).

Chose the default ray tracing method. Sound does not travel in a straight line in water.
By providing a sound velocity profile, SonarWiz will model the true sound ray path
through the water column based on measured sound velocity gradients.

After all bathymetry files and sound velocity profiles have been imported. Use the Tide
and Sound Velocity Manager (see Section 4.4) to override the default values set here.

4.5.5 Default Filters

It is sometimes useful to run automatic filters on all incoming data. You can set up those
automatic filters in the remaining sections of the Project Level Settings dialog. The filters
and their settings are described in detail in Section 4.8 on page 74.

4.5.6 Saving and Applying Settings

It is possible to save a group of Project Settings and give them a name for future use.
For example, perhaps you need different settings for data collected in shallow water and
data collected in deeper channels.

You can use the Save As… button to give a name to a group of settings and it will be
added to the Project Settings Drop down at the top of the dialog.

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Figure 51: Saving a group of settings under a name

After the settings have been saved you can switch between the named groups using the
Current Project Settings Group drop down list:

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Figure 52: Switching saved settings groups using the drop down

When a bathymetry file is loaded into SonarWiz, it is assigned the settings from the
active settings group. Future changes to the default settings group will have no effect on
the files already loaded into the project. If you want to override the settings stored in an
existing file, you can use the Make Others Like This… button to assign the current
project settings to all selected files.

4.6 Merge

Merging combines the raw sonar data with auxiliary attitude and navigation information
to create bathymetric soundings. You cannot display or otherwise work with bathymetry
without first merging the data sets.

The Merge operation in SonarWiz consists for 4 steps:

1. Select one or more files for merging or re-merging

2. Review and overwrite the process settings table for all selected files
3. Review how sounding uncertainty will be computed (required for CUBE gridding)

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4. Overwrite the automatic filter settings for this group of files

Merging or Re-merging a file:

 Computes or re-computes the bathymetry according to the current state of the vessel,
tide and sound velocity settings, etc.
 Resets the amplitude values back to their original state erasing any signal processing
that might have been applied.
 Computes the total propagated uncertainty for soundings according to the new settings
of the error model
 (Optionally) resets flagged samples so they can be visualized and edited again
 Re-runs the automatic filters on the new data set.

Before Merging, you must:

1. Successfully Import bathymetry files so that they show a Yellow or Green merge state icon

Figure 53: A group of bathymetry files ready to merge

2. (Optionally) Assign tide and sound velocity profiles using the Tide Manager
3. (Optionally) Load external navigation files if needed

To start a Merge process select the Merge icon from the Bathymetry tool bar
or from the Bathymetry files context menu in the Project Explorer. Each step in the
merge wizard will be described below.

4.6.1 Merge File Selection

The first step in the Merge process is to select the bathymetry files to merge. You can
select them all using the Check All box at the top of the dialog.

NOTE: Only bathymetry files that are checked on in the Project Explorer can be merged.
If you have accidently turned them all off and you try to Merge you will see a warning
there are no files to merge!

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Figure 54: Merge file selection dialog

When you have selected the files to merge click the Next> button.

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4.6.2 Merge – Auxiliary Data Selection

Figure 55: Merge auxiliary data selection dialog

The second page in the Merge wizard presents the settings that will be used to merge
the file. Initially, these will match the default project settings (see Section 4.5 on page
59). After the first merge, the file will remember the last set of settings that applied.

Whatever changes you make to the settings in this dialog will apply to all the files that
are being merged.

Note that the Downsample filter found in the merge settings dialog removes is not a
regular filter because it removes data from further processing. All other filters simply flag
the data but retain the values in storage. It is recommended to use the downsample filter
for sonars that produce excessively high-volume output. It will greatly increase the
processing time of the rest of the program and it can improve the precision of the
soundings as well.

When you are satisfied with the process settings, click Next

4.6.3 Merge – Error Model Data

An optional error model can be applied to the soundings to compute total propagated
uncertainty for use with the CUBE gridding algorithm. There are four options:

No Error Model - sounding uncertainty will be set to zero

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Sonar Provided Model - SonarWiz will use the uncertainty values stored in the
bathymetry file (not all sonars provide uncertainty)

Simple IHO Model - Assume the sounding uncertainty just barely meets the specified
IHO Survey Order specifications.

This is a simple, worst-case model. Most modern sonars have error budgets much less
than what this option produces. However, it is easy to compute and allows you to use
the CUBE gridder (which is excellent) even for data you know little about.

Full Error Model - Do a total propagated uncertainty calculation to estimate the

sounding uncertainty based on the known location and performance of equipment
installed on the platform.

The full error model computation requires detailed information about the configuration of
the vessel lever arms and the performance of your instruments.

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Figure 56: Full Cube parameters entry dialog

4.6.4 Merge -- Filter Settings

Override the preset filter settings for the group of files being merged. See Section 4.8.1
on page 74 for details.

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Figure 57: Automatic Filter settings

If you are satisfied with the automatic filter settings, Click FINISH to begin the merge
operation.

4.6.5 Merge Resolution and Troubleshooting

If everything is in order, you will see a Processing Bathymetry Files dialog to show the
progress through the Merge operation:

Figure 58: Merge progress dialog

If the Merge operation is successful, the Merge indicator next to each bathymetry file will
turn Green to indicate that the file has computed bathymetry and it is up to date:

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Figure 59: Successful merge resolution

You should now see be able to visualize bathymetry in the main window according to
your selected Bathymetry Drawing Mode (see Section 2.7 on page 26).

If an error occurs during merge, the Merge status icon will turn Red. You may find helpful
messages about what might have gone wrong in the SonarWiz Output window

Sometimes the bathymetry doesn’t look the way you expect.

Table 20: Merge trouble shooting tips

Problem Suggestion

I Can’t Merge Do the files have overlapping Position, Attitude and Sonar
Data (open the File properties from the Project Explorer)

Did you assign a tide or sound velocity profile and then later
turn it off or remove it from the project?

Merge was successful Check that the file is check to draw in the Project Explorer.
but there is no
bathymetry Check that the Bathymetry Drawing mode is set to Draw
Raw Bathymetry

Check that the Opacity slider is all the way to the right

Re-merge, turn off all filters. You may have removed all the
data

Check that the project coordinate system matches the

coordinate system of the sonar data (for sonars that record
in projected units).

Bathymetry looks Turn off the automatic filters and re-merge.

wrong
Check that the vessel configuration is correct, was a
transducer mount reversed is it pointed in the correct
direction? Use the Swath editor 3D view to examine the

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swale and make sure it is flat on the seafloor and not pointed
into space.

Check the settings for speed of sound, does the profile look
ok? A freshwater Sound velocity in saltwater (or reversed)
can cause problems.

For US Customers: have you mixed Feet and Meters

somewhere (Vessel configuration, Map projection, Speed of
sound)?

Bathymetry is wavy Check that the lever arms are correct. Is the mount moving
in the water?

Try reversing the sign of the heave or attitude roll and pitch

Check for timing latency between the Motion Sensor and

the Sonar

4.7 Filter Navigation and Attitude

After merging, the navigation and attitude editor should be used to ensure that there are
no spikes or deviations in the navigation. If edits are made, the affected lines should be
re-merged.

TIP: Use the Navigation and Attitude Editor to low-pass filter antenna heights which can
then be used during merge operations to form a dynamic tide.

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4.8 Filter Bathymetry

4.8.1 Automatic Filters

SonarWiz has a number of automatic filters. These can be run during the Merge process
after bathymetry has been computed or they can be run at any time using the
Bathymetry > Filter tool in the Bathymetry toolbar.

The following sections describe how the filters operate.

4.8.1.1 Reset Filter Flags

Once a sounding has been flagged it will no longer be used for bathymetry and
amplitude computations or visualizations. The reset filter flags option will clear flagged
samples by flag class during subsequent merger or filter operations.

4.8.1.2 Channel Filter

Turn on or off, particular channels for processing. SonarWiz assigns channel 0 to all
single channel systems and port-facing transducers in dual-head systems. Channel 1 is
reserved for starboard-facing transducers in dual-head systems.

4.8.1.3 Manufacturer Flag Filter

If enabled, honor flagging done by acquisition software. (Recommended)

4.8.1.4 Amplitude Filter

If enabled, calculates the mean sample amplitude of each ping and flags all samples that
fall below the specified ratio of the mean.

4.8.1.5 Range Filter

If enabled, flags all soundings closer to the transducer than Filter Near Range, and flags
all sounding beyond Filter Far Range

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4.8.1.6 Cutoff Angle Filter

If enabled, flags all soundings between the Inner Minimum Cutoff Angle and the Inner
Maximum Cutoff Angle. Also, flags all soundings beyond the Outer Minimum Cutoff
Angle and beyond the Outer Maximum Cutoff Angle

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4.8.1.7 Sample Density Filter

If enabled, divides the swath cross-section into bins. Flags all soundings in bins that do
not have the minimum number of samples in them. Equidistant bins are defined by
horizontal and vertical bin size; equiangular bins are defined by angle and range.

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Equidistant Bins:

Equiangular Bins:

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4.8.1.8 Static Box Filter

If enabled, flags soundings that fall outside the defined box based on minimum and
maximum depth and minimum and maximum horizontal.

4.8.1.9 Dynamic Box Filter

The Dynamic Box Filter is similar to the Static Box Filter, except that box is centered on
the mean depth of the ping and the width and height of the box are defined as multiples
of the water depth.

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4.8.1.10 Along-Track Filter

If enabled, divides the ping cross-section into horizontal bins. For each bin, it calculates
the mean depth. Points which fall beyond the threshold distance from the mean depth
are flagged. The bins in the along-track filter are updated over multiple pings with greater
weight placed on the most recent pings.

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4.8.2 Swath Editor

The swath editor is useful for manually editing one track line at a time. You can edit in a
variety of 2D and 3D cross-sections.

1. Select a trackline to edit

2. Select Bathymetry > Swath Editor

3. Configure the Swath Editor:

3.1 Turn on the Sidebar to see configuration options

3.2 The available survey lines are shown at the top of the sidebar. Select a new survey
line by clicking on the name

3.3 The General Section controls the display of points in the editor

3.4 The Colors section allows you to change the color map of points including changing
the color attributes from bathymetry (default) to amplitude

3.5 The General Section Sweep length (pings) setting controls how much of the track
line is shown in one page. Page through the file using page up, page down, the Space
Bar or the mouse scroll wheel

3.6 Open a 3D view of the data by clicking the 3D button on the ribbon interface.

Additional shortcut keys are available by press the H key

4.8.3 Area Editor

The Area Editor is useful for manually editing trouble spots in the data that cross multiple
track lines. It is also very good at editing around submerged targets with complex

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geometry. The Area editor works with both the raw point cloud data and grid surfaces
derived from the point cloud.

1. Open the Area Editor. You can open the area editor in two ways:

1.1 Right-click a grid in the Project Explorer and Select Grid Editor. In this mode, the
grid itself can be edited in addition to the underlying bathymetric soundings. Or ...

1.2 Select the Bathymetry > Area Editor Icon and draw a polygon around an area to
edit. This will generate a temporary grid in the selection polygon, and the editor will
automatically go to selection editor mode where you can edit the soundings
immediately.

2. If the editor was opened with a grid, draw a selection box to edit by holding down
SHIFT+Left click on the mouse to draw a small selection box. You can move the box by
right-clicking the box with the mouse (or SHIFT+ARROW keys) and rotate the box by
CTRL+left clicking one of the corner anchors of the box. Hit ENTER to open the
selection editor mode.

3. Once in Selection Editor Mode, the Subset Manager sidebar controls the display of
points similar to the Swath Editor.

4. Filter and manually edit the soundings in the subset windows and click Update Grid in
the ribbon to see the results of the edit on the grid surface.

5. Close the Subset editor mode by clicking the Clear icon in the ribbon or you can move
the selection box in the Grid View and hit Enter to open a new selection of points.

6. Sometimes it is useful to work on the grid directly rather than the point cloud. You can
switch to the Grid Editing tab and edit the grid manually, removing spikes and
interpolating gaps. The clean grid can then be used with the Grid Surface filter to
quickly flag Soundings that are far from the edited grid surface

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4.9 Patch Test Calibration

4.10 Process Amplitude

4.10.1 Importing Backscatter Data

Swath bathymetry amplitude data is always imported and coincident with bathymetric
soundings in SonarWiz. Only one backscatter record type (beam averaged, sidescan,
Snippets, TruePix, etc) can be imported per bathymetric file, so for file formats that
provide more than one backscatter record per ping such as Kongsberg ALL, Hypack
HSX and Reson S7K, the user must choose the backscatter source before importing the
file.

Determining what backscatter records are available in a swath bathy file can be done by
opening a Record Type Summary report from the Tools ribbon menu in SonarWiz.

When importing a bathymetric file, open the File Type Specific Options… dialog, click
on the tab for the desired file type, and select the backscatter source packet.

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If the across-track resolution of the backscatter record does not exactly match the
bathymetry sounding resolution, the user must also select how to map the backscatter
onto to the bathymetric soundings. There are generally two available options:

1. Plot backscatter at beam detection points (default). In this mode, the footprint of
each beam is computed and the corresponding time series of backscatter samples is
extracted from the selected backscatter record. Then, the backscatter values are filtered
to remove null values, sorted by amplitude value, and finally the median backscatter of
the remaining samples in the footprint is assigned to the sounding.
2. Interpolate backscatter positions between beams. In this mode, each backscatter
sample in the time series is converted into a sounding by linearly interpolating the
corresponding bathymetry beam angles and ranges from the raw bathymetry data.
In general, option 1 produces the best results while maintaining reasonable across-track
resolution. Most modern shallow water systems are capable of sub-decimeter sounding
density. It is usually unnecessary to increase the sounding density beyond this and the
median filter applied to the amplitude time series footprint reduces backscatter
scintillation. It is always recommended to use Option 1 when the backscatter record
includes targets proud of the seabed such as wrecks, pilings or other overhanging
structures, as backscatter interpolation doesn’t work well over complex 3D structures.

4.10.2 Amplitude Units

SonarWiz works in log linear units (dB) wherever possible. For backscatter packet types
that report amplitude values (DN) in dB, these amplitude values are copied into the
unprocessed sonar sounding without modification. Examples include Kongsberg ALL
(packets 83, 88, 89) and Reson S7K (7058). For amplitude packets reported in linear
units such as Reson S7K (packet 7006, 7007, 7018, 7028), R2Sonic (Bathymetry,
Snippets, TruePix), EdgeTech JSF, the data are converted to log-linear units using the
following formula:

𝑆𝑜𝑛𝑎𝑟𝑊𝑖𝑧 𝐴𝑚𝑝𝑙𝑖𝑡𝑢𝑑𝑒 = 20𝑙𝑜𝑔(𝐷𝑁)

4.10.3 Raw Backscatter Visualization

Unprocessed backscatter values can be visualized as soon as bathymetry has been

computed using the Merge operation. Also, at any time, re-merging a dataset will reset
the backscatter to its unprocessed state.

To see the backscatter values open the Color Control from the Map Toolbar. In the
DataType drop down box, select Backscatter. At this point, you should see a histogram
of the backscatter values, a color bar showing how colors have been assigned to the
histogram and the soundings in the main window of SonarWiz will switch to display the
backscatter values in their current state of processing.

It is possible and recommended to use backscatter values for coloring soundings in all of
the 3D editors in SonarWiz. See the Color section of these tools for available options.

4.10.4 Backscatter Processing

In order to improve backscatter mosaics, SonarWiz provides 3 backscatter processing

algorithms that can be applied to individual track lines alone or in series. All three

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algorithms are statistical and are designed to adjust the backscatter intensity of
individual soundings so that backscatter values are more consistent across the survey
area. Backscatter processing does not affect the bathymetry in any way, although clean
bathymetry will produce better backscatter results.

4.10.5 Empirical Gain Normalization (EGN)

EGN is designed to provide a global correction to sonar amplitude files to correct for
across track artifacts in beam amplitude due to:

 differences in transducer angular response

 systematic differences in reflectivity due to beam geometry
 differences in acoustic transmission losses
 Systematic artifacts in the sonar equipment and installation such as differences between
beam sectors, damaged or weathered transducers, port/starboard interference, etc.

EGN works under the assumption that the sonar was operated consistently (same
transmit power, pulse-width, and gains) over the survey area and that all changes in the
received echo level were due to changes in the seafloor composition and beam
geometry. By stacking thousands of pings from throughout the survey area, the
algorithm isolates the systematic artifacts in the sonar pulse from the natural variations
of the seafloor. The resulting correction tables are system-specific and can account for
many unforeseen variations in amplitude due to imperfections in the hardware (age,
damage) or less than ideal mounting situations.

EGN may fail to produce satisfactory results if the survey was not collected with
backscatter processing in mind. In particular, the sonar should be operated with as little
modification to power and gains as possible. The statistical nature of the procedure
works best with large data sets.

4.10.6 Automatic Gain Compensation (AGC)

AGC is a local correction which is particularly useful for removing strong along track and
across track artifacts. There are two parameters. The first is an amplitude target value
and the second is a window size specified as a fraction of the across track ping width.
The window is moved across the ping and the mean amplitude value of the window is
determined. The difference between the window average amplitude and the target value
is the correction applied to the center sounding in the window (EL).

𝑎𝑚𝑝𝑙𝑖𝑡𝑢𝑑𝑒 = (𝑊𝑖𝑛𝑑𝑜𝑤𝑎𝑣𝑒𝑟𝑎𝑔𝑒 − 𝑇𝑎𝑟𝑔𝑒𝑡) + 𝐸𝐿

AGC is a strong filter and can remove regional variations in amplitude. However, it can
enhance local target detection and is extremely effective at removing pitch and roll
artifacts in amplitude data.

4.10.7 Nadir Filter

The nadir filter is a specialized version of AGC. It is designed to reduce the nadir artifact
found in the center of swath bathymetry files. The nadir filter has a single parameter
which specifies the width of the zone to be corrected by the nadir filter in degrees port
and starboard of the nadir beam. The filter first automatically determines a target

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amplitude value for each ping by examining the amplitude values immediately outside
the specified nadir zone. Second, the AGC filter is run on the samples inside the nadir
zone. This usually results in reducing the bright amplitude values immediately adjacent
to the nadir beams. Finally, the corrected amplitude values replace the original values
inside the nadir zone. At the margins of the nadir zone, the corrected values are blended
gradually with the original amplitude values to prevent the introduction of a visible seam
between the corrected and uncorrected data.

4.11 Grid Bathymetry Data

4.12 Grid Operations

Grids are rectangular regions comprised of evenly spaced rows and columns. The
intersection of a row and column is called a grid node. Rows contain grid nodes with the
same Y coordinate, and columns contain nodes with the same X coordinate, Gridding
generates a Z value at each grid node by interpolating or extrapolating the data values.

To better visualize the quality of the bathymetry, create a rough-draft grid of the data at
this time.

1. Zoom the main SonarWiz window to the extents of your data (Ctrl+F)
2. Right-click the Grids branch in the SonarWiz Project Explorer and select Create New Grid…
3. Set an appropriate Grid Cell Size for the area (1m)
4. Assign an Output Grid File Root name (test)
5. Select Primary Grid Surface: Depth
6. Select Grid Algorithm: Cube
7. (optionally) Select Optional Grid Outputs such as: Uncertainty, Hypothesis Count and
Hypothesis Strength

Inspect the resulting grids for blunders in Vessel configuration, Tides, incorrect Sound
Velocity artifacts, improper filter settings (too much filtering, not enough filtering). Correct
the errors and repeat the steps up to this point. Finally, identify areas in the grid that will
require manual editing.

5 Patch Test Calibration Tool

5.1 Scope

This document describes how to perform a calibration or “Patch Test” using the CTI
Patch Test Calibration tool.

5.2 Introduction

The “Patch” test is a field calibration procedure designed to identify and correct for
constant orientation and timing biases between the sonar system and the integrated
motion sensor as installed on the survey vessel. A patch test is usually the first data
collected after mobilizing a sonar system for survey operations, and should be repeated
whenever the sonar or auxiliary sensors are moved or modified. The patch test serves to

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shake down the equipment before data collection begins in earnest, and provides
important quality control information for data processing.

The patch test is based upon the idea that the seafloor should appear the same
regardless of the azimuth, speed or motion history of the vessel. The tests consist of a
series of paired line geometries over a patch of seafloor (hence the name) or a target on
the seafloor where any mismatches of the target between the two lines can be explained
by only one of the unknown variables: yaw, pitch, roll or time delay.

The patch test procedures described in this document are based on information in
Lecture 24 of the Multibeam Sonar Training Course (Clarke, deMoustier, Mayer and
Wells). These procedures are suitable for all sonar types and will produce good results,
however, CTI recommends that you follow the patch test procedure recommended by
your sonar manufacturer, if available.

5.3 Prerequisites

Before beginning the patch test procedure:

1. Ensure that the vessel is properly configured in the CTI Vessel Editor (VE).
a. Check that the position source lever arms are accurate to 1 cm.
b. Check that the motion sensor lever arms are accurate to 1 cm and that the motion
sensor orientation angles (if any) are accurate to <2 degrees.
c. Check that the sonar transducer lever arms are accurate to 1 cm and that the sonar
orientations are at the manufacturer’s default values.
d. Ensure that the water line is located properly relative to the Vessel Reference Point
(VRP).
2. Load auxiliary data
a. Sound velocity profiles in the patch test area should be loaded with proper position and
time information
b. Tide files (if used) should be loaded
c. Post-processed position data (e.g. Applanix SBET files) should be loaded
3. Merge and filter the patch test data sets
a. Apply attitude and heave to the data
b. Ray-trace the data through a sound velocity profile
c. Apply best-available vertical control (antenna position, tides, etc.)
d. Down sample and filter the data aggressively to produce a clean test surface.

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5.4 The Patch Test Calibration (PTC) user interface

The PTC interface consists of 5 main areas (see Figure 60):

Figure 60 - Main user interface for the Patch Test Calibration (PTC) tool

A 3D view of the seafloor. This view shows the gridded bathymetry of the selected lines.
Arrows above the seafloor display indicate the position of the vessel and the direction of
travel for each data set loaded into the PTC.

To change the orientation in the 3D view, left-click the seafloor and move the mouse. To
change the vertical exaggeration, use the slider on the right of the 3D view display.
Further options used to control the display of the 3D view (such as grid resolution and
line colors) are set on Settings Tab described below.

To draw a profile across the 3D view. Press and hold the SHIFT key while left-dragging
with the mouse. Draw the profile where desired and a 3D view of the profile will appear
to indicate the position of the profile. Drawing a new profile will replace any existing older
profile.

The Profile Display. When a profile has been drawn across the 3D view, the profile pane
will open to display the raw bathymetry and profile lines for each of the datasets in the
profile. The profile colors correspond to the data set colors in the 3D view. The profiles
are linked to the calibration values shown in the calibration pane and are updated
dynamically as the calibration values are changed.

The Patch Test Pane. The patch test pane is where the calibration type is selected,
configured and calibration results displayed.

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Figure 61 - Calibration pane of the PTC

The Calibration pane controls the patch test being performed and shows the results of
the test. There are 4 main components:

1. Vessel and Device selection. If only one vessel is available, the drop down will be grayed out.
2. Calibration test type selection and configuration.
3. Calibration test results.
4. Calibration values table. The table shows the test name, channel description, current value,
and new value. The current value column is the value stored in the vessel editor and the
value that will be applied to data sets during Merge operations. The New value is the result
of any operations in the PTC.

4. The Side Tabs. The side tabs include the Patch Test tab (shown by default), the
Settings Tab, and the Selected Survey Lines tab. The patch test tab has already been
described, the Settings tab contains a number of settings which control the display of the
PTC including the survey line colors and the resolution of the grid in the 3D view. The
Selected Survey Lines tab allows the user to control which lines are active during
calibration tests.

5. The tool bar. The toolbar contains a number of commands for activating functions

in the PTC. The most important of which are the recalculate button which

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begins an automatic calibration test, and the Save to Vessel button which is
used to store the new vessel calibration values back in the vessel database.

5.5 Patch Test Procedure

The ideal seafloor for patch testing is a flat bottom with a few very strong targets such as
rock reefs, pipelines or slopes which the patch tests will utilize as targets for aligning the
sonar system.

Patch test lines do not need to be particularly long (< 500 m is usually sufficient),
however it is important that the motion sensor and positioning system are stable during
the sensitive data collection portion of the line. Some motion sensors have a run-out
period after turns where horizontal accelerations from the turn affect the beginning of the
line. This should be accounted for in your patch test line planning (and in your survey
planning, of course).

It is recommended that the vessel be steered by autopilot at all times during data
collection to maintain straight parallel lines. The track lines should be oriented in such a
way that the vessel can maintain steerage without excessive crabbing or pitching.

The patch test data can be collected in any order that is convenient for the vessel. In
fact, it is sometimes necessary to improvise a patch test from data collected without a
calibration pattern in mind. However, the patch test processing should be done in the
following recommended order as some of the later tests depend on previous results.

Technically, the patch test calibration applies to a single transducer/receiver pair. On

dual-headed systems, it is necessary to modify the patch test pattern to ensure that each
transducer is calibrated against itself (that is, each line must be run with port-to-port
overlap and then starboard-to-starboard overlap). In practice, many dual-headed
systems (such as interferometers) are mounted on a common head assembly where
independent measurement of heading and pitch is impractical. For these systems, it is
usually acceptable to solve for a single pitch and heading offset and apply those values
to both transducers. The roll offsets for dual-headed systems should still be solved for
independently.

5.6 Position Time Delay

The position time delay test measures the time latency of the positioning system and
should be the first test completed in the patch test sequence. This test is performed by
running two lines in the same direction over a target at two different speeds as shown in
Figure 62. Both single-head and dual-headed systems perform the test in the same way,
for dual-headed systems run the tests for each transducer separately.

Note that, ∆𝑥 is close to positioning uncertainty for modern systems. For example, a 6
knots vs 12 knots speed difference with 1 second time delay is only 3 m separation at
the seafloor. It would be very difficult to detect timing differences <500 ms using this
technique.

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Fast (blue) and slow (green) pass over the target position

Apparent position
of target in sonar
display separates
between the fast
line and the slow
line if there is a
time lag in the
positioning system.

∆𝑥 Figure 62 - Solving for time delay

To perform the time delay test using the PTC. Load two file data sets collected over a
target, traveling in the same direction at two different speeds. An example is shown in
Figure 63 over a pipe diffuser. The scour around the pipe diffuser will serve as the
target.

Figure 63 - Time delay patch test over a pipe diffuser

To perform the time delay test:

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1. Open the PTC by clicking on the Patch Test Button drop down arrow on the toolbar. Select
polygonal area to run patch test… option, and then draw a polygon around the area of interest
as shown in Figure 63.
2. Move the 3D view of the seafloor by using the left mouse button. Arrange the view so that you
can draw a profile across the scour depression caused by the pipe diffuser.5
3. Select Position Latency in the Calibration Type drop down:

Figure 64 - Select position latency the Calibration type drop down.

4. Hold down the Shift key and use the left mouse button to draw a profile along the track lines
across the scour depression as shown in Figure 65.

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Figure 65 - Drawing the profile for a time latency test in the PTC

5. Select the minimum and maximum latency values to test and the step size as shown in Figure
66.

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Figure 66 - Setting minimum and maximum values for latency test

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6. Click the Recalculate button to run the automatic latency test.

Figure 67 - Results of the position latency test.

The Recalculate button will try every latency value between the Minimum and Maximum
latency value set in Step 5. The value which minimizes the difference between the two

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profiles will be returned as a V-graph (#2) and numerically in the New column of the
Position Latency row (#3) in the Calibration Values table as shown in Figure 67.

In the example here, the latency value is 0.0 s. this is the expected result from modern
equipment conditioned by time synchronization hardware.

6b. optionally, you can manually move the slider bar to change the latency values.
The 2D profiles will update to show the results of the calculation.

6c. optionally, you can manually enter a value directly in the Calibration values table
(new column).

When you are satisfied with the results of the test. Click the Save to Vessel icon in the

toolbar . Any row in the Calibration values table with a check in the Save
checkbox will be stored in the vessel file. The value in the New column will be stored in
the vessel and become the Current value.

Figure 68 - Calibration values results table

Exit the PTC and re-merge the data with the new time latency values.

5.7 Pitch Bias

The pitch bias test resolves static bias in the pitch angle of the sonar. The pitch test
requires a line be surveyed in inverse directions at any speed.

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Apparent
position of
target is offset
∆𝑝 from true
position of
target due to
pitch
misalignment

Figure
∆𝑥69 - Pitch bias test configuration
The pitch test requires that the time delay is solved. The pitch test is insensitive to gyro or roll biases.
However, ∆p is difficult to resolve in shallow water (see

Table 21). Both single-head and dual-headed systems perform the test in the same way,
for dual-headed systems run the tests for each transducer separately.

Table 21 - Apparent target offset of a 1 degree pitch error

Water Depth (m) ∆𝒙 (m)

20 0.34 (no chance)

200 3.40 (limit of detection)

2000 34.0 (no problem)

To perform the pitch test using the PTC. Load two file data sets collected over a target,
traveling in the opposite direction on the same line. An example is shown in over a pipe
diffuser. The scour around the pipe diffuser will serve as the target.

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Figure 70 - Survey design for pitch test

In the PTC, Patch Test tab, select Calibration Type: pitch from the Calibration Type
dropdown and then draw a profile along the two data sets directly over the target as
shown in Figure 71.

Figure 71 - Profile directly along the two datasets over the scour depression target

Running the pitch test in the PTC is exactly the same as for the time delay. Set the
minimum and maximum test values and click the Recalculate button in the toolbar. For
this profile, the pitch bias calculated by the PTC was 0.4 degrees as shown in

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Figure 72 - Results of pitch bias test

Save the new pitch bias value to the vessel by clicking the Save to Vessel icon

Re-merge the data.

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5.8 Roll Bias

The roll patch test resolves the static roll bias. The roll test differs significantly between
single-head and dual-head systems. For single-head systems two data sets are
collected in opposite directions over the same track line, any speed. For dual-headed
systems two parallel lines are collected in opposite directions, at any speed. In both
cases, the test works best over a flat seabed. The dual-head roll test is repeated for
each transducer.

Single-head Roll Test

Apparent seafloor offset from true seafloor by roll bias

Figure 73 - Single-head roll bias test configuration

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Figure 74 - Example of a single-head roll test patch

Open the PTC and select Roll in the Calibration type dropdown box:

Figure 75 - Calibration type roll selected in the Patch Test tab of the PTC

Then draw a profile perpendicular to the track lines as shown in Figure 76. The cross-
section will be a profile across the track of the two data sets.

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Figure 76 - Profile drawn perpendicular to the track lines for a roll test in the PTC

The roll test bias is computed in the PTC using the same steps as before. The roll bias
for this data set was +0.2 degrees as shown in Figure 77.

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Figure 77 - Roll bias results for a single-transducer roll bias test

Save the results to the vessel file by clicking the Save to Vessel button in the toolbar,
exit the PTC and remerge the data.

Dual-head Roll Bias Test

Dual headed systems including dual-head multibeams and most interferometers must
calibrate each transducer separately. The roll bias test pattern is therefore modified to
use parallel lines to make it possible to overlap port-to-port and starboard-to-starboard
as shown in Figure 78. The minimum number of parallel lines is 3 which gives one

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overlap for each of the port and starboard transducers. Five to seven parallel lines are
more typical where the extra overlaps are used for redundancy.

Apparent seafloor offset from true seafloor by roll bias

Figure 78 - Dual-head roll calibration configuration

An example of a 6-line patch test pattern collected for a dual-headed interferometer is

shown in Figure 79. Ideally, the roll test should be performed over a flat seabed, the
smoothest area in the pattern is towards the bottom of the survey area. The extra lines
will provide some redundancy for the calculated results.

Figure 79 - Example of a roll bias patch test pattern collected by a GeoSwath Plus interferometer

Open the PTC on the rectangular area towards the bottom of the survey pattern shown
in Figure 79. The PTC supports dual-channel systems using the same interface as a
single-channel system. The extra channels are listed in the Calibration type drop down
and the extra offset angles are listed in the Calibration values table. For a dual-headed

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system there will be a roll value for channel 0 (port) and channel 1 (starboard), and
likewise for pitch, heading and position latency.

Figure 80 - Example of the PTC showing the additional channels for the dual-headed system

To start the roll calibration. Select Calibration type: Roll (Tx0):

Figure 81 - Select the port transducer for roll test (tx0)

Draw a profile line perpendicular to the track lines. Draw it across all of the available
track lines as shown in Figure 82, the PTC will calculate the result of each available
overlap and report the average offset value.

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Figure 82 - For dual-headed systems the roll bias test uses a profile drawn across all of the available track
lines

When manually adjusting the Roll value using the slider bar in the PTC with Calibration
type Tx0 selected. You should see only the port-facing transducer beams rising and
falling. The starboard beams are not part of the test and remain fixed at their current roll
values. Using the recalculate button to automatically run the Tx0 Roll test will similarly
only evaluate the port-facing transducer. The results for this dataset are shown in Figure
83. Note that the V-graph shows the results for 2 different overlap solutions for Tx0 and
it is the average value between the two solutions that is stored in the New results column
of the Calibration values table. Also note that the center value of the test is about -60
degrees. This corresponds to the roll (elevation) offset entered into the vessel editor
when configuring the interferometric system. Interferometric transducers do not point
straight down like multibeams and instead are inclined upward by about 60-degrees (-30
degrees from horizontal).

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Figure 83 - Tx0 Roll results

To repeat the test with the starboard channel, select Roll (Tx1) from the Calibration type
drop down and recalculate the test.

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Figure 84 - Roll test results for the starboard channel (Tx1)

In this case, there were 3 overlapping pairs of lines used in the test, resulting in 3 v-
graph results in the PTC test results. The average roll offset for the starboard channel
was -60.1 degrees.

To save these values to the vessel, click the Save to Vessel button and re-merge the
data.

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5.9 Heading Bias

The heading patch test calculates the static bias in heading or yaw between the sonar
system and the motion sensor. Like the roll test above, the line pattern must be modified
for dual-headed systems so that port-to-port and starboard-to-starboard transducers are
compared. As a rule of thumb, heading bias can be resolved to no better than about ½ of
the beam width of the sonar. The single-transducer test is not sensitive to other biases
since both lines are run in the same direction, however, the dual-head heading test is
run in opposite directions and is therefore sensitive to time offset and pitch bias

Single Head Heading Test

Apparent position of target is offset by the heading bias

Figure 85 - Configuration of heading (Yaw) bias patch test

The single-head heading bias test consists of two parallel lines run at the same speed
and in the same direction. A target located between the two lines is used to calculate the
heading bias. Because the lines are run in the same direction and at the same speed,
timing delays and pitch bias effect both lines similarly and are therefore not important
(this is not true for dual-headed systems run in opposite directions!). Roll bias will result
in the target vertically separating, but that should not bias heading the results (though a
vertical offset will cause problems for the PTC automatic convergence algorithm, you
can still align the profiles by eye using the manual slider).

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Figure 86 - Example of single-head heading test over pipe scour depression

Open the PTC over the area highlighted and select the Heading test from the
Calibration type drop down box as shown in Figure 87.

Figure 87 - Select the Heading calibration type in the PTC

Draw the profile line down the middle of the target scour depression, bisecting the two
parallel track lines as shown in Figure 88.

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Figure 88 - For a heading test, draw the profile between the two parallel track lines, directly over the target

For this example, the optimal solution was found to be a heading bias of +0.2 degrees
as shown in Figure 89.

Save the results to the vessel by clicking the Save To Vessel button. Exit the PTC and
re-merge the lines.

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Figure 89 - Heading bias computation

Dual-Head Heading Test

The dual-headed heading test is similar to the dual-headed roll test in that the parallel
lines must be run in the opposite direction so that port-to-port and starboard-to-starboard
overlap is maintained (see Figure 90). It is invalid to compare the port beams to the
starboard beams on a 2-headed system. As with the single-head heading test, a target
must be identified between the two lines which is used to calibrate the heading bias.
Because the lines are being run in opposite directions, time delay and pitch bias must be
solved before the heading test is started.

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Starboard to Starboard Port to Port

Figure 90 - In dual-head heading test 2 parallel

Apparent position lines
of need to be
target run in opposite
is offset by the directions
heading tobias
maintain port-
to-port and starboard-to-starboard transducer overlap.

Figure 91 shows a patch test data set collected over a large dune field. These dunes
provide excellent targets for calibrating the heading bias of this dual-head system. Not
only are the targets easy to identify in the bathymetric profiles, but the visual line formed
by the contours makes it easy to see whether or not the alignment was successful. Other
good targets for heading calibrations include man-made pipelines, linear rock reefs or
glacial erratics.

Figure 91 – The dune field in this dual-headed patch test provides several good spots for doing a heading
calibration

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Figure 92 - 3D view of the patch test area showing port-to-port and starboard-to-starboard overlap

Opening the PTC and examining the dune field we can find several areas with good
port-to-port and starboard-to-starboard overlap against which we can run our calibration
tests. Start the test by selecting Heading (Tx0) calibration type from the dropdown box
(Figure 93)

Figure 93 - Select heading (Tx0) from the Calibration type drop down

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Draw the profile parallel to the track lines with port-to-port overlap. The profile line goes
directly over a prominent dune which will be the target used for our heading calibration
as shown in Figure 94. The results of the calibration was a new heading orientation of for
the port transducer of 181.5 degrees or +1.5 degrees from the values originally entered
in the Vessel Editor for the port-facing transducer (Figure 95).

Figure 94 - Profile drawn between the two heading calibration tracklines with port-to-port transducer overlap.

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Figure 95 - Results of port-transducer (tx0) heading calibration

For the starboard transducer (Tx1) we switch the Calibration type dropdown box to
Heading Tx 1 and draw the profile down the middle of the two lines with starboard-to-
starboard overlap. Here again, there is a large dune to provide a target for our heading
calculations (Figure 96)

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Figure 96 - Starboard transducer profile is drawn between track lines with starboard-to-starboard overlap.

The result of the starboard transducer heading calibration is shown in Figure 97 and is
about half the value for Tx 0 (port: +1.4, starboard: +0.7).

To save these values click the Save to Vessel button and re-merge the data.

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Figure 97 - Results of heading calibration on starboard transducer (Tx 1)

5.10 Conclusion

We recommend that patch test lines be collected at the beginning of every cruise to
verify the equipment installation and demonstrate that the system is performing to
specifications.

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Be sure that a) sensor lever arms are accurate to the centimeter level; b) that the
bathymetric sonar mount is rigid and inflexible and c) that all auxiliary equipment is
performing properly.

Patch test results can be ruined by sound velocity artifacts. Be sure to collect accurate
environmental data! You must have real-time sound velocity measurements at the head
and up-to-date sound velocity profile casts in the patch test area to prevent refraction
artifacts form affecting the calibration results.

The test lines do not need to be long or take more than a few minutes to collect each.
The important part is to maintain the accurate geometry of the lines and to find good
targets for performing the heading and pitch tests.

The Patch Test Calibration tool is flexible. There are other patch test protocols than the
ones described in this manual. The PTC should be able to assist you with these
calculations as well.

5.11 References

Clarke, J.H., deMoustier, C., Mayer, L. and Wells, D. (2008) Lecture 24 Notes, 46th
Multibeam Sonar Training Course, OMG, University of New Brunswick; CCOM,
University of New Hampshire. San Diego, CA. 7 to 12 January 2008. Pp. 799--914

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